Whole blood assay to measure response to type i IFNS and detect auto-antibodies neutralizing ifns

Abstract

The present invention provides methods, assays and kits for evaluation and assessment of IP-10 (CXCL10) expression, particularly IFN induction of IP-10, to determine the presence of inborn errors of the Type I IFN or Type II IFN response pathway and / or auto-antibodies directed against, and particularly neutralizing, Type I IFNs or Type II IFNs in a patient. The methods, assays and kits including for assessment and evaluation of individuals prior to vaccination with live attenuated virus vaccines, particularly including yellow fever vaccines and COVID-19 vaccines, to assess risk for vaccine-associated disease and adverse events, and for evaluation, treatment and management of patients, particularly including those who develop vaccine-associated disease. Identification of inborn errors of the Type 1 IFN response pathyway and / or auto-antibodies directed against, and particularly neutralizing, Type I IFNs are associated with severe viral illness, including COVID-19 disease, and vaccine-associated disease, particularly with live attenuated virus vaccines, particularly including yellow fever vaccines, as well as arboviral diseases, including WNV and TSE encephalitis.

Description

WHOLE BLOOD ASSAY TO MEASURE RESPONSE TO TYPE I IFNS AND DETECTAUTO-ANTIBODIES NEUTRALIZING IFNSSTATEMENT OF GOVERNMENT RIRHTS

[0001] This invention was made with government support under numbers R01AI127564, RO 1 Al 163029, and UL1TR001866 awarded by the National Institutes of Health. The government has certain rights in the invention.FIELD OF / THE INVENTION

[0002] The present invention relates generally to the evaluation and assessment of IP- 10 (CXCL10) expression, particularly IFN induction of IP- 10, to determine the presence of inborn errors of the Type I IFN or Type II IFN response paihyway and / or auto-antibodies directed against, and particularly neutralizing, Type I IFNs or Type II IFN in a patient. Identification of inborn errors of the Type I IFN or Type II IFN response pathyway and / or auto-antibodies directed against, and particularly neutralizing, Type I IFNs or Type II IFN are associated with severe viral illness, including hypoxemic pneumonia such as with COVID- 19 disease, influenza and MERS, and vaccine-associated disease, particularly with live attenuated virus vaccines, particularly including yellow fever vaccines as well as viral encephalitis, including West Nile Virus and Tick Borne virus encephalitis.BACKGROUND OF THE INVENTION

[0003] Type I IFNs ate associated with severe viral illness, including hypoxemic pneumonia such as COVID- 19, influenza, and MERS, and vaccine-associated disease, particularly with live attenuated virus vaccines, particularly including yellow fever vaccines, as well as viral encephalitis, including West Nile virus and Tick Borne virus encephalitis. Notably, these conditions are Arboviral diseases (arthropod-bom viral diseases). Assocation with other arboral diseases such as Zika and Chikunguya has also been shown. The Type II IFN, particuiary IFN-y, is an important effector of the immune system and has a protective and effective role against ifectious disease an in diverse types of infection.

[0004] IFN-y-inducible protein 10 (IP- 10, CXCL10), a chemokine secreted from ceils stimulated with type I and II IFNs and LPS, is a chemoattractant for activated T cells. Expression of IP- 10 is seen in many Th 1 -type inflammatory diseases, where it is thought to play an important role in recruiting activated T cells into sites of tissue inflammation. IP- 10 was initially identified as an early response gene induced by IFN-y in U937 cells (a monocyielike cell line) ( Luster, A. D. et al (1985) Nature 315:672.). IP- 10 is constitutively expressed at low levels in thymic, splenic, and lymph node stroma, however, expression can be highly induced in a variety of cells, including endothelial cells, keratinocytes, fibroblasts, mesangial cells, astrocytes, monocytes, and neutrophils by stimulation withIFN-ot, IFN-fJ, IFN-y, or EPS and in T ceils by Ag activation (Luster, A. D,, and J. V, Ravetch (1987) J. Exp. Med. 166:1084; Vaoguri, P., and J. M. Farber (1990) J. Biol. Ghent 265:15049; Ohmori, ¥., and T. A. Hamilton (1990) Biochem. Brophys, Res. Commun. 168:1261).

[0005] Auto-Abs against type I IFNs have been described in patients with various conditions, including myasthenia gravis and / or thymoma (30-75%), systemic lupus erythematosus (SLE) (10-14%), and in patients on type I IFN treatment (Bello-Rivero, 1. et al. (2004) J Autoimmun 23, 63-73; Meager, A. et al. (2003) Clin Exp Immunol 132, 128-136; Bradford, H. F. et al. (2023) Cell Rep Med 4, 100894; Gupta, S. et al. (2016) Arthritis Rheumatol 68, 1677-1687; Panem, S. et al (1982) J Immunol 129, 1-3; Vallbracht, A. et al (1981) Nature 289, 496-497). They are relatively rare in the general population (in <0.5% (auto-Abs neutralizing high concentrations of type I IFNs) and <2% (auto-Abs neutralizing low concentrations of type I IFNs)) of individuals under the age of 65 years, however, their prevalence increases sharply thereafter, reaching ~4% and ~8%, respectively, in individuals over the age of 70 years (Bastard, P. et al. (2021) Science Immunology 6 (2021); Fuel, A. wt al (2022) J Exp Med 219, doi.org:10. l084 / jem.20211387); Casanova JL et ai. The Ouroboros of Autoimmunity. Nature Immunology 2024. The underlying cause of the auto-Abs neutral izing type I IFNs remains unexplained in most cases.

[0006] Auto-Abs against type I IFNs were first discovered in 1981-1984 by Ion Gresser. They were found in autoimmune polyendocrine syndrome type 1 (APS-1) patients in 2006, which led to use of their detection as a diagnostic marker of this condition (Levin, M. (2006) PLoS Med 3, ©292; Meager, A. et al. (2006) PLoS Med 3, ©289). More recently with the COVID-19 pandemic, the pathogenic role of these auto-antibodies in viral diseases became widely accepted. In approximately 15% of cases of critical COVID-19 pneumonia, patients were found to have pre-existing auto-Abs neutralizing type I IFNs (Bastard, P. et al. (2020) Science 370, doi.org:10.l 126 / science.abd4585; Bastard, P. et al. (2021) Science Immunology 6, doi.org: 10.1126 / sciimmunol.abl4340; Casanova, J. A.-O. & Abel, L. A.-O. (2021) Science, doi.org: 10.1126 / science.abj7965; Manry, J. et al. (2022) Proc Natl Acad Sci U S A 119, e2200413119). Auto-Abs neutralizing type 1 IFNs also underlie ~5% of cases of critical influenza paeumonia (Zhang, Q. et al. (2022) J .Exp Med 219, doi.org:10.1084 / jem.20220514), ~25% of hospitalizations for Middle East respiratory syndrome (MERS) pneumonia (Puel, A et ai (2022) J Exp Med 219, doi.org:10.1084 / jem.202H387; Hale, B. G. (2023) European Journal of Immunology 53, 2250164; Alotaibi, F. et al. (2023) Influenza and other Respiratory Viruses 17, https: / / doi.org:10.1111 / irv.l3116), "-30-40% of severe adverse reactions to the live attenuated virus vaccine against yellow fever virus (YFV-17D) (Le Hir, A. et al. (2023) J Travel Med (2023), doi.org:doi:10.1093 / jtm / taad!60; Bastard, P. et al. (2021) J Exp Med 218, doi.org: 10.1084 / jem.20202486) and, strikingly, '-40% of cases of West Nile virus encephalitis (Gervais, A. et al (2023) J Exp Med 220, doi.org: 10.1084 / jem.20230661) as well as 10% of cases of Tick borne virus encephalitis (JEM in press). These auto-Abs have a major clinical impact, are presentbefore viral infection, and are causal for severe disease. They are also universal, as they have been found in > 40 countries worldwide, across latitudes and longitudes, and across ancestries.

[0007] Current procedures for detecting auto-Abs neutralizing type I IFNs are based on in vitro cell- based assays and usually involve assessments of STAT1 phosphorylation (p-STATl) by flow cytometry after the stimulation of PBMCs with type I IFNs in the presence of plasma or serum from the patient or control (Shaw. ER et al (2022) Curr Protoc 2(8), doi.orgtdoi: 10.1002 / cpzl .511 ; Bastard, P. et al (2020) Science 370, doi.org: 10.1126 / science.abd4585). More sensitive luciferase reporter cell-based assays have also recently been developed (Bastard, P. et al (2021 ) Science Immunology 6, doi.org: 10.1126 / sciimmunol.abl4340). If the patient plasma or serum contains neutralizing auto-Abs against type I IFNs, cytokines are neutralized and, thus, unable to signal through their receptors, resulting in low levels of p-STATl or luciferase activity. By contrast, in the absence of such antibodies, the type I IFNs can induce high levels of firefly luciferase activity.

[0008] Inborn errors of type I interferons have been found to be associated with various viral diseases, including in up to 5% of COVID-19 disease patients with critical pneumonia under 60 years old where mutations particularly in the TLR3 and TLR7 genes were identified (Zhang Q et al (2022) Nature 603:587-593, doi.org / 10.1038 / s41586-022-04447-0). Similarly, gennline mutations in TLR3, IRF7 and IRF9 have been shown to underlie critical and life threatening influenza pneumonia (Ciancanellu MJ et al (2015) Science 348, 448-453; Hernandez N et al (2018) J Exp Med 215:2567-2585; Lira HK et al (2019) Nature 216:2038-2056). Detection of relatively rare inborn errors of the type I IFN response pathway is complex and currently requires individual and specific assessment of common gene mutations, each gene being evaluated separately.

[0009] There is a need for rapid and effective methods, assays, kits and approaches io readily identify those individuals with an altered or ineffective Type I or Type II interferon response pathway. There is a need for methods, assays, kits and approaches to readily identify those individuals al greater risk for severe viral disease in order that they can be more aggressively managed and clinically treated. There is a need for rapid identification of clinical, physiological, genetic aspects in patients that will characterize their risk of severe disease and identify' their susceptibilities and for the suitable and applicable treatment for those patients. There is need to for methods to identify' those individuals at risk for vaccine-associated disease, such as Yellow fever vaccine associated disease including YEL- AVD and YEL-AND. The present invention addresses such unmet needs in the field, including as to infectious disease susceptibility, virus infections and vaccine-accociated disease by virtue of a simple and all-encompassing approach to identify those most at risk and further point to additional testing, evaluation for those patients or indivisuals and to provide treatment options.

[0010] The citation of references herein shall not be construed as an admission that such is prior art to the present invention.SUMMARY OF THE INVENTION

[0011] In a general aspect, the present invention relates to a single marker and readout for rapid and cost-effective assessment of multiple parameters relevant to the IFN response pathway, particularly to the presence of inborn errors of the Type I or Type II IFN response pathyway and / or auto-antibodies directed against, and particularly neutralizing, Type I IFNs or Type II IFN in a patient or individual. Methods, assays and kits based on the marker and readout are provided. In a particular aspect, the invention relates to a single marker readout for rapid and cost-effective assessment of alterations in the Type I IFN pathway or the Type II IFN pathway, particularly wherein a single marker readout and approach can predict alterations in one or the other pathway.

[60012] The basis of the marker readout, methods, assays and kits is the IFN-inducible protein IP- 10 (also designated CXCL10), a chemokine secreted from cells stimulated with type I and II IFNs. In accordance with the invention, alteration of the IFN-response pathyway by virue of one or more auto- antibody specific for a type I IFN, or for type II IFN, or genetic mutation, particularly loss of function or loss of activity, in one or more gene in the type I IFN response pathway, and / or type II IFN response pathway, results in blockage ofIFN-mediated induction of IP- 10. Failure of induction of IP- 10, such as by IFNy, or by one or more of IFNa2, IFNp or IFNa, is indicative of one or more auto-antibody specific for a type I or type II IFN, or genetic mutation, particularly loss of function or loss of activity, in one or more gene in the in the type I IFN response pathway, and / or type II IFN response pathway, in a sample from a patient and in that patient or individual. The invention provides a simple, straightforward, single marker readout to predict type I IFN response pathway alteration, and / or type II IFN response pathway alteration, particularly the presence of one or more IFN type specific auto-antibody or a detrimental / loss of function mutation in one or genes in the IFN response pathway.

[0013] The invention provides a single marker and readout for rapid and cost-effective assessment of the presence of inborn errors of the Type 1 IFN response pathyway and / or auto-antibodies directed against, and particularly neutralizing, Type I IFNs in a patient or individual. The invention provides a single marker and readout for rapid and cost-effective assessment of the presence of inborn errors of the Type II IFN response pathway and / or auto-antibodies directed against, and particularly neutralizing, Type II IFNs in a patient or individual.

[0014] The quantification of IP- 10 upon stimulation of whole blood with IFN-alpha, -beta, -gamma, and -omega is a suitable readout to screen for autoantibodies neutralizing type I IFNs (alpha, beta, omega) and type II IFN (gamma), as well as genetic disorders of either signaling pathway.

[0015] The assay, methods and kits hereof have application and use with regard to and for (i) viral pneumonia, (ii) viral encephalitis (in particular due to arboviruses), and (iii) adverse reactions to live viral vaccines. The invention provides a whole blood assay to detect auto-antibodies neutralizing type I IFNs and as risk factor of various diseases or conditions, particularly including severe viral diseases (COVID-19, critical influenza pneumonia, Middle East respiratory syndrome (MERS) pneumonia, West Nile virus encephalitis), and severe adverse reactions to live attenuated vaccines, such as the liveattenuated virus vaccine against yellow fever virus (YFV-17D). The whole blood assay can also permit the detection of auto-Abs neutralizing type II IFN and as risk factor of various diseases or conditions, particularly including in patients with mycobacterial disease, including BCG disease, atypical mycobacteriosis, and tuberculosis, as well as other intra-macrophagic bacteria, fungi, and parasites.

[0016] The invention provides a whole blood assay that permits the detection of genetic defects in the type I and / or type II IFN response pathways.

[0017] In an aspect, the assays, methods and kits hereof include a positive control, In particular, the positive control can provide assurance that auto-Abs are being detected. In art aspect, a control mAh against IFN receptor is added to blood from a healthy person. This provides a positive control to be sure auto-Abs to IFNs can and are able to be detected in the samples to be tested.

[0018] In an aspect the approach, assay, methods, kits provides rapid results, particularly results within 24 hours. The approach, assay, methods, kits provides rapid results, particularly results within 1 day, and particularly in less than a day, within 12-24 hours or within 12 hours. The approach, assay, methods, kits provides rapid results, particularly results within hours. This is m comparison to alternative assays, methods wherein results require 2-4 days, and also wherein multiple markers or readouts must be evaluated rather than a single predictive readout. Results herein are provided within 24h compared to classical assays (2-4 days).

[0019] The present invention relates to genetic aspects of the interferon gene pathway that are correlated with and render patients susceptible to vaccine-associated disease, particularly yellow fever vaccine related disease, including YEL-AVD and YEL-AND, or particularly Sars-Cov2 vaccine related disease, including disease caused by, resulting from, associated with or related to live attenuated coronavirus vaccine(s). The invention further relates to auto-antibodies directed against and specific for type I interferon proteins, the presence of which are correlated with and render patients susceptible to severe viral disease, such as severe COVID- 19 disease, influenza, White Nik Virus, and / or to vaccine-associated disease.

[0020] The evaluation of IP-10 induction via the methods and assays provided herein pennits the prediction or detection of the presence of one or more auto-antibodies directed against and specific for type I interferon proteins. The presence of one or more auto- antibodies directed against and specific for type I interferon proteins has been correlated with severe viral disease, particularly induing severe COVID-19 disease, and to vaccine-associated disease. The evaluation of IP- 10 induction via the methods and assays provided herein permits the prediction or detection of the presence of one or more auto-antibodies directed against and specific for type II interferon proteins. In some aspects, the correlation is to susceptiblity to vaccine-associated disease, particularly live vaccines. The presence of one or more auto-antibodies directed against and specific for type II interferon proteins has been correlated with susceptibility to infectious disease, severe viral disease and to vaccine-associated disease. In some aspects, the correlation is to susceptiblity to vaccine-associated disease, particularly yellow fever vaccine-associated disease, including YEL-AVD and YEL-AND. In some aspects, severeviral disease includes coronavirus, such as COVID-19, influenza (flu), West Nile Virus (WNV). In some aspects, severe viral disease includes COVID-19, critical influenza pneumonia, Middle East respiratory syndrome (MFRS) pneumonia, West Nile virus encephalitis.

[0021] Auto-antibodies directed against and specific for type I interferon proteins includes autoantibodies targeted against one (or more) of most of the individual subtypes of type I IFNs. In particular, the autoantibodies target an individual subtype of type I IFN which is capable of inducing IP- 10. The presence of the auto-antibody, particularly neutralizing auto-antibody, targeting one or more individual subtype of type I IFN which ordinarily can or does induce IP-10, prevents or blocks or drastically reduces IP-10 induction with IFN. This results in the absence of IP-10 induction, or very significant reduction of IP-10 induction, with IFN in the methods and assays of the invention. Thus, the absence of induction of IP-10, or a significantly reduced induction of IP-10, or the absence of IP-10 protein, antigen or gene expression upon stimulation of a sample of blood, plasma, serum from a patient indicates that the patient has or harbors auto-antibody directed against and specific for one of more subtype of type I IFN. In some aspects, the auto-antibody is particularly targeted against IFN-a2, IFN- 3, or IFN-ffi.

[0022] The auto-antibody / ies may be specific for one or more type I IFN selected from:(i) IFN-a2 and IFN-p(it) IFN-a2 and IFN-w;(iii) IFN-«2, IFN-® and IFN-P;(iv) IFN-a2, IFN-tn, IFN-p, IFN-al , IFN-a6, IFN-ctl3, IFN-al 4 and IFN-a!6; and(v) IFN-a2, IFN-®, IFN-al, IFN-a6, IFN-al3, IFN-al4 andlFN-a!6.

[0023] In another aspect, the patient may have or produce one or more auto-antibody directed against IFN-s and / or IFN-K.

[0024] The lack of IP-10 induction or a significantly limited IP- 10 induction in response to IFN, particularly one or more of IFNy, IFN-a2, lFN-£, or IFN-o), can be indicative and diagnostic of Auto- antibodies directed against and specific for type I or type II interferon proteins includes autoantibodies targeted against one (or more) of most of the individual subtypes of type I IFNs or type II IFN. Auto- antibodies directed against and specific for type II interferon proteins includes autoantibodies targeted against one (or more) of most of the individual subtypes of type II IFNs, in particular, the autoantibodies targeted an individual subtype of type II IFN which is capable of inducing IP-10, such as IFN-y. The presence of the auto-antibody, particularly neutralizing auto-antibody, targeting one or more individual subtype of type II IFN which ordinarily can or does induce IP- 10. pre vents or blocks or drastically reduced IP-10 induction with IFN. This results in the absence of IP-10 induction, or very significant reduction of IP- 10 induction with IFN in the methods and assays of the invention. Thus, the absence of induction of IP- 10, or a significantly reduced induction of IP-10, or the absence of IP-10 protein, antigen or gene expression upon stimulation of a sample of blood, plasma, serum from a patientindicates that the patient has or harbors auto-antibody directed against and specific for one of more subtype of type II IFN. In some aspects, the auto-antibody is particularly targeted against IFN-y.

[0025] The evaluation of IP- 10 induction via the methods and assays provided herein permits the prediction or detection of the presence of genetic defects in the type I and / or type II IFN response pathways. In embodiments, the genetic defect is a loss of function (LOF) mutation. In embodiments, the genetic defect is in one or more of the ZFAM2 or TYK2 genes. In embodiments, the genetic defect is a mutation in one or more of the IFNAR2 or TYK2 genes. In embodiments, the genetic defect is in one or more of the IFNARl, IFNAR2, TYK2 or IRF9 genes. In embodiments, the genetic defect is a mutation in one or more of the IFNARl, IFNAR2, TYK2 or IRF9 genes. In embodiments, the genetic defect or mutation is in one or more of theTYK2, IFNARl, STATI, STAT2, IRF7, IFIH1,TLR3, TBK1, IRF3, TICAMI, UNC93B1, TRAF3, or TLR7 genes.

