WO2021205013A1 - Compositions and methods for treating covid-19 - Google Patents

Abstract

The disclosure relates to compositions and methods for reducing the risk of developing severe illness or cytokine release syndrome associated with viral respiratory diseases such as COVID-19, by determining a subject's IL-1 genotype pattern and in some cases administering inflammation inhibitors. The IL-1 genotype is determined by obtaining information regarding the subject's single nucleotide polymorphism (SNP) alleles for: each of the rsl7561, rsl6944 and rsll43634 polymorphic loci, each of the rsl6944, rsll43623 and rs4848306 polymorphic loci; or each of the rsl7561, rsl6944, rsll43634, rsll43623 and rs4848306 polymorphic loci

Description

COMPOSITIONS AND METHODS FOR TREATING COVID-19

CROSS REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to U.S. provisional application number 63/007,625, filed on April 9, 2020, the contents of which are incorporated by reference in their entirety herein.

BACKGROUND OF THE INVENTION

[0002] The severe acute respiratory syndrome caused by coronavirus-2 (SARS-CoV-2) emerged toward the end of 2019, and by March 2020 was declared a global pandemic. The disease resulting from SARS-CoV-2 is referred to as COVID-19 and has a range of clinical effects on infected populations, ranging from mild symptoms to potentially life threatening clinical expressions of the disease. The fatality rate for COVID-19 was estimated to be approximately 3.7% overall in 2020, and is age-dependent, disproportionately affecting those over 60 years of age or who have pre-existing conditions, including cardiovascular disease, uncontrolled diabetes mellitus, and hypertension. COVID-19 pathophysiology has overlapping characteristics with diseases associated with previous coronavirus outbreaks, such as SARS and MERS. As with SARS and MERS, COVID-19 affects the pulmonary system, and severe cases are associated with aggressive inflammation and cytokine release syndrome (CRS) produced by viral replication and exuberant inflammatory responses. Uncontrolled pulmonary inflammation and CRS are complications resulting in severe symptoms and death in certain COVID-19 patients. There thus exists a need in the art for additional methods to treat and prevent CRS and other inflammation related disorders associated with COVID-19. This disclosure provides compositions and methods for the treatment and prevention of COVID-19 induced inflammation and CRS.

SUMMARY OF THE INVENTION

[0003] The disclosure provides methods of reducing a risk of developing severe COVID-19 symptoms, such as those requiring hospitalization, or cytokine release syndrome (CRS) associated with COVID-19 in a subject, reducing the severity of COVID-19 symptoms, or cytokine release syndrome (CRS) induced by COVID-19, and treating COVID 19 or CRS from COVID-19 in a subject.

[0004] In some embodiments of the methods of the disclosure, the methods comprise: (a) identifying a subject who has or is at risk of developing COVID-19; (b) obtaining information regarding the subject’s single nucleotide polymorphism (SNP) alleles for: (i) each of the rsl7561 polymorphic locus, the rsl6944 polymorphic locus and the rsl 143634 polymorphic locus; (ii) each of the rsl 6944 polymorphic locus, the rsl 143623 polymorphic locus and the rs4848306 polymorphic locus; or (iii) each of the rsl7561 polymorphic locus, the rsl6944 polymorphic locus the rsl 143634 polymorphic locus, the rsl 143623 polymorphic locus and the rs4848306 polymorphic locus; (c) diagnosing the subject as having a positive IL-1 genotype pattern obtained in (b) if the IL-1 genotype of the subject is selected from the group consisting of: (i)

T/T or T/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl6944 and T/T or T/C at rsl 143634; (ii) G/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; (iii) G/G, T/T, G/T or T/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl6944 and C/C at rsl 143634; (iv) T/T or T/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl 6944 and T/T or T/C at rsl 143634; (v) G/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; (vi) G/G, T/T, G/T or T/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl6944 and C/C at rsl 143634;

(vii) T/T or T/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl6944 and T/T or T/C at rsl 143634; (viii) G/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; (ix) (G/G, T/T, G/T or T/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl6944 and C/C at rsl 143634; (x) T/T or T/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944 and T/T or T/C at rsl 143634; (xi) G/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; (xii) G/G, T/T, G/T or T/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944 and C/C at rsl 143634; (xiii) T/T or T/G at rsl7561, C/C at rsl6944 and T/T/ or T/C at rsl 143634; (xiv) G/G at rsl7561, C/C at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; (xv) G/G, T/T,

