Methods for identifying individuals at high risk of developing coronavirus infection and treatments for such individuals.

Abstract

Provided herein are methods for treating a subject suffering from a coronavirus infection, and methods for identifying a subject at increased risk for a coronavirus infection.

Description

[Technical Field]

[0001] This disclosure provides methods for treating subjects who have or are susceptible to coronavirus infection, methods for identifying subjects who have or are at high risk of developing coronavirus infection, and methods for diagnosing coronavirus infection. [Background technology]

[0002] Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was discovered in Wuhan, China at the end of 2019 and causes coronavirus disease 2019 (COVID-19). Symptoms of COVID-19 range from flu-like symptoms such as fever, cough, and headache, to respiratory failure, acute immune reaction, and death, although it is estimated that most infected individuals show little to no symptoms, even if they are present. As of September 2020, the disease had more than 30 million known cases and more than 940,000 known deaths worldwide, with many more cases and deaths likely undetected. Known risk factors include, in particular, male gender, older age, race, obesity, cardiovascular and kidney disease, chronic obstructive pulmonary disease (COPD), and dementia.

[0003] One of the characteristics of COVID-19 infection is that it can be fatal for some people, while others of comparable age and overall health may be completely asymptomatic. Increased risk of severe illness is associated, among other risk factors, with sex (male), race, age, and obesity. However, the rationale for such differences is currently unclear, but the ability to predict the severity of symptoms in individuals with COVID-19 infection will be a valuable tool for identifying at-risk populations. The ability to identify, monitor, and isolate these populations as needed will represent a significant advance in managing the current COVID-19 pandemic. [Overview of the project]

[0004] This disclosure provides a method for treating a subject with a therapeutic agent that treats or inhibits coronavirus infection, wherein the subject is infected with or susceptible to developing coronavirus infection, and the method is determined by the following steps: i) determining a polygene risk score (PRS) of the subject, a) obtaining or having obtained a biological sample from the subject; and b) performing or having performed a genotyping assay on the biological sample to determine whether the subject has a genotype that includes one or more genetic variants associated with susceptibility to and / or severity of coronavirus infection; wherein the PRS score is determined by the presence or absence of genetic variants and the subject's gene type for each genetic variant. ii) reflecting modosycnoziness and heterozygosity; if the subject's PRS score is below a desired threshold, administering or continuing to administer a standard dose of a treatment agent that treats or inhibits coronavirus infection, and / or monitoring the subject for the onset of coronavirus infection and / or progression of coronavirus infection; or iii) if the subject has a PRS score above a desired threshold, administering or continuing to administer a standard dose of a treatment agent that treats or inhibits coronavirus infection, where the presence of a PRS score above a desired threshold indicates an increased risk of the subject developing coronavirus infection and / or developing severe coronavirus infection.

[0005] This disclosure provides a method for identifying subjects at increased risk of developing coronavirus infection or severe coronavirus infection, the method comprising determining a polygenetic risk score (PRS) of the subject, by: a) obtaining or having obtained a biological sample from the subject; and b) performing or having performed a genotyping assay on the biological sample to determine whether the subject has a genotype comprising one or more genetic variants associated with susceptibility to and / or severity of coronavirus infection; wherein the PRS score reflects the presence or absence of genetic variants and the subject's homozygosity and heterozygosity for each genetic variant; if the subject's PRS score is below a desired threshold, the subject has a reduced risk of developing coronavirus infection or severe coronavirus infection; and if the subject's PRS score is above a desired threshold, the subject has an increased risk of developing coronavirus infection or severe coronavirus infection.

[0006] The accompanying drawings incorporated herein and constituting part thereof illustrate several embodiments and are useful in illustrating the principles of this disclosure together with the description of this disclosure. [Brief explanation of the drawing]

[0007] [Figure 1] The study shows an association between a high COVID-19 genetic risk score (GRS) and hospitalization or severe illness rates in COVID-19-positive patients with one or more established COVID-19 risk factors. [Figure 2] This data shows COVID-19 positive patients and COVID-19 patients requiring hospitalization, categorized by age, sex, and confirmed COVID-19 comorbidities across several cohorts. [Figure 3-1] This shows the sample sizes for various COVID-19 patient categories across several cohorts. [Figure 3-2]Same as above. [Figure 4-1] Shows genetic variants shown to be associated with the risk of COVID-19 in previous GWAS. [Figure 4-2] Same as above. [Figure 4-3] Same as above. [Figure 5-1] Shows the hospitalization risks of COVID-19 positive patients of different ancestries grouped by GRS and polygenic risk scores (PRS). [Figure 5-2] Same as above. [Figure 5-3] Same as above. [Figure 5-4] Same as above. [Figure 6-1] Shows the risks of severe illness in COVID-19 positive patients of various ancestries grouped by GRS and PRS. [Figure 6-2] Same as above. [Figure 6-3] Same as above. [Figure 6-4] Same as above.

Mode for Carrying Out the Invention

[0008] Various terms related to aspects of the present disclosure are used throughout this specification and the claims. Unless otherwise indicated, such terms are to be given their ordinary meaning in the art. Other specifically defined terms are to be interpreted in a manner consistent with the definitions provided herein.

[0009] Unless otherwise explicitly stated, no method or embodiment described herein is intended to be construed as requiring its steps to be performed in a particular order. Therefore, unless a method claim specifically states in the claims or description that the steps should be limited to a particular order, no order is implied in any way. This also applies to any possible ambiguities for interpretation, including logical issues relating to the arrangement of steps or operational flows, plain meanings arising from grammatical structure or punctuation, or the number or types of embodiments described herein.

[0010] As used herein, unless otherwise clearly indicated by the context, the singular forms "a," "an," and "the" refer to multiple objects. As used herein, the terms “subject” and “patient” are interchangeable. A subject may include any animal, including mammals. Mammals include, but are not limited to, livestock (e.g., horses, cattle, pigs), pet animals (e.g., dogs, cats), laboratory animals (e.g., mice, rats, rabbits), and non-human primates. In some embodiments, the subject is human.

[0011] As used herein, “nucleic acid,” “nucleic acid molecule,” “nucleic acid sequence,” “polynucleotide,” or “oligonucleotide” may include polymeric forms of nucleotides of any length, and may include DNA and / or RNA, and may be single-stranded, double-stranded, or multi-stranded. One strand of a nucleic acid also refers to its complementary strand.

[0012] As used herein, the term “including” may, in certain embodiments, be replaced as desired with “consisting of” or “essentially consisting of.” As used herein, the terms “treat,” “treating,” and “treatment,” and “inhibit,” “inhibiting,” and “inhibition” refer to eliciting a desired biological response, such as a therapeutic effect or a preventive effect, respectively. In some embodiments, the therapeutic effect includes one or more of the following after administration of the drug or composition containing the drug: reduction / mitigation of coronavirus infection such as COVID-19; reduction / mitigation of the severity of coronavirus infection such as COVID-19 (e.g., reduction or inhibition of the onset of COVID-19 infection); reduction / mitigation of symptoms and infection-related effects; delay of the onset of symptoms and infection-related effects; reduction of the severity of symptoms of infection-related effects; reduction of the severity of acute episodes; reduction of the number of symptoms and infection-related effects; reduction of the incubation period of symptoms and infection-related effects; improvement of symptoms and infection-related effects; reduction of secondary symptoms; reduction of secondary infections; prevention of recurrence of coronavirus infection such as COVID-19; reduction of the number or frequency of recurrent episodes; increase of the incubation period between symptomatic episodes; increase of the time to sustained progression; acceleration of recovery; or increase in the effectiveness of alternative treatments or decrease in resistance; and / or increase in the survival period of the affected host animal. The preventive effect may include complete or partial avoidance / suppression or delay of the onset / progression of coronavirus infections such as COVID-19 after the administration of the treatment protocol (e.g., complete or partial avoidance / suppression or delay), and an increase in the survival time of the affected host animal. Treatment of coronavirus infections such as COVID-19 includes treatment of subjects already diagnosed with any form of coronavirus infection, such as COVID-19, at any clinical stage or clinical symptom, delaying the onset or progression or exacerbation or worsening of symptoms or signs of coronavirus infections such as COVID-19, and / or prevention and / or reduction of the severity of coronavirus infections such as COVID-19.

[0013] As used herein, the terms “coronavirus infection” or “CoV infection” refer to infection caused by coronaviruses such as SARS-CoV-2, MERS-CoV, or SARS-CoV. This term includes coronavirus respiratory infections, which often occur in the lower respiratory tract. Symptoms include high fever, dry cough, shortness of breath, pneumonia, gastrointestinal symptoms such as diarrhea, organ failure (renal failure and renal insufficiency), septic shock, and death in severe cases. Severe coronavirus infections may be characterized by hospitalization, cytokine storm, shortness of breath, pneumonia, organ failure, septic shock, chest pain or chest tightness, and / or speech impairment or loss of motor function.

[0014] As used herein, the term “comorbidity” refers to one or more diseases or conditions in a subject that may increase the severity of coronavirus infection or may be associated with an increased risk of having severe coronavirus infection. Comorbidities include, but are not limited to, hypertension, coronary artery disease, heart failure, type 2 diabetes, chronic kidney disease, asthma, chronic obstructive pulmonary disease (COPD), and Alzheimer's disease.

[0015] This disclosure relates, in general, to the finding that stratification of subjects by COVID-19 polygeneic risk score (COVID-PRS or PRS) may be useful in identifying subjects who are more likely to benefit from treatment with an anti-spike SARS-CoV-2 monoclonal antibody cocktail (REGN10933 + REGN10987; casirivimab and imdevimab), independently of conventional clinical criteria such as age or other comorbidities (e.g., cardiovascular disease).

[0016] This disclosure provides a method for treating a subject with a therapeutic agent that treats or inhibits coronavirus infection, the subject being infected with or susceptible to developing coronavirus infection. The method includes the step of determining a polygenic risk score (PRS) of the subject. In some embodiments, the PRS is determined by taking or having taken a biological sample from the subject and performing or having performed a genotyping assay on the biological sample to determine whether the subject has a genotype containing one or more genetic variants associated with susceptibility to developing coronavirus infection and / or severity of coronavirus infection. The PRS score reflects the presence or absence of genetic variants and the subject's homozygosity and heterozygosity to each genetic variant. If the subject's PRS score is below a desired threshold, the subject is administered or continues to be administered a standard dose of the therapeutic agent that treats or inhibits coronavirus infection, and / or the subject is monitored for the development and / or severity of coronavirus infection. If a subject has a PRS score exceeding the desired threshold, administer or continue administering a treatment that treats or inhibits coronavirus infection to the subject at the same or greater dose than the standard dose. The presence of a PRS score exceeding the desired threshold indicates that the subject is at increased risk of developing coronavirus infection and / or developing severe coronavirus infection.