[0026] In an embodiment, the genetic defect or mutation is in one or more of theor TYK2 genes. In an embodiment, the genetic defect or mutation is in one or more of the IFNARl, IFNAR2, TYK2 or 1RF9 genes. In an embodiment, the genetic defect or mutation is in one or more of the IFNAR2, TYK2, IFNARl, STATI or STA T2 genes. In an embodiment, the genetic defect or mutation is in one or more of the IFNARl, TYK2. IFNARl, STATI, STAT2, TLR3 or TLR7 genes. In an embodiment, the genetic defect or mutation is in one or more of the IFNARl, TYK2, IFNARl, IRF7, IFIH1, TLR3, TBK1, IRF3, TICAMI, or UNC93B1 genes. In an embodiment, the genetic defect or mutation is in one or more of the IFNARl, TYK2, IFNARl, STATI, STAT2, IRF7, IFIH1, TLR3, TBK1, IRF3 , TICAMI or UNC93B1 genes. In an embodiment, the genetic defect or mutation is in one or more of the IFNARl, TYK2, IFNARl, STATI, STAT2, IRF7, IFIH1, TLR3, TBK1, IRF3, TICAMI, UNC93B1 or TRAF3 genes. In an embodiment, the genetic defect or mutation is in one or more of the IFNARl, TYK2, IFNARl, STATI, STAT2, IRF7, TFIHl, TLR3, TBK1, IRF3, TICAMI, UNC93B1, TRAF3, or TLR7 genes.

[0027] Thus, the lack of IP-10 induction or a significantly limited IP-10 induction in response to IFN, particularly one or more of IFN-y, IFN-a2, IFN-j3, or IFN-oj, can be indicative and diagnostic of a genetic defect in the type I IFN and / or type II IFN response pathways. A mutation in one or more of the IFN response pathway genes, including in aspects a loss of function (LOF) mutation in one or more of the IFN response pathway genes, will result in lack of IP- 10 induction or a significantly limited IP- 10 induction in response to IFN. The one or more of the IFN response pathway genes may be selected from one or more of 1FNAR2 or TYK2 genes: one or more of the IFNARl, IFNAR2, TYK2 or IRF9 genes; one or more of the IFNARl, TYK2, IFNARl, STATI orSTATl genes; one ormore ofthe / FAARZ, TYK2, IFNARl, STATI, STAT2, TLR3 or TLR7 genes; one or more of the IFNARl, TYK2. IFNARl, IRF7, TFIHl, TLR3, TBK1, IRF3, TICAMI, or UNC93B1 genes; one or more of the IFNARl, TYK2. IFNARl, STATI, STAT2, IRF7, IFIH1, TLR3, TBK1, 1RF3 , TICAMI or UNC93BI genes: one or more of the IFNARl, TYK2, IFNARl, STATI, STAT2, IRF7, IFIH1, TLR3, TBK1, IRF3, TICAMI. UNC93BlorT / L4F3 genes; or one or more of the 1FNAR2, TYK2, IFNARl, STAT1. STAT2, IRF7, IFIHl, TLR3, TBKI, IRF3, TICAMI, UNC93BI, TRAF3, or TLR7 genes.

[0028] In another aspect, the invention provides a single marker assay evaluation, which indicates the possible presence of one (or more) inborn errors of type I IFN immunity. In an aspect, the invention provides a single marker assay evaluation, which indicates the possible presence of one (or more) inborn errors of type I IFN immunity which are associated with and identifiable in patients with severe viral disease, such as severe COVID- 19, severe influenza pneumonia. In particular, variations in type 11FN- related autosomal genes have been identified in patients with life-threatening COVID- 19 pneumonia. This and exemplary' type I IFN-related autosomal gene mutations has been described, for example in W02022 / 020569, published January 27, 2022, which is incorporated herein by reference,{00029] In accordance with the invention, by virtue of failed IFN induction of IP- 10, loss of function (LOF) mutations in one or more of IFNARl, IFNAR2, TYK2 and ZRF9 can be identified. In accordance with the invention, by virtue of failed IFN induction of IP-10, loss of function (LOF) mutations in one or more of IFNAR2, TYK2, IFNARl, STAT1, STAT2, IRF7, IFIHl, TLR3, TBKI, IRF3, TICAMI, UNC93B1, TRAF3 and TLR7 can be identified. In one embodiment, by virtue of failed IFN induction of IP-10, loss of function (LOF) mutations in one or more of IFNAR2, TYK2, IFNARl, STAT1, STAT2. IRF7, IFHH, TLR3, TBKI, IRF3, TICAMI, UNC93B1, TRAF3 and TLR7, or in one or more of IFNARl, IRF7, IFIHl, TLR3, TBKI, IRF3, TICAMI, UNC93B1, IFNAR2, STAT1, STAT2 or TRAF3 genes can be identified in patients with severe viral disease, such as severe viral pneumonia or encephalitis. In one embodiment, by virtue of failed IFN induction of IP- 10, loss of function (LOF) mutations in one or more of IFNARl, 1RF7, IFIHl, TLR3, TBKI, IRF3, TICAMI, UNC93B1, IFNAR2, STAT1, STAT2 or TRAF3 genes can be identified in patients with severe COVID- 19 and associated with aspects of severe COVID- 19 disease. In one embodiment, by virtue of failed IFN induction of IP- 10, loss of function (LOF) mutations in one or more of IFNARl, IRF7, IFIHl, TLR3, TLR7, TBKI, IRF3, TICAMI, UNC93B1, IFNAR2, STAT'l, STAT2 or TRAF3 genes can be identified in patients with severe COVID- 19 and associated with aspects of severe CO VID-19 disease.

[0030] Identification or indication / prediction, by virtue of failed IFN induction of IP-10, of any one or more of a LOF mutation or a mutation resulting in significantly reduced or inactive type-I and / or type II IFN pathway gene selected from one or more of IFNARl, IRF7, IFIHl, TI..R3, TLR7, TBKI, I.RF3. TICAMI, UNC93B1, IFNAR2, STAT1, STAT2, TRAF3 or IRF9, one or more of the IFNARl, IFNAR2, TYK2 or IRF9, one or more of IFNARl, IRF7, IFIHl, TLR3, TBKI, IRF3. TICAMI, UNC93B1, IFNAR2, STAT1, STAT2. TRAF3 or IRF9, one or more of IFNARL IRF7, IFIHl, TLR3, TBKI, IRF3, TICAMI, UNC93B1, IFNAR2, STATI, STAT2 or TRAF3 one or more of IFNARl, IRF7, IFIHL TLR3, TBKI, IRF3, TICAMI, UNC93B1 and IFNAR2, or one or more of IFNARl, IRF7, IFIHl, TLR3, TBKI, IRF3, TICAMI and UNC93B1 in an individual positive for SARS-CoV-2 infection provides critical information that the individual is altered in type I or type II IFN response and most vulnerable to severe disease. Identification of any one or more of a LOF mutation or a mutation in oneor more such gene resulting in significantly reduced or inactive protein encoded thereby in an individual, particularly a male individual, positive for SARS-CoV-2 infection provides critical information that the individual is altered in type I IFN response and in protective type I IFN immunity against SARS-CoV-2 and most vulnerable to severe disease, particularly to severe pulmonary and lung disease. Such an individual(s) or patient(s) must be managed and treated differently and with particular and specific care so as to avoid severe disease and pneumonia.

[0031] The presence of inborn errors of type I or type II interferon immunity or auto-antibodies against Type I IFNs or Type II IFN dictates and defines aspects and approaches to therapy for severe viral disease, such as severe COVID-19 disease, severe influenza. Also, the presence of inborn errors of type I or type II interferon immunity or auto-antibodies against Type I IFNs or type II IFN can dictate and define aspects and approaches to therapy for vaccine-associated disease, particularly live-attenuated vaccine-associated disease, such as yellow fever vaccine-associated disease, such as coronavirus vaccine-associated disease, such as COVID-19 vaccine-associated disease, such as live-attenuated CO VID-19 vaccine -associated disease. In certain embodiments, by virtue of failed IFN induction of IP- 10, the presence of loss of function recessive or dominant, homozygous or heretpzygous mutations in type I IFN genes results in an altered and / or nonfunctional or ineffective immune or IFN-mediated response to vires infection, thereby resulting in pathological and severe COVID-19 disease with SARS- CoV-2 infection. In certain embodiments, the presence of auto-antibodies directed against Type I IFNs results in an altered and / or nonfunctional or ineffective immune or IFN-mediated response to virus infection and live attenuated virus vaccination, thereby resulting in pathological and severe yellow fever vaccine-associated disease or in pathological and severe coronavirus vaccine-associated disease, such as live-attenuated CO VID- 19 vaccine-associated disease. Identification of the type I IFN or type II IFN pathway gene mutation present in a patient permits and enables the specific and targeted therapy such as administering the IFN protein which production or function is lost to the patient. The prediction of the presence of autoantibody(ies) or loss of function mutation(s) in the type I and / or type 11 IFN pathway via a single marker readout provides and permits rapid and effective management of disease, altered approach to therapy, avoidance of live attenuated vaccine(s), and indicates risk of such.[ 000032] The invention provides a method for predicting an altered type I IFN pathway or altered type II IFN pathway in a patient or individual comprising:(a) isolating a blood or serum sample from said patient or individual;(b) combining the blood or serum with IFN selected from IFNy, and one or more of IFNa2, EFNfJ or IFN® for a period of time so as to permit IFN induction; and(c) evaluating the induction, elevation, or increased expression ofIP-10 in response to IFNy, and one or more ofIFNo.2, IFNP or IFN©; wherein the failure of induction, elevation, or increased expression of IP-10 in response to IFNy, or in response to one or m ore of IFNa2, IFNp or IFN® indicates the presence of an autosomal recessive IFN deficiency or loss-of-fimction (LOF) mutation in a type I IFN or type II IFN pathway or responserelevant gene, or the presence of anti-type I IFN or anti-type 51 IFN specific auto-antibodies (auto- Abs) in the patient or individual.

[0033] In an embodiment of the method, the failure of IFNa2, IFN£ or IFNco mediated induction indicates the presence of an autosomal recessive IFN deficiency or loss-of-function (LOF) mutation in a type I IFN pathway or response relevant gene, or the presence of anti-type I IFN specific auto- antibodies (auto-Abs) in the patient or individual; and wherein the failure of IFNy mediated induction indicates the presence of an autosomal recessive IFN deficiency or loss-of-fimction (LOF) mutation in a type II IFN pathway or response relevant gene or the presence of anti-type II IFN specific auto-Abs, particularly anti-IFNy auto-Abs, in the patient or individual.

[0034] In embodiments, a method is provided further comprising:(d) evaluating the blood or serum sample for auto-antibodies specific for one or more type I IFN selected from:(i) IFN-ct2 and IFN-®;(ii) IFN-a2, IFN-m and IFN-0;(iii) IFN-a2, IFN-®, IFN-p and IFN-e;(iv) ll v-o.2, IFN-O), IFN-& IFN-e and IFN-K;(v) IFN-O.2, IFN-®, IFN-p and IFN-al / 13;(vi) IFN-a2, IFN-®, IFN-p, IFN- a 1 / 13 and IFN-al4;(vii) IFN-a2, IFN-co, IFN-p, IFN- al / 13, IFN-al 4 and IFN-a7:(viii) IFN-a2, IFN-®, IFN- al / 13, IFN-aI4. IFN-a7(ix) IFN-a2, IFN-®, IFN-p, IFN-e, IFN-al , IFN-a2, IFN-a6, IFN-al3, IMal4 and IFN- al 6; and(x) IFN-a2, IFN-w, IFN-al, IFN-a2, IFN-a6, !FN-al3, !FN-al4 and IFN-al6; or(e) evaluating the blood or serum sample for auto-antibodies specific for one or more type II IFN selected from IFNy,

[0035] In embodiments, the method further comprises:(d) evaluating the blood or serum sample for a LOF mutation in one or more type I IFN pathway gene or type II IFN pathway gene selected from:(i) IFNAR2 or TYK2-(i) IFNARl, IFNAR2, TYK2 or IRF9;(in) IFNAR2, TYK2, IFNARL STAT1 m STAT2;(iv) ZFMLR2, TYK2, IFNARl, STAT1, STAT2, TLR3 or TLR7;(v) IFNARL, TYK2, IFNARl, IRF7, IFIH1, TLR3, TBK1, IRF3. TTCAM1, or UNC93B1 ;(vi) IFNAR2, TYK2, IFNARl, STAT1, STAT2, IRF7,IFIH1, TLR3, TBK1, IRF3 , TICAM1 or UNC93BI;(vii) IFNARL, TYK2, IFNARl, STAT1, STAT2, 1RF7, IFIH1, TLR3, TBK1, IRF3 , TICAM1,UNC93B1M TRAF3; or(viii) IFNAR2, TY.K2, 1FNAR1, STAT1, STAT2, IRF7, IFIH1, TLR3, TBK1, IRF3 , TICAMI, UNC93B1, TRAF3, or TLR7;(e) wherein, a patient or individual determined to have an autosomal recessive IFN deficiency or LOF mutation is administered one or more Type I or Type II IFN to replace the function lost due to the mutation and / or is administered an immune-modulatory agent that increases or facilitates type I or type II IFN-mediated response.

[0836] In an embodiment of the method, the patient or individual determined to have a LOF mutation is administered IFN-a2 or IFN-p or IFN-y.

[0037] In another embodiment, the method further comprises:(d) evaluating the blood or serum sample for auto-antibodies specific for one or more type I IFN selected from:(i) IFN-a2 and IFN-®;(11) IFN-a2, IFN-® and IFN-p;(iii) IFN-O2, IFN-®, IFN-p and IFN-s:(iy) IFN-«2, IFN-®, IFN-p, IFN-e and IFN-K;(v) IFN-a2, IFN-®, IFN-0 and IFN-al / 13;(vi) IFN-a2, 1FN-®, IFN-p, IFN- al / 13 and IFN-aU;(vii) IFN-a2, IFN-®, IFN-p, IFN- al / 13, IFN-al 4 arid IFN-a7;(viii) IFN-a2, IFN-®, IFN- al / 13, IFN-aI4, IFN-a7(ix) IFN-a2, 1FN-®, IFN-P, IFN-e, IFN-al, IFN-a2, IFN-a6, IFN -al 3, IFN-al4 and IFN- al 6; and(x) IFN-O2, IFN-co, IFN-al, IFN-a2, IFN-a6, IFN-al3, IFN-al4 and IFN-al6; and(e) evaluating the blood or serum sample for a LOF mutation in one or more type I IFN pathway gene or type II IFN pathway gene selected from:(i) IFNAR2 or 7TK2;(ii) IFNAR1, IFNAR2, TYK2 or IRF9;(iii) ZRV4R2, TYK2, 1FNAR1, STAT1 or STAT2;(iv) IFNAR2, TYK2, IFNAR1, STAT1, STAT2, TLR3 or T.LR7;(v) W14A2, TYK2. IFNAR1, IRF7, IFIH1, TLR3, TBK1, IRF3, TIC AMI, or LWC9J8I ;(vi) IFNAR2, TYK2, IFNAR1, STAT1, STAT2, IRF7. IFIHL TLR3, 7’8K1, IRF3 , TICAMI or UNC93B1;(vii) IFNAR2, TYK2, IFNAR1, STAT1, STAT2, IRF7, IFIH1, TLR3, TBKl, 1RF3 , TICAMI, UNC93BIor TRAF3; or(viii) IFNAR2, TYK2, IFNAR1, STAT1. STAT2, IRF7, IFIH1, TLR3, TBKl, IRF3 , TICAMI, UNC93B1, TRAF3, or TLR7; or(f) evaluating the blood or serum sample for auto-antibodies specific for one or more type II IFN selected from IFNy.

[0038] In some embodiments or aspects, the blood or serum sample is evaluated for neutralizing antibodies,

[88839] In some embodiments, wherein anti-type I IFN or anti-type II IFN auto-antibodies are identified, plasmapheresis is then conducted on the patient or individual to deplete the antibodies, or wherein B cells, such as auto-reactive B cells, and / or plasmacytes or plasmablasts are depleted in the patient or individual.

[0040] In some embodiments, wherein anti-type I IFN or anti-type II IFN auto-antibodies are identified, a patient or individual having auto-Abs against one or more of IFN-o2, IFN-o, IFN-s, IFN- al, IFN-sfo, IFN-al3, IFN-al4 or IFN-al6 and not having auto-Abs against IFN-p is treated by administering IFN-p.

[0041] In some embodiments, a patient or individual having auto-Abs against one or more of £FN-a2 or IFN-O) and not having auto-Abs against IFN-p is treated by administering IFN-p.

[0042] In. some embodiments, a patient or individual having auto-Abs against one or more Type I IFN selected from IFN-w, IFN-s, IFN-p, IFN-K, and not having auto-Abs against IFN-u2 is treated by administering IFN-a2.

[0043] In some embodiments, a patient or individual not having auto-Abs against IFN-P is treated by administering IFN-p.

[0044] In some embodiments, a patient or individual having auto-Abs against one or more Type I IFN is treated by administering an IFN subtype which is not neutralized by the patient’s or individual’s auto- Abs.

[0045] In some embodiments, a patieni or individual having one or more anti-type I IFN auto-antbody is not administered a viral vaccine, particularly a live attenuated or inactivated viral vaccine, or wherein a patient or individual positive for or at risk for infection or severe virus infection, or having vaccine- associated disease is treated to remove or deplete the auto-Abs and / or is administered a type I IFN or type II IFN against which they do not have auto-Abs and / or is administered an immune-modulatory agent that increases or facilitates type I IFN-mediated response or type II IFN-mediated response.

[0846] In some embodiments, the patient or individual is suffering from or at risk of infection selected from SARS-CoV-2 infection, influenza infection, West Nile Virus infection, Middle East respiratory syndrome (MERS), intra-macropbage infection, mycobacterial disease and tuberculosis.

[0047] In an aspect of the invention, methods are provided for predicting the presence of an autosomal recessive IFN deficiency or loss-of-function (LOF) mutation in a type I IFN pathway or response relevant gene, or Hie presence of anti-type I IFN specific auto-Abs in a patient or individual positive for or at risk for SARS-CoV-2 infection, influenza infection, West Nile Virus infection, Middle East respiratory syndrome (MERS), intra-macrophage infection, mycobacterial disease or tuberculosis, having CO VID- 19 disease, prior to vaccination with live atenuated vaccine (LAV), or having vaccine-associated disease and thereby determining treatment and treating the patient or individual, wherein a patient or individual having one or more auto-antbody is not administered the vaccine or wherein a patient or individual positive for or at risk for SARS-CoV-2 infection, influenza infection. West Nile Virus infection, Middle East respiratory syndrome (MERS), intra-macrophage infection, mycobacterial disease, or tuberculosis, having COVID-19 disease, or having vaccine-associated disease is treated to remove or deplete the auto- Abs and / or is administered a type I IFN against which they do not have auto- Abs and / or is administered an immune-modulatory agent that increases or facilitates type I IFN- mediated response.

[0048] In an embodiment, the LAV is a COVID- 19 / SARsCoV-2 vaccine or is a yellow fever vaccine, In another embodiment, the vaccine- associated disease is COVID-I9 / SARsCoV-2 vaccine-associated disease or is yellow fever virus (YFV) vaccine-associated disease.

[0049] The invention provides an assay for predicting an altered type I IFN pathway or altered type II IFN pathway in a patient or individual comprising:(a) contactin g a sample of blood or serum sample from the patient or individual with IFN selected from IFNy, and one or more of IFNa2, IFN$ or IFNe) for a period of time so as to permit IFN induction; and(b) evaluating the induction, elevation, or increased expression of IP- 10 in response to IFNy, and one or more of !FNa2, IFNp or IFN®; wherein the failure of induction, elevation, or increased expression of IP- 10 in response to IFNy, or in response to one or more of IFNa2, IFNp or IFN® indicates the presence of an autosomal recessive IFN deficiency or loss-of-function (LOF) mutation in a type I IFN or type II IFN pathway or response relevant gene, or the presence of anti-type I IFN or anti-type II IFN specific auto-antibodies (auto- Abs) in the patient or individual.

[0050] In an embodiment, the assay comprises:(a) contacting a sample of blood or serum sample from the patient or individual with IFNy, and one or more of IFNa2, IFNp or IFN® for a period of time so as to pennit IFN induction; and(b) evaluating the induction, elevation, or increased expression of IP- 10 in response to IFNy and one or more of IFNa2, IFNp or IFN®.