G/T or T/G at rsl7561, C/C at rsl6944 and C/C at rsl 143634; (xvi) T/T or T/G at rsl7561, C/T at rsl 6944 and T/T or T/C at rsl 143634; (xvii) C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rs 16944; (xviii) C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rs 16944; (xix) C/C at rs4848306, C/G at rsl 143623, C/T at rsl6944; and (xx) C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944; and (d) administering an inflammation inhibitor to the subject diagnosed with a positive IL-1 genotype pattern in step (c); thereby reducing the risk of the subject for developing CRS associated with COVID-19, reducing the severity of the CRS in the subject, or treating CRS associated with COVID-19. In some embodiments, the methods further comprise administering a COVID-19 therapy.

[0005] The disclosure further provides methods of predicting a risk of or predisposition to developing cytokine release syndrome (CRS) associated with COVID-19 in a subject, comprising: (a) identifying a subject who has or is at risk of developing COVID-19; (b) obtaining information regarding the subject’s single nucleotide polymorphism (SNP) alleles for: (i) each of the rsl7561 polymorphic locus, the rsl6944 polymorphic locus and the rsl 143634 polymorphic locus; (ii) each of the rsl 6944 polymorphic locus, the rsl 143623 polymorphic locus and the rs4848306 polymorphic locus; or (iii) each of the rsl7561 polymorphic locus, the rsl6944 polymorphic locus the rsl 143634 polymorphic locus, the rsl 143623 polymorphic locus and the rs4848306 polymorphic locus; (c) diagnosing the subject as having a positive IL-1 genotype pattern obtained in (b) if the IL-1 genotype of the subject is selected from the group consisting of: (i) T/T or T/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl 6944 and T/T or T/C at rsl 143634; (ii) G/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; (iii) G/G, T/T, G/T or T/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl 6944 and C/C at rsl 143634; (iv) T/T or T/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl6944 and T/T or T/C at rsl 143634; (v) G/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; (vi) G/G, T/T, G/T or T/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl6944 and C/C at rsl 143634; (vii) T/T or T/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl 6944 and T/T or T/C at rsl 143634; (viii) G/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; (ix) (G/G, T/T, G/T or T/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl6944 and C/C at rsl 143634; (x) T/T or T/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944 and T/T or T/C at rsl 143634; (xi) G/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; (xii) G/G, T/T, G/T or T/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944 and C/C at rsl 143634; (xiii) T/T or T/G at rsl7561, C/C at rsl6944 and T/T/ or T/C at rsl 143634; (xiv) G/G at rsl7561, C/C at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; (xv) G/G, T/T, G/T or T/G at rsl7561, C/C at rsl6944 and C/C at rsl 143634; (xvi) T/T or T/G at rsl7561, C/T at rsl6944 and T/T or T/C at rsl 143634; (xvii) C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl 6944; (xviii) C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl 6944; (xix) C/C at rs4848306, C/G at rsl 143623, C/T at rsl 6944; and (xx) C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944; and thereby predicting the risk of or predisposition to developing cytokine release syndrome (CRS) associated with COVID-19 in the subject. In some embodiments, the methods further comprise measuring at least one biomarker associated with the development of CRS. In some embodiments, the methods further comprise administering an inflammation inhibitor. In some embodiments, the methods further comprise administering a COVID-19 therapy.