[0017] Genetic factors may play a significant role in the risk of developing coronavirus infection and may potentially influence a subject's response to drug treatment. The PRS combines information from numerous genetic variants obtained from infection-related studies to create a single composite quantitative measure that reflects each subject's genetically derived risk of infection. Subjects with a higher number of coronavirus infection risk alleles will have a higher PRS than subjects with fewer alleles. Risk can be assessed at several thresholds, such as percentiles or standard deviation units of the population distribution. Genetic loci associated with coronavirus infection risk, including any genetic variants described herein, can be used by the PRS to stratify subjects, which would be useful in identifying subjects likely to benefit from treatment with any of the inhibitors described herein, regardless of conventional clinical criteria.

[0018] PRS calculations can identify individuals most susceptible to developing coronavirus infections, such as Covid-19. Furthermore, PRS calculations may allow for the identification of individuals most likely to respond to any of the inhibitors described herein.

[0019] In some embodiments, subjects at high risk of developing coronavirus infection may be selected based on PRS, which comprises a weighted sum of multiple genetic variants associated with the development of coronavirus infection and is calculated using at least about 2, at least about 3, at least about 4, at least about 5, at least about 6, at least about 7, at least about 8, at least about 9, at least about 10, at least about 20, at least about 30, at least about 40, at least about 50, at least about 60, at least about 70, at least about 80, at least about 100, at least about 120, at least about 150, at least about 200, at least about 250, at least about 300, at least about 400, at least about 500, or at least about 1,000 genetic variants, and if a patient has a PRS above a threshold score, one of the inhibitors described herein is administered and / or one of the isolation techniques described herein is practiced.

[0020] In some embodiments, the disclosure includes a large number of alleles in a risk assessment, for example, at least about 500,000 genetic variants, at least about 1,000,000 genetic variants, at least about 2,000,000 genetic variants, at least about 3,000,000 genetic variants, at least about 4,000,000 genetic variants, at least about 5,000,000 genetic variants, or at least about 6,000,000 genetic variants, or at least about 6,500,000 genetic variants, or at least about 7,000,000 genetic variants, or at least about 8,000,000 genetic variants, or at least about 9,000,000 genetic variants, or at least about 10,000,000 genetic variants.

[0021] In some embodiments, the Disclosure provides a method for determining PRS in a subject, the method of determining at least about 2 genetic variants from a coronavirus risk database, at least about 3 genetic variants, at least about 4 genetic variants, at least about 5 genetic variants, at least about 6 genetic variants, at least about 7 genetic variants, at least about 8 genetic variants, at least about 9 genetic variants, at least about 10 genetic variants, at least about 15 genetic variants, at least about 20 genetic variants, at least about 30 genetic variants, at least about 40 genetic variants, at least about 50 genetic variants, at least about 60 genetic variants, at least about 70 genetic variants, at least about 100 genetic variants, at least about 200 genetic variants, at least about 500 genetic variants, and at least about 1 This involves determining whether 000 genetic variants, at least approximately 2000 genetic variants, at least approximately 5000 genetic variants, at least approximately 10,000 genetic variants, at least approximately 20,000 genetic variants, at least approximately 50,000 genetic variants, at least approximately 75,000 genetic variants, at least approximately 100,000 genetic variants, at least approximately 500,000 genetic variants, at least approximately 1,000,000 genetic variants, at least approximately 2,000,000 genetic variants, at least approximately 3,000,000 genetic variants, at least approximately 4,000,000 genetic variants, at least approximately 5,000,000 genetic variants, or at least approximately 6,000,000 genetic variants are present in a biological sample derived from the subject, where the presence of a risk allele increases PRS and the presence of an alternative allele decreases PRS.

[0022] In some embodiments, the Disclosure provides a method for determining the risk of a subject developing coronavirus infection, comprising: identifying whether a coronavirus genetic variant is present in a biological sample from the subject; and calculating a PRS of the subject based on the identified genetic variant, wherein the PRS is calculated by summing the weighted risk scores associated with each identified genetic variant.The number of identified genetic variants is at least approximately 2, at least approximately 3, at least approximately 4, at least approximately 5, at least approximately 6, at least approximately 7, at least approximately 8, at least approximately 9, at least approximately 10, at least approximately 15, at least approximately 20, at least approximately 30, at least approximately 40, at least approximately 50, at least approximately 95, at least approximately 100, at least approximately 200, at least approximately 500, at least approximately 1000, at least approximately 2000, at least approximately 5000, and at least approximately 10,000 genetic variants. Target variants, at least approximately 20,000 genetic variants, at least approximately 50,000 genetic variants, at least approximately 75,000 genetic variants, at least approximately 100,000 genetic variants, at least approximately 500,000 genetic variants, at least approximately 1,000,000 genetic variants, at least approximately 2,000,000 genetic variants, at least approximately 3,000,000 genetic variants, at least approximately 4,000,000 This could be 10,000,000 genetic variants, or at least approximately 5,000,000 genetic variants, or at least approximately 6,000,000 genetic variants, or at least approximately 6,500,000 genetic variants, or at least approximately 7,000,000 genetic variants, or at least approximately 8,000,000 genetic variants, or at least approximately 9,000,000 genetic variants, or at least approximately 10,000,000 genetic variants.

[0023] In some embodiments, the Disclosure provides a method for determining the risk of a subject developing coronavirus infection, the method comprising: identifying whether a coronavirus genetic variant is present in a biological sample from the subject; calculating the subject's PRS based on the identified genetic variant; and assigning the subject to a risk group based on the PRS. The PRS may be divided into quintiles, for example, upper quintile, middle quintile, and lower quintile, where the upper quintile of the polygene score corresponds to the highest genetic risk group and the lower quintile of the polygene score corresponds to the lowest genetic risk group.The number of identified genetic variants is at least approximately 2, at least approximately 3, at least approximately 4, at least approximately 5, at least approximately 6, at least approximately 7, at least approximately 8, at least approximately 9, at least approximately 10, at least approximately 15, at least approximately 20, at least approximately 30, at least approximately 40, at least approximately 50, at least approximately 95, at least approximately 100, at least approximately 200, at least approximately 500, at least approximately 1000, at least approximately 2000, at least approximately 5000, and at least approximately 10,000 genetic variants. Target variants, at least approximately 20,000 genetic variants, at least approximately 50,000 genetic variants, at least approximately 75,000 genetic variants, at least approximately 100,000 genetic variants, at least approximately 500,000 genetic variants, at least approximately 1,000,000 genetic variants, at least approximately 2,000,000 genetic variants, at least approximately 3,000,000 genetic variants, at least approximately 4,000,000 This could be 10,000,000 genetic variants, or at least approximately 5,000,000 genetic variants, or at least approximately 6,000,000 genetic variants, or at least approximately 6,500,000 genetic variants, or at least approximately 7,000,000 genetic variants, or at least approximately 8,000,000 genetic variants, or at least approximately 9,000,000 genetic variants, or at least approximately 10,000,000 genetic variants.

[0024] In some embodiments, the Disclosure relates to a method for selecting a subject or candidate at risk of developing coronavirus infection, wherein the subject or candidate is at risk of developing coronavirus infection and is comprised of at least about two genetic variants related to coronavirus, at least about three genetic variants, at least about four genetic variants, at least about five genetic variants, at least about six genetic variants, at least about seven genetic variants, at least about eight genetic variants, at least about nine genetic variants, at least about ten genetic variants, at least about fifteen genetic variants, at least about twenty genetic variants, at least about thirty genetic variants, at least about forty genetic variants, at least about fifty genetic variants, at least about ninety-five genetic variants, at least about one hundred genetic variants, at least about two hundred genetic variants, at least about five hundred genetic variants, at least about one thousand genetic variants, and at least about two thousand genetic variants. , at least approximately 5,000 genetic variants, at least approximately 10,000 genetic variants, at least approximately 20,000 genetic variants, at least approximately 50,000 genetic variants, at least approximately 75,000 genetic variants, at least approximately 100,000 genetic variants, at least approximately 500,000 genetic variants, at least approximately 1,000,000 genetic variants, at least approximately 2,000,000 genetic variants, at least approximately 3,000, 000 genetic variants, at least approximately 4,000,000 genetic variants, at least approximately 5,000,000 genetic variants, or at least approximately 6,000,000 genetic variants, or at least approximately 6,500,000 genetic variants, or at least approximately 7,000,000 genetic variants, or at least approximately 8,000,000 genetic variants, or at least approximately 9,000,000 genetic variants, or at least approximately 10,000,The present invention provides a method comprising: identifying whether 000 genetic variants are present in a biological sample derived from each subject or candidate; calculating a polygenic risk score (PRS) for each subject or candidate based on these identified genetic variants; and selecting subjects or candidates for a desired risk group.

[0025] For all coronavirus risk assessments, incorporating a large number of genetic variants offers the advantage of improved predictive power. This disclosure further provides the risk assessments outlined above, for example, incorporating at least 500,000, at least 1,000,000, at least 2,000,000, at least 3,000,000, at least 4,000,000, at least 5,000,000, or at least 6,000,000 genetic variants, or at least 6,500,000 genetic variants, or at least 7,000,000 genetic variants, or at least 8,000,000 genetic variants, or at least 9,000,000, or at least 10,000,000 genetic variants related to coronavirus.

[0026] In some embodiments, the Disclosure relates to a method for selecting a population of subjects or candidates at high risk of developing coronavirus infection, wherein the population consists of at least about two genetic variants related to coronavirus, at least about three genetic variants, at least about four genetic variants, at least about five genetic variants, at least about six genetic variants, at least about seven genetic variants, at least about eight genetic variants, at least about nine genetic variants, at least about ten genetic variants, at least about fifteen genetic variants, about 20 genetic variants, at least about 30 genetic variants, at least about 40 genetic variants, at least 50 genetic variants, at least 95 genetic variants, at least 100 genetic variants, at least 200 genetic variants, at least 500 genetic variants, at least 1000 genetic variants, and at least 2000 genetic variants. Variants, at least 5,000 genetic variants, at least 10,000 genetic variants, at least 20,000 genetic variants, at least 50,000 genetic variants, at least 75,000 genetic variants, at least 100,000 genetic variants, at least 500,000 genetic variants, at least 1,000,000 genetic variants, at least 2,000,000 genetic variants, at least 3,000, 000 genetic variants, at least 4,000,000 genetic variants, at least 5,000,000 genetic variants, or at least 6,000,000 genetic variants, or at least 6,500,000 genetic variants, or at least 7,000,000 genetic variants, or at least 8,000,000 genetic variants, or at least 9,000,000 genetic variants, or at least 10,000,The present invention provides a method comprising: identifying whether 000 genetic variants are present in a biological sample derived from each subject or candidate; calculating the PRS derived from each subject or candidate based on these identified genetic variants; and selecting subjects or candidates from the high-risk group.