[0051] In an embodiment, the assay further comprises evaluating the presence of auto-antibodies directed against one or more Type I IFN or Type II IFN, comprising:(c) contacting the sample of blood or serum with one or more recombinant type I IFN protein selected from IFN-a2, IFN-to, IFN-3, and IFN-y, wherein each IFN protein is labeled with a distinct detectable tag or marker to form an antibody-protein complex;(d) contacting any antibody-protein complex of (a) with one or more labeled anti-human immune globulin molecule that will bind and label auto-antibody bound to any one or more IFN protein; and(e) specifically and selectively detecting each type I IFN protein bound by specific auto-Ab thereto.

[0052] In an embodiment, one or more recombinant type I IFN protein is labeled with a fluorescent marker. In an embodiment, one or more recombinant type I IFN protein is covalently coupled to a magnetic bead with a fluorescent marker. In another embodiment, each of the one or more recombinant type I IFN proteins is covalently coupled to a magnetic bead with a distinct and differential fluorescent marker. In another embodiment, the one or more labeled anti-human immune globulin molecule that will bind and label bound auto-antibody is a labeled non-human animal derived anti-human IgG.

[0053] In an embodiment, the presence of neutralizing auto-antibodies is determined.

[0054] In an embodiment of the assay, the blood or serum sample is further evaluated for a LOF mutation in one or more type I IFN pathway gene or type II IFN pathway gene comprising assessing one or more gene mutation by virtue of one or more probe directed against one or more type I IFN pathway gene or type II IFN pathway gene selected from:(i) 7FW.4F2 or TYK2'(ii) IFNAR1 , IFNAR2, TYK2 or WP;(iii) IFNAR2, TYK2, 1FNAR1, STAT1 or STAT2;W IFNAR2, TYK2, IFNAR1, STAT1, STAT2, TLR3 or TIFF;(y) IFNAR2, TYK2, IFNAR1, IRF7, IFIH1, TLR3, TBK1,IRF3, TICAM1, or UNC93B1 ;(vi) IFNAR2, TYK2, IFNARL STAT1, STAT2, IRF7, IFIHJ, TLR3, TBK1, IRF3 , TICAM1 or UNC93B1;(vii) IFNAR2, TYK2, IFNAR1, STAT1, STAT2, IRF7JFIH1, TLR3, TBK1, IRF3 , TICAM1, UNC93B1 or TRAF3; or(viii) IFNAR2, TYK2, IFNAR1, STAT / , STAT2, IRF7, IFIffl, 1ZR3, TBK1, IRF3 , TIC AMI. UNC93B1, TRAF3, or TLR7.

[0055] The invention further provides a kit for evaluating or predicting an altered type I IFN pathway or altered type II IFN pathway in a patient or individual comprising:(a) IFN selected from IFN?, and one or more of IFNct2, IFNp or IFN®; and(b) an agent, antibody or probe capable of binding IP- 10 protein; for a period of time so as to pennit IFN induction; and(c) a means for specific and selective detection of each IP- 10 protein bound by the agent, antibody or probe; wherein the failure of induction, elevation, or increased expression of IP-10 in response to IFNy, or in response to one or more of IFN«2, IFN0 or IFNo indicates an altered type I IFN pathway or altered type II IFN pathway.

[0056] In an embodiment, the kit further comprises a means for determining the presence of an autosomal recessive IFN deficiency or loss-of-function (LOF) mutation in a type I IFN or type II IFN pathway or response relevant gene, or the presence of anti-type I IFN or anti-type II IFN specific auto- antibodies (auto-Abs) in the patient or individual.(00057] In an embodiment, a kit is provided for evaluating the presence of auto-antibodies directed against one or more Type I IFN or Type II IFN in a patient or individual, wherein the kit further comprises:(a) one or more recombinant type I IFN protein selected from IFN-a2, IFN-<a, IFN-P and IFN-y, wherein each IFN protein is labeled with a distinct detectable tag or marker;(b) one or more labeled anti-human immune globulin molecule that will bind and label auto- antibody bound to any one or more IFN protein;(c) a means for specific and selective detection of each type I IFN protein bound by specific auto- Ab thereto,J000S8] In another embodiment, one or more recombinant type I IFN protein is labeled with a fluorescent marker, or wherein one or more recombinant type I IFN protein is covalently coupled to a magnetic bead with a fluorescent marker. In an embodiment, each of the one or more recombinant type I IFN proteins is covalently coupled to a magnetic bead with a distinct and differential fluorescent marker.

[0059] In some embodiments, the kit provides for further evaluating the blood or serum sample for a LOF mutation in one or more type I IFN pathway gene or type II IFN pathway gene comprising assessing one or more gene mutation, wherein the kit further comprises of one or more probe directed against one or more type I IFN pathway gene or type II IFN pathway gene selected from:(i) IFNAR2 or TYK2;(ii) IFNARI, IFNAR2, TYK2 or IRF9:(iii) IFNAR2, TYK2, IFNARI, STAT! mSTAT2;(iv) IFNAR2, TYK2, IFNARI, STAT1, STAT2, TLR3 or TLR7;(v) IFNAR2, TYK2, IFNARI, IRF7, IFIHI, TLR3, TBKI, IRF3, TICAM1, or UNC93B1 ;(vi) IFNAR2, TYK2, IFNARI, STAT1, STAT2, IRF7, IFIHI, TLR3, TBKL IRF3 , TICAM1 or UNC93B1;(vii) 1FNAR2, TYK2, IFNARI, STAT1, STAT2, IRF7, IFIHI, TLR3, TBKI, IRF3 , TICAMI, UNC93BIor TRAF3; or(viii) IFNAR2, TYK2, IFNARI, STAT1, STAT2, IRF7, IFIHI, TLR3, TBKI, IRF3 , TIC AMI, UNC93B1, TRAF3, cr TLR7.

[0960] In embodiments, the assays or kits provide for evaluating a patient or individual positive for or at risk for SARS-CoV-2 infection or having COVID-19 disease or prior to vaccination with live attenuated vaccine or having vaccine-associated disease for the presence of an autosomal recessive IFN deficiency or loss-of- function (LOF) variation or mutation in a type I IFN pathway or response relevant gene and thereby determining treatment or whether the patient or individual can be safely vaccinated or should be vaccinated and / or treating the patient or individual, wherein a patient or individual determined to have an autosomal recessive IFN deficiency or LOF mutation is administered one or more Type IIFN to replace the function lost due to the mutation and / or is administered an immune-modulatory agent that increases or facilitates type I IFN-mediated response.

[0061] In an embodiment, the patient or individual determined to have a LOF mutation is administered a Type 1 IFN. In another embodiment, the patient or individual determined to have a LOF mutation is administered IFN-a2 or IFN-p or IFN-y.

[0062] Other objects and advantages will become apparent to those skilled in the art from a review of the ensuing detailed description, which proceeds with reference to the following illustrative drawings, and the attendant claims.BRIEF DESCRIPTION OF THE DRAWINGS

[0063] The patent or patent application contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the U.S. Patent and Trademark Office upon request and payment of the necessary fee.

[0064] FIG. 1A to IF: IP-10 (CXCLI0) induction after the stimulation of whole blood from healthy donors with type I IFNs (A and C) IP- 10 induction, assessed with plasma supernatants alter the stimulation of whole blood with various concentrations of glycosylated IFN-a2 for 16 h, as measured by LEGENDplex™. Blood samples were collected 8 to 24 h before stimulation. Three (A) or nine (C) healthy donors were tested once for each set of conditions. (B) CXLC10 mRNA induction after the stimulation of PBMCs from three healthy donors with I ng / mL glycosylated IFN-«2 for 6 h, as measured by RT-qPCR. (D) Fold-induction of IP- 10 after the stimulation of whole blood with 1 ng / mL glycosylated IFN-u2 for 16 h, as measured by LEGENDplex™. Nine healthy donors were tested once each. Blood samples were collected 8 to 24 h before stimulation. (E and F) IP- 10 induction, assessed with plasma supernatants after the stimulation of whole blood with various concentrations of glycosylated IFN-p (E) or glycosylated IFN-co (F) for 16 b, as measured by LEGENDplex™. Blood samples were collected 8 to 24 h before stimulation. Five healthy donors were tested once for each set of conditions.

[0065] FIG. 2A and 2B (A) IL -6 induction after the stimulation of whole blood from three healthy donors with various concentrations of glycosylated IFN-&2 for 16 h. IL-6 levels were assessed in plasma supernatants by LEGENDplex™. (B) CXCL10 fold-induction after the stimulation of PBMCs from nine healthy donors with 1 ng / mL glycosylated IFN-a2 for 6 h, as assessed by RT-qPCR.

[0066] FIG. 3A to 3D: Whoie-transeriptome analysis after PBMC stimulation with IFN-u2(A) Volcano plot analysis of bulk RNAseq performed on total mRNA extracted from the PBMCs of three healthy donors after stimulation with 1 ng / mL glycosylated IFN~a2 for 6 h. The labeled genes (MSRI.GBPiPl, APOBEC3A, SIGLECI, IDO1, SERPING1, EPHB2, NEURL3, BATF2, BCL2L14, OTOF, IFITM3, ERICH3, PRLR, LINCO2068, CXCL10, APOBEC3B, HESXi, CXCL11 andCCL8) are the top 20 genes displaying the highest levels of induction relative to non-stimulated conditions. (B- C-D) Volcano plot analysis showing the transcripts induced in cDC2 cells (B), classical monocytes (C),and non-classical monocytes (D), as determined by scRNAseq (Parse Bioscience). PBMCs of three healthy donors were stimulated with 1 ng / mL glycosylated IFN-a2 for 6 h and whole mRNA was extracted.

[0067] FIG. 4A to 4G: Assessment of other potential target proteins after the stimulation of whole blood from healthy donors with type I IFNs (A) I-TAC induction after the stimulation of whole blood from three healthy donors with various concentrations of glycosylated IFN-a2 for 16 h. I- TAC levels were assessed in plasma supernatants by LEGENDplex™. (B-D) CD 169 induction after the stimulation of whole blood from three healthy donors with glycosylated IFN-a2, IFN-P or IFN-®. CD169 levels were assessed by ELISA. (E-G) MCP-2 induction after the stimulation of whole blood from three healthy donors with various concentrati ons of glycosylated IFN-a2, IFN-P and IFN-to. MCP- 2 levels were assessed in plasma supernatants by LEGENDplex™.

[0068] FIG. SA to 5H: Evaluation of tech n leal parameters and assessment of the effects of other cytokines (human IFN-c, IFN-K, and IFN-y, and cynomolgus monkey and mouse IFN-a2) on IP- 10 induction. (A) IP- 10 induction after stimulation with 100 U / mL or 1,000 U / mL recombinant human IFN-s, IFN-K or IFN-y for 16 h. Three healthy donors were tested for each set of conditions. IP- 10 levels were then assessed in plasma supernatants by LEGENDplex™. (B) IP-10 induction after stimulation with 100 U / mL or 1,000 U / mL recombinant human IFN-s, IFN-K or IFN-y for 16 h. Three healthy donors were tested for each set of conditions. IP- 10 levels were then assessed in plasma supernatants by ELISA. (C) Effect of time between collection and stimulation on IP- 10 induction. IP- 10 levels were assessed in plasma supernatants by LEGENDplex™ after the stimulation of whole blood with I ng / mLor -y for 16 h. Three healthy donors were tested for each set of conditions. (D) Effect of the matrix on which blood is collected. Lithium heparin, EDTA and citrate tubes were used to collect blood from three healthy donors. Whole-blood samples were stimulated with 1 ng / mL IFN-a2, ~P, -co or -y for 16 h, IP- 10 levels were then assessed in plasma supernatants by LEGENDplex™. (E) Kinetics of IP- 10 induction (effect of stimulation time). Whole blood from two healthy donors was stimulated with the indicated concentrations of IFNs for 2 h, 4 h, 6 h, 8 h, 10 h, 12 h, 14 h and 16 h. IP- 10 levels were then assessed in plasma supernatants by LEGENDplex™. (F) Effect of the presence or absence of 5% CCh on IP-10 production after the stimulation of whole blood from three healthy donors with I ng / mL IFN-a2, -p, -m or -y for 16 b. -CO?: stimulation at 37°C without CO2 supplementation, +CO2: stimulation at 37°C with 5% CO2 supplementation (G) IP-10 induction after the stimulation of whole blood from HDs with 1 pg / mL anti-IFNARI or anii-IFNAR2 neutralizing mAbs The mAbs were incubated with whole blood for 30 minutes before stimulation with IFNs. (II) IP- 1 D induction after the stimulation of whole blood from HDs with 10 pg / mL anti-IFNARI or anti-IFNAR2 neutralizing mAbs. The mAbs were added at the same time as the IFNs.

[0069] FIG, 6A to 6Ft IP-10 induction after the stimulation of whole blood from patients with impaired type I IFN-dependent immunity'. (A) IP- 10 induction after the stimulation of whole blood from five APS-1 patients and nine healthy donors with 10 ng / mL glycosylated IFN-a2 (left), IFN-p(middle) or IFN-to (right) for 16 h. IP-10 levels were measured in plasma supernatants by ELISA. Whole blood from three APS • 1 patients and five healthy donors was also stimulated with 1 ,000 U / mL IFN-y as a control. IP- 10 levels were compared between the HD and APS-1 groups by implementing non-parametric Mann-Whitney tests in GraphPad Prism. Ns: not significant: **: P-value < 0.001 (B) IP- 10 induction after the stimulation of whole blood from five APS-1 patients and nine healthy donors with 1 ng / mL glycosylated IFN-a2 (left), IFN-p (middle) or IFN-m (right) for 16 h. IP- 10 levels were measured in plasma supernatants by ELISA. Whole blood from three APS-1 patients and five healthy donors was also stimulated with 100 U / mL IFN-y as a control. Multiple Mann-Whitney tests were performed to compare the HD and APS-1 groups for each set of stimulation conditions, IP- 10 levels were compared between the HD and APS-1 groups in non-parametric Mann- Whitney tests implemented in GraphPad Prism. Ns: not significant **: P-value < 0.001 (C) IP- 10 induction in plasma supernatants after the stimulation of whole blood from a patient neutralizing low concentrations of IFN-a2 (1 ng / mL - 100 pg / mL) in a luciferase assay. Whole-blood samples from the patient and three healthy donors were stimulated with glycosylated type 1 (10 ng / mL) or type II ( 1 ,000 U / mL) IFNs for 16 h. IP- 10 levels were then assessed in plasma supernatants by ELISA. (D) TP- 10 induction in plasma supernatants after the stimulation of whole blood from a patient neutralizing low concentrations of IFN-a2 (1 ng / mL - 100 pg / mL) in a luciferase assay. Whole-blood samples from the patient and three healthy donors were stimulated with glycosylated type I (1 ng / mL) or type II (100 U / mL) IFNs for 16 h. IP- 10 levels were then assessed in plasma supernatants by ELISA. (E) IP- 10 induction in plasma supernatants after the stimulation of whole blood from a patient with the NFKB2 p52LO!7lKB8GOfmutation, a female patient with NEMO deficiency (incontinentia pigmenti), and a patient with auto-Abs neutralizing type I IFNs with no genetic diagnosis. TC: Travel control. Whole-blood samples were stimulated with glycosylated type I (1 ng / mL) or type II (100 U / mL) IFNs for 16 h. IP- 10 levels were then assessed in plasma supernatants by ELISA. (F) IP- 10 induction in plasma samples from patients with autosomal recessive IFNAR1, IFNAP2, TYK2, or IRF9 deficiency. Whole-blood samples from the patients and three healthy donors were stimulated with glycosylated type I (1 ng / mL) or type II (100 U / mL) IFNs for 16 h. IP-10 levels were then assessed in plasma supernatants by ELISA. A TC blood sample from a healthy individual was available for the one of the IFNAR27' patients. These samples were stimulated >48 h after blood sampling. The blood of the TYK2’'" patient was stimulated 24 h after blood sampling. The blood of the IRF9’Apatient was stimulated 6 h after blood sampling.

[0070] FIG. 7 depicts IP- 10 induction after the stimulation of whole blood from a patient with auto- Abs neutralizing IFNy. IP- 10 induction was measured after the stimulation of whole blood from one patient (anti-IFN-y patient) and one travel control (TC) with 100 or 1,000 U / mL IFN-y, or with 10 ng / mL glycosylated IFN-a2, IFN-p, or IFN-ei (as controls) for 16 h. IP- 10 levels were measured in plasma supernatants by ELISA. The patient (pink) could almost completely neutralize 100 U / mL IFN- y, but not 1,000 U / mL, and not type I IFNs. By contrast, the travel control (gray) could not neutralize any of the IFNs and concentrations tested.DETAILED DESCRIPTION[09071 j In accordance with the present invention there may be employed conventional molecular biology, microbiology, and recombinant DNA techniques within the skill of the art. Such techniques are explained folly in the literature. See, e.g., Sambrook et al, "Molecular Cloning: A Laboratory Manual" (1989); "Current Protocols in Molecular Biology" Volumes I-II1 [Ausubel, R. M., ed. (1994)1; "Cell Biology: A Laboratory Handbook" Volumes I-III [J. E. Celis, ed, (1994))]: "Current Protocols in Immunology" Volumes MH [Coligan, J. E., ed. (1994)]; "Oligonucleotide Synthesis" (MJ. Gait ed. 1984); "Nucleic Acid Hybridization" [B.D. Hames & S.J. Higgins eds. (1985)]; "Transcription And Translation" [B.D. Hanies & S.J. Higgins, eds. (1984)1; "Animal Cell Culture” [R.I. Freshney, ed. (1986)]; "Immobilized Cells And Enzymes" [IRL Press, (1986)]; B. Perbal, "A Practical Guide To Molecular Cloning" (1984).

[0072] Therefore, if appearing herein, the following terms shall have the definitions set out below.A. TERMINOLOGY

[0073] The term “antibody” describes an immunoglobulin whether natural or partly or wholly synthetically produced. The term also covers any polype pts de or protein having a binding domain which is, or is homologous to, an antibody binding domain. CDR grafted antibodies are also contemplated by this term. An "antibody" is any immunoglobulin, including antibodies and fragments thereof, that binds a specific epitope. The term encompasses polyclonal, monoclonal, and chimeric antibodies. The tern “artibody(ies)” includes a wild type immunoglobulin (Ig) molecule, generally comprising four full length polypeptide chains, two heavy (H) chains and two light (L) chains, or an equivalent Ig homologue thereof (e.g., a camelid nanobody, which comprises only a heavy chain); including full length fonctional mutants, variants, or derivatives thereof, which retain the essential epitope binding features of an Ig molecule, and including dual specific, bispecific, multispecific, and dual variable domain antibodies; Immunoglobulin molecules can be of any class (e.g., IgG, IgE, IgM, IgD, IgA, and IgY), or subclass (e.g,, IgGl, IgG2, lgG3, IgG4, IgAl, and IgA2). Also included within the meaning of the term “antibody” are any “antibody fragment”.[0(1974] An “antibody fragment” means a molecule comprising at least one polypeptide chain that is not fall length, including (i) a Fab fragment, which is a monovalent fragment consisting of the variable light (VL), variable heavy (VH), constant light (CI..) and constant heavy I (CHI) domains; (ii) a F(ab')2 fragment, which is a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (ii i) a heavy chain portion of an Fab (Fd) fragment, which consists of the VH and CHI domains; (iv) a variable fragment (Fv), which consists of the VL and VH domains of a single arm of an antibody, (v) a domain antibody (dAb) fragment, which comprises a single variable domain (Ward, E.S. et al., Nature 341, 544-546 (1989)); (vi) a camelid antibody; (vii) an isolated complementarity determining region (CDR); (viii) a Single Chain Fv Fragment wherein a VH domain and a VL domainare linked by a peptide linker which allows the two domains to associate to form an antigen binding site (Bird et al, Science, 242, 423-426, 1988; Huston et al, PNAS USA, 85, 5879-5883, 1988); (ix) a diabody, which is a bivalent, bispecific antibody in which VH and VL domains are expressed on a single polypeptide chain, but using a linker that is too short to allow for pairing between the two domains on the same chain, thereby forcing the domains to pair with the complementarity domains of another chain and creating two antigen binding sites (WO94 / 13804; P. Holliger et al Proc. Natl. Acad. Sci. USA 90 6444-6448, (1993)); and (x) a linear antibody, which comprises a pair of tandem Fv segments (VH- CH1-VH-CH1) which, together with complementarity light chain polypeptides, form a pair of antigen binding regions; (xi) multivalent antibody fragments (scFv dimers, trimers and / or tetramers (Power and Hudson, J Immunol. Methods 242: 193-204 9 (2000)); (xii) a minibody, which is a bivalent molecule comprised of scFv fused to constant immunoglobulin domains, CH3 or CH4, wherein the constant CH3 or CH4 domains serve as dimerization domains (Olafsen T et al (2004) Prot Eng Des Sei 17(4):315- 323; Hollinger P and Hudson PJ (2005) Nature Biotech 23(9): 1126-1136); and (xiii) other non-foll length portions of heavy and / or light chains, or mutants, variants, or derivatives thereof, alone or in any combination.