[0006] In some embodiments of the methods of the disclosure, step (c) comprises diagnosing the subject as having a positive IL-1 genotype pattern obtained in (b) if the IL-1 genotype of the subject is selected from the group consisting of: (xxi) any allele at rsl7561, C/C at rs4848306, G/G at rsl 143623, C/T at rsl6944, and any allele at rsl 143634; (xxii) any allele at rsl7561, C/T at rs4848306, G/G at rsl 143623, C/C at rsl6944, and any allele at rsl 143634; (xxiii) any allele at rsl7561, C/C at rs4848306, G/C at rsl 143623, C/T at rsl6944, and any allele at rsl 143634 (xiv) any allele at rsl7561, C/C at rs4848306, G/G at rsl 143623, C/C at rsl6944, and any allele at rsl 143634; (xxv) T/G or T/T at rsl7561, C/T at rs4848306, G/G at rsl 143623, C/T at rsl 6944, and T/C or T/T at rsl 143634; (xxvi) T/G or T/T at rsl7561, C/C at rs4848306, C/G at rsl 143623, T/T at rsl6944, and T/C or T/T at rsl 143634; and (xxvii) T/G or T/T at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944, and T/C or T/T at rsl 143634 [0007] In some embodiments of the methods of the disclosure, the subject has tested positive for severe acute respiratory syndrome coronavirus (SARS-CoV-2). In alternative embodiments, the subject is known, or is suspected, to have been exposed to SARS-CoV-2. In alternative embodiments, the subject is not known or suspected of having SARS-CoV-2. [0008] In some embodiments of the methods of the disclosure, the methods further comprise measuring at least one biomarker associated with the development of CRS. In some embodiments, the at least on biomarker is selected from the group consisting of C-C motif chemokine ligand 20 (CCL20), Prostaglandin E2 (PGE2), interleukin 1 (IL-1), interleukin 2 (IL- 2), IL-2R, interferon gamma (IFNy), interleukin 5 (IL-5), interleukin 6 (IL-6), interleukin 10 (IL- 10), tumor necrosis factor alpha (TNFa), monocyte chemoattractant protein- 1 (MCP-1), interleukin 6 signal transducer (gpl30), Fms-related tyrosine kinase 3 ligand (Flt3L), C-X3-C motif chemokine ligand 1 (CX3CL1), colony stimulating factor 2 (CSF), alanine aminotransferase (ALT), aspartate aminotransferase (ART), lactate dehydrogenase (LDH), C- reactive protein (CRP), ferritin, and D-dimer. In some embodiments, the at least one biomarker is selected from the group consisting of IL-2, IL-2R, IL-6, IL-10, TNFa, ALT, ART, LDH, CRP, ferritin, and D-dimer. In some embodiments, the at least one biomarker comprises a two- cytokine max fold change of at least 75 fold each, a one cytokine max fold change of at least 250, a C-reactive protein level of greater than or equal to 200 mg/L, or a combination thereof. In some embodiments, the cytokine, or cytokines, are selected from the group consisting of IL-1, IL-2, IL-2R, PTNGg, IL-5, IL-6, IL-10, TNFa, MCP-1, gpl30, Flt3L, CX3CL1 and CSF.

[0009] In some embodiments of the methods of the disclosure, the inflammation inhibitor is administered prior to the manifestation of COVID-19 symptoms. In some embodiments, the inflammation inhibitor is administered after the manifestation of initial COVID-19 symptoms but prior to the onset of CRS. In some embodiments, the initial COVID-19 symptoms comprise one or more of fever, cough, fatigue, loss of taste/smell, gastroenteritis and myalgia. In some embodiments, the inflammation inhibitor is administered after or concurrent with the onset of CRS.

[0010] In some embodiments of the methods of the disclosure, the inflammation inhibitor is an IL-1 inhibitor. In some embodiments, the IL-1 inhibitor comprises an inflammasome modulator. In some embodiments, the inflammasome modulator can cross the blood brain barrier. In some embodiments, the inflammasome modulator comprises Diacerein, Sarei-To, Binimetinib, Can-04, Rilonacept, XL- 130, Givinostat or Ammonium trichloro-tellurate. In some embodiments, the IL-1 inhibitor is an IL-la inhibitor or an IL-Ib inhibitor. In some embodiments, the IL-la inhibitor is selected from the group consisting of Bermekimab, ABT- 981, Isunakinra, AC-701, Sairei-To, Can-04, XL-130, a MABpl antibody and Givinostat. In some embodiments, the L-Ib inhibitor is selected from the group consisting of ABT-981, Anakinra, Anakinra Biosimilar, APX-002, Binimetinib, CAN-04, Diacerein, DLX-2681, Givinostat, Isunakinra, Rilonacept, SER-