How to predict and treat the severity of COVID-19

Abstract

The present invention relates generally to coronavirus disease 2019 (COVID-19), and more particularly to predicting the severity of COVID-19 manifestations in patients or individuals at risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) based on the level of chemokine (C-X-C motif) ligand 16 (CXCL16) expression and / or rs10490770 genotype.

Description

[Technical field]

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS This application claims priority to co-pending U.S. Provisional Patent Application No. 63 / 264,896, filed December 3, 2021, the entirety of which is incorporated herein as if fully set forth. [Background technology]

[0002] SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or sometimes 2019-nCoV), a spherical positive single-stranded RNA virus, is causing the ongoing pandemic of coronavirus disease 2019 (COVID-19). To date, SARS-CoV-2 has infected over 126 million individuals worldwide and caused over 2.7 million deaths. SARS-CoV-2 is a strain of the SARS-CoV species in the Betacoronavirus genus.

[0003] Like other coronaviruses, SARS-CoV-2 has four structural proteins: S (spike), E (envelope), M (membrane), and N (nucleocapsid). The S, E, and M proteins form the viral envelope, while the N protein is located in the core of the virus particle, binds to viral RNA, and is involved in conformation into the viral particle. Some betacoronaviruses also contain hemagglutinin-esterase (HE) protein on the particle surface, which may enhance entry into host cells.

[0004] The spike protein is a trimeric class I fusion protein that is highly glycosylated and protrudes from the virion surface, facilitating attachment to and entry into host cells. In some coronaviruses, the S protein consists of two subunits, S1 and S2, on the surface of the viral particle. In other coronaviruses, including SARS-CoV-2, the S protein contains S1 and S2 domains but remains intact on the surface of the viral particle until it is cleaved in endocytic vesicles during viral entry.

[0005] Fusion of the S protein with the host cell membrane involves significant structural rearrangements of the S protein: the receptor-binding domain (RBD) of the S1 subunit of the S protein undergoes a conformational movement from a "down" conformation that is inaccessible to the S1 subunit's bound receptor to an "up" conformation that is accessible to the receptor. The "up" conformation appears to be less stable than the "down" conformation.

[0006] The S2 domain controls viral entry into host cells. Angiotensin-converting enzyme 2 (ACE2), a type I membrane protein, is widely expressed throughout human tissues, including lung, heart, kidney, intestine, and adipose tissue. ACE2 has been identified as the host cell receptor for previous SARS-CoV strains and is the target of the SARS-CoV-2 S protein RBD. RBD binding is thought to occur on the outer surface of the ACE2 protein, whereas angiotensin substrate binding occurs within a deep cleft of the protein.

[0007] Recently, a 3.5 angstrom resolution structure of the S protein was reported. As mentioned above, the S protein is cleaved into two subunits, the S1 and S2 subunits. This cleavage of the S protein by host proteases is important for viral infection and viral escape from cells via lysosomes.

[0008] During infection, the S protein is cleaved by host cell proteases to expose the fusion peptide of the S2 domain. Cleavage of the S protein occurs between the S1 and S2 domains, followed by cleavage within the S2 domain (S2') proximal to the fusion peptide. This results in fusion of the viral and cellular membranes and release of the viral genome into the cytoplasm of the host cell. Cleavage at both sites is thought to be necessary for viral entry into the host cell.

[0009] CXCR6 and CXCL16 Recent genome-wide association studies have identified a gene cluster on chromosome 3 (3p21.31; rs73064425) containing the C-X-C motif chemokine receptor 6 (CXCR6) gene that is at higher risk for severe manifestation of COVID-19. This DNA segment is approximately 50 kb in size and includes LZTFL1, SLC6A20, FYCO1, CCR9, and XCR1 in addition to the CXCR6 gene. Another variant, rs10490770 (T>C), is associated with higher hospitalization rates, severe disease (leading to severe respiratory failure and venous thromboembolism), and death. Genetic variants within this segment that are associated with severe COVID were inherited from Neanderthals and are carried by a high percentage of individuals in South Asia and Europe.