[0075] As antibodies can be modified in a number of ways, the term "antibody" should be construed as covering any specific binding member or substance having a binding domain with the required specificity. Thus, this term covers antibody fragments, derivatives, functional equivalents and homologues of antibodies, including any polypeptide comprising an immunoglobulin binding domain, whether natural or wholly or partially synthetic. Chimeric molecules comprising an immunoglobulin binding domain, or equivalent, fused to another polypeptide are therefore included.

[0076] The term “comprise” generally used in the sense of include, that is io say permitting the presence of one or more features or components.[0(1077] The term “consisting essentially of' refers to a product, such as a peptide sequence, of a defined number of residues which is not covalently attached to a larger product.

[0078] The term "oligonucleotide," as used herein in referring to a probe of use the present invention, is defined as a molecule comprised of two or more ribonucleotides, preferably more than three. Its exact size will depend upon many factors which, in turn, depend upon the ultimate function and use of the oligonucleotide. The term "primer" as used herein refers to an oligonucleotide, which is capable of acting as a point of initiation of synthesis when placed under conditions in which synthesis of a primer extension product, which is complementary to a nucleic acid strand, is induced, i.e., in the presence of nucleotides and an inducing agent such as a DNA polymerase and at a suitable temperature and pH. The primer may be either single-stranded or double-stranded and must be sufficiently long to prime the synthesis of the desired extension product in the presence of the inducing agent. The exact length of the primer will depend upon many factors, including temperature, source of primer and use of the method. For example, for diagnostic applications, depending on the complexity of the target sequence.the oligonucleotide primer typically contains 15-25 or more nucleotides, although it may contain fewer nucleotides.[00079 = The term "agent" means any molecule, including polypeptides, antibodies, polynucleotides, chemical compounds and small molecules. In particular the term agent includes compounds such as test compounds or drug candidate compounds.

[0080] The term "assay” means any process used to measure a specific property of a protein or of a compound. A "screening assay" includes a process used to characterize or select proteins or polypeptides based upon their activity, which may include signalling or downstream protein or response activity. A "screening assay" includes a process used to characterize or select compounds based upon their activity' from a collection of compounds.

[0081] The term "preventing” or "prevention" refers to a reduction in risk of acquiring or developing a disease or disorder (i.e., causing at least one of the clinical symptoms of the disease not to develop) in a subject that may be exposed to a disease-causing agent, or predisposed to the disease in advance of disease onset. The term "prophylaxis" is related to and encompassed in the term ‘prevention’, and refers to a measure or procedure the purpose of which is to prevent, rather than to treat or cure a disease. Non- limiting examples of prophylactic measures may include the administration of vaccines; the administration of low molecular weight heparin to hospital patients at risk for thrombosis due, for example, to immobilization; and the administration of an anti-malarial agent such as chloroquine, in advance of a visit to a geographi cal region where malaria is endemic or the risk of contracting malaria is high.[000S2| "Therapeutically effective amount" means that amount of a drag, compound, antibody, or pharmaceutical agent that will elicit the biological or medical response of a subject that is being sought by a medical doctor or other clinician. In particular, with regard to gram-positive bacterial infections and growth of gram-positive bacteria, the term “effective amount” is intended to include an effective amount of a compound or agent that w ill bring about a biologically meaningful decrease in the amo unt of or extent of disease or flare free time period and or increase in length of a subject’s survival or period disease-free or in remission or free of flare(s). The phrase "therapeutically effective amount" is used herein to mean an amount sufficient to prevent, and preferably reduce by at least about 30 percent, more preferably by at least 50 percent, most preferably by at least 90 percent, a clinically significant change, or enhanced survival or disease-free period by at least about 30 percent, more preferably by at least 50 percent, most preferably by at least 90 percent.

[0083] The term "treating" or "treatment" of any disease, condition, or infection refers, in one embodiment, to ameliorating the disease or infection (i.e., arresting the disease or growth of the infectious agent or bacteria or reducing the manifestation, extent or severity of at least one of the clinical symptoms thereof) In another embodiment "treating" or "treatment” refers to ameliorating at least one physical parameter, which may not be discernible by the subject, In yet another embodiment, "treating” or "treatment" refers to modulating the disease or infection, either physically, (e.g., stabilization of adiscernible symptom), physiologically, (e.g,, stabilization of a physical parameter), or both. In a further embodiment, "treating" or "treatment" relates to slowing the progression of a disease or reducing an infection.

[0084] The phrase "pharmaceutically acceptable" refers to molecular entities and compositions that are physiologically tolerable and do not typically produce an allergic or similar untoward reaction, such as gastric upset, dizziness and the like, when administered to a human.

[0005] As used herein, "pg" means picogram, "ng" means nanogram, "ug” or "pg" mean microgram, "mg" means milligram, "ul" or "pl" mean microliter, "ml" means milliliter, "I" means liter.B. DETAILED DISCLOSURE.

[0086] Type I interferons (IFNs) are key components of the immediate antiviral response and are critical for restricting viral replication and spread. Type I IFNs work through autocrine and paracrine type I IFN receptor (IFNAR) signalling. It has recently been reported that minimal amounts of type I IFNs have been detected in the peripheral blood or lungs of patients with severe COVID- 19 (Blanco- Melo D et al (2020) Cell 181 : 1036-1045 (doi.org / 10.1016 / j.cell.2020.04.026); Hadjaj J et al (2020) Science 10.1126 / science.abc6027). However, the kinetics and requirements of systemic and local immune system response and immune modulators, including IFN responses, during COVID-19 are unclear and largely unknown, as are the specific contribution and requirements of response, including IFN responses, as they may contribute to COVID-19 pathogenesis and disease severity. Understanding and recognition of aspects and IFN responses, particularly those of the type I IFNs, correlated, associated with or even causative of an altered or ineffective response to SARS-CoV-2 infection is important, if not essential, in order to best and most quickly and appropiately identify a COVID-19 patient at significant risk or likelihood of severe COVID-19 disease so as to monitor, treat or specifically manage them in terms of therapeutic approaches or agents.

[99987] There are 17 type I IFN genes in humans, which encode 16 proteins (because two IFN alpha genes encode proteins of Identical sequence). IFN beta is unique and ubiquitous. IFN kappa is unique and expressed in the skin. IFN epsilon in the reproductive tract. IFN omega is expressed ubiquitously but more so by leukocytes, as are the 12 IFN alpha types. The known auto-Abs neutralize the 12 alpha IFNs (there may be cases that neutralize only some alphas), or the omega, or both, and more rarely the beta. The assay and test provided in accordance with the instant invention can detect auto-Abs against each of the 16 IFNs.

[0088] Human type I IFNs are a large subgroup of interferon proteins that help regulate the activity of the immune system . The mammalian type I IFNs are designated IFN-a (alpha), IFN-p (beta), IFN-K (kappa), IFN-s (epsilon) and IFN-ca (omega). All type I IFNs bind a specific cell surface receptor complex the IFN-a receptor (IFNAR) that consists of IFNAR1 and IFNAR2 chains. The IFN-a proteins are produced mainly by plasmacytoid dendritic cells (pDCs) and are involved in innate immunity against viral infection. IFN-a proteins comprise 13 subtypes IFN-al, IFN-a2, IFN-a4, IFN-a5, IFN-a6, IFN-a7, IFN-a8, IFN-a 10, IFN-al 3, IFN-al4, IFN-al 6, IFN-al 7 and IFN-a21. Several recombinantIFN proteins are approved as therapeutic proteins and available and in clinical use. Recombinant IFN- a is available as a thereapeutic protein as either Intron® A (interferon alfa-2b) or Roforon®-A (interferon alfa-2a) and is administered by subcutaneous, intravenous or intramuscular injection. Pegyiated forms of IFN-a are also available particularly pegyiated interferon alfa-2a (trade name Pegasys) and pegyiated interferon alfa-2b (tradename Pegintron). Recombinant Interferon beta IFN-p is available as a therapeutic in several marketed and approved forms including Avonex (interferon beta la), Rebif (interferon beta la), Plegridy (peginterferon beta la), Betaferon (interferon beta lb), Extavia (interferon beta lb). Pegyiated IFN-p is available as plegridy (Biogen). There is one known type II IFN which is IFN-y.

[0089] The present invention has discovered that the presence of inborn errors of type I or Type II interferon immunity or auto-antibodies against Type I IFNs or Type II IFN can be evaluated by assessment of a single marker readout, particularly induction of IP- 10 via IFN. In certain embodiments, the presence of loss of function recessive or dominant, homozygous or heretozygous mutations in type I IFN genes results in an altered and / or nonfunctional or ineffective immune or IFN- mediated induction of IP-10. Identification of the IFN gene mutation or the IFN specific auto- antibody present in a patient permits and enables the specific and targeted therapy such as administering the IFN protein which function is lost to the patient.

[0090] The presence of auto antibodies directed against Type I IFNs (or to type II IFN. IFN-y), results in an altered and / or nonfunctional or ineffective immune or IFN -mediated response to virus infection, thereby, for example, resulting in pathological and severe COVID-19 disease with SARS-CoV-2 infection. Patients with auto-antibodies against an IFN type will not respond to treatment with that IFN subtype, and in fact administration of that subtype could be harmful and dangerous. The recognition that up to 10% of severe COVID-19 patients have circulating neutralizing auto-Abs directed against specific IFN proteins now provides approaches and methods for identifying these patients, even and particularly at early stage of disease or upon initial recognition of SARS-CoV-2 infection so that they can be differentially managed and treated.

[0091] The invention provides a method for predicting an altered type 1 IFN pathway or altered type II IFN pathway in a patient or individual comprising:(a) isolating a blood or serum sample from said patient or individual;(b) combining the blood or serum with IFN selected from IFNy, and one or more of IFNo2, IFN|3 or IFN® for a period of time so as to permit IFN induction; and(c) evaluating the induction, elevation, or increased expression of IP- 10 in response to IFNy, and one or more of IFNo2, IFNp or IFN®; wherein the failure of induction, elevation, or increased expression of IP-10 in response to IFNy, or in response to one or more of IFNa2, IFN|$ or IFN® indicates the presence of an autosomal recessive IFN deficiency or loss-of-function (LOF) mutation in a type I IFN or type II IFN pathway or responserelevant gene, or the presence of anti-type I IFN or anti-type II IFN specific auto-antibodies (auto- Abs) in the patient or individual.

[0092] In an embodiment of the method, the failure of IFNa2, IFNp or IFN® mediated induction indicates the presence of an autosomal recessive IFN deficiency or loss-of-function (LOF) mutation in a type I IFN pathway or response relevant gene, or the presence of anti-type I IFN specific auto- antibodies (auto-Abs) in the patient or individual; and wherein the failure of IFNy mediated induction indicates the presence of an autosomal recessive IFN deficiency or loss-of-function (LOF) mutation in a type II IFN pathway or response relevant gene or the presence of anti-type II IFN specific auto-Abs, particularly anti-IFNy auto-Abs, in the patient or individual,

[0093] In embodiments, a method is provided further comprising:(d) evaluating the blood or serum sample for auto-antibodies specific for one or more type I IFN selected from:(i) IFN-a2 and IFN-®;(ii) IFN-a2, IFN-a) and IFN-£;(iii) IFN-&2, IFN-ffi, IFN-P and IFN-E;(iv) IFN-u2, IFN-®, IFN-p, IFN-s and IFN-K;(v) IFN-a2, IFN-a, IFN-p and IFN-al / 13;(vi) IFN-a2, IFN-a, IFN-& IFN- a 1 / 13 and IFN-al4;(vii) IFN-a2, IFN-®, IFN-£, IFN- a 1 / 13 , IFN-a 14 and IFN-a? ;(viii) IFN-a2, IFN-a, IFN- al / 13, IFN-al4, IFN-a7(ix) IFN-s2, IFN-a, IFN~P, IFN-s, IFN-a 1, IFN-u2, IFN-a6, IFN-al3, IFN-a 14 andlFN- aI6; and(x) IFN-a2, IFN-o, IFN-al , IFN-a2, IFN-a6, IFN-al 3, !FN-al4 and IFN-al 6; or(e) evaluating the blood or serum sample for auto-antibodies specific for one or more type II IFN selected from IFNy.

[0094] In embodiments, the method further comprises:(d) evaluating the blood or serum sample for a LOF mutation in one or more type I IFN pathway gene or type II IFN pathway gene selected from:(i) IFNAR2 ot TYK2;(ii) IFNARL IFNAR2, TYK2 or IRF9;(iii) IF.NAR2, TYK2, IFNARI, STAT1 orSTAT2;(iv) IFNARL, TYK2, IFNARI , STAT1 , STAT2, TLR3 or TLR7;(v) IFNAR2, TYK2, IFNARI, IRF7, IFIHI, TLR3, TBKL IRF3, TIC AMI, or UNC93B1 ;(vi) IFNARL, TYK2, IFNARI, STAT1, STAT2, IRF7, IFIHI, TLR3, TBK1JRF3 , TIC AMI or UNC93BI;(vii) IFNAR2, TYK2, IFNARI, STALL STAT2, IRF7, IFIHI, TLR3, TBK1, IRF3 , TICAMI.UNC93BIor TRAF3; or(viii) 1FNAR2. TYK2, IFNAR1, STAT1. STAT2, 1RF7, IFW, TLR3, TBK1, IRF3 , TICAM1, UNC93BI, TRAF3. or TLR7;(e) wherein a patient or individual determined to have an autosomal recessive IFN deficiency or LOF mutation is administered one or more Type I or Type H IFN to replace the function lost due to the mutation and / or is administered an immune-modulatory agent that increases or facilitates type I or type II IFN-mediated response.

[0095] Various IFN type I or type II pathway mutations are known and have been described. Numerous IFN gene variations and mutations are described, including particularly wherein the mutations result in loss of function of an IFN, including in WO 2022 / 020569, published January' 27, 2022, and in Zhang Q et al (2020) Science 370(6515) eabd4570, incorporated by reference herein.

[0096] In an embodiment of the method, the pati ent or individual determined io have a LOF mutation is administered IFN-a2 or IFN-0 or IFN-y.

[0097] In another embodiment, the method further comprises:(d) evaluating the blood or serum sample for auto-antibodies specific for one or more type I IFN selected from:(i) TFN-a2 and IFN-®;(ii) IFN-a2, IFN-® and IFN-p;(iii) IFN-a2 , IFN-® , 1FN-P and IFN-E;(iv) IFN-a2, IFN-ro, IFN-p, IFN-s and IFN-K;(v) IFN-a2, IFN-®, IFN-£ and IFN-al / 13;(vi) IFN-a2, IFN-®, IFN-fJ, IFN- al 713 and IFN-al4;(vii) IFN-a2, IFN-®, IFN-p, IFN- al / 13, IFN-al 4 and IFN-a7;(viii) IFN-a2, IFN-®, IFN- a 1 / 13, IFN-al 4, IFN-a7(ix) IFN-a2, IFN-®, TFN-jJ, IFN-E, IFN-al , IFN-a2, IFN-a6, IFN-al3, IFN-al4 and IFN- al 6; and(x) IFN-a2, IFN-®, IFN-al, IFN-a2, IFN-a6, IFN-al3, IFN-al 4 and !FN-al6; and(e) evaluating the blood or serum sample for a LOF mutation in one or more type I IFN pathway gene or type II IFN pathway gene selected from:(i) IFNAR2 or 71 W2;(ii) IFNAR1, 7FNAR2, TYK2 or IRF9;(iii) IFNAR2. TYK2, IFNAR1, STAT1 or STAT2;(iv) IFNAR2, TYK2, 1FNARL STAT1, STAT2, TLR3 or TLR7;(y) IFNAR2, TYK2, IFNAR1, IRF7, 7FIH1, TLR3, TBK1, IRF3, TICAM1. or UNC93B1 ;(vi) IFNAR2, TYK2, IFNAR1, STAT1, STAT2. 1RF7, IFIHI, TLR3, TBK1, IRF3 , TICAM1 or UNC93BI;(vii) IFNAR2, TYK2, IFNARI, STAT1, STAT2. IRF7, 1FIH1, TLR3, TBK1, IRF3 , HCAM1, UNC93B]or TRAP 3; or(viii) IFNAR2, TYK2, IFNARI, STAT1, STAT2, IRF7, IFIH1, TLR3, TBKL IRF3 , TICAMI, UNC93B1, TRAF3, or TLR7; or(f) evaluating the blood or serum sample for auto-antibodies specific for one or more type II IFN selected from IFNy.

[0098] In some embodiments or aspects, the blood or serum sample is evaluated for neutralizing antibodies.