[0027] In some embodiments, the number of identified genetic variants is at least two. In some embodiments, the number of identified genetic variants is at least three. In some embodiments, the number of identified genetic variants is at least four. In some embodiments, the number of identified genetic variants is at least five. In some embodiments, the number of identified genetic variants is at least six. In some embodiments, the number of identified genetic variants is at least seven. In some embodiments, the number of identified genetic variants is at least eight. In some embodiments, the number of identified genetic variants is at least nine. In some embodiments, the number of identified genetic variants is at least ten. In some embodiments, the number of identified genetic variants is at least twenty. In some embodiments, the number of identified genetic variants is at least twenty. In some embodiments, the number of identified genetic variants is at least thirty. In some embodiments, the number of identified genetic variants is at least forty. In some embodiments, the number of identified genetic variants is at least 50. In some embodiments, the number of identified genetic variants is at least 70. In some embodiments, the number of identified genetic variants is at least 100. In some embodiments, the number of identified genetic variants is at least 500. In some embodiments, the number of identified genetic variants is at least 1,000. In some embodiments, the number of identified genetic variants is at least 2,000. In some embodiments, the number of identified genetic variants is at least 5,000.In some embodiments, the number of identified genetic variants is at least 10,000. In some embodiments, the number of identified genetic variants is at least 20,000. In some embodiments, the number of identified genetic variants is at least 50,000. In some embodiments, the number of identified genetic variants is at least 75,000. In some embodiments, the number of identified genetic variants is at least 100,000. In some embodiments, the number of identified genetic variants is at least 500,000. In some embodiments, the number of identified genetic variants is at least 1,000,000. In some embodiments, the number of identified genetic variants is at least 2,000,000. In some embodiments, the number of identified genetic variants is at least 3,000,000. In some embodiments, the number of identified genetic variants is at least 4,000,000. In some embodiments, the number of identified genetic variants is at least 5,000,000. In some embodiments, the number of identified genetic variants is at least 6,000,000. In some embodiments, the number of identified genetic variants is at least 6,500,000. In some embodiments, the number of identified genetic variants is at least 7,000,000. In some embodiments, the number of identified genetic variants is at least 8,000,000. In some embodiments, the number of identified genetic variants is at least 9,000,000. In some embodiments, the number of identified genetic variants is at least 10,000,000.

[0028] In some embodiments, the genetic variant associated with susceptibility to developing coronavirus infection and / or the severity of coronavirus infection includes one or more (or all) of the single nucleotide polymorphisms (SNPs) rs73064425, rs2531743, rs143334143, rs9411378, rs10735079, rs2109069, rs74956615, and rs2236757. In some embodiments, the genetic variant associated with susceptibility to developing coronavirus infection and / or the severity of coronavirus infection is rs73064425. In some embodiments, the genetic variant associated with susceptibility to developing coronavirus infection and / or the severity of coronavirus infection is rs2531743. In some embodiments, the genetic variant associated with susceptibility to developing coronavirus infection and / or the severity of coronavirus infection is rs143334143. In some embodiments, the genetic variant associated with susceptibility to developing coronavirus infection and / or the severity of coronavirus infection is rs9411378. In some embodiments, the genetic variant associated with susceptibility to developing coronavirus infection and / or the severity of coronavirus infection is rs10735079. In some embodiments, the genetic variant associated with susceptibility to developing coronavirus infection and / or the severity of coronavirus infection is rs2109069. In some embodiments, the genetic variant associated with susceptibility to developing coronavirus infection and / or the severity of coronavirus infection is rs74956615. In some embodiments, the genetic variant associated with susceptibility to developing coronavirus infection and / or the severity of coronavirus infection is rs2236757. These SNPs were identified by examining the literature of GWAS containing more than 1,000 COVID-19 cases, with a p-value of 5e-8.

[0029] In some embodiments of the present disclosure, the risk assessment includes the highest weighted PRS scores including, but not limited to, the top 50%, 55%, 60%, 70%, 80%, 90%, or 95% of the PRS scores of the patient population.

[0030] [[ID=*3]] In some embodiments, the identified genetic variants include the most risk - associated genetic variants among the genetic variants related to the coronavirus or genetic variants having weighted risk scores in the top 10%, top 20%, top 30%, top 40%, or top 50%.

[0031] In some embodiments, the identified genetic variants include genetic variants related to the development of coronavirus infection in the top 10%, top 20%, top 30%, top 40%, or top 50% of the p - value range. In some embodiments, each identified genetic variant has a p - value of about 10

[0032] , , , about 10 -2 , about 10 -3 , about 10 -4 , about 10 -5 , about 10 -6 , about 10 -7 , 10 -8 , about 10 -9 , about 10 -10 , about 10 -11 , about 10 -12 , about 10 -13 , or about 10 -14 , or about 10 -15 , or about 10 -8 and includes genetic variants related to the development of coronavirus infection having a p - value less than 5×10

[0032] In some embodiments, identified genetic variants include genetic variants associated with the development of coronavirus infection in high-risk patients, where the odds ratio (OR) is approximately ≥1.0, ≥1.5, ≥1.75, ≥2.0, or ≥2.25 for the top 50% of the distribution compared to the rest of the reference population; or approximately ≥1.5, ≥1.75, ≥2.0, ≥2.25, ≥2.5, or ≥2.75. In some embodiments, the odds ratio (OR) may be in the range of approximately 1.0 to approximately 1.5, approximately 1.5 to approximately 2.0, approximately 2.0 to approximately 2.5, approximately 2.5 to approximately 3.0, approximately 3.0 to approximately 3.5, approximately 3.5 to approximately 4.0, approximately 4.0 to approximately 4.5, approximately 4.5 to approximately 5.0, approximately 5.0 to approximately 5.5, approximately 5.5 to approximately 6.0, approximately 6.0 to approximately 6.5, or approximately 6.5 to approximately 7.0. In some embodiments, high-risk patients include patients with PRS scores in the upper end of the decile, quintile, or tertile in the reference population.

[0033] In some embodiments, the identified genetic variants include the genetic variant with the highest genetic variant capacity in the reference population. In some embodiments, the capacity of the genetic variant is calculated with respect to the risk of developing coronavirus infection based on statistical significance, strength of association, and / or probability distribution.

[0034] In some embodiments, the genetic variant score is calculated using a PRS calculation method such as the LDPred method (or its variations and / or versions), which is a Bayesian approach that calculates the posterior mean effect of all variants based on prior (effect size in prior GWAS) and posterior reduction based on linkage disequilibrium. LDPred produces the PRS using genome-wide diversity with weights derived from a set of GWAS summary statistics. See Vilhjalmsson et al., Am.J.Hum.Genet., 2015, 97, 576-92. In some embodiments, alternative approaches to calculating genetic variant scores may be used, including SBayesR (Lloyd-Jones, LR, world wide web at “biorxiv.org / content / biorxiv / early / 2019 / 01 / 17 / 522961.full.pdf”), Pruning and Thresholding (P&T) (Purcell, Nature, 2009, 460, 748-752), and COJO (Yang et al., Nat. Genet., 2012, 44, 369-375). SBayesR is a Bayesian approach similar to LDPred, but allows for greater flexibility with posterior mean effects. Pruning and Thresholding uses a minimum p-value threshold between variants (the p-value associated with the variant from the source data file) and r 2 A threshold (LD criterion) must be specified. P&T identifies the variant with the smallest p-value in each region, and then, under that variant, the specified r 2 Larger than r 2 P&T "collates" all other variants within a region that have a value. In P&T, an indicator variant represents all variants in the collection (only indicator variants are included in P&T, and all other variants are excluded). COJO, or Conditional Co-association Analysis, is conceptually similar to P&T, but after conditioning with an indicator variant, it incorporates additional variants in a given LD block into the score if they show an independent contribution to the risk of developing coronavirus infection.

[0035] In some embodiments, the ability of the genetic variant is calculated using the LDPred method, where the ρ value is approximately 0.0001 to approximately 0.5. In some embodiments, the ability of the genetic variant is calculated using the LDPred method, where the ρ value is approximately 0.5. In some embodiments, the ability of the genetic variant is calculated using the LDPred method, where the ρ value is approximately 0.1. In some embodiments, the ability of the genetic variant is calculated using the LDPred method, where the ρ value is approximately 0.05. In some embodiments, the ability of the genetic variant is calculated using the LDPred method, where the ρ value is approximately 0.01. In some embodiments, the ability of the genetic variant is calculated using the LDPred method, where the ρ value is approximately 0.005. In some embodiments, the ability of the genetic variant is calculated using the LDPred method, where the ρ value is approximately 0.001. In some embodiments, the ability of the genetic variant is calculated using the LDPred method, where the ρ value is approximately 0.0005. In some embodiments, the ability of a genetic variant is calculated using the LDPred method, where the ρ value is approximately 0.0001.

[0036] In some embodiments, the PRS score reflects the presence or absence of genetic variants, the homozygosity and heterozygosity of the subject for each genetic variant, and their association with susceptibility to coronavirus infection. In some embodiments, the PRS score reflects the presence or absence of genetic variants, the homozygosity and heterozygosity of the subject for each genetic variant, and their association with the severity of coronavirus infection. In some embodiments, the PRS score reflects the presence or absence of genetic variants, the homozygosity and heterozygosity of the subject for each genetic variant, and their association with susceptibility to coronavirus infection and the severity of coronavirus infection.

[0037] In some embodiments, susceptibility to developing coronavirus infection is characterized by confirmed infection (i.e., a positive test result). In some embodiments, the severity of coronavirus infection is characterized by hospitalization, cytokine storm, shortness of breath, pneumonia, organ failure, septic shock, chest pain or chest tightness, and / or speech impairment or motor loss. In some embodiments, the severity of coronavirus infection is characterized by hospitalization. In some embodiments, the severity of coronavirus infection is characterized by a cytokine storm. In some embodiments, the severity of coronavirus infection is characterized by shortness of breath. In some embodiments, the severity of coronavirus infection is characterized by pneumonia. In some embodiments, the severity of coronavirus infection is characterized by organ failure. In some embodiments, the severity of coronavirus infection is characterized by septic shock. In some embodiments, the severity of coronavirus infection is characterized by chest pain or chest tightness. In some embodiments, the severity of coronavirus infection is characterized by speech impairment or motor loss.

[0038] In some embodiments, the PRS score is combined with a comorbidity score. If the combination of the subject's PRS score and comorbidity score falls below a desired threshold, the subject is administered or continues to be administered a standard dose of a treatment that treats or inhibits coronavirus infection, and / or the subject is monitored for the onset and / or progression of coronavirus infection. If the combination of the subject's PRS score and comorbidity score exceeds a desired threshold, the subject is administered or continues to be administered a standard dose of a treatment that treats or inhibits coronavirus infection at the same or a higher dose. If the combination of the PRS score and comorbidity score exceeds a desired threshold, it indicates that the subject has an increased risk of developing coronavirus infection and / or an increased risk of developing severe coronavirus infection. In some embodiments, the subject has only 1 to 5 comorbidities. In some embodiments, the subject has only 1 to 4 comorbidities. In some embodiments, the subject has only 1 to 3 comorbidities. In some embodiments, the subject has only 2 or 3 comorbidities.