[0010] Chemokine (CXC motif) ligand 16 (CXCL16) is synthesized as a transmembrane molecule and expressed as a cell surface binding molecule and a soluble chemokine. CXCL16 interacts with CXCR6 on leukocytes and other cells promoting chemotaxis or cell adhesion. Inflammatory cytokines such as IFNγ and TNFα promote CXCL16 expression. Upon release, CXCL16 binds to CXCR6. + It has previously been implicated in the pathogenesis of lung injury where it functions as a chemoattractant for T cells, natural killer (NK) cells, B cells, and dendritic cells. CXCL16 levels have been shown to be elevated in the serum of patients with acute lung injury. Summary of the Invention

[0011] In one embodiment, the invention provides a method of treating a patient diagnosed with coronavirus disease 2019 (COVID-19) comprising measuring an expression level of chemokine (C-X-C motif) ligand 16 (CXCL16) in the patient, and if the expression level of CXCL16 is associated with a more severe COVID-19 manifestation, treating the patient for a more severe COVID-19 manifestation, regardless of the severity of the patient's actual COVID-19 manifestation.

[0012] In another embodiment, the present invention provides a method of treating a patient diagnosed with coronavirus disease 2019 (COVID-19), comprising determining that the patient has a genotype associated with a more severe COVID-19 manifestation at the rs10490770 single nucleotide polymorphism (SNP) site and treating the patient for a more severe COVID-19 manifestation, regardless of the actual severity of the patient's COVID-19 manifestation.

[0013] In yet another embodiment, the invention provides a method of predicting severity of a coronavirus disease 2019 (COVID-19) manifestation in a patient diagnosed with or at risk for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), comprising determining an expression level of chemokine (C-X-C motif) ligand 16 (CXCL16) in the patient; and if the CXCL16 expression level is associated with a more severe COVID-19 manifestation, predicting that the patient will experience a more severe COVID-19 manifestation; or if the CXCL16 expression level is not associated with a more severe COVID-19 manifestation, predicting that the patient will experience a less severe COVID-19 manifestation.

[0014] In yet another embodiment, the invention provides a method of predicting severity of coronavirus disease 2019 (COVID-19) manifestations in a patient diagnosed with COVID-19 or an individual at risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), comprising determining the rs10490770 genotype of the patient or individual, and predicting that the patient or individual is likely to not experience severe COVID-19 manifestations if the patient's or individual's rs10490770 genotype is determined to be TT, or predicting that the patient or individual is likely to experience severe COVID-19 manifestations if the patient's or individual's rs10490770 genotype is not TT.

[0015] These and other features of the present invention will be more readily understood from the following detailed description of the various aspects of the invention taken in conjunction with the accompanying drawings which illustrate various embodiments of the invention. [Brief description of the drawings]

[0016] [Figure 1] 1 shows baseline plasma CXCL16 levels in COVID-19 patients and COVID negative control subjects. [Diagram 2] 1 shows baseline plasma CXCL16 levels in COVID-19 patients who died and those who survived the disease. [Diagram 3] 1 shows baseline plasma CXCL16 levels in COVID-19 patients according to the severity of COVID-19 manifestations. [Figure 4] FIG. 1 shows plots of CXCL16 levels, BMI, and age in COVID-19 patients who died and those who survived the disease, showing correlation with CXCL16 levels. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0017] Please note that the drawings of the present invention are not to scale. The drawings are intended to depict only typical aspects of the present invention and therefore should not be considered as limiting the scope of the present invention. In the drawings, like numbers represent like elements between the drawings.

[0018] Applicant's ODYSSEY study is a double-blind, Phase 3 study with planned randomization of a total of 300 hospitalized severely COVID-19 patients. The inclusion criteria for the study are as follows: 1. You are an adult aged between 18 and 90 years old; 2. Laboratory-confirmed COVID-19 infection; 3. Pneumonia confirmed by chest radiography or computed tomography; 4. Fever of 36.6°C or higher under the armpit, 37.2°C or higher in the mouth, or 37.8°C or higher in the rectum was confirmed after admission or use of antipyretics; 5. PaO2 / FiO2 ≦ 300; and 6. The patient is hospitalized.

[0019] Key exclusion criteria included: 1. Unable to provide informed consent, or to have an authorized relative or designated person provide informed consent, or unable to comply with the requirements of the protocol; 2. Known allergy to tradipitant or other neurokinin-1 antagonists; 3. Pregnancy; 4. Uncontrolled HIV infection, HBV infection, or HCV infection; 5. Other uncontrolled medically significant illness; 6. Participating in clinical trials of other investigational drugs; 7. Alanine aminotransferase > 5 × upper limit of normal or creatinine clearance < 50 m 174 l / min; 8. Requirement of artificial respiration for more than 72 hours.