[0099] In some embodiments, wherein anti-type I IFN or anti-type II IFN auto-antibodies are identified, plasmapheresis is then conducted on the patient or individual to deplete the antibodies, or wherein B cells, such as auto-reactive B cells, and / or plasmacytes or plasmablasts are depleted in the patient or individual.[000100] In some embodiments, wherein anti-type I IFN or anti-type II IFN auto-antibodies are identified, a patient or individual having auto-Abs against one or more of IFN-ot2, IFN-a, JFN-e, IFN- otl, IFN-a6, IFN-« 13, ffN-al4 or IFN-al6 and not having auto-Abs against IFN-p is treated by administering IFN-p.[090101] In some embodiments, a patient or individual having auto-Abs against one or more of IFN-a2 or IFN-ro and not having auto-Abs against IFN-P is treated by administering IFN-J3.[099102] In some embodiments, a patient or individual having auto-Abs against one or more Type I IFN selected from IFN-a, IFN-E, IFN-0, IFN-K, and not having auto-Abs against IFN-a2 is treated by administering IFN-a2.[000103] In some embodiments, a patient or individual not having auto-Abs against IFN-p is treated by administering IFN-p.[000104] In some embodiments, a patient or individual having auto-Abs against one or more Type I IFN is treated by administering an IFN subtype which is not neutralized by the patient’s or individual’s auto-Abs.[000105] In some embodiments, a patient or individual having one or more anti-type I or type II IFN auto-antbody is not administered a viral vaccine, particularly a live attenuated or inactivated viral vaccine, or wherein a patient or individual positive for or at risk for infection or severe virus infection, or having vaccine-associated disease is treated to remove or deplete the auto-Abs and / or is administered a type I IFN or type II IFN against which they do not have auto-Abs and / or is administered an immune- modulatory agent that increases or facilitates type I or type II IFN-mediated response.[000106] In some embodiments, the patient or individual is suffering from or at risk of infection selected from SARS-CoV-2 infection, influenza infection, West Nile Virus infection, Middle East respiratory syndrome (MERS), intra-macrophage infection, mycobacterial disease and tuberculosis.[000107] In an aspect of the invention, methods are provided for predicting the presence of an autosomal recessive IFN deficiency or loss-of-function (LOF) mutation in a type I IFN pathway or response relevant gene, or the presence of anti-type I IFN specific auto-Abs in a patient or individualpositive for or at risk for SARS-CoV-2 infection, influenza infection, West Nile Virus infection, Middle East respiratory syndrome (MERE), intra-macrophage infection, mycobacterial disease or tuberculosis, having COVID-19 disease, prior to vaccination with live atenuated vaccine (LAV), or having vaccine- associated disease and thereby determining treatment and treating the patient or individual, wherein a patient or individual having one or more auto-antbody is not administered the vaccine or wherein a patient or individual positive for or at risk for SARS-CoV-2 infection, influenza infection, West Nile Virus infection, Middle East respiratory syndrome (MERS), intra-macrophage infection, mycobacterial disease, or tuberculosis, having COVID-19 disease, or having vaccine-associated disease is treated to remove or deplete the auto-Abs and / or is administered a type I IFN against which they do not have auto- Abs and / or is administered an immune-modulatory agent that increases or facilitates type I IFN- mediated response,[0901O8] In an embodiment, the LAV is a COVlD-19 / SARsCo¥-2 vaccine or is a yellow fever vaccine. In another embodiment, the vaccine-associated disease is COVID-19 / SARsCoV-2 vaccine- associated disease or is yellow fever virus (YFV) vaccine -associated disease.[000109] In accordance with the method, the blood or serum sample may be evaluated for neutralizing antibodies. The sample may be further evaluated for neutralizing antibodies, for example, once auto-Abs are identified. The blocking of downstream effects or specific activity of an IFN type or subtype can be assessed and determined. One skilled in the art will know and have available approaches to assess IFN-specific activity and mediated effects. Thus, as an example if auto-Abs are identified against IFN-«2, antibody blocking of IFN-a2-mediated activity can be evaluated. In an example, cells may be incubated with IFN-o2 and patient plasma and assessed for pSTATl induction. The instant examples describe neutralization assays which can be conducted. [0011 0] In an embodiment, a method is provided for prevention of severe CO VID-19 disease. Identification of existing auto-Abs in a patient and specific treatment or mediation directed io remove or reduct the auto-Abs or to administer an alternative IFN which is not neutralized, could prevent the onset of severe COVED- 19 disease in a SARS-CoV-2 infected individual.[000111] In an embodiment of the method, plasmapheresis is conducted on the patient or individual to deplete the antibodies, or wherein B cells, such as auto-reactive B cells, and / or plasmacytes or plasmablasts are depleted in the patient or individual. Plasmaphersis is a known and readily available process wherein plasma is separated from blood cells. The plasma may replaced with another solution such as saline or albumin, or the plasma is treated and then returned to the patient’s body. Plasmapheresis is utilized clinically in various instances, including to remove antibodies from blood. Approaches to deplete B cells, such as auto-reactive B cells, plasmacytes or plasmablasts are known and available in the art. Monoclonal antibodies capable of depleting plasmablasts include daratumumab (Darzalex) or isatuximab (Sarclisa), which are directed against CD38. Rituximab (Rituxan, Truxima) is a chimeric monoclonal antibody directed against CD20, which is primarily found oti the surface of immune system B cells, and triggers B cell death with binding. Approachesutilized to reduce antibody or B cell responses in auto-immune diseases for example may also be considered or utilized. Once auto-Abs are reduced or depleted, in an embodiment, IFN therapy and administration of for example IFN-a or another Type I or Type II IFN protein can proceed.[000112] Alternatively, a patient may be treated with or administered an IFN agent or protein against which they do not have auto-Abs. A patient or individual having auto-Abs against one or more Type I or Type II IFN may be treated by administering an IFN subtype which is not neutralized by the patient’s or individual’s auto-Abs. A patient or individual having auto-Abs against one or more of Type I IFN may be treated by administering an IFN-a subtype which is not neutralized by the patient’s or individual’s auto-Abs. A patient or individual having auto-Abs against one or more of IFN-a2, IFN-a, IFN-s, IFN-al, IFN-a2, IFN-a6, IFN-al 3, IFN-a 14 or IFN-al 6 and not having auto- Abs against IFN-p may treated by administering IFN-|3. A patient or individual having auto-Abs against one or more Type I IFN selected from IFN-®, IFN-e, IFN-P, IFN-K, and not having auto-Abs against IFN-a2 is treated by administering IFN-c.2. Suitable IFN-a and IFN-P for administration is known and available.[000113] In another alternative, a patient may be treated with or administered a high dose of the IFN agent or protein against which they do have auto-Abs, such that the dose is high enough whereby some IFN present is not able to be neutralized and is active. This type of approach has been utilized in patients with auto-Abs against and neutralizing GM-CSF, whereby the patients have been dosed with enough of the GM-CSF such that it does work.[000114] The invention provides an assay for predicting an altered type I IFN pathway or altered type II IFN pathway in a patient or individual comprising:(a) contacting a sample of blood or serum sample from the patient or individual with IFN selected from IFNy, and one or more of IFNa2, IFNp or IFN® for a period of time so as to permit IFN induction; and(b) evaluating the induction, elevation, or increased expression of IP-10 in response to IFNy, and one or more of IFNa2, IFNp or IFN®; wherein the failure of induction, elevation, or increased expression of IP- 10 in response to IFNy, or in response to one or more of IFNa2, IFNP or IFN® indicates the presence of an autosomal recessive IFN deficiency or loss-of-fimction (LOF) mutation in a type I IFN or type II IFN pathway or response relevant gene, or the presence of anti-type I IFN or anti-type II IFN specific auto-antibodies (auto- Abs) in the patient or individual.[000115] In an embodiment, the assay comprises:(a) contacting a sample of blood or serum sample from the patient or individual with IFNy, and one or more of IFNa2, IFNp or IFNw for a period of time so as to permit IFN induction; and(b) evaluating the induction, elevation, or increased expression of IP-10 in response to IFNy and one or more of IFNa2, IFNp or IFN®.[000116] In an embodiment, the assay further comprises evaluating the presence of auto- antibodies directed against one or more Type I IFN or Type II IFN, comprising:(c) contacting the sample of blood or serum with one or more recombinant type I IFN protein selected from IFN-α2, IFN-®, IFN-fk and IFN-y, wherein each IFN protein is labeled with a distinct detectable tag or marker to form an antibody-protein complex;(d) contacting any antibody-protein complex of (a) with one or more labeled anti-human immune globulin molecule that will bind and label auto-antibody bound to any one or more IFN protein; and(e) specifically and selectively detecting each type I IFN protein bound by specific auto-Ab thereto.[000117] In accordance with the methods and assays and kits provided herein, the induction, elevation, or increased expression of IP-10 is determined by direct detection and / or measurement of IP- 10, by such as by ELIS A, such as by binding with an antibody directed against IP- 10. In aspects, the antibody directed against IP- 10 can be detected and measured via a detectable label or marker. In aspects, the expression or amount of IP- 10 is evaluated by assessing or determining IP- 10 protein levels, IP- 10 RNA levels, or IP- 10 gene expression levels. The induction, elevation, or increased expression of IP- 10 may be a quantitative measure or may be more qualitative, whereby the presence or absence of IP-10 is evaluated and the amount of IP-10 is no t specifically determined.£000118] In an embodiment, one or more recombinant type I IFN protein is labeled with a fluorescent marker. In an embodiment, one or more recombinant type I IFN protein is covalently coupled to a magnetic bead with a fluorescent marker. In another embodiment, each of the one or more recombinant type I IFN proteins is covalently coupled to a magnetic bead with a distinct and differential fluorescent marker. In an embodiment, IP-10 protein is labeled with a fluorescent marker or is detected via a marker, such as a fluorescent marker. In an embodiment, a ligand or antibody capable of binding and / or recognizing IP- 10 protein is labeled with a fluorescent marker or is detected via a fluorescent marker. In an embodiment, IP- 10 protein is covalently coupled to a magnetic bead with detectable marker, such as a fluorescent marker. In an embodiment, a ligand or antibody capable of binding and / or recognizing IP- 10 protein is covalently coupled to a magnetic bead with a detectable marker, such as a fluorescent marker. In another embodiment, each of the one or more recombinant type I IFN proteins is covalently coupled to a magnetic bead with a distinct and differential fluorescent marker. In another embodiment, the one or more labeled anti-human immune globulin molecule that will bind and label bound auto-antibody is a labeled non-human animal derived anti-human IgG. For example a labeled goat anti-Human IgG or labeled rabbit anti-human IgG may be utilized.[000119] In an embodiment, the presence of neutralizing auto-antibodies is determined. Whether an antibody is neutralizing can be determined utilizing any approaches or methods known and available to the skilled artisan. Neutralizing antibodies will block their target protein’s activity. Neutralizing antibodies against IFN-a2, for example will eliminate STAT1 phosphorylation in response to IFN-a2. [888120] In an embodiment of the assay, the blood or serum sample is further evaluated for a LOF mutation in one or more type I IFN pathway gene or type II IFN pathway gene comprisingassessing one or more gene mutation by virtue of one or more probe directed against one or more type I IFN pathway gene or type II IFN pathway gene selected from:(i) IFNAR2 or TYK2;(li) ZfoW 1 , IFNAR2, TYK2 or ZRFP;(iii) IFNA.R2, TYK2, IFNAR1, STAT1 or STAT2;(iv) IFNAR2, TYK2. IFNARL STAT1, STAT2, TLR3 or TLR7;(v) 1FNAR2, TYK2, IFNARL 1RF7, IFIH1, TLR3, TBK1, IRF3, TICAM1, or UNC93B1 ;(vi) IFNAR2, TYK2, IFNARL STAT1, STAT2, [RF7, IFIHL TLR3, TBK1, IRF3 , TICAMI or UNC93B1;(vii) IFNAR2, TYK2, IFNARL STALL STAT2, IRF7. IFIHL TLR3, TBK1, IRF3 , TICAM1, UNC93B1QV TRAF3; or(viii) IFNAR2, TYK2, IFNARL STAT1, STAT2, IRF7, IFIH1, TLR3, TBK1, IRF3 , TICA.M1, UNC93B1, TRAF3, or TLR7.[000121] The invention further provides a kit for evaluating or predicting an altered type I IFN pathway or altered type II IFN pathway in a patient or individual comprising:(a) IFN selected from IFNy, and one or more of IFNa2, IFNP or IFN®; and(b) an agent, antibody or probe capable of binding IP-10 protein; for a period of time so as to permit IFN induction; and(c) a means for specific and selective detection of each IP-10 protein bound by the agent, antibody or probe; wherein the failure of induction, elevation, or increased expression of IP-10 in response to IFNy, or in response to one or more of IFNa2, IFN[J or IFN® indicates an altered type I IFN pathway or altered type II IFN pathway.[000122] In an embodiment, the kit further comprises a means for determining the presence of an autosomal recessive IFN deficiency or loss-of-function (LOF) mutation in a type I IFN or type II IFN pathway or response relevant gene, or the presence of anti-type I IFN or anti-type II IFN specific auto-antibodies (auto-Abs) in the patient or individual.[000123] In an embodiment, a kit is provided for evaluating the presence of auto-antibodies directed against one or more Type I IFN or Type II IFN in a patient or individual, wherein the kit further comprises:(a) one or more recombinant type 1 IFN protein selected from IFN-a2, IFN-®, IFN-p and IFN-y, wherein each IFN protein is labeled with a distinct detectable tag or marker;(b) one or more labeled anti-human immune globulin molecule that will bind and label auto- antibody bound to any one or more IFN protein;(c) a means for specific and selective detection of each type I IFN protein bound by specific auto-Ab thereto.[000124] In another embodiment, one or more recombinant type I IFN protein is labeled with a fluorescent marker, or wherein one or more recombinant type I IFN protein is covalently coupled to a magnetic bead with a fluorescent marker. In an embodiment, each of the one or more recombinant type I IFN proteins is covalently coupled to a magnetic bead with a distinct and differential fluorescent marker. Alternatively, each of the one or more recombinant type I IFN proteins may covalently coupled to a magnetic bead with a distinct and differential fluorescent marker. This permits determination of any and all applicable anti-type I IFN auto-Abs in a single step, and indicates which, including if more than one, type I IFN is targeted by antibodies in the patient sample. Suitable fluorescent markers, including magnetic beads or such other suitable bead or selectable tag having fluorescent markers are known and available to one skilled in the art. Fluorescent markers may include for example fluorescein, rhodamine, Texas Red, green fluorescent protein, auramine, AMCA blue and Lucifer Yellow. The fluorescent protein may be selected from one or more of a blue / UV protein, a cyan protein, a green protein, a yellow protein, an orange protein, a red protein, a far-red protein, a near-IR protein, a long stokes shift protein, a photactivatible protein, a photoconvertible protein and a photo switchable protein. Examples of blue / UV fluorescent proteins include TagBFP and Sapphire. Examples of Cyan proteins include ECFP and derivatives thereof, Cerulean, TagCFP and rnTFPl. Examples of green proteins include GFP and derivatives thereof, Emerald, monomeric azami green. Examples of yellow proteins include EYFP and derivatives thereof, and examples of orange proteins include monomeric kusabira orange and derivatives thereof. Red fluorescent proteins are known in the art and include for example REP and derivatives thereof, mRaspberry. roCheny, mStrawberry, mRuby.[000125] In some embodiments, the kit provides for further evaluating the blood or serum sample for a I, OF mutation in one or more type I IFN pathway gene or type II IFN pathway gene comprising assessing one or more gene mutation, wherein the kit further comprises of one or more probe directed against one or more type I IFN pathway gene or type II IFN pathway gene selected from:(i) IFNAR2 or TYK2;(ii) IFNAR / , IFNAR2, TYK2 or IRF9;(iii) IFNAR2, TYK2, IFNAR!, STAT1 or STAT2;(iv) IFNAR2, TYK2, IFNAR1, STAT1, STAT2, TLR3 or TLR7;(v) IFNAR2, TYK2. IFNAR! , IRF7, IFI.H1, TLR3, TBKI, IRF3, TICAM1, or UNC93B1 ;(vi) IFNAR2, TYK2, IFN ARI, STAT1, STAT2, IRF7, IFIH1, TLR3, TBK1,IRF3 , TICAM1 or UNC93B1;(vii) 1FNAR2, TYK2, IFNAR! , STAT1, STAT2, IRF7, IFIH1, TLR3, TBKI, IRF3 , TICAMJ, UNC93B1OI TRAF3, or(yiii) 1FNAR2, TYK2, IFNAR!, STAT1, STAT2, IRF7JFIH1, TLR3, TBK1,1RF3 , TICAM1, UNC93B1, TRAF3, or TLR7.[000126] In embodiments, the assays or kits provide for evaluating a patient or individual positive for or at risk for SARS-CoV-2 infection or having COVID- 19 disease or prior to vaccinationwith live attenuated vaccine or having vaccine-associated disease for the presence of an autosomal recessive IFN deficiency or loss-of-function (LOF) variation or mutation in a type I IFN pathway or response relevant gene and thereby determining treatment or whether the patient or individual can be safely vaccinated or should be vaccinated and / or treating the patient or individual, wherein a patient or individual determined to have an autosomal recessive IFN deficiency or LOF mutation is administered one or more Type I IFN to replace the function lost due to the mutation and / or is administered an immune-modulatory agent that increases or facilitates type I IFN-mediated response.[000127] In an embodiment, the patient or individual determined to have a LOF mutation is administered a Type I IFN. In another embodiment, the patient or individual determined to have a LOF mutation is administered IFN-a2 or IFN-P or IFN-y.[000128] Evaluation of RNA or protein expression may be conducted using any method known in the art. Protein expression or induction may be determined via antibody(ies) specific for one or more such protein, Also, in accordance with the methods of the invention, RNA expression may be assessed by RT PCR or may be determined by RNA sequencing. In accordance with the method, protein expression may be assessed using specific antibodies, assessing for protein activity, utilizing protein ligands. Protein expression may be evaluated utilizing one or more protein markers, such as one or more antibody specific for the protein or by a suitable readout of the amount of protein, such as a label, dye, ligand etc. Where an RNA or gene is indicated by name, its corresponding information can be derived by ne skilled in the art, such as via determination of the gene ID, a database listing, corresponding database nucleic acid or protein sequence. The sequence enables development and utilization of a nucleic acid probe, directed or specific antibody, protein assay, etc to determine expression, amount, level, activity of the corresponding nucleic acid such as RNA or of the corresponding protein. This and these approaches for evaluation of RNA or protein expression, of RNA or protein levels / amounts, or of RNA or protein activity are within the knowledge and ability of one skilled in the art.[000129] The present invention also relates to a variety of diagnostic applications, including methods for detecting and evaluating the expression of or altered presence (increased or decreased amount) of the markers provided herein, particularly including the protein IP- 10 (CXCL10) or the gene, RNA markers or their associated proteins as decribed and provided herein. Thus, the expression of a gene, presence or amount of RNA, or presence or amount of associated or encoded protein is evaluated. RNA may be evaluated by assessing transcriptome changes. RNA may be evaluated by RNA sequencing, RNA may be evaluated and determined by RT-PCR. Nucleic acid probes for evaluation and PCR can be designed, selected and utilized by one skilled in the art, including based on the gene and nucleic acid sequence(s) known and available corresponding to the markers listed and in the marker sets provided herein.[000130] Protein may be evaluated by reference to their ability to be recognized by a specific antbody directed thereto. Antibodies immunospecific for any one of the markers provided herein may be knownand available to the public and may be accessed via the scientific community or purchased from a commercial vendor. Readily searchable databases or web browsers may be utilized for example for identifying potential suppliers for such antibodies.[000151] 'There are various exemplary known and available antibodies specifically directed against IP-10 (CXCL-10). Capture and detector antibodies are known and available. These include: Abeam antibodies ab3 l6903 and ab289906 as well as rabbit monocloal to human IP- 10 ab283681; R&D systems mouse monoclonal antibody MAB266 and clone # 33036; Thermo Fisher Scientific antibodies MAB-33342 and 7-01225.[000132] Proteins, peptides or peptide complexes can be identified, targeted, labeled, and / or quantitated in blood or serum, on ceils or in cells, including cell(s) in peripheral blood. Diagnostic applications include in vitro and in vivo applications well known and standard to the skilled artisan and based on the present description. Diagnostic assays and kits for in vitro assessment and evaluation of IP- 10 (CXCL-10) may be utilized to diagnose, evaluate and monitor patient samples including those known to have or suspected of having severe viral infection response or a Type I or Type IT IFN alteration, mutation, auto-antibody.[000133] In a further embodiment, commercial test kits suitable for use by a medical specialist may be prepared to determine the presence or absence of aberrant, differential or increased expression of one or more or of a subset of markers, genes, RN As, relevant proteins described herein. One class of kits will contain at least the labeled marker or its binding partner, for instance a nucleic acid probe, primer, or an antibody specific thereto, and directions, of course, depending upon the method selected. The kits may also contain peripheral reagents such as buffers, stabilizers, etc.