[0039] In some embodiments, the comorbidity score reflects the presence or severity of comorbidities selected from the group consisting of hypertension, coronary artery disease, heart failure, type 2 diabetes, chronic kidney disease, asthma, chronic obstructive pulmonary disease (COPD), and Alzheimer's disease, or a combination thereof. In some embodiments, the comorbidity is hypertension. In some embodiments, the comorbidity is coronary artery disease. In some embodiments, the comorbidity is heart failure. In some embodiments, the comorbidity is type 2 diabetes. In some embodiments, the comorbidity is chronic kidney disease. In some embodiments, the comorbidity is asthma. In some embodiments, the comorbidity is COPD. In some embodiments, the comorbidity is Alzheimer's disease.

[0040] The presence or absence of any genetic variant described herein in a biological sample derived from a subject, and / or the determination of whether the subject has any genetic variant described herein, can be performed by any of the methods described herein. In some embodiments, these methods may be performed in vitro. In some embodiments, these methods may be performed in situ. In some embodiments, these methods may be performed in vivo. In any of these embodiments, nucleic acid molecules may be present in cells obtained from the subject.

[0041] In any embodiment described herein, nucleic acid molecules may be present in cells obtained from the subject. In any embodiment described herein, the genotyping assay may be performed in vitro.

[0042] In some embodiments, the genotyping assay includes sequencing at least a portion of the nucleotide sequence of a genomic nucleic acid molecule in a biological sample. In some embodiments, the genotyping assay includes sequencing at least a portion of the nucleotide sequence of an mRNA molecule in a biological sample. In some embodiments, the genotyping assay includes sequencing at least a portion of the nucleotide sequence of a cDNA molecule generated from an mRNA molecule in a biological sample. In some embodiments, the genotyping assay includes sequencing at least a portion of the nucleotide sequence of one or more nucleic acid molecules and / or adjacent nucleic acid regions encoding LZTFL1, SLC6A20, CCHCR1, ABO, OAS3, DPP9, RAVER1, and / or IFNAR2. In some embodiments, the genotyping assay includes sequencing an entire nucleic acid molecule in a biological sample.

[0043] In some embodiments, the genotyping assay comprises: a) amplifying at least a portion of a nucleic acid molecule encoding LZTFL1, SLC6A20, CCHCR1, ABO, OAS3, DPP9, RAVER1, and / or IFNAR2, and / or an adjacent region of nucleic acid; b) labeling the amplified nucleic acid molecule with a detectable label; c) contacting the labeled nucleic acid molecule with a support containing a mutation-specific probe; and d) detecting the detectable label.

[0044] In some embodiments, a genotyping assay includes contacting nucleic acid molecules encoding LZTFL1, SLC6A20, CCHCR1, ABO, OAS3, DPP9, RAVER1, and / or IFNAR2, and / or adjacent nucleic acid regions, in a biological sample with a mutation-specific probe containing a detectable label, and detecting the detectable label.

[0045] In some embodiments, nucleic acid molecules are present in cells obtained from the subject. In some embodiments, the genotyping assay is performed in vitro. In any embodiment described herein, the coronavirus infection may be Middle East Respiratory Syndrome (MERS), Severe Acute Respiratory Syndrome (SARS), or Coronavirus Disease 2019 (COVID-19). In any embodiment described herein, the coronavirus infection may be MERS. In any embodiment described herein, the coronavirus infection may be SARS. In any embodiment described herein, the coronavirus infection may be COVID-19.

[0046] In any embodiment described herein, the method may further include testing the subject for the presence of SARS-CoV-2. In any embodiment described herein, therapeutic agents for treating or inhibiting coronavirus infection include lopinavir / ritonavir, chloroquine, hydroxychloroquine, remdesivir, ribavirin, azithromycin, falapirivir, ivermectin, enfuvirtide, amantadine, rimantadine, preconalil, acyclovir, zidovudine, lamivudine, formivirsen, rifampicin, zanamivir, oseltamivir, peramivir, NP-120 (ifenprodil), faviravir / favipiravir, TMJ2 (T J003234), TZLS-501, APN01, tocilizumab, galidesivir, sarilumab, SNG001, AmnioBoost, AT-100, colchicine, leronlimab, BPI-002, OYA1, artemisinin, OT-101, Sepsivac, Prezcobix (darunavir and cobicistat), baricitinib, BXT-25, dexamethasone, duvelisib, or interferons such as recombinant interferon, or any combination thereof. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is lopinavir / ritonavir. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is chloroquine. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is hydroxychloroquine. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is remdesivir. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is ribavirin. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is azithromycin. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is favipiravir. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is ivermectin. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is enfuvirtide.

[0047] In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is amantadine. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is rimantadine. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is preconalil. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is acyclovir. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is zidovudine. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is lamivudine. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is homivirsen. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is rifampicin. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is zanamivir. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is oseltamivir. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is peramivir. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is NP-120 (ifenprodil). In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is faviravir / favipiravir. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is TMJ2 (TJ003234). In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is TZLS-501. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is APN01. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is tocilizumab.In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is galidesivir. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is sarilumab. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is SNG001. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is AmnioBoost. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is AT-100. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is colchicine. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is leronlimab. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is BPI-002. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is OYA1. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is artemisinin. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is OT-101. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is Sepsivac. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is Prezcobix (darunavir and cobicistat). In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is baricitinib. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is BXT-25. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is dexamethasone. In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is duvelisib.In any embodiment described herein, the therapeutic agent for treating or inhibiting coronavirus infection is an interferon, such as recombinant interferon.

[0048] In some embodiments, the therapeutic agent for treating or inhibiting coronavirus infection is an anti-inflammatory agent, an antimalarial agent, an antibody or its antigen-binding fragment that specifically binds to SARS-CoV-2 virus particles, or a COVID-19 vaccine, bromhexine hydrochloride (BHH), 4-(2-aminomethyl)benzenesulfonyl fluoride hydrochloride (AEBSF), nafamostat mesylate, or a polyamide. In some embodiments, the antimalarial agent is chloroquine or hydroxychloroquine. In some embodiments, the anti-inflammatory agent is camostat mesylate. In some embodiments, the anti-inflammatory agent is an antibody such as sarilumab, tocilizumab, or gymcirumab. In some embodiments, the COVID-19 vaccine is an inactivated / dead virus vaccine, an attenuated live virus vaccine, or a viral subunit vaccine.

[0049] In some embodiments, the therapeutic agent for treating or inhibiting coronavirus infection is the antibody cocktail REGN-COV2. In some embodiments, the therapeutic agent for treating or inhibiting coronavirus infection is the antibody cocktail REGN-COV2, or antigen-binding fragments of one or both monoclonal antibodies in the antibody cocktail REGN-COV2. In some embodiments, the therapeutic agent for treating or inhibiting coronavirus infection is any anti-SARS-CoV-2 spike glycoprotein antibody disclosed in U.S. Patent No. 10,787,501, or its antigen-binding fragment, or any combination thereof.

[0050] In some embodiments, the therapeutic agent for treating or inhibiting coronavirus infection is the antibody cocktail REGN-COV2 or anti-IL-6 antibody, or a combination thereof. In some embodiments, the therapeutic agent for treating or inhibiting coronavirus infection is the antibody bamranivimab (LY-CoV555). In some embodiments, the therapeutic agent for treating or inhibiting coronavirus infection is the antibody cocktail REGN-COV2, anti-IL-6 antibody, or antibody bamranivimab (LY-CoV555), or any combination thereof, or optionally, a combination with any other therapeutic agent described herein.

[0051] In some embodiments, the dose of a therapeutic agent for treating or inhibiting coronavirus infection may be increased by about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, or about 90% (i.e., more than the standard dose) for subjects that are heterozygous or homozygous for one or more of the genetic variants described herein, compared to subjects that do not have any of the genetic variants described herein (which may receive a standard dose). In some embodiments, the dose of a therapeutic agent for treating or inhibiting coronavirus infection may be increased by about 10%, about 20%, about 30%, about 40%, or about 50%. Furthermore, the dose of a therapeutic agent for treating or inhibiting coronavirus infection in subjects that are heterozygous or homozygous for one or more of the genetic variants described herein may be administered more frequently than in subjects that do not have any or more of the genetic variants described herein.

[0052] Therapeutic agents that treat or inhibit coronavirus infection may be repeated, for example, after 1 day, 2 days, 3 days, 5 days, 1 week, 2 weeks, 3 weeks, 1 month, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 2 months, or 3 months. Repeated doses may be the same or different doses. Doses may be repeated once, twice, three times, four times, five times, six times, seven times, eight times, nine times, ten times, or more. For example, according to a specific drug regimen, subjects may receive treatment over a long period (e.g., six months, one year, or more).

[0053] The administration of therapeutic agents for treating or inhibiting coronavirus infection may be carried out by any preferred route, including, but not limited to, parenteral, intravenous, oral, subcutaneous, intra-arterial, intracranial, intrathecal, intraperitoneal, topical, intranasal, or intramuscular. Pharmaceutical compositions for administration are preferably sterile, substantially isotonic, and manufactured under GMP conditions. Pharmaceutical compositions may be supplied in unit dosage forms (i.e., dosages for single administration). Pharmaceutical compositions may be formulated using one or more physiologically and pharmaceutically acceptable carriers, diluents, excipients, or auxiliary materials. This formulation depends on the chosen route of administration. The term "pharmaceutically acceptable" means that the carrier, diluent, excipient, or auxiliary material is compatible with the other components of the formulation and is substantially harmless to its recipient.

[0054] This disclosure also provides a method for identifying subjects at high risk of developing coronavirus infection or severe coronavirus infection. This method includes determining the subject's PRS by obtaining or having obtained a biological sample from the subject, and performing or having performed a genotyping assay on the biological sample to determine whether the subject has a genotype containing one or more genetic variants associated with susceptibility to and / or severity of coronavirus infection. The PRS score reflects the presence or absence of genetic variants and the subject's homozygosity and heterozygosity to each genetic variant. If the subject's PRS score is below a desired threshold, the subject is at reduced risk of developing coronavirus infection or severe coronavirus infection. If the subject has a PRS score above a desired threshold, the subject is at increased risk of developing coronavirus infection or severe coronavirus infection.

[0055] In some embodiments, the PRS score reflects the presence or absence of genetic variants, the homozygosity and heterozygosity of the subject for each genetic variant, and their association with susceptibility to coronavirus infection. In some embodiments, the PRS score reflects the presence or absence of genetic variants, the homozygosity and heterozygosity of the subject for each genetic variant, and their association with the severity of coronavirus infection. In some embodiments, the PRS score reflects the presence or absence of genetic variants, the homozygosity and heterozygosity of the subject for each genetic variant, and their association with susceptibility to coronavirus infection and the severity of coronavirus infection. The severity of coronavirus infection is described herein. Any genetic variant described herein, or any combination thereof (such as rs73064425, rs2531743, rs143334143, rs9411378, rs10735079, rs2109069, rs74956615, and rs2236757) may be used to generate the PRS.

[0056] In some embodiments, the PRS score is combined with a comorbidity score, and if the combination of the subject's PRS score and comorbidity score falls below a desired threshold, the subject has a reduced risk of developing coronavirus infection or severe coronavirus infection; if the combination of the subject's PRS score and comorbidity score exceeds the desired threshold, the subject has an increased risk of developing coronavirus infection or severe coronavirus infection. In some embodiments, the subject has only 1 to 5 comorbidities. In some embodiments, the subject has only 1 to 4 comorbidities. In some embodiments, the subject has only 1 to 3 comorbidities. In some embodiments, the subject has only 2 or 3 comorbidities. Comorbidities may be selected from any of those described herein.