[0020] Patients will be followed for up to 28 days to record clinical outcomes. Clinical course will be recorded using 7-point clinical status defined as follows: 1- death; 2- Hospitalized for mechanical ventilation or ECMO; 3- Hospital admission for non-invasive ventilation or high-flow oxygen supplementation; 4- Hospital admission due to need for supplemental oxygen; 5- Hospitalization not requiring supplemental oxygen but requiring ongoing medical care; 6- Hospitalization without needing supplemental oxygen or continuing medical care; 7- Not hospitalized.

[0021] Details of the COVID-19 patients and COVID negative control subjects are shown in Tables 1 and 2 below.

[0022] [Table 1]

[0023] [Table 2]

[0024] As used herein, a more severe COVID-19 manifestation means that the patient is hospitalized and on mechanical ventilation or ECMO (WHO=2 in ODYSSEY study) and a less severe COVID-19 manifestation means any other degree of severity other than death (WHO=3, 4, 5, 6, or 7 in ODYSSEY study). Patients who die from COVID-19 are clearly patients who have presented with a severe COVID-19 manifestation, but for purposes of the methods described herein, e.g., for predicting the severity of COVID-19 manifestations in living patients and / or for treating those living patients, consideration of patients who have already died from COVID-19 is not relevant.

[0025] Plasma concentrations of CXCL16 in hospitalized, otherwise unexcluded COVID-19 patients (n=114) and SARS-CoV-2 negative control subjects (n=37) will be assessed using an ELISA assay to characterize the CXCR6 / CXCL16 axis in the pathogenesis of severe COVID-19. DNA samples of patients and controls will be collected for subsequent sequencing.

[0026] The results show elevated levels of CXCL16 in hospitalized COVID-19 patients. As shown in Figure 1, baseline CXCL16 levels are higher (p=0.0235) in COVID-19 patients with severe manifestations (WHO=2) than in patients with less severe manifestations (WHO=3, 4, or 5), while the differences between all COVID-19 patients (WHO=2, 3, 4, or 5) and COVID negative control subjects are not significantly different. CXCL16 expression of approximately 600 pg / mL or higher is associated with more severe manifestations of COVID-19. These results do not correlate with the age, BMI, or sex of the patients.

[0027] Thus, according to one embodiment of the present invention, the severity of a patient's COVID-19 infection can be predicted by determining the patient's CXCL16 expression level. If the level of CXCL16 expression is associated with more severe COVID-19 manifestations (i.e., 600 pg / mL or higher), it can be predicted that the patient will experience more severe COVID-19 manifestations. In contrast, if the level of CXCL16 expression is not associated with more severe COVID-19 manifestations (i.e., less than 600 pg / mL), it can be predicted that the patient will experience less severe COVID-19 manifestations. Such predictions can be made for patients diagnosed with COVID-19, or for individuals at risk of infection with SARS-CoV-2 and developing COVID-19.

[0028] Similarly, a patient diagnosed with COVID-19 can be treated based on such a determination. For example, upon determining that the level of CXCL16 expression is associated with a more severe COVID-19 manifestation, treating the patient can include treating the patient for the more severe COVID-19 manifestation, regardless of the level of severity of the COVID-19 manifestation that the patient exhibits. Such treatment can include inhibiting CXC16 activity in the patient, for example, by administering to the patient an anti-CXCL16 antibody in an amount sufficient to inhibit CXCL16 activity in the patient. Both monoclonal and polyclonal CXCL16 antibodies are known and available, for example, from Invitrogen.

[0029] CXCL16 levels were also significantly (p=0.0004) higher in COVID-19 patients who ultimately died from the disease than in those who were alive at the end of the study. As seen in Figure 2, the average CXCL16 levels in patients who ultimately died from COVID-19 were more than twice as high as the average in patients who did not die.

[0030] These results are replicated in a subsequent study of 70 COVID-19 patients, as shown in Figure 3. Here, patients with the most severe COVID-19 manifestations (WHO=2) again had significantly higher baseline CXCL16 levels than patients with less severe manifestations (WHO=3-7).

[0031] The combined results from both studies suggest that CXCL16 concentrations correlate with COVID-19 mortality. Figure 4 shows plots of CXCL16 concentrations, BMI, and age in COVID-19 patients. Black circles represent patients who died from COVID-19.

[0032] At CXCL16 concentrations above 700 pg / mL, the mortality rate in COVID-19 patients is approximately 25%. This increases to almost 50% in patients with a BMI above 26 and age above 52 years. All patients who died from COVID-19 in this study were in this group.