[000134] In accordance with the present disclosure, the gene listings provided present information with which an ordinarily skilled practitioner can access the amino acid sequences of the proteins and nucleic acid sequences of the encoding genes identified herein as including loss of function variations and mutations. A stepwise protocol or means for identification of the sequences listed herein may include the artisan accessing one of the publicly available databases and entering a relevant ensembl number or gene name or symbol io identify the sequence and relevant marker information. Such information may be used to design probes for detection of any of the proteins, genes therein or to identify commercially available probes or antibodies therefore or thereof. Primers for detection of nucleic acid sequences encoding any of the proteins listed in the tables presented herein are also envisioned as are primers for PCR including RT PCR. Such primers may be used to detect RNA expression levels or to detect the presence of a specific variation or mutation in the nucleic acid. The design of primers for detecting the presence of a specific variation or mutation listed herein is a matter of routine practice with the nucleic acid sequence in hand as provided by publicly available websites such as those mentioned above. Such probes and primers are useful for the kits described herein.[000135] Human protein encoding sequencs and amino acid sequences for the various referenced type I interferon (IFN) pathway proteins arc known and available. For example, protein sequences inpublic databases are known and include the following: IRJF7 (NP 004022.2), TLR3 (NP_003256.l), TBK l (NP_037386.1, NMJ13254.4), IR.F3 (AAH09395), TICAMl (NP .891549), IFNARl (NP 000620.2), UNC93B1 (NPJ 12192.2), IFIH1 (AAI11751.1, NPJ71451.2), IFNAR2 (NP_001276054.1), IRF9 (NPJ)01372329.1), STAT I (NP_009330.1), STAT2 (NP 005410.1), TRAF3 (NP ...003291 ,2) and TLR7 (NP 057646.1; AAZ99026.1).[000136] In an embodiment of the method, the variation or mutation in one or more type I IFN pathway gene selected is determined via a delectably labeled primer or oligonucleotide specific for the mutation, wherein hybridization and detection of the labeled primer or oligonucleotide is diagnostic for the presence of the mutation and LOF of the type I IFN in the patient or individual. In an embodiment of the method, the variation or mutation in one or more type I IFN pathway or response relevant gene is determined via a detestably labeled primer or oligonucleotide specific for the mutation, wherein hybridization and detection of the labeled primer or oligonucleotide is diagnostic for the presence of the mutation and LOF of the type I IFN in the patient or individual. [000137] In an embodiment of the method, the variation or mutation in one or more type I IFN pathway gene is determined via whole genome or whole exome sequencing. In an embodiment of the method, the variation or mutation in one or more type I IFN pathway or response relevant gene is determined via whole genome or whole exome sequencing. One skilled in the art can readily undertake and conduct sequencing, even targeted gene region sequencing to identify or screen for one or more variations or mutations, including loss of function mutations, in the IFN response relevant genes identified and provided herein.[000138] In other embodiments of the invention and methods provided herein, a patient or individual may first be screened or evaluated for the presence and / or levels of type I IFN in their blood, plasma or serum. In a particular embodiment, a patient or individual may first be screened or evaluated for the presence and / or levels of IFN-a, particularly IFN-a2, IFN-J3 and / or IFN-y in their blood, plasma or serum. Thus assays and methods are provided comprising first evaluating a patient or individual for levels of type I TFNs and / or type II IFN (IFN-y); in the event that IFN levels are low or undetectable, the patient or individual may be evaluated for IFN-mediated IP- 10 induction, and then for mutations in type I or type II IFNs or IFN pathway genes. Assays and methods are provided comprising first evaluating a patient or individual for levels of type I IFNs, in a particular aspect for levels of IFN-a; in the event that IFN levels, particularly in an aspect IFN-a levels are low or undetectable, the patient or individual is evaluated for IFN-mediated IP- 10 induction, and then for auto-Abs against type I IFNs. The patient or individual thereby identified as having auto-Abs is identified as likely to progress to severe viral disease and is treated to remove or deplete the auto-Abs and / or is administered a type I IFN against which they do not have auto-Abs andfor is administered an immune-modulatory agent that increases or facilitates type I IFN-mediated response.[000139] The methods provided herein have applicability io various virus infections, including respiratory viruses and respiratory' viral disease, Thus, the methods of the invention are applicable inpatients suspected of or at risk of infection with rhinovirus, respiratory syncytial virus, influenza virus, coronavirus, parainfluenza virus and / or adenovirus. Ths invention is applicable prior to vaccination with a live or live attenuated vaccine, for example prior to vaccination with yellow fever vaccine, which is a live vaccine. Thus, with development, implementation and administration of a live or live attenuated COVID- 19 / SARS-CoV-2 vaccine, testing of individuals prior to vaccination, particularly to evaluate the presence if neutralizing auto-Abs to type I IFN(s) would be beneficial and very important. Further, in instances where a patient may have recovered from severe COVID- 19 infection, it would be beneficial to assess the presence of auto-Abs against type I IFNs and / or the presence of one or more LOF mutation in the IFN-related autosomal genes described herein so as to have that information available in further instances of any viral exposure or infection, In addition, relatives of those who have experienced or succumbed to COVID-19 disease should be evaluated, particularly in view of die autosomal recessive mutations that lead to severe CO VID-19 disease. In as much as the presence of auto-Abs and even of LOF mutations have been generally not evident by way of clinical manifestations even prior to SARS-CoV-2 infection, family relatives or children may also be carrying one or more mutation(s) or may have auto-Abs.[000140] The methods and approaches described herein are applicable to LAVs other than yellow fever, including MMR, and also LAVs in development or under consideration for coronavirus, particularly Sars-Cov-2. Several LAVs are presently in development for Sars-Cov-2. For example, Sanchez-Felipe L et al 2020 describe the development of a candidate vaccine (YF-S0) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that uses live-attenuated yellow fever 17D (YF17D) vaccine as a vector to express a noncleavable prefusion form of the SARS-CoV-2 spike antigen.[000141] The invention may be better understood by reference to the following non-limiting Examples, which are provided as exemplary of the invention. The following examples are presented in order to more folly illustrate the preferred embodiments of the invention and should in no way be constated, however, as limiting the broad scope of the invention.EXAMPLE 1[800142] Human inborn errors of the type I IFN response pathway and auto-Abs neutralizing IFN-a, -p, and / or -ft) can underlie severe viral illnesses. We report a simple assay for ths detection of both types of conditions. We stimulated whole blood from healthy individuals and patients with inborn errors of type I IFN immunity or auto-Abs against type I IFNs with glycosylated human IFN-a2, -p, or -o). As controls, we added a monoclonal antibody (mAb) blocking the type I IFN receptor and stimulated blood with IFN'-v (type II IFN). Of the molecules we tested, IP- 10 (also known as CXCL10 and encoded by the interferon- stimulated gene (ISG) CXCL10) was the molecule most strongly induced by type I and type II IFNs in the whole blood of healthy donors in an ELISA-like assay. In patients with inherited IFNAR1, IFNAR2, TYK2, or IRF9 deficiency, IP-10 was induced only by IFN-y, whereas, in thosewith auto-Abs neutralizing specific type I IFNs, IP- 10 was also induced by the type 1 IFNs not neutralized by the auto-Abs. The measurement of type I and II IFN-dependent IP- i 0 induction therefore constitutes a simple procedure and approach for detecting rare inborn errors of the type I IFN response pathway and more common auto-Abs neutralizing type I IFNs.[000143] Human inborn errors of the type 1 IFN pathway and auto-Abs neutralizing type I IFNs can underlie various life-threatening viral diseases, including viral pneumonias and encephalitis. Inborn errors of the type I IFN pathway are rare, but millions of people worldwide are thought to have auto- Abs neutralizing type I IFNs. There is currently no quick, easy, and affordable diagnostic test for identifying these conditions in clinical laboratories. We have filled this gap by developing a simple assay for their detection. This assay is sensitive, easy, robust, affordable, and provides results quickly, thus meeting the requirements of clinical laboratories.[000144] Introduction[000145] Auto-Abs against type I IFNs were first described in 1981 -1984 in a single patient with disseminated shingles’’3. They may be produced due to monogenic inborn errors of tolerance to self, as in almost all patients with autosomal recessive autoimmune polyendocrine syndrome type 1 (APS-1), a disease caused by biallelic loss-of-fiinction AIRE variants44. Other related genetic etiologies include deleterious variants in men hemizygous for deleterious X-linked FOXP3" (causing immune dysreguiation polyendocrinopathy enteropathy X-linked (IPEX) recessive syndrome) or women heterozygous for X-linked IKBKG variants78, (Rosain J. et al. 2024, in preparation) causing incontinentia pigmenti, IP. a dominant X-linked disorder. Biallelic variants of the autosomal genes RAG1, RAG^-11'13, NIK, and RELB14, and monoallelic variants of AIRE?,h, NFKB214, IKZF216,17, and CTLA416can also underlie the production of these auto-Abs. These genes are expressed in thymocytes (e.g. RAG1, RAG2, FOXP3, IKZF2, CTLA4, NFKB2, IKBKG) and / or in thymic stromal cells (AIRE, IKBKG, IKZF2, NFKB2, NIK, RELB) and / or in T cells (NIK, RELB), and their defects impair central T-cell tolerance, Auto-Abs against type I IFNs can also be found in patients with conditions with a less well-delineated genetic architecture, including myasthenia gravis and / or thymoma (30-75%), systemic lupus erythematosus (SLE) (10-14%), and in patients treated with type I IFN13'24. In the general population, they are found in <0.5% (auto-Abs neutralizing high concentrations of type I IFNs) and <2% (auto-Abs neutralizing low concentrations of type 1 IFNs) of individuals under the age of 65 years, and their prevalence increases sharply thereafter, reaching -4% and ~8%, respectively, in individuals over the age of 70 years25,25. The underlying cause of the auto-Abs neutralizing type I IFNs remains unexplained in most cases.[000146] Auto-Abs against type I IFNs were long thought to be clinically silent1 ,26'29. Their discovery in APS-1 patients in 2006 led to their use of their detection as a diagnostic marker of this condition4-6. It has been suggested that they influence the course of diabetes in APS-1 patients6, and the severity of disease in SLE patients2021-30-31. However, it was not until the CO VID- 19 pandemic that their pathogenic role in viral diseases was widely accepted. Most unvaccinated SARS-CoV-2-infected APS-I patients were hospitalized for hypoxemic COVID- 19 pneumonia32'34. Moreover, -15% of cases of critical COVID-19 pneumonia were found to be due to pre-existing auto-Abs neutralizing type IThese findings were replicated worldwide30,333''-69. Auto-Abs neutralizing type I IFNs also underlie -5% of cases of critical influenza pneumonia70, ~25% of hospitalizations for Middle East respiratory syndrome (MERS) pneumonia26,29,71, ~ 30-40% of severe adverse reactions to foe live attenuated virus vaccine against yellow fever virus (YFV-17D)72,73and, strikingly, -40% of cases of West Nile virus encephalitis74. These auto-Abs have a major clinical impact, with odds ratios (OR) for severe disease in carriers increasing with the concentration and number of type I IFNs neutralized, typically reaching values greater than 10, and often greater than 1 OO25,28, / 4. These auto-Abs are present before viral infection and are causal for severe disease28,36.[000147] Current procedures for detecting auto-Abs neutralizing type I IFNs are based on in vitro cell-based assays. They usually involve assessments of STAT] phosphorylation (p-STATl) by flow cytometry after the stimulation of PBMCs with type I IFNs in the presence of plasma or serum from the patient or control10,75. More sensitive luciferase reporter cell-based assays have also recently been developed8,25. In the STAT1 phosphoiylation assays, the blocking activity of auto-Abs is evaluated by assessing STAT1 phosphorylation in healthy control PBMCs stimulated with type I IFNs in the presence of 10% serum or plasma from the patient or a healthy control10,7’. In the luciferase assays, HEK293T cells are transfected with a plasmid containing the firefly luciferase gene under the control of a promoter inducible by type I IFN s due to the presence of five interferon-sensitive response element (ISRE) repeats, and a plasmid encoding the Renilla luciferase (as a control for transfection)9,25. The cells are then stimulated with type I IFNs in the presence of 10% plasma or serum from a patient or a healthy control. If this plasma or serum contains neutralizing auto-Abs against type I IFNs, these cytokines are neutralized and, thus, unable to signal through their receptors, resulting in low levels of firefly luciferase activity’. By contrast, in the absence of such antibodies, the type I IFNs can induce high levels of firefly luciferase acti vity.[000148] These assays are robust and sensitive, but time-consuming, labor-intensive, and expensive. The flow cytometry assays take one to two days, and the luciferase assay, four days. Moreover, the flow cytometry-based assays have a limited throughput, preventing their use to screen large numbers of individuals. They are also costly, at an estimated USS6-10 for the testing of a single sample. These limitations account for the restriction of their use to only a small number of laboratories worldwide, typically research laboratories in the wealthiest countries. Furthermore, these assays use 1 :10 dilutions of plasma, and this dilution may result in an underestimation of the prevalence of auto- Abs against type I IFNs. Finally, methods for auto-Ab detection based on antibody structure (ELISA) rather than neutralizing function, are simpler and cheaper, but nevertheless have drawbacks as neutralizing auto-Abs can escape ELISA detection, and the auto-Abs detected by ELISA may be non- neutralizing2534,74,76. Indeed, the correlation between the structural and functional detection of these auto-Abs depends on many factors, only some of which are known7'''''9. The detection of neutralizingauto-Abs is globally important, in terms of public health, as there are at least 100 million carriers and the spectrum of known clinical consequences of these auto-Abs is continually expanding. We therefore set out to develop a simple, quick, and affordable method for detecting auto-Abs neutralizing type 1 IFNs that could be easily implemented in clinical practice in clinical laboratories worldwide.[000149] METHODS[0001 SO | Whole blood stimulation with IFNsFresh blood from healthy donors, IFNAR- or TYK2-deficient patients, or individuals with auto-Abs neutralizing type I IFNs was collected in lithium heparin tubes (except for the comparison between lithium heparin, EDTA and citrate tubes). The healthy donors were blood donors recruited through the French Blood Bank, aged 18-68 years and with no known medical or genetic condition. The blood was stimulated with a serial 10- fold dilutions of human glycosylated IFN-a2 (Merck, catalog number: H6041-10UG), IFN-]3 (Peprotech, catalog number: 300-02BC), IFN-® (Origene. catalog number: TP721113), IFN-s (Biotechne, catalog number: 9667-ME-025), IFN-K (Cusabio, catalog number: CSB-YP889172HU), IFN-y (IMUKIN) mouse IFN-a2 (R&D, catalog number: 12100-1) or cynomolgus monkey IFN-«2 (R&D, catalog number: 14110-1), or was left unstimulated (NS), in a final volume of 200 or 500 pL. After 16 h (or less in time-course experiments) of stimulation at 37°C, under an atmosphere containing 5% COz, the plasma was collected and stored at -80°C or used directly for the assessment of cytokine or chemokine production. The mAbs used as controls to block typeI IFNs were preincubated with blood and used at a concentration of 3 pg / mL(anti-IFNAR2 mAb, PBL, Catalog No.: 21385) or at a dilution of 1 :50 (Human Type I IFN Neutralizing Antibody Mixture, PBL, Catalog No.: 39000). A total minimal volume of 1 mL is enough to test a blood sample in all the above conditions. Healthy donors tested were aged 20-69 years old, including males and females.[000151] Assessment of type I IFNs response in whole blood[000152] LEGENDplex™[000153] The type I IFNs response was assessed using the LEGENDplex™ Human Anti-Virus Response Panel (13-plex) (Biolegend, catalog number: 740349), the LEGENDplex™ Human Inftammarion Panel 1 (13-plex) (Biolegend, catalog number: 740809), and the LEGENDplex™ HU Proinflammatory Chemokine Panel 1 (13-plex) (Biolegend catalog number: 740985) according to the manufacturer’s protocol.[000154 [ IP-10 EUSA[000155] IP-10 detection was performed by ELISA on plasma supernatant after whole-blood stimulation with IFN, in accordance with the manufacturer’s protocol (.R&D, catalog number: DIP 100). [090156] CD169 ELISA[000157] CD169 detection was performed by ELISA on plasma supernatant after whole-blood stimulation with IFN, in accordance with the manufacturer’s protocol (Abeam, catalog number: ab213757).[000158][000159] Two million PBMCs were obtained from each of three healthy donors and stimulated with glycosylated IFN-a2 (Merck, catalog number: H6041-10UG) for 6 h in Roswell Park Memorial Institute (RPMI) medium + 10% FBS. RNA was then extracted with an RNA extraction kit (Zymo Research, catalog number: ZR1051). Total RNA sequencing was performed with an Illumina NovaSeq S2 flow cell (read length: 100 bp) with a read depth of 30 M. All FASTQ sequences passed quality control tests and were aligned with the GRCh38 reference genome with STAR (2.6. Id), BAM files were converted to a raw count expression matrix with featurecount. Raw count data were normalized with DEseq2. The ensemble ID targeting multiple genes was collapsed (average) and a final gene data matrix was used for a modular repertoire analysis, as previously described102,103or for geneset enrichment analysis (GSEA: fgsea) with hallmark gene sets (gsea-msigdb.org / ).[000160] scRNAseq[000161] For scRNASeq analysis following stimulation, we isolated fresh PBMCs from three healthy donors, and washed them three times with PBS plus 0.5% FCS. We fixed the ceils with the Evercode™ Cell Fixation v2 kit (Parse Biosciences, cat. number ECF2101), according to the manufacturer’s protocol. We then prepared libraries with the E vercode’MWT v2 kit (Parse Biosciences, cat. number ECW02135) and sequenced them with an Illumina NovaSeq 6000 sequencer. We preprocessed sequences with CellRanger. We sequenced about 10,000 cells per sample. scRNA-seq FASTQ files from 8 sublibraries were demultiplexed into 22 samples with the splitpipe pipeline (vl.0.4p) from Parse Biosciences. Demultiplexed FASTQ files from HD1, HD2, and HD3 were aligned with the GRCh38 / hg38 human reference genome with standard alignment protocols. The expression matrices were integrated with the Seurat package (v4.3.0) in R. Initial quality control was performed manually based on standard metrics to filter out low-quality data. The filtered data were further integrated with Harmony (Korsunsky et al., 2019). Cell-type annotation involved two sequential rounds of graph-based clustering. Clusters were identified on the basis of canonical marker gene expression, facilitated by the SingleR pipeline (Aran et al., 2019) with reference to the MouacoImmuneData (Monaco et al., 2019). Pseudobulk differential expression analysis was performed with DESeq2 (Love et al., 2014). The results were visualised with volcanoplots generated with the Enhanced Volcano package (Blighe, Rana, and Lewis, 2018) in R.[000162] RT-qPCR[ 000163 [ RNA was isolated from peripheral blood mononuclear cells with the Zymo Quick-RNAMiniprep Kit (Zymo Research, catalog number: ZR1051), according to the manufacturer’s protocol. Reverse transcription was performed with the High-Capacity RNA-to-cDNA™ Kit (Applied Biosystems, catalog number: 4368814), according to the manufacturer’s protocol. The cDNA obtained was then subjected to qPCR with Applied Biosystems Taqman assays for CXCL10 and the p- glucuronidase (GUS) house-keeping gene for normalization, and with Fast Advanced Master Mix -Taqman™ Real-Time PCR (Applied Biosystems, catalog number: 4444557). The resuits are expressed according to the ACt or AACt method.[000164] Statistical analysis[000165] For each set of stimulation conditions, the distributions of IP-10 quantification data in pg / mL were compared between the HD and APS- 1 groups in non-parametric Mann- Whitney tests implemented in GraphPad Prism.[000166] RESULTS[000167] IP-10 is the most strongly induced by type I IFNs in blood of all the molecules tested [000168] We stimulated whole blood (collected on lithium heparin 4 h to 48 h before stimulation and kept at room temperature with gentle shaking) from three healthy donors with various concentrations (1 pg / inL to I pg / mL) of glycosylated recombinant human IFN-a2, or left it unstimulated (non stimulated, NS). After 16 hours, we assessed the production of a panel of 25 potentially relevant cytokines and chemokines (IL-10, IL-6, TNF, IP-10, IFN-X1, IL-8, IL-12.p70, IFN-I2 / 3, GM-CSF, IL- 10, MCP-1, IL-17A, IL- 18, IL-23, IL-33, Eotaxin, TARC, RANTES, MIP-la, MIG, ENA-78, MIP-3a, GROa, I-TAC, and MIP-lp) in LEGENDplex™ multiplex assays (an EL, ISA-like assay) on the supernatant IP-10 (encoded by CXCL10) had the highest absolute induction levels of all the proteins tested, for all three controls (with mean fold-induction over non-stimulated of 42-fold for for stimulation with I ng / ml, and with detectable but low levels at baseline (Figure 1A). IL-6 displayed a much lower level of induction (4-fold), also varying considerably between the individuals tested (Figure 2A). The remaining molecules tested were poorly induced (data not shown). At the mRNA level, RT-qPCR revealed a strong induction of CXCL10 expression in the fresh PBMCs of the three healthy donors tested after 6h of stimulation with 1 ng / mL IFN-o2 (Figure IB). A study of nine additional healthy donors confirmed the consistent production of IP-10 in response to type I IFN stimulation, with detection by LEGENDplex™ (Figure 1C). With 1 ng / mL IFN-a2, a 30- to 100-fold induction (mean: 70-fold, SD: 40-fold) was observed for IP-10 protein levels, and a 10- to 80-fold induction (mean: 30- fold, SD: 20) was observed for CXCL10 mRNA levels (Figures ID, 2B). Finally, we measured IP-10 induction after stimulation with the other two major type I IFNs: IFN-0 and IFN-OJ. Stimulation with I ng / mL or 10 ng / mL IFN-0 induced high levels of IP- 10 (>4,000 pg / ml..), whereas lower concentrations of IFN-0 resulted in litle or no induction (Figure IE). Glycosylated IFN-O) induced IP-10 less strongly than IFN-a2 and IFN-p, but the resulting IP- 10 levels were high enough for consistent detection when 1 ng / mL IFN was used for stimulation (Figure IF). Overall, we identified IP-10 as a protein strongly induced by type I IFNs and easily detectable by an ELISA-like assay on blood. The use of an IFN concentration of 1 ng / mL yielded a strong response for all three type I IFNs tested and a sensitivity similar to that of the previously described classical luciferase-based neutralization assay25.