[0057] The genotyping assay may be any genotyping assay, such as any assay described herein. In some embodiments, the genotyping assay includes sequencing at least a portion of the nucleotide sequence of a genomic nucleic acid molecule in a biological sample. In some embodiments, the genotyping assay includes sequencing at least a portion of the nucleotide sequence of an mRNA molecule in a biological sample. In some embodiments, the genotyping assay includes sequencing at least a portion of the nucleotide sequence of a cDNA molecule produced from an mRNA molecule in a biological sample. In some embodiments, the genotyping assay includes sequencing at least a portion of the nucleotide sequence of one or more nucleic acid molecules and / or adjacent nucleic acid regions encoding LZTFL1, SLC6A20, CCHCR1, ABO, OAS3, DPP9, RAVER1, and / or IFNAR2. In some embodiments, the genotyping assay includes sequencing an entire nucleic acid molecule in a biological sample.

[0058] In some embodiments, the genotyping assay comprises: a) amplifying at least a portion of a nucleic acid molecule encoding LZTFL1, SLC6A20, CCHCR1, ABO, OAS3, DPP9, RAVER1, and / or IFNAR2 polypeptides, and / or an adjacent region of nucleic acid; b) labeling the amplified nucleic acid molecule with a detectable label; c) contacting the labeled nucleic acid molecule with a support containing a mutation-specific probe; and d) detecting the detectable label.

[0059] In some embodiments, a genotyping assay includes contacting nucleic acid molecules encoding LZTFL1, SLC6A20, CCHCR1, ABO, OAS3, DPP9, RAVER1, and / or IFNAR2, and / or adjacent nucleic acid regions, in a biological sample with a mutation-specific probe containing a detectable label, and detecting the detectable label.

[0060] In some embodiments, nucleic acid molecules are present in cells obtained from the subject. In some embodiments, the genotyping assay is performed in vitro. In some embodiments, the coronavirus infection is any coronavirus infection described herein.

[0061] In some embodiments, the method further includes testing subjects for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In some embodiments, the method further includes separating subjects at high risk of developing coronavirus infection into a high-risk group, and / or isolating and / or monitoring subjects at high risk of developing coronavirus infection.

[0062] The determination of whether a subject has any of the genetic variants described herein in a biological sample derived from the subject, and / or whether a subject has any of the genetic variants described herein, can be made by any of the methods described herein. In some embodiments, these methods may be performed in vitro. In some embodiments, these methods may be performed in situ. In some embodiments, these methods may be performed in vivo. In any of these embodiments, nucleic acid molecules may be present in cells obtained from the subject.

[0063] The biological sample may be derived from any cells, tissues, or bodily fluids of the subject. The sample may include any clinically appropriate tissue, such as a bone marrow sample, tumor biopsy specimen, fine-needle aspiration biopsy specimen, or a sample of bodily fluids such as blood, gingival crevicular exudate, plasma, serum, lymph, ascites, cystic fluid, or urine. In some cases, the sample may include an oral swab. The sample used in the methods disclosed herein will vary depending on the assay format, the nature of the detection method, and the tissue, cells, or extract used as the sample. Depending on the assay used, the biological sample may be treated differently. For example, when detecting any genetic variant described herein, a pretreatment designed to isolate or concentrate the sample for genomic DNA may be employed. Various techniques may be used for this purpose. When detecting the level of any variant mRNA molecule, various techniques may be used to concentrate the mRNA of the biological sample. Various methods may be used to detect the presence or level of mRNA, or the presence of a specific variant genomic DNA locus. In some embodiments, the methods described herein may further include, for example, obtaining a biological sample from the subject.

[0064] In any embodiment described herein, the assay or determination step may include sequencing of the entire nucleic acid molecule. In some embodiments, only the variant genomic nucleic acid molecule is analyzed. In some embodiments, only the variant mRNA molecule is analyzed. In some embodiments, only the variant cDNA molecule obtained from the mRNA molecule is analyzed.

[0065] Examples of techniques for sequencing nucleic acids include, but are not limited to, chain terminator (Sanger) sequencing and dye terminator sequencing. Other methods include non-sequencing nucleic acid hybridization methods, which involve using labeled primers or probes on purified DNA, amplified DNA, and fixed cell preparations (fluorescence in situ hybridization (FISH)). In some methods, the target nucleic acid molecule may be amplified before detection or simultaneously with detection. Examples of nucleic acid amplification techniques include, but are not limited to, polymerase chain reaction (PCR), ligase chain reaction (LCR), strand displacement amplification (SDA), and nucleic acid sequence-based amplification (NASBA). Other methods include, but are not limited to, ligase chain reaction, strand displacement amplification, and thermophilic SDA (tSDA).

[0066] Hybridization techniques may utilize stringent conditions to ensure that the probe or primer specifically hybridizes to its target. In some embodiments, polynucleotide primers or probes under stringent conditions hybridize to their target sequence to a detectably higher degree than other non-target sequences (including up to 10 times the background, such as at least 2 times, at least 3 times, at least 4 times, or more than the background). Stringent conditions are sequence-dependent and vary in different contexts.

[0067] Appropriate stringing conditions to promote DNA hybridization (e.g., washing with 6× sodium chloride / sodium citrate (SSC) at approximately 45°C, followed by washing with 2× SSC at 50°C) are known or can be found in Current Protocols in Molecular Biology, John Wiley & Sons, NY (1989), 6.3.1-6.3.6. Typically, stringing conditions for hybridization and detection include a salt concentration of less than approximately 1.5 M Na at pH 7.0–8.3. + Ions, typically about 0.01–1.0 M Na + The conditions would be an ionic concentration (or other salt) and a temperature of at least about 30°C for short probes (e.g., 10-50 nucleotides) and at least about 60°C for longer probes (e.g., over 50 nucleotides). Stringent conditions can also be achieved by adding an destabilizer (e.g., formamide). Optionally, the wash buffer may contain about 0.1% to about 1% SDS. The hybridization duration is generally less than about 24 hours, usually about 4 to about 12 hours. The wash duration should be long enough to reach equilibrium.

[0068] In any embodiment described herein, any variant described herein can be detected using mutation-specific polymerase chain reaction techniques. Mutation-specific primers may be used, as DNA polymerase will not extend if a mismatch with the template is present.

[0069] In any embodiment described herein, the assay or determination step may include contacting a biological sample with a primer or probe, such as a mutation-specific primer or a mutation-specific probe, which, under stringent conditions, specifically hybridizes to one of the genetic variants described herein rather than a corresponding reference nucleic acid molecule, and determining whether hybridization has occurred.

[0070] In some embodiments, the assay or determination step includes RNA sequencing (RNA-Seq). In some embodiments, the assay or determination step also includes reverse transcription of mRNA to cDNA by reverse transcriptase polymerase chain reaction (RT-PCR), etc.

[0071] In some embodiments, this method utilizes probes and primers of sufficient nucleotide length to bind to a target nucleic acid sequence and specifically detect and / or identify any genetic variant described herein. The operator may achieve this result by determining hybridization or reaction conditions. The nucleotide length may be any length sufficient for use in selected detection methods, including any assay described or exemplified herein. Such probes and primers can specifically hybridize to a target nucleotide sequence under high stringency hybridization conditions. While probes and primers may have complete nucleotide sequence identity of consecutive nucleotides within the target nucleotide sequence, probes that are distinct from the target nucleotide sequence and retain the ability to specifically detect and / or identify the target nucleotide sequence can be designed by conventional methods. The probes and primers may have approximately 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity or complementarity with the nucleotide sequence of the target nucleic acid molecule.

[0072] Mutation-specific probes or primers may contain nucleic acid sequences that are complementary to and / or hybridize to any genetic variant or its complement as described herein, or that specifically hybridize to such variants. In some embodiments, a mutation-specific probe or primer contains or comprises at least about 5, at least about 8, at least about 10, at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, at least about 20, at least about 21, at least about 22, at least about 23, at least about 24, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, or at least about 50 nucleotides. In some embodiments, mutation-specific probes and primers contain or comprise at least 15 nucleotides. In some embodiments, mutation-specific probes and primers contain or comprise at least 15 to at least about 35 nucleotides. In some embodiments, the mutation-specific probe or mutation-specific primer hybridizes to any variant genomic nucleic acid molecule, any variant mRNA molecule, and / or any variant cDNA molecule under stringent conditions.

[0073] In some embodiments, to determine whether any nucleic acid molecules in a biological sample contain any of the genetic variants described herein, the biological sample may be subjected to an amplification method using a primer pair comprising a first primer derived from a 5' adjacent sequence adjacent to the variant location to generate an amplicon indicating the presence of the variant. In some embodiments, the amplicon may range from the length of the primer pair plus one nucleotide base pair to any length of amplicon that can be produced by the DNA amplification protocol. This distance may range from one nucleotide base pair to the limit of the amplification reaction, or about 20,000 nucleotide base pairs. Optionally, the primer pair is adjacent to a region comprising the variant location and a location containing at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more nucleotides on each side of the variant location.

[0074] Similar amplicons can be generated from mRNA and / or cDNA sequences. PCR primer pairs can be derived from known sequences, for example, by using computer programs intended for this purpose, such as the PCR Primer Analysis Tool in Vector NTI version 10 (Informax Inc., Bethesda Md.); PrimerSelect (DNASTAR Inc., Madison, Wis.); and Primer3 (version 0.4.0.COPYRGT., 1991, Whitehead Institute for Biomedical Research, Cambridge, Mass.). Furthermore, primers can be manually identified by visually examining sequences using known guidelines.

[0075] In any embodiment described herein, the isolated mutation-specific probe or mutation-specific primer comprises at least about 15 nucleotides, wherein the mutation-specific probe or mutation-specific primer comprises a nucleotide sequence complementary to a portion of the nucleotide sequence of any genetic variant described herein. In some embodiments, such isolated nucleic acid molecules comprise at least about 5, at least about 8, at least about 10, at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, at least about 20, at least about 21, at least about 22, at least about 23, at least about 24, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, and at least about 55 , containing or consisting of at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, at least about 200, at least about 300, at least about 400, at least about 500, at least about 600, at least about 700, at least about 800, at least about 900, at least about 1000, at least about 2000, at least about 3000, at least about 4000, or at least about 5000 nucleotides. In some embodiments, such isolated nucleic acid molecules contain or consist of at least about 5, at least about 8, at least about 10, at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, at least about 20, at least about 21, at least about 22, at least about 23, at least about 24, or at least about 25 nucleotides. In some embodiments, the isolated nucleic acid molecule contains or consists of at least about 18 nucleotides. In some embodiments, the isolated nucleic acid molecule contains or consists of at least about 15 nucleotides.In some embodiments, the isolated nucleic acid molecule consists of or contains about 10–35, about 10–30, about 10–25, about 12–30, about 12–28, about 12–24, about 15–30, about 15–25, about 18–30, about 18–25, about 18–24, or about 18–22 nucleotides. In some embodiments, the isolated nucleic acid molecule consists of or contains about 18–30 nucleotides. In some embodiments, the isolated nucleic acid molecule contains or contains at least about 15–at least about 35 nucleotides.