[0033] The results show that there is no correlation between CXCL16 levels and IFN-γ or TNF-α expression.

[0034] Genetic analysis reveals an association between the rs10490770 variant and severe COVID-19 infection. Carriers of the rs10490770 T>C variant have a significantly (p<0.002) higher risk of death when compared to wild-type patients.

[0035] Thus, embodiments of the present invention may include similar methods of predicting the severity of COVID-19 or treating COVID-19 based on determining a patient's rs10490770 genotype. For example, determining that a COVID-19 patient or individual at risk of SARS-CoV-2 infection has a rs10490770 genotype associated with more severe COVID-19 manifestations (i.e., a non-TT genotype) may predict that the patient or individual is likely to experience more severe COVID-19 manifestations. Conversely, if a patient or individual is determined to have a TT genotype at the rs10490770 site, it may predict that the patient or individual is likely to experience less severe COVID-19 manifestations.

[0036] Such predictions can be used to treat COVID-19 patients. For example, upon determining that a patient has a non-TT rs10490770 genotype, the patient can be treated for a more severe COVID-19 manifestation, regardless of the actual severity of the patient's COVID-19 manifestation. Such treatment can include, for example, inhibiting CXCL16 activity in the patient. Such inhibition can include administering to the patient an anti-CXCL16 antibody in an amount sufficient to inhibit CXCL16 activity. As noted above, monoclonal and polyclonal CXCL16 antibodies are known in the art.

[0037] As used herein, the singular forms "a," "an," and "the" are intended to include the plural forms unless the context clearly dictates otherwise. It will be further understood that the terms "comprises" and / or "comprising," when used herein, specify the presence of stated features, integers, steps, operations, elements, and / or components, but do not exclude the presence or addition of one or more other features, integers, steps, operations, elements, components, and / or groups thereof.

[0038] This written description uses examples to disclose the invention, including the best mode, and also enables one of ordinary skill in the art to practice the invention, including making and using any devices or systems, and performing any related or incorporated methods. The patentable scope of the invention is defined by the claims, and may include other examples that occur to those skilled in the art. Such other examples are intended to be within the scope of the claims if they have structural elements that do not differ from the literal language of the claims, or if they include equivalent structural elements that do not differ insubstantially from the literal language of the claims.

Claims

Claim 1: An agent comprising an anti-chemokine (C-X-C motif) ligand 16 (CXCL16) antibody for use in a method of treating a patient diagnosed with coronavirus disease 2019 (COVID-19), the method comprising: determining the level of expression of chemokine (CXC motif) ligand 16 (CXCL16) in said patient; or Determining that the patient has a genotype associated with severe COVID-19 symptoms due to the rs10490770 single nucleotide polymorphism (SNP) site; and administering to the patient the anti-CXCL16 antibody in an amount sufficient to inhibit CXCL16 activity if the level of CXCL16 expression is 600 pg / mL or greater, or if the rs10490770 genotype is a non-TT genotype, or both. The agent comprising:

2. 1. A method for predicting the severity of coronavirus disease 2019 (COVID-19) manifestations in a patient diagnosed with COVID-19 or an individual at risk for infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), comprising: Determining the rs10490770 genotype of the patient or individual; and predicting that the patient or individual is unlikely to experience severe COVID-19 symptoms if the patient's or individual's rs10490770 genotype is determined to be TT; or If the patient's or individual's rs10490770 genotype is determined to be other than TT, predicting that the patient or individual is likely to experience severe COVID-19 symptoms. The method comprising:

3. An agent comprising an anti-chemokine (C-X-C motif) ligand 16 (CXCL16) antibody for use in a method of treating a patient diagnosed with coronavirus disease 2019 (COVID-19), the method comprising: and predicting the severity of coronavirus disease 2019 (COVID-19) manifestations in a patient diagnosed with COVID-19, the method comprising: determining the rs10490770 genotype of said patient or individual; and predicting that the patient or individual is unlikely to experience severe COVID-19 symptoms if the patient's or individual's rs10490770 genotype is determined to be TT; or If the patient's or individual's rs10490770 genotype is determined to be other than TT, predicting that the patient or individual is likely to experience severe COVID-19 symptoms. Including, administering to said patient an amount of said anti-CXCL16 antibody sufficient to inhibit CXCL16 activity if said patient's or individual's rs10490770 genotype is determined to be not TT.

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