[000169] Genome-wide expression analysis confirms the suitability of IP- 10 as a candidate target[000170] We then used an unbiased genome-wide approach to determine whether IP- 10 was a strong candidate. We stimulated PMBCs from three healthy donors with 1 ng / mL IFN-a2 for 6 h and performed bulk RNAseq. We found that CXCL10 was among the top 20 most strongly induced transcripts (Figure 3A). We corroborated these results by performing single-cell (sc)RNAseq analysis on the same samples, revealing high levels of CXCL10 induction by IFN-a2 in type 2 conventional dendritic cells (cDC2), classical and non-classical monocytes, naive and memory B cells, memory CD8, CD4 Th2 cells, CD4 Thl7 T cells and 'NK cells (Figure 3B-D, Table 1). We also determined whether the proteins corresponding to the other 19 transcripts in this top 20 were expressed at the cell surface or secreted, and whether monoclonal antibodies were commercially available for their detection (Table 2). We measured the induction of these potential targets by ELISA, after 16 h of stimulation with type I IFNs. We found that I-TAC (encoded by CXCLU, the most strongly induced gene identified in the RNAseq experiment) was poorly detectable with high background levels for protein detection (Figure 4A). CD169 (encoded by S1GLEC1) induction by IFN-a2 or IFN-J3 gave only a weak signal (maximum of 750 pg / mL and 1,000 pg / mL, respectively) with a relatively high background (250 pg / mL in the absence of stimulation) (Figures 4B-C). Stimulation with IFN-w resulted in generally higher levels of CD 169 production (2,000 pg / mL) (Figure 4D). Whole-blood stimulation with 1 ng / mL type 1 1FN resulted in no more than an eight-fold induction of CD 169, a much weaker induction than for IP- 10, and CD 169 was therefore not considered a strong candidate for the assay in the conditions tested. Finally, we tested MCP-2 (encoded by CCLS) as the fourth and last secreted protein displaying high levels of induction at the mRNA level according to RNAseq results (Figures 4E-G). We found that MCP-2 was less strongly induced by 1 ng / mL IFN-a2 (median: 204 pg / mL), IFN-p (median: 834 pg / mL), and IFN-ra (median: 54 pg / mL) than IP - 10, as determined by LEGENDplex™. Overall, IP- 10 remained the most robust candidate.[000171] Table 1: CXCL10 expression in different cell subpopulations. PBMCs from three healthy donors were stimulated with 1 ng / mL IFN-a2 for 6 h, and scRNAseq was performed (Parse Bioscience). cDC2: type 2 conventional dendritic cells; ClassMono: classical monocytes; NClasMono: non-classical monocytes; BNv: naive B cells; CD8CM: CD8 ‘ central memory T cells; BMin: memory B cells; CD4TH2: CD4+T helper 2 cells; CD4Thl 7: CD4Th2: CD4+T helper 17 cells; NK: natural killer ceils; CD4Treg: CD4+T regulator cells; CD4Thl : CD4+T helper I cells; MATT: mucosal- associated invariant T cells; CD8Nv: CD8+naive T cells.TABLE 1Cell typeAdj listed P Value cDC2 9.08043133 3.93E-13 3.41E-UClassMono 7.07152808 1.81E-08 2.63E-07NClasMono 6.88990241 1.12E-06 4.19E-05BNv 4.93703754 I.58E-43 8.2 IE-42CD8CM 4.62740916 1.29E-06 4.49E-05BMm 4.41136895 4.40E-43 3.41E-41CD4Th2 3.16694567 1.62E-10 3.68E-09CD4Thl7 2.§ 1563776 L97E-06 . ft.48r.-05>NK 2.35180089 7.48E-06 > 9.97E-05CD4Treg 2.58354929 1 30E-02 1.05E-01CD4Thl i .54400230 2.85E-02 1.10E-01MATT i .40797691 4.32E-02 2.27E-01CD8Nv 1.10810034 1.02E-01 2.62E-011000J 72J The top 20 genes induced after the stimulation of PBMCs from healthy donors with 1 ng / mL IFN~a2 for 6 h, as determined by RNAseq are provided below in TABLE 2. For each gene, we indicate the mode of expression of the corresponding protein, the immune cells in which it is expressed at RNA level according to public databases (Human Protein Atlas), whether the corresponding protein is detected in blood immunoassays (Human Protein Atlas), and whether monoclonal antibodies are commercially available.TABLE 2> >[000173 ] IP-10 is also induced after whole-blood stimulation with IFN-y bid not with IFN-s and IFN-K[000174] Human IFN-s and IFN-K are restricted to the fesnale reproductive tract and the skin, respectively, unlike the other type I IFNs, which are broadly expressed80"82. Efforts to detect auto-Abs neutralizing IFN-s or IFN-K have, therefore, been limited, as such antibodies would be expected to have a narrower biological and medical relevance than those against IFN-a, IFN-3, or IFN-®. Moreover, these IFNs with low affinity for their receptor are unable to induce detectable STAT I phosphorylation and firefly luciferase activity in the widely used neutralization assays, even at high concentrations, precluding the detection of auto-Abs targeting them in these assays. This poor detection probably results from their affinity for the IFNAR1-IFNAR2 heterodimer being more than three orders of magnitude lower than that of the other type 1 IFNs8’. We nevertheless evaluated the ability of these IFNs to induce IP-10 following the stimulation of fresh, whole-blood samples, in the conditions described above. We also assessed the activity of IFN-y in this assay to serve as a control for blood stimulation, as IP- 10 has been reported io be type II IFN-inducibles4, We thought of using an IFN-a from another primate species as a control but we found that cynomolgus monkey IFN-a2, which is 92% identical to human IFN-u2, stimulated human cells but was also neutralized by human auto-Abs against IFN-a2 (data not shown). Stimulation with 10 ng / mL IFN-s or IFN-K (the highest concentration used) led to the detection of IP- 10 at levels similar to those observed in the absence of stimulation, suggesting that these IFNs were unable to induce IP- 10, at least in these conditions of stimulation and detection in ceils (Figare 5A). By contrast, stimulation with 100 U / mL or 1,000 U / mL recombinant IFN-v (IFN-ylb, unglycosylated) led to the production of almost 3,000 pg / mL IP-10, a level similar to that observed with 1-10 ng / mL IFN-o.2, IFN-p, or IFN-a. This finding is consistent with IP-10 being inducible by IFN-y and suggests that our test could also be used to detect auto-Abs neutralizing IFN-y or to diagnose inborn errors of IFN-y-dependent immunity76,77. IFN-y can, therefore, be used at least as a control for tests on patients with inborn errors of the type I IFN-dependent and type II IFN-mdependent response pathways, and patients with auto-Abs against type I but not type II IFNs. It should be noted that the blood samples used here were collected more than 24 hours before the assay, which may have decreased the amount of IP- 10 detected. A classical ELISA was performed on these plasma supernatants and yielded similar results, with slightly higher sensitivity (Figure 5B). Thus, IP- 10 can be induced by the three major human type I IFNs, but not by the tissue-restricted IFN-s and IFN-K, and it is also induced by type II IFN. IP-10 is, therefore, a suitable target molecule for the detection of auto-Abs neutralizing thecorresponding type I or type II IFNs. Moreover, IFN-y can be used as a control in screens for auto-Abs neutralizing type I IFNs only, and vice versa.[000175] Assessment of experimental conditions likely to affect IP- 10 production[000176] We then investigated technical parameters that might modify IP- 10 induction in the assay, such as the time between blood sampling and stimulation, and the matrix used for blood sampling (containing clot activators or anticoagulants). We tested the blood of three healthy donors sampled 4 h, 24 h, 48 h and 72 h before stimulation with 1 ng / mL IFN, The strongest IP-10 response was obtained following the stimulation of blood samples obtained four hours before the assay (3,000-4,000 pg / mL) (Figure SC). Collecting the blood sample 24 h before stimulation almost halved the amount of IP-10 produced in the assay, although the response to IFN-y remained strong. IP- 10 production after stimulation with type I IFNs was similar for blood samples collected 24 h or 48 h before the assay but was much lower for blood samples collected 72 h before the assay (Figure 5C). We then compared the IP-10 response to stimulation with IFN between blood samples collected in tubes containing lithium heparin, ethylenediamine tetraacetic acid (EDTA) or citrate. Blood collected in lithium heparin and stimulated with 1 ng / mL type I IFN produced 2,000-3,000 pg / mL IP- 10, but IP-10 levels were much lower for blood samples collected in EDTA (<600 pg / mL) and almost no IP-10 was detected for blood samples collected in citrate (Figure 5D). We then studied the kinetics of IP-10 production following IFN stimulation. We stimulated blood samples collected in lithium heparin from two healthy donors with 1 ng / mL type I IFN and 100 U7mL IFN-y, 16 hours after sampling. Plasma supernatants were collected 2 h, 4 h, 6 h. 8 h, 10 h, 12 h, 14 h and 16 h post-stimulation for the assessment of IP-10 production. IP- 10 was detectable as early as 4 h after stimulation, and relatively high levels were detected after 6 h of stimulation (Figure 5E). Beyond this timepoint, IP- 10 levels continued to increase, slowly but steadily, to reach a plateau after 14-16 h of stimulation. Finally, we compared IP- 10 responses following the stimulation with IFN of blood incubated with and without 5% CO2, as clinical laboratories do not use incubators with COr-enriched atmospheres. We found no difference in IP-10 induction between these conditions (Figure 5F). Also, we showed that mAbs blocking IFNAR.2 or a cocktail of mAbs neutralizing all type I IFNs prevented or strongly impaired the induction of IP-10 by any type I IFN (data not shown). This observation provided an important control for diagnostic purposes for patients with suspected auto-Abs against type I IFNs or genetic deficiencies of the type 1 IFN response pathway. Overall, these data suggest that, for optimal results, blood should be 1) stimulated very soon after sampling (preferably within 24 h), ii) imperatively collected in lithium heparin-containing tabes, and iii) stimulated at least 6 h and, ideally, between 14 and 16 h.]W®177] IP-40 is not induced by type I IFNs in patients with auto-Abs neutralizing type IIFNs1000178] We collected whole-blood samples in lithium heparin for nine healthy individuals and five APS-1 patients. These samples were stimulated, 8 h to 24 h after their collection, with 10 ng / mL or 1 ng / mL of IFN-a2, IFN-3, or IFN-ffi. Plasma samples from the healthy donors were simultaneouslytested negative for auto-Abs neutralizing type I IFNs, whereas the plasma samples from the five APS- 1 patients were previously found to neutralize 10 ng / mL IFN-a2a and IFN~o>, and one of these samples also neutralized 1 ng / mL IFN-p- Of note, these neutralization values were obtained in a luciferase- based neutralization assay in the presence of a 1 : 10 dilution of plasma, implying a neutralization of 10 times higher concentrations in vivo. These APS-1 patients also had high titers of auto-Abs on ELISA (data not shown). After 16 h of stimulation, we measured IP- 10 levels in the supernatant by ELISA (Figure 6A-B). After stimulation with 10 ng / mL IFNs, strong IP-10 induction (up to >10,000 pg / mL) was observed for the nine healthy donors tested, in all conditions of stimulation (Figure 6A). By contrast, tests on ths five APS-1 patients revealed an abolition of IP-10 induction after stimulation with IFN-a2 or IFN-«>, at all concentrations tested (0.1, 1, and 10 ng / mL), and after stimulation with 0.1 or 1 ng / mL IFN-P, thereby demonstrating the neutralizing activity of the auto-Abs of these patients. Blood samples from five healthy donors and three APS-1 patients were also stimulated with 1,000 U / mL IFN- y, leading to strong IP-10 induction in the samples of both patients and controls. After stimulation with 1 ng / mL IFNs, IP- 10 levels remained high in blood from healthy donors, whereas 1FN-O2 and IFN-w were completely neutralized by all blood samples from APS - 1 patients; the samples from three of these patients completely neutralized IFN-P and the sample from another one of these patients partially neutralized IFN-P (Figure 6B). IP- 10 induction was similar in patients and healthy donors after stimulation with 100 U / mL IFN-y. We then tested blood from a patient with severe CO VID-19 pneumonia and auto-Abs neutralizing low concentrations of IFN-a2 (i.e., 1 ng / mL and 100 pg / mL, as previously tested in luciferase-based neutralization assays), but without a genetic diagnosis. In the whole-blood assay, blood from this patient neutralized 10 ng / mL IFN-a2 (equivalent to 1 ng / mL IFN- a2 in the luciferase assay, due to the 1 :10 dilution of the plasma). The patient’s blood sample also completely neutralized 1 ng / mL IFN-a2 (equivalent to 100 pg / mL in the luciferase assay) and, interestingly, also partially neutralized I ng / mL IFN-P and IFN-CT, whereas the samples from the healthy donors did not (.Figures 6C-D). IP-10 production following IFN-y stimulation was normal in both the patient and controls. Finally, we tested blood from a patient heterozygous for an autosomal NFKB2 p52LOt7lKB8°Ofallele carrying auto-Abs neutralizing 10 ng / mL !FN-a2 and IFN-w, a woman heterozygous for an X-linked NEM&Ofallele carrying carries auto-Abs neutralizing 10 ng / mL IFN-®, and a patient with auto-Abs neutralizing 10 ng / mL of all type I IFNs with no genetic diagnosis. These neutralization data previously obtained in the luciferase assay were fully reproduced in our whole-blood IP-10 assay (Figure 6E). Thus, IP-10 is not induced by rype I IFNs in patients with auto-Abs neutralizing high or low concentrations of the corresponding type I IFNs, This assay is at least as sensitive as the luciferase assay, and perhaps even more sensitive, given that it uses whole blood rather than plasma.[099179 ] IP-10 is not induced by the activation of whole blood from patients with IEI affecting the type I IFN response pathwayWe assessed the impact of a genetic deficiency of the type I IFN response pathway by stimulating fresh blood from patients with autosomal recessive, complete IFNAR18>SS, IFNAR289-90, TYK291’93, or IRF994deficiency. We first showed that pre-incubation with mAbs blocking IFNAR1 or IFNz\R2 prevented the induction of IP-10 by any type I IFN (Figure SG-H). This observation also provided an important control for diagnostic purposes for patients with suspected auto-Abs against type I IFNs or genetic deficiciencies of the type I IFN response pathway. Leukocytes from patients with complete TYK2 deficiency display a profound, but not complete impairment of responses to type I IFN, IL-10, IL-12, and IL-2392 9J-95. Following the stimulation of whole blood from a TYK2-deficient patient or from a IFN ARI -deficient patient with 1 IFN-a2, IFN-<s, or IFN-p, IP-10 was produced in amounts similar to those observed in the absence of stimulation, attesting to a complete lack of response; by contrast, blood from the healthy donors tested responded normally. IP-10 production after IFN-y stimulation was normal in both patients and controls (Figure 6F). The results for one of the two IFNAR2-deficient patients were identical, with a complete lack of response, whereas the other IFN AR2 -deficient patient produced very small, but nevertheless detectable amounts of IP- 10 after stimulation with IFN-β or IFN-oj, This was perhaps due to the affinity of these two IFNs for their receptors (IFN ARI and IFNAR2) being higher than that of IFN-a2 for its receptor, allowing some signal transduction through IFNARl alone56(Figure 6F). The levels of IP- 10 produced following stimulation with IFN-y were slightly lower for the IFNAR2-deficient patients than for the three healthy donors (but similar to that of the travel control of the IFNAR2 -deficient patient) and the TYK2-deficient patient, probably because their blood samples were not stimulated until 48 h and 36 h after their collection. This highlights the necessity of a (travel) control sample drawn at the same time as that of the patient, to ensure correct interpretation. Interestingly, the IRF9-deficient patient displayed weak but detectable IP-10 induction after stimulation with all type I IFNs, perhaps mediated by STAT homodimers in the absence of STAT1-STAT2-IRF9 heterotrimers (Figure 6F). Thus, IP-10 induction in response to stimulation with 1 ng / mL type IFN of any of the three subtypes was severely or totally abolished in the whole-blood samples of patients with genetic defects of the type IFN pathway tested. As in patients with auto-Abs neutralizing type I IFNs, these inborn errors of the type I IFN response pathway impaired type I IFN-induced IP- 10 production. These findings suggest that this assay can be used to detect both genetic defects of the type I IFN response pathway (as shown for mutations of TYK2, IRF9tand possibly STAT!, STAT2, and mutations of STAT1 also affecting the type II IFN pathway) and auto-Abs neutralizing type I IFNs.[000180] DISCUSSION[000181] Human IP-10 was initially reported to be strongly induced by type II IFN stimulation in (J937 cells97. It is also induced by type I and III IFNs (also known as IFN-As: IFN-X.1 (IL-29), IFN-A.2 (IL-28a), IFN-A3 (lL-28b) and IFN-A4) in human umbilical vein endothelial (HUVEC) cells and is, therefore, considered to be an interferon-stimulated gene (ISG) without selectivity for any particular type of IFN98"100. The function of human IP-10 at whole-body level is unknown, as no IP-10-deficienthumans have ever been identified. Mice with genetic defects resulting in an absence of IP-10 display impaired T-cell proliferation in response to allogeneic and antigenic stimulation, impaired IFN-y secretion by T cells in response to antigenic challenge, and an impaired ability to control the replication of mouse hepatitis virus in the brain9'. We show here that human IP- 10 is induced by !FN-a2, IFN-fJ, IFN-ffi, or IFN-y, as shown by LEGENDplex™ and ELISA, in whole blood ftom healthy individuals, but not in whole blood from patients with circulating auto-Abs neutralizing the corresponding type I IFNs, or patients with inborn errors of immunity (1EI) affecting the type I IFN response pathway. The detection of IP- 10 by ELISA or ELISA-like techniques is, therefore, a suitable readout for screens for common auto-Abs neutralizing type I IFNs and, possibly, rarer auto-Abs neutralizing type II IFN. The prior incubation of blood from healthy donors with mAbs that block IFN ARI or IFNAR2 can be used as a control. Human IFN-y can be used as a control in assays screening for auto-Abs neutralizing type I IFNs or genetic defects of the type I IFN receptor. High concentrations of type I IFNs could also be used as a control, although this would increase the cost of the assay, and an appropriate concentration of IFNs not neutralized by potent auto-Abs remains to be determined. The use of whole blood rather than plasma or serum in this assay indirectly allows the detection, or at least the suspicion of auto-Abs neutralizing any form of human type I IFN or genetic defects of the type I IFN response pathway. Indeed, there is no other known mechanism that could explain a lack of response to IFN-ct2, -p, and / or -w in a patient whose leukocytes respond to IFN-y.[000182] This new assay has several advantages over the classic neutralization assays performed in research laboratories25. First, it is based on whole-blood stimulation and does not, therefore, require the prior processing of blood samples with the purification of cells, plasma, or serum. Second, the stimulation step is both easy and rapid (6 h or overnight), providing a convenient organization of testing over a period of less than two days that is compatible with standard work schedules in diagnostic laboratories. Third, the plasmas collected and left unstilulated (NS conditions) can be analyzed directly by ELISA for the structural detection of the auto-Abs to corroborate any neutralization observed. Fourth, various types of ELISA are commonly used in diagnostic laboratories, as these assays are cheap and robust, with a high throughput, and can easily be scaled up. Fifth, the assay provides results rapidly (potentially within 10 h from the start of the assay, taking into account the times required for stimulation and IP-10 detection), and certainly more reapidly than the classical assays used in research laboratories (2-4 days). Sixth, the materials and reagents required are already in use in most, if not all diagnostic laboratories. No sophisticated or expensive machines are needed. Seventh, the cost of this assay is reasonable, at an estimated USS3-5 per sample and set of conditions, about half the cost of previous tests. Overall, this assay is a sensitive and robust tool for the detection of auto-Abs neutralizing IFNs and inborn errors of the type I IFN response pathway, and is compatible with the technical constraints of a diagnostic laboratory. 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Induction of interferon-inducible protein- 10 and monokine induced by interferon-gamma from human endothelial cells infected with Influenza A virus. Arch Virol 149(1 (2003) hitox <foi crgtdoi: 10.1007 / s00705 -003-0208-499 Brownell, J. et al. Direct, Interferon-Independent Activation of the CXCL10 Promoter by NF- KB and Interferon Regulatory' Factor 3 during Hepatitis C Virus Infection. Journal of Virology 88, 1582-1590 (201 D htri ,« t 2\ r , l *' K '100 Sauty, A. et al. The T Cell-Specific CXC Chemokines IP- 10, Mig, and I-TAC Are Expressed by Activated Human Bronchial Epithelial Cells 1. The Journal of Immunology 162, 3549-3558 (1999). https >101 Bastard, P. et al. Greater risk of COVID- 19 pneumonia in children with autoantibodies neutralizing IFN-a than in those with autoantibodies neutralizing IFN-w. J Exp Med 221(2) (2023). ht'ps: / / doi.org:doi; 10.1084 / jem.20231353102 Bastard, P. el al. Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs. Science Immunology 8(90) (2022). https.fopfofouEXAMPLE 2[000184] The above example established detection of IP- 10 by ELISA or ELISA-like techniques as a suitable readout for screens for common auto-Abs neutralizing type I IFNs and proposed its applicability with regard to rarer auto- Abs neutralizing type II IFN. IFN-y is the single type II IFN. An additional stud}-' was conducted to further evaluate and establish the applicability of the test and approach to detect inborn errors in the type II IFN response pathway and auto-antibodies against type II IFN.[000185] IP-10 induction in a patient with auto-Abs neutralizing IFN-y was assessed (results shown in FIG. 7). IP-10 induction was measured after the stimulation of whole blood from an anti-IFN-y patient versus a travel control (TC). Two different concentrations of IFN-y were evaluated, as well as glycosylated IFN-a2, IFN-P, or IFN-® (as controls), with IP-10 levels measured in plasma supernatants by ELISA. The anti-IFN-y patient sample almost completely neutralized 100 U / niL IFN-y as would be expected and IP-10 levels in response to IFN-y were on the order of the non stimulated (NS) baseline. At a high IFN-y concentration ( 1 ,000 U / ml) the antibody was not able to neutralize. Also, the anti-IFN- y patient sample did not neutralize the type I IFNs and IP-10 levels were induced. By contrast, the travel control (TC) could not neutralize any of the IFNs and concentrations tested. This study demonstrates that altered IP-10 induction could identify and screen samples with auto-antibodies against type II IFN.Thus, detection of IP- 10, determined via ELISA or ELISA-like techniques for example, provides a suitable readout for screens for auto-Abs neutralizing type II IFN, particularly auto-Abs neutralizing IFN-y.[000186| This invention may be embodied in other forms or carried out in other ways without departing from the spirit or essential characteristics thereof. The present disclosure is therefore to be considered as in all aspects illustrated and not restrictive, the scope of the invention being indicated by the appended Claims, and all changes which come within the meaning and range of equivalency are intended to be embraced therein.[000187] Various references are cited throughout this Specification, each of which is incorporated herein by reference in its entirety.