[0076] In any embodiment described herein, the isolated nucleic acid molecule hybridizes to at least about 15 consecutive nucleotides of a nucleic acid molecule that is at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% identical to any genetic variant described herein. In some embodiments, the isolated nucleic acid molecule consists of or contains about 15 to about 100 nucleotides, or about 15 to about 35 nucleotides. In some embodiments, the isolated nucleic acid molecule consists of or contains about 15 to about 100 nucleotides. In some embodiments, the isolated nucleic acid molecule consists of or contains about 15 to about 35 nucleotides.

[0077] In some embodiments, the mutation-specific probe and mutation-specific primer include DNA. In some embodiments, the mutation-specific probe and mutation-specific primer include RNA.

[0078] In some embodiments, the probes and primers described herein (including mutation-specific probes and mutation-specific primers) have nucleotide sequences that specifically hybridize to any nucleic acid molecule or its complement disclosed herein. In some embodiments, the probes and primers specifically hybridize to any nucleic acid molecule disclosed herein under stringent conditions.

[0079] In some embodiments, primers (including mutation-specific primers) may be used in second-generation sequencing or high-throughput sequencing. In some cases, primers (including mutation-specific primers) may be modified. In particular, primers may include various modifications used in different steps of, for example, massively parallel signature sequencing (MPSS), Polony sequencing, and 454 pyrosequencing. Modified primers may be used in multiple steps of the process, including biotinylated primers in the cloning step, and fluorescently labeled primers used in the bead-loading and detection steps. Polony sequencing is generally performed using a paired-end tag library in which each molecule of the DNA template is approximately 135 bp long. Biotinylated primers are used in the bead-loading step and emulsion PCR. Fluorescently labeled degenerate nonamer oligonucleotides are used in the detection step. Adapters may include 5'-biotin tags for immobilizing the DNA library onto streptavidin-coated beads.

[0080] In any embodiment described herein, the probe (e.g., a mutation-specific probe) may include a label. In some embodiments, the label is a fluorescent label, a radioisotope label, or biotin.

[0081] The probes and / or primers described herein (including mutation-specific probes and mutation-specific primers) contain or consist of about 15 to about 100 nucleotides, about 15 to about 35 nucleotides, and / or a total of these. In some embodiments, the probes and primers described herein (including mutation-specific probes and mutation-specific primers) have nucleotide sequences that specifically hybridize to any genetic variant disclosed herein or its complement. In some embodiments, the probes and primers (including mutation-specific probes and mutation-specific primers) specifically hybridize to any genetic variant disclosed herein under stringent conditions. In the context of this disclosure, “specifically hybridize” means that the probe or primer (including mutation-specific probes and mutation-specific primers) does not hybridize to any genomic nucleic acid molecule described herein that is not related to coronavirus, a reference mRNA molecule described herein, and / or any reference cDNA molecule described herein.

[0082] Isolated nucleic acid molecules (e.g., probes and primers) may also be ligated to or fused to heterologous nucleic acid sequences (e.g., in vectors) or heterologous labels. For example, the isolated nucleic acid molecules disclosed herein may be in a vector containing isolated nucleic acid molecules and heterologous nucleic acid sequences, or as an exogenous donor sequence containing isolated nucleic acid molecules and heterologous nucleic acid sequences. Isolated nucleic acid molecules may be ligated to or fused to heterologous labels. Labels may be directly detectable (e.g., fluorophores) or indirectly detectable (e.g., haptens, enzymes, or fluorophore enchanters). Such labels may be detectable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means. Examples of such labels include radioactive labels, dyes, pigments, chromogens, spin labels, and fluorescent labels. Labels may also be, for example, chemiluminescent substances; metal-containing substances; or enzymes, resulting in enzyme-dependent secondary signal generation. The term “label” may also refer to a “tag” or hapten, which is a conjugated molecule that, when subsequently added together with a substrate, can selectively bind to a conjugated molecule used to generate a detectable signal. For example, biotin can be used as a tag together with the avidin or streptavidin conjugate of horseradish peroxidase (HRP) to bind to the tag, and the presence of HRP can be detected by examining it with a colorimetric substrate (e.g., tetramethylbenzidine (TMB)) or a chemiluminescent substrate. Exemplary labels that can be used as tags to facilitate purification include, but are not limited to, myc, HA, FLAG or 3XFLAG, 6XHis or polyhistidine, glutathione-S-transferase (GST), maltose-binding proteins, epitope tags, or the Fc portion of immunoglobulins. Numerous labels include, for example, particles, fluorophores, haptens, enzymes, and their colorimetric, chemiluminescent, and chemiluminescent substrates, as well as other labels.

[0083] The disclosed nucleic acid molecules (e.g., probes and primers) may include, for example, nucleotides, or unnatural nucleotides or modified nucleotides (such as nucleotide analogs or nucleotide substitutions). Such nucleotides include nucleotides containing modified bases, sugars, or phosphate groups, or nucleotides incorporating unnatural moieties into their structure. Examples of unnatural nucleotides include, but are not limited to, dideoxynucleotides, biotinylated nucleotides, aminated nucleotides, deaminated nucleotides, alkylated nucleotides, benzylated nucleotides, and fluorophore-labeled nucleotides.

[0084] Nucleic acid molecules disclosed herein (e.g., probes and primers) may also include one or more nucleotide analogs or substitutions. A nucleotide analog is a nucleotide containing modifications to either the base moiety, sugar moiety, or phosphate moiety. Modifications to the base moiety include, but are not limited to, native and synthetic modifications of A, C, G, and T / U, as well as different purine or pyrimidine bases (e.g., pseudouridine, uracil-5-yl, hypoxanthin-9-yl(I), and 2-aminoadenine-9-yl). Modified bases include, but are not limited to, 5-methylcytosine (5-me-C), 5-hydroxymethylcytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl derivatives and other alkyl derivatives of adenine and guanine, 2-propyl derivatives and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine, and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyluracil and cytosine, 6-azouracil, cytosine and thiocytosine. Examples include mine, 5-uracil (pseudracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo (e.g., 5-bromo), 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine, 7-methyladenine, 8-azaguanine, 8-azaadenine, 7-deazaguanine, 7-deazaadenine, 3-deazaguanine, and 3-deazaadenine.

[0085] Nucleotide analogs may also include modifications of the sugar moiety. Modifications of the sugar moiety include, but are not limited to, natural and synthetic modifications of ribose and deoxyribose. Sugar modifications include modifications at the 2' position such as OH;F;O-, S-, or N-alkyl;O-, S-, or N-alkenyl;O-, S-, or N-alkynyl; or O-alkyl-O-alkyl, where the alkyl, alkenyl, and alkynyl are substituted or unsubstituted, C 1~10 Alkyl or C 2~10 Alkenyl and C 2~10Examples of modifications that may involve alkynyls include, but are not limited to, -O[(CH2) n O] m CH3, -O(CH2) n OCH3, -O(CH2) n NH2, -O(CH2) n CH3, -O(CH2) n -ONH2, and -O(CH2) n ON[(CH2) n CH3)2 can also be mentioned, but it is not limited to these. Other modifications at the 2' position include C 1~10 Examples of modifications include, but are not limited to, alkyl groups, substituted lower alkyl groups, alkaryl groups, aralkyl groups, O-alkaryl groups or O-aralkyl groups, SH, SCH3, OCN, Cl, Br, CN, CF3, OCF3, SOCH3, SO2CH3, ONO2, NO2, N3, NH2, heterocycloalkyl groups, heterocycloalkaryl groups, aminoalkylamino groups, polyalkylamino groups, substituted silyl groups, RNA cleavage groups, reporter groups, intercalators, groups for improving the pharmacokinetic properties of oligonucleotides, or groups for improving the pharmacodynamic properties of oligonucleotides, and other substituents having similar properties. Similar modifications may also occur at other positions on the sugar, particularly on the 3'-terminal nucleotide or at the 3' position of the sugar in 2'-5' linked oligonucleotides, and at the 5' position of the 5'-terminal nucleotide. Modified sugars may also include sugars with modifications to the oxygen of the bridging ring, such as CH2 and S. Nucleotide sugar analogs may also have sugar mimes, such as a cyclobutyl moiety instead of pentofuranosyl sugars.

[0086] Nucleotide analogs may also be modified at the phosphate moiety. Modified phosphate moieties include, but are not limited to, moieties that can be modified so that the bond between two nucleotides contains phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkyl phosphotriesters, methyl and other alkylphosphonates (including 3'-alkylene phosphonates and chiral phosphonates), phosphinates, phosphoramides (including 3'-aminophosphoramides and aminoalkyl phosphoramides), thionophosphoramides, thionoalkyl phosphonates, thionoalkyl phosphotriesters, and boranophosphates. These phosphate bonds or modified phosphate bonds between two nucleotides may be via 3'-5' or 2'-5' bonds, which may have opposite polarity, e.g., 3'-5' to 5'-3' or 2'-5' to 5'-2'. Various salts, mixed salts, and free acid forms are also included. Peptide nucleic acids (PNAs) are another example of nucleotide substitutions.

[0087] This disclosure also provides supports comprising a substrate to which any one or more of the probes disclosed herein are bound. A solid support is a solid-phase substrate or support to which molecules, e.g., any of the probes disclosed herein, can be associated. One form of a solid support is an array. Another form of a solid support is an array detector. An array detector is a solid support in which multiple different probes are coupled in an array, grid, or other organized pattern. A form for a solid-state substrate is a microtiter dish (e.g., a standard 96-well type). In some embodiments, a multi-well slide glass containing typically one array per well may be used.

[0088] In any embodiment described herein, the coronavirus infection may be Middle East Respiratory Syndrome (MERS), Severe Acute Respiratory Syndrome (SARS), or Coronavirus Disease 2019 (COVID-19). In any embodiment described herein, the coronavirus infection may be MERS. In any embodiment described herein, the coronavirus infection may be SARS. In any embodiment described herein, the coronavirus infection may be COVID-19.

[0089] In any embodiment described herein, any of the methods may further include testing the subject for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

[0090] In any embodiment described herein, any method may further include separating individuals at high risk of developing coronavirus infection into a high-risk group, and / or isolating and / or monitoring such individuals. In any embodiment described herein, any method may further include quarantine of individuals whose risk of developing coronavirus infection has increased. In some embodiments, individuals at high risk of developing coronavirus infection are isolated in a quarantine area or ward, or provided with a private room, or their movement or access to non-carrier or non-infected individuals or unprotected healthcare workers is limited or restricted, and / or they are provided with dedicated patient care equipment. In some embodiments, when isolation is implemented, healthcare workers who come into contact with individuals at high risk of developing coronavirus infection are required to wear protective clothing. In some embodiments, the methods disclosed herein further include monitoring the condition of individuals at high risk of developing coronavirus infection. In some embodiments, monitoring the subject's condition includes periodically testing the subject for the presence of coronavirus infection and / or periodically evaluating the subject for the presence of symptoms of coronavirus infection, as described herein. In some embodiments, isolation or quarantine measures are implemented for a certain period (e.g., two weeks, three weeks, one month, two months, three months, six months, or a period exceeding six months). In some embodiments, isolation or quarantine measures are maintained for a certain period after the subject no longer tests positive for the presence of coronavirus infection. In some embodiments, isolation or quarantine measures are maintained as long as the subject exhibits symptoms of coronavirus infection. In some embodiments, isolation or quarantine measures are maintained for a certain period after the subject no longer exhibits symptoms of coronavirus infection.

[0091] In any embodiment described herein, if a subject is identified as being at high risk of developing coronavirus infection, the subject may be treated with a therapeutic agent that treats or inhibits coronavirus infection, as described herein.

[0092] All patent documents, websites, other publications, accession numbers, etc., cited above or below are referred to by reference in whole for all purposes to the same degree as if each individual item were specifically and individually indicated to be referred to in that manner. Where different sequences of versions relate to different accession numbers at different points in time, the version related to the accession number at the effective filing date of this application is intended. The effective filing date means the earlier of the actual filing date or the filing date of the priority application, where the accession number is referenced, if applicable. Similarly, where different versions of publications, websites, etc., are published at different points in time, the most recent published version at the effective filing date of this application is meant unless otherwise noted. Any feature, step, element, embodiment, or aspect of this disclosure may be used in combination with other features, steps, elements, embodiments, or aspects unless otherwise specifically noted. While this disclosure has been described in some detail by illustrations and examples for the purposes of clarity and understanding, it will be apparent that certain changes and modifications may be practiced within the scope of the appended claims.

[0093] The following examples are provided to illustrate the embodiments in more detail. They are intended to illustrate, and not limit, the claimed embodiments. The following examples provide disclosures and descriptions of how the compounds, compositions, articles, devices and / or methods described herein are prepared and evaluated, and are intended to be purely illustrative and not to limit any claims. While efforts have been made to ensure accuracy with respect to numerical values ​​(e.g., quantities, temperatures, etc.), some degree of error and deviation may be expected. Unless otherwise indicated, parts are parts by weight, temperatures are °C or ambient temperature, and pressures are atmospheric pressure or near atmospheric pressure. [Examples]

[0094] Example 1: Genetic association study of COVID-19 outcomes Genetic association studies on COVID-19 outcomes across individuals with COVID-19 and those without a history of SARS-CoV-2 infection were compiled from three studies and four ancestry groups. Among COVID-19 cases, hospitalized patients were more likely to be older, have non-European ancestry, and have pre-existing cardiovascular and pulmonary disease (see Figure 2). Using these data, two groups of COVID-19 outcomes were defined: five phenotypes associated with disease risk in COVID-19 cases, and two phenotypes associated with disease severity (see Figure 3).

[0095] Example 2: Identification of genetic variants that modulate disease severity after SARS-CoV-2 infection To identify genetic variants that modulate disease severity after SARS-CoV-2 infection, eight independent associations with disease risk reported in recent GWAS involving over 1,000 cases were studied (r 2Reproducing the results of <0.05) (see Figure 4), we hypothesized that some of these published risk variants may also modulate disease severity. After considering multiple studies, six variants showed a directionally consistent and significant association with at least one of our five disease risk phenotypes: LZTFL1 rs73064425 (3p21.31; MAF=7%, OR=1.42, p=7x10 -11 ); rs2531743 near SLC6A20 (3p21.31;MAF=42%,OR=1.06,p=9x10 -4 ); MHC's rs143334143(6p21.33;MAF=7%,OR=1.36,p=6x10 -4 );ABO's rs9411378(9q34.2;MAF=23%,OR=1.12,p=6x10 -10 ); DPP9's rs2109069(19p13.3;MAF=31%,OR=1.06,p=10 -4 ); and IFNAR2's rs2236757(21q22.1;MAF=29%,OR=1.13,p=2x10 -4 ). The column labeled "Reference" in Figure 4 refers to Pairo-Castineria et al., "Genetic mechanisms of critical illness in Covid-19", medRxiv, 2020 (Worldwide Web "medrxiv.org / content / 10.1101 / 2020.09.24.20200048v2.full.pdf+html") and Shelton et al., "Trans-ethnic analysis reveals genetic and non-genetic associations with COVID-19 susceptibility and severity", medRxiv, 2020 (Worldwide Web "medrxiv.org / content / 10.1101 / 2020.09.04.20188318v1").

[0096] Example 3: High COVID-19 GRS is associated with hospitalization or severe illness. This study also aims to determine whether genetics can help identify individuals at high risk of severe illness for whom preventive or therapeutic interventions can be prioritized. In particular, it focused on four variants (LZTFL1, MHC, DPP9, and IFNAR2, within / neighboring) that have been identified as being associated with COVID-19 susceptibility and also modulate COVID-19 severity. Using these variants, a GRS was constructed for individuals with COVID-19, and after adjusting for established risk factors (age, sex, comorbidities, etc.), the risk of hospitalization and severe illness was compared between patients with high GRS and all other cases. This analysis identified one high GRS (top 10%) (OR=3.91, 95% CI 1.94-8.36, p=2x10). -4 Individuals with one or two established risk factors (OR=5.32, 95%CI 1.89-19.7, p=0.004) were strongly associated with hospitalization risk (see Figure 1). Notably, however, in individuals with many (three or more) risk factors, there was no association between high GRS and hospitalization risk (OR=0.98, 95%CI 0.47-2.21, p=0.96). These individuals had a very high risk of hospitalization regardless of GRS (approximately 80%). Similar results were observed for the risk of severe illness (see Figure 1). In summary, these results suggest that using GRS calculated with variants associated with disease severity can identify COVID-19 cases at high risk of developing a poor disease outcome in patients with few or no established risk factors for severe COVID-19. This is important because many of these individuals may not be prioritized for prophylactic or therapeutic intervention under current guidelines.

[0097] Example 4: The polygene risk score (PRS) predicts the severity of COVID-19 disease and the risk of hospitalization in the UKB European ancestry cohort. The PRS combines information from numerous genetic variants derived from infection-related studies to create a single composite quantitative assessment criterion for each individual that reflects each individual's genetically derived infection risk. Individuals with a higher number of coronavirus infection risk alleles have a higher PRS than individuals with fewer alleles. The PRS was calculated for COVID-19 patients and incorporated into logistic regression models of COVID-19 outcomes for each patient ancestry group in each cohort. Higher PRS scores predicted an increased risk of hospitalization in the European ancestry group of the UKB cohort, and this predictive power increased when combined with the GRS (see Figure 5). Similar results were obtained when this analysis was repeated for the risk of severe illness in COVID-19 cases (see Figure 6).

[0098] Example 5: Use of the COVID-19 Polygene Risk Score (COVID-PRS) to identify targets for spike SARS-CoV-2 monoclonal antibody cocktail treatment (predictive) COVID-PRS may further elucidate genetic factors associated with the risk of severe COVID-19 disease by evaluating patients hospitalized with severe or critical COVID-19 (compared to a non-severe control group) in sarilumab (kevzara) and / or anti-spike clinical trials. Furthermore, COVID-PRS may be assessed using virological and clinical efficacy endpoints in patients enrolled in anti-spike SARS-CoV-2 monoclonal antibody trials (casiribimab and imdevimab). Specifically, COVID-PRS may be tested using the following endpoints (but not limited to these): the presence of baseline antibodies against SARS-CoV-2 S protein and / or N protein (i.e., "SeroAb positive" vs. "SeroAb negative" status); baseline viral shedding (log10 copies / mL) as measured by RT-qPCR in NP swabs; change from baseline in viral shedding endpoints; and change from baseline in clinical status (on a 7-point ordinal scale).

[0099] COVID-PRS may be associated with differences in the proportion of SeroAb-positive patients and / or differences in baseline viral shedding. Differences in viral shedding or change from baseline in clinical status between placebo and treatment groups may vary by COVID-PRS layer. These analyses may assess the impact of PRS on the underlying biological mechanisms of COVID-19 disease and identify subsets of patients who may benefit more from anti-spike SARS-CoV-2 monoclonal antibody treatment.

[0100] The following are additional optional endpoint variables that may be used in the evaluation of COVID-PRS. Clinical, demographic, laboratory, PK / PD, and biomarker / safety endpoints may include, but are not limited to, baseline demographics and clinical characteristics; baseline laboratory and biomarker values ​​and changes from baseline; serum concentrations of casirivimab and imudevimab and corresponding PK parameters; immunogenicity adverse events (ADA) to casirivimab and imudevimab; and the proportion of patients with SAEs that occurred during treatment.

[0101] Common efficacy endpoints include, but are not limited to, the time-weighted mean change in viral shedding from baseline; the time until negative RT-qPCR is generated in all tested samples (and subsequently, no positive RT-qPCR is generated in any tested samples); the percentage of patients with viral loads below the detection limit at each visit; and the percentage of patients with viral loads below the limit of quantification at each visit.

[0102] Evaluation items for hospitalized patients may include, but are not limited to, the percentage of patients whose clinical condition improved by at least 1 or 2 points; the percentage of patients who initiated high-intensity oxygen therapy; the number of days on oxygen supplementation, high-intensity oxygen therapy, or mechanical ventilation; the length of hospital stay; the percentage of patients who were readmitted after discharge; the percentage of patients admitted to the intensive care unit (ICU); the length of stay in the ICU; and the all-cause mortality rate.

[0103] While not limited to specific criteria, outpatient evaluation items may include: the proportion of patients who have visited a healthcare facility one or more times or two or more times in relation to COVID-19; the total number of healthcare visits related to COVID-19; the proportion of patients hospitalized due to COVID-19; the proportion of patients who have received one or more outpatient or telemedicine consultations due to COVID-19; the proportion of patients requiring oxygen use, high-intensity oxygen therapy, or mechanical ventilation due to COVID-19 (if applicable); the length of hospital stay due to COVID-19 (if applicable); the proportion of patients with all-cause mortality; the time to the first onset of symptoms consistent with COVID-19 (asymptomatic cohort only); and the duration of symptoms consistent with COVID treatment.

[0104] In addition to those described herein, various modifications of the subject matter described herein will be apparent to those skilled in the art from the foregoing description. Such modifications shall also fall within the scope of the attached claims. Each reference cited herein (including, but not limited to, bibliographic articles, U.S. and non-U.S. patents, published patent applications, published international patent applications, GeneBank accession numbers, etc.) is incorporated herein by reference in whole and for all purposes.