Claims

WHAT IS CLAIMED IS:

1. A method for predicting an altered type I IFN pathway or altered type II IFN pathway in a patient or individual comprising:(a) isolating a blood or serum sample from said patient or individual;(b) combining the blood or serum with IFN selected from IFNy, and one or more of IFNa2, IFNP or IFN® for a period of time so as to permit IFN induction; and(c) evaluating the induction, elevation, or increased expression of IP-10 in response to IFNy, and one or more of IFNa2, IFNp or IFNa; wherein the failure of induction, elevation, or increased expression of IP-10 in response to IFNy, or in response to one or more of IFNa2, IFNp or IFN® indicates the presence of an autosomal recessive IFN deficiency or loss-of-fonction (LOF) mutation in a type I IFN or type IT IFN pathway or response relevant gene, or the presence of anti-type I IFN or anti-type II IFN specific auto-antibodies (auto- Abs) in the patient or individual.

2. The method of claim 1, wherein the failure of IFNa2, IFN£ or IFNffl mediated induction indicates the presence of an autosomal recessive IFN deficiency or loss-of-fonction (LOF) mutation in a type I IFN pathway or response relevant gene, or the presence of anti-type I IFN specific auto- antibodies (auto-Abs) in the patient or individual; and wherein the failure of IFNy mediated induction indicates the presence of an autosomal recessive IFN deficiency or loss-of-fonction (LOF) mutation in a type 11 IFN pathway or response relevant gene or the presence of anti-type 11 IFN specific auto-Abs, particularly anti-IFNy auto-Abs, in the patient or individual.3, The method of claim 1 further comprising:(d) evaluating the blood or serum sample for auto-anlibodies specific for one or more type I IFN selected from:(i) IFN-a2 and IFN-w;(ii) IFN-®2, IFN-to and IFN-p;(iii) IFN-a2, IFN-©, IFN-p and IFN-s;(iv) IFN-a2, IFN-©, IFN-(3, IFN-s and IFN-K;(v) !FN-a2, IFN-to, IFN-P and IFN-al / 13;(vi) IFN-a2, IFN-®, IFN-p, IFN- al / 13 and IFN-al4;(vii) IFN-a2, IFN-©, IFN-3, IFN- al / 13, IFN-al4 and IFN-a7;(viii) IFN-a2, IFN-o, IFN- al / 13, IFN-al4, IFN-a7(ix) IFN-O2, IFN-m, IFN-P, IFN-s., IFN-aL IFN-a2, IFN-a6, IFN-al3, IFN-al4 andIFN-aI6; and(x) IFN-s2, IFN-<a, IFN-cel, IFN-a2, IFN-e6, IFN-al3, IFN-al4 and!FN-al6; or(e) evaluating the blood or serum sample for auto-antibodies specific for one or more type II IFN selected from IFNy.

4. The method of claim 1 further comprising:(d) evaluating the blood or serum sample for a LOF mutation in one or more type I IFN pathway gene or type II IFN pathway gene selected from:(ii) IFNARI, IFNAR2, TYK2 or IRF9;{m) IFNAR2, TYK2, IFNARI, STATI or STAT2;(iv) IFNAR2, TYK2, IFNARI, STATI, STAT2, TLR3 or TLR7;(v) IFNAR2, TYK2, IFNARI, IRF7, IFIH1, TLR3, TBK1, IRF3, TICAMI, or UNC93B1 ;(vi) IFNAR2, TYK2, IFNARI, STATI, STAT2, IRF7, IFIH1, TLR3, TBK1, IRF3 , TICAMI or UNC93BI;(vii) IFNAR2, TYK2. IFNARI, STATI, STAT2, IRF7, IFIHI, TLR3, TBKIJRF3 , TICAMI, UNC93Blor TRAF3; or(viii) IFNAR2, TYK2, IFNARI, STATI, STAT2, IRF7, IFIHI, TLR3, TBK1, IRF3 ,TICAMI, UNC93BL TRAF3, or TLR7;(e) wherein a patient or individual determined to have an autosomal recessive IFN deficiency or LOF mutation is administered one or more Type I or Type II IFN to replace the function lost due to the mutation and / or is administered an immune-modulatory agent that increases or facilitates type I or type II IFN-mediated response.

5. The me thod of claim 4, wherein the patient or individual determined to have a LOF mutation is administered IFN-a2 or IFN-P or IFN-y.

6. The method of claim 1 further comprising:(d) evaluating the blood or serum sample for auto-antibodies specific for one or more type I IFN selected from:(i) IFN-&2 and IFN-©;(ii) IFN-a2, IFN-© and IFN-P;(iii) IFN-«2, IFN-®, IFN-P and IFN-E;(iv) IFN-a2, IFN-©, IFN-P, IFN-E and IFN-K;(v) IFN-a2, IFN-ffl, IFN-P and IFN-al / 13 ;(vi) IFN-a2, IFN-©, IFN-P, IFN- al / 13 and IFN-al4;(vii) IFN-a2, IFN-©, IFN-P, IFN- al / 13, IFN-al4 andlFN-a7;(viii) IFN-«2, IFN-O), IFN- al / 13, IFN-aI4, IFN-a7(ix) IFN-a2, lFN-<», IFN-P, IFN-e, IFN-al, IFN-&2, IFN-a6, IFN-al3, IFN-al 4 and IFN-al 6; and(x) IFN-a2, IFN-ca, IFN-al, IFN-ot2, IFN-a6, IFN-al3, IFN-al 4 and IFN-al 6; and(e) evaluating the blood or serum sample for a LOF mutation in one or more type I IFN pathway gene or type II IFN pathway gene selected from:(i) / FFAR2 or TYK2;(ii) IFNARi , IFNAR2, TKO or IRF9;(iii) IFNAR2, TYK2, IFNAR1, STAT! or STAT2;(iv) IFNAR2, TYK2, IFNARl, STAT], STAT2, TLR3 or TLR7;(v) IFNAR2, TYK2, IFNARl. ISF7, IFIH1, TLR3, TBKI, IRF3, TICAMI, or UNC93B1 ;(vi) IFNAR2, TYK2, IFNARl, STATI, STAT2, IRF7, IFIH1, TLR3, TBKI, IRF3 , TICAM1 or UNC93B1;(vii) IFNAR2, TYK2, IFNARl, STATI, STAT2, IRF7, TFIffl, TLR3, TBKI, IRF3 , TICAML UNC93Blor TRAF3; or(viii) IFNAR2, TYK2, IFNARl, STATI, STAT2, IRF7, IFIH1, TLR3, TBKI, IRF3 , TICAM1, UNC93B1, TRAF3, or TLR7; or(f) evaluating the blood or serum sample for auto-antibodies specific for one or more type 11 IFN selected from IFNy.

7. The method of any of claims 3 or 6, wherein the blood or serum sample is evaluated for neutralizing antibodies.

8. The method of any of claims 1 , 2, 3, 6 or 7, wherein anti -type I IFN or anti-type II IFN auto- antibodies are identified and plasmapheresis is then conducted on the patient or individual to deplete the antibodies, or wherein B cells, such as auto-reactive B cells, and / or plasmacytes or plasmablasts are depleted in the patient or individual.

9. The method of any of claims I, 2, 3, 6 or 7, wherein anti-type I IFN or anti-type II IFN auto- antibodies are identified and wherein a patient or individual having auto-Abs against one or more of IFN-a2, IFN-co, IFN-s, IFN-al, TFN-a6, IFN-al 3, IFN-a14 or IFN-al 6 and not having auto-Abs against IFN-P is treated by administering IFN-p,10. 'The method of any of claims 1 , 2, 3, 6 or 7. wherein a patient or individual having auto-Abs against one or more of IFN-a2 or IFN-a and riot having auto-Abs against IFN-p is treated by administering IFN-p.

11. The method of any of claims 1 , 2, 3, 6 or 7, wherein a patient or individual having auto-Abs against one or more Type 1 IFN selected from IFN-ffi, IFN-s, IFN-p, IFN-K, and not having auto-Abs against IFN-a2 is treated by administering IFN-a2.

12. The method of any of claims L 2, 3, 6 or 7, wherein a patient or individual not having auto-Abs against IFN-P is treated by administering IFN-p.

13. The method of any of claims 1, 2, 3, 6 or 7. wherein a patient or individual having auto-Abs against one or more Type I IFN is treated by administering an IFN subtype which is not neutralized by the patient’s or individual’s auto-Abs.

14. The method of any of claims 1, 2, 3, 6 or 7, wherein a patient or individual having one or more anti-type I IFN auto-antbody is not administered a viral vaccine, particularly a live attenuated or inactivated viral vaccine, or wherein a patient or individual positive for or at risk for infection or severe virus infection, or having vaccine-associated disease is treated to remove or deplete the auto- Abs and / or is administered a type I IFN or type II IFN against which they do not have auto-Abs and / or is administered an immune-modulatory agent that increases or facilitates type I IFN-mediated response.

15. The method of any of claims 1-13, wherein the patient or individual is suffering from or at risk of infection selected from SARS-CoV-2 infection, influenza infection, West Nile Virus infection, Middle East respiratory’ syndrome (MERS), intra-macrophage infection, mycobacterial disease and tuberculosis.

16. The method of any of claims 1-7, for predicting the presence of an autosomal recessive IFN deficiency or loss-of-function (LOF) mutation in a type I IFN pathway or response relevant gene, or the presence of anti-type I IFN specific auto-Abs in a patient or individual positive for or at risk for SARS-CoV-2 infection, influenza infection, West Nile Virus infection, Middle East respiratory syndrome (MERS), intra-macrophage infection, mycobacterial disease or tuberculosis, having COVID- 19 disease, prior to vaccination with live attenuated vaccine (LAV), or having vaccine- associated disease and thereby determining treatment and treating the patient or individual, wherein a patient or individual having one or more auto-antbody is not administered the vaccine or wherein a patient or individual positive for or at risk for SARS-CoV-2 infection, influenza infection, West NileVirus infection, Middle East respiratory syndrome (MERE), intra-macrophage infection, mycobacterial disease, or tuberculosis, having COVID-19 disease, or having vaccine-associated disease is treated to remove or deplete the auto-Abs and / or is administered a type I IFN against which they do not have auto-Abs and / or is administered an immune-modulatory agent that increases or facilitates type I IFN-mediated response.

17. The method of claim 16, wherein the LAV is a COVID-19 / SARsCoV-2 vaccine or is a yellow fever vaccine.

18. The method of claim 16, wherein the vaccine-associated disease is COVID-19 / SARsCoV-2 vaccine-associated disease or is yellow fever virus (YFV) vaccine-associated disease,19. An assay for predicting an altered type I IFN pathway or altered type II IFN pathway in a patient or individual comprising:(a) contacting a sample of blood or serum sample from the patient or individual with IFN selected from IFNy, and one or more of IFNa2, IFNp or IFN© for a period of time so as to permit IFN induction; and(b) evaluating the induction, elevation, or increased expression of IP- 10 in response to IFNy, and one or more of IFNu2, IFNp or IFN®; wherein the failure of induction, elevation, or increased expression of IP-10 in response to IFNy, or in response to one or more of IFNa2, IFNp or IFN® indicates the presence of an autosomal recessive IFN deficiency or loss-of-fiinction (LOF) mutation in a type I IFN or type II IFN pathway or response relevant gene, or the presence of anti-type I IFN or anti-type II IFN specific auto-antibodies (auto- Abs) in the patient or individual.

20. The assay of claim 19, comprising:(a) contacting a sample of blood or serum sample from the patient or individual with IFNy, and one or more of IFNa2, IFNp or IFN® for a period of time so as to permit IFN induction; and(b) evaluating the induction, elevation, or increased expression of IP- 10 in response to IFNy and one or more of IFNa2, IFNB or IFN®.

21. The assay of claim 19 or 20, further comprising evaluating the presence of auto-antibodies directed against one or more Type I IFN or Type II IFN, comprising:(c) contacting the sample of blood or serum with one or more recombinant type I or type II IFN protein selected from IFN-a2, IFN-®, IFN-P, and IFN-y, wherein each IFN protein is labeled with a distinct detectable tag or marker to form an antibody-protein complex;(d) contacting any antibody-protein complex of (a) with one or more labeled anti-human immune globulin molecule that will bind and label auto-antibody bound to any one or more IFN protein; and(e) specifically and selectively detecting each type I or type II IFN protein bound by specific auto- Ab thereto.

22. The assay of claim 21, wherein one or more recombinant type I or type II IFN protein is labeled with a fluorescent marker.

23. The assay of claim 21, wherein one or more recombinant type I or type II IFN protein is covalently coupled to a magnetic bead with a fluorescent marker.

24. The assay of claim 21 or 23, wherein each of the one or more recombinant type I or type II IFN proteins is covalently coupled to a magnetic bead with a distinct and differential fluorescent marker,25. T he assay of claim 21, wherein the one or more labeled anti-human immune globulin molecule that will bind and label bound auto-antibody is a labeled non-human animal derived anti- human IgG.

26. The assay of any of claims 21-25, wherein the presence of neutralizing auto-antibodies is determined.

27. The assay of claim 19 or 20, further evaluating the blood or serum sample for a LOF mutation in one or more type I IFN pathway gene or type II IFN pathway gene comprising assessing one or more gene mutation by virtue of one or more probe directed against one or more type I IFN pathway gene or type II IFN pathway gene selected from:(i) IFNAR2 or TYK2-(ii) IFNAR1, IFNAR2, TYK2 or 1RF9;(iii) IFNAR2, 77X2, IFNARi, STAT1 or STAT2;(iv) IFNAR2, TYK2, IFNAR1, STAT1, STAT2, TLR3 or TLR7;(v) 1FNAR2, TYK2, IFNAR1, IRF7, IFIHl, TLR3, TBK1, IRF3, TICAM1, or UNC93B1 ;(vi) IFNAR2, TYK2, IFNAR1, STAIR STAT2, IRF7, IFIHl, TLR3, TBK1, IRF3 , TICAM1 or UNC93BI;(vii) IFNAR2, TYK2, IFNAR1, STAT1, STAT2, IRF7, IFIHl, TLR3, TBKI, IRF3 ,TICAM1, UNC93Blor TRAF3; or(viii) IFNAR2, TYK2, 1FNARI, STAT1, STAT2, IRF7, IFIH1, TLR3, TBK1, IRF3 , TICAM1, UNC93B1, TRAF3, or TLR7.

28. A kit for evaluating or predicting an altered type I IFN pathway or altered type II IFN pathway in a patient or individual comprising:(a) IFN selected from IFNy, and one or more of IFNa2, 1FN|J or IFN®; and(b) an agent, antibody or probe capable of binding IP- 10 protein; for a period of time so as to permit IFN induction: and(c) a means for specific and selective detection of each IP-10 protein bound by the agent, antibody or probe: wherein the failure of induction, elevation, or increased expression of IP- 10 in response to IFNy, or in response to one or more of IFNa2, IFNp or IFN® indicates an altered type I IFN pathway or altered type II IFN pathway.

29. The kit of claim 28, wherein kit further comprises a means for determining the presence of an autosomal recessive IFN deficiency or loss-of- function (LOF) mutation in a type I IFN or type II IFN pathway or response relevant gene, or the presence of anti-type I IFN or anti-type II IFN specific auto-antibodies (auto-Abs) in the patient or individual,30. The kit of claim 28 or 29 for evaluating the presence of auto-antibodies directed against one or more Type I IFN or Type II IFN in a patient or individual, wherein the kit farther comprises:(a) one or more recombinant type I or Type II IFN protein selected from IFN-a2, IFN-®, IFN-p and IFN-y, wherein each IFN protein is labeled with a distinct detectable tag or marker;(b) one or more labeled anti-human immune globulin molecule that will bind and label auto-antibody bound to any one or more IFN protein;(c) a means for specific and selective detection of each type I IFN protein bound by specific auto- Ab thereto.31 . The kit of claim 30, wherein one or more recombinant type I or type II IFN protein is labeled with a fluorescent marker, or wherein one or more recombinant type I or type II IFN protein is covalently coupled to a magnetic bead with a fluorescent marker.

32. The kit of claim 30 or 31. wherein each of the one or more recombinant type I or type II IFN proteins is covalently coupled to a magnetic bead with a distinct and differential fluorescent marker.

33. The kit of claim 28 or 29, for further evaluating the blood or serum sample for a LOF mutation in one or more type I IFN pathway gene or type II IFN pathway gene comprising assessingone or more gene mutation, wherein the kit forther comprises of one or more probe directed against one or more type I IFN pathway gene or type II IFN pathway gene selected from:(i) IFNAR2 or TYK2;(ii) IFNARI, IFNAR2, 71X2 or IRF9;(iii) IFNAR2, TYK2' , IFNARI, STAT1 or STAT2:(iv) IFNAR2, TYK2, IFNARI , STAT1 , STAT2, TLR3 or TLR7;(v) TFNAR2, TYK2, IFNARI, IRF7, IFIH1, TLR3, TBK1, IRF3, TICAM1, or UNC93B1 ;(vi) IFNAR2, TYK2, IFNARI, STAT1, STAT2, IRF7, IFIHI, TLR3, TBKI, IRF3 , TIC AMI or UNC93B1;(vii) IFNAR2, TYK2, IFNARI, STAT1. STAT2, IRF7, IFIHI, TLR3, TBKI, IRF3 , TICAMI, UNC93B1OT TRAF3; or(viii) IFNAR2, TYK2, IFNARI, STAT1, STAT2, IRF7, IFIHI, TLR3, TBKI, IRF3 , TICAM1, UNC93B1, TRAF3, or TLR7.

34. The assay of claim 27 or the kit of claim 33 for evaluating a patient or individual positive for or at risk for SARS-CoV-2 infection or having COVID- 19 disease or prior to vaccination with live attenuated vaccine or having vaccine-associated disease for the presence of an autosomal recessive IFN deficiency or loss-of-fimction (LOF) variation or mutation in a type I or type II IFN pathway or response relevant gene and thereby determining treatment or whether the patient or individual can be safely vaccinated or should be vaccinated and / or treating the patient or individual, wherein a patient or individual determined to have an autosomal recessive IFN deficiency or LOF mutation is administered one or more Type I or Type II IFN to replace the function lost due to the mutation and / or is administered an immune-modulatoiy agent that increases or facilitates type I or type II IFN- mediated response.

35. The assay or kit of claim 34, wherein the patient or individual determined to have a LOF mutation is administered a Type I or Type II IFN.

36. The assay or kit of claim 34, wherein the patient or individual determined to have a LOF mutation is administered IFN-o2 or IFN-p or IFN-y.

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