Claims

1. The use of a therapeutic agent for treating or inhibiting coronavirus infection in the manufacture of a pharmaceutical product for treating a person who has contracted or is susceptible to developing coronavirus infection, wherein the treatment is: The polygene risk score (PRS) of the aforementioned subject is Obtaining or having obtained a biological sample from the aforementioned subject, and To determine whether the subject has a genotype that includes at least one genetic variant related to susceptibility to the onset of coronavirus infection and / or the severity of coronavirus infection, a genotyping assay is performed on the biological sample or is being performed. This includes determining by The PRS score reflects i) the presence or absence of the at least one genetic variant in the target genotype, and ii) the homozygosity or heterozygosity of the target with respect to each of the at least one genetic variant. In the aforementioned procedure, if the subject has a PRS score below a desired threshold, the therapeutic agent for treating or inhibiting the coronavirus infection is administered to the subject at a standard dose or the administration is continued. If the subject has a PRS score exceeding a desired threshold, the therapeutic agent that treats or inhibits the coronavirus infection is administered to the subject in an amount exceeding the standard dose, or administration is continued. If the PRS score exceeds the desired threshold, the subject has an increased risk of developing the coronavirus infection and / or an increased risk of developing a severe coronavirus infection. The aforementioned therapeutic agents include lopinavir / ritonavir, chloroquine, hydroxychloroquine, remdesivir, ribavirin, azithromycin, farapirivir, ivermectin, enfuvirtide, amantadine, rimantadine, preconalil, acyclovir, zidovudine, lamivudine, formivirsen, rifampicin, zanamivir, oseltamivir, peramivir, ifenprodil, faviravir / favipiravir, TMJ2 (TJ003234), and TZL. S-501, APN01, tocilizumab, galidesivir, sarilumab, SNG001, AT-100, colchicine, leronlimab, BPI-002, OYA1, artemisinin, OT-101, Sepsivac, darunavir and cobicistat, baricitinib, BXT-25, dexamethasone, duvelisib, interferon, antibody cocktail REGN-COV2, or anti-IL6 antibody, or any combination thereof. The at least one genetic variant associated with susceptibility to developing coronavirus infection and / or severity of coronavirus infection includes single nucleotide polymorphisms (SNPs) rs73064425, rs2531743, rs143334143, rs9411378, rs10735079, rs2109069, rs74956615, and rs2236757, The aforementioned use.

2. The use according to claim 1, wherein the PRS score also reflects the association between the at least one genetic variant and susceptibility to coronavirus infection.

3. The use according to claim 1, wherein the PRS score also reflects the association between the at least one genetic variant and the severity of coronavirus infection.

4. The use according to claim 1, wherein the PRS score also reflects the association between the at least one genetic variant and susceptibility to coronavirus infection and the severity of coronavirus infection.

5. The use according to any one of claims 1 to 4, wherein the severity of the coronavirus infection is characterized by hospitalization, cytokine storm, shortness of breath, pneumonia, organ failure, septic shock, chest pain or chest tightness, and / or speech impairment or loss of motor function.

6. A use according to any one of claims 1 to 5, The PRS score is combined with a comorbidity score based on the number of comorbidities the subject has; If the subject's PRS score and comorbidity score combined fall below a desired threshold, the subject is administered or continues to be administered the therapeutic agent that treats or inhibits the coronavirus infection at a standard dose; If the subject's PRS score and comorbidity score combined exceed a desired threshold, the subject is administered or continues to be administered the therapeutic agent that treats or inhibits the coronavirus infection in an amount exceeding the standard dose; Herein, the use of the above indicates that the combined PRS score and comorbidity score exceed the desired threshold, which indicates that the subject has an increased risk of developing the coronavirus infection and / or an increased risk of developing a severe coronavirus infection.

7. The use according to claim 6, wherein the subject has one to five comorbidities, one to four comorbidities, one to three comorbidities, or two or three comorbidities.

8. The use according to claim 6 or 7, wherein the comorbidity score reflects the presence or severity of comorbidities, including hypertension, coronary artery disease, heart failure, type 2 diabetes, chronic kidney disease, asthma, chronic obstructive pulmonary disease (COPD), or Alzheimer's disease.

9. The use according to any one of claims 1 to 8, wherein the therapeutic agent is an antibody cocktail of anti-IL-6 antibodies, REGN-COV2, or a combination thereof.

10. The use according to any one of claims 1 to 9, wherein the genotyping assay comprises sequencing at least a portion of the nucleotide sequence of a genomic nucleic acid molecule in the biological sample, at least a portion of the nucleotide sequence of an mRNA molecule in the biological sample, or at least a portion of the nucleotide sequence of a cDNA molecule generated from the mRNA molecule in the biological sample.

11. The use according to any one of claims 1 to 10, wherein the genotyping assay comprises sequencing at least a portion of the nucleotide sequence of a region of at least one nucleic acid molecule and / or an adjacent nucleic acid molecule encoding LZTFL1, SLC6A20, CCHCR1, ABO, OAS3, DPP9, RAVER1, and / or IFNAR2.

12. The use according to claim 11, wherein the genotyping assay comprises sequencing the entirety of at least one nucleic acid molecule encoding LZTFL1, SLC6A20, CCHCR1, ABO, OAS3, DPP9, RAVER1, and / or IFNAR2, and / or the entirety of a region of an adjacent nucleic acid molecule.

13. The aforementioned genotype determination assay, a) Amplifying at least a portion of the region of the at least one nucleic acid molecule and / or an adjacent nucleic acid molecule that encodes LZTFL1, SLC6A20, CCHCR1, ABO, OAS3, DPP9, RAVER1, and / or IFNAR2, b) Labeling the amplified nucleic acid molecule with a detectable label, c) Contacting the labeled nucleic acid molecule with a support containing a mutation-specific probe, d) Detecting the detectable sign, The use according to claim 11, including the use described in claim 11.

14. The aforementioned genotype determination assay, Contacting at least one nucleic acid molecule encoding LZTFL1, SLC6A20, CCHCR1, ABO, OAS3, DPP9, RAVER1, and / or IFNAR2, and / or a region of an adjacent nucleic acid molecule, with a mutation-specific probe containing a detectable label, To detect the aforementioned detectable sign, The use according to claim 11, including the use described in claim 11.

15. The use according to any one of claims 1 to 14, wherein the coronavirus infection includes Middle East Respiratory Syndrome (MERS), Severe Acute Respiratory Syndrome (SARS), or Coronavirus Disease 2019 (COVID-19).

16. The use according to any one of claims 1 to 15, wherein the procedure further comprises testing the subject for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

17. The use of a polygene risk score (PRS) to assess the risk of a subject developing coronavirus infection or developing severe coronavirus infection, wherein the assessment is: The polygene risk score (PRS) of the aforementioned subject is Obtaining or having obtained a biological sample from the aforementioned subject, and This includes determining whether the subject has a genotype that includes at least one genetic variant related to susceptibility to the onset of coronavirus infection and / or the severity of coronavirus infection by performing or having performed a genotyping assay on the biological sample, The PRS score reflects i) the presence or absence of the at least one genetic variant, and ii) the homozygosity and heterozygosity of the subject for each of the at least one genetic variants. If the subject has a PRS score below the desired threshold, then the subject has a reduced risk of developing coronavirus infection or developing severe coronavirus infection, and If the subject has a PRS score exceeding a desired threshold, the subject has an increased risk of developing coronavirus infection or developing severe coronavirus infection. The at least one genetic variant associated with susceptibility to developing coronavirus infection and / or severity of coronavirus infection includes single nucleotide polymorphisms (SNPs) rs73064425, rs2531743, rs143334143, rs9411378, rs10735079, rs2109069, rs74956615, and rs2236757, The aforementioned use.

18. The use according to claim 17, wherein the PRS score also reflects the association between the at least one genetic variant and susceptibility to coronavirus infection.

19. The use according to claim 17, wherein the PRS score also reflects the association between the at least one genetic variant and the severity of coronavirus infection.

20. The use according to claim 17, wherein the PRS score also reflects the association between the at least one genetic variant and susceptibility to coronavirus infection and the severity of coronavirus infection.

21. The use according to any one of claims 17 to 20, wherein the severity of the coronavirus infection is characterized by hospitalization, cytokine storm, shortness of breath, pneumonia, organ failure, septic shock, chest pain or chest tightness, and / or speech impairment or loss of motor function.

22. The PRS score is combined with a comorbidity score based on the number of comorbidities the subject has. If the subject's PRS score and comorbidity score combined fall below the desired threshold, then the subject's risk of developing coronavirus infection or severe coronavirus infection is reduced. The use according to any one of claims 17 to 21, wherein if the subject's PRS score and comorbidity score combined exceed a desired threshold, the subject has an increased risk of developing coronavirus infection or developing severe coronavirus infection.

23. The use according to claim 22, wherein the subject has one to five comorbidities, one to four comorbidities, one to three comorbidities, or two or three comorbidities.

24. The use according to claim 22 or 23, wherein the comorbidity score reflects the presence or severity of comorbidities, including hypertension, coronary artery disease, heart failure, type 2 diabetes, chronic kidney disease, asthma, chronic obstructive pulmonary disease (COPD), or Alzheimer's disease.

25. The use according to any one of claims 17 to 24, wherein the genotyping assay comprises sequencing at least a portion of the nucleotide sequence of a genomic nucleic acid molecule in the biological sample, at least a portion of the nucleotide sequence of an mRNA molecule in the biological sample, or at least a portion of the nucleotide sequence of a cDNA molecule generated from the mRNA molecule in the biological sample.

26. The use according to any one of claims 17 to 25, wherein the genotyping assay comprises sequencing at least a portion of the nucleotide sequence of a region of at least one nucleic acid molecule and / or an adjacent nucleic acid molecule encoding LZTFL1, SLC6A20, CCHCR1, ABO, OAS3, DPP9, RAVER1, and / or IFNAR2.

27. The use according to claim 26, wherein the genotyping assay comprises sequencing the entirety of at least one nucleic acid molecule encoding LZTFL1, SLC6A20, CCHCR1, ABO, OAS3, DPP9, RAVER1, and / or IFNAR2, and / or the entirety of a region of an adjacent nucleic acid molecule.

28. The aforementioned genotype determination assay, a) Amplifying at least a portion of the region of the at least one nucleic acid molecule and / or an adjacent nucleic acid molecule that encodes LZTFL1, SLC6A20, CCHCR1, ABO, OAS3, DPP9, RAVER1, and / or IFNAR2, b) Labeling the amplified nucleic acid molecule with a detectable label, c) Contacting the labeled nucleic acid molecule with a support containing a mutation-specific probe, d) Detecting the detectable sign, The use according to claim 26, including the use described in claim 26.

29. The aforementioned genotype determination assay, Contacting at least one nucleic acid molecule encoding LZTFL1, SLC6A20, CCHCR1, ABO, OAS3, DPP9, RAVER1, and / or IFNAR2, and / or a region of an adjacent nucleic acid molecule, with a mutation-specific probe containing a detectable label, To detect the aforementioned detectable sign, The use according to claim 26, including the use described in claim 26.

30. The use according to any one of claims 17 to 29, wherein the coronavirus infection includes Middle East Respiratory Syndrome (MERS), Severe Acute Respiratory Syndrome (SARS), or Coronavirus Disease 2019 (COVID-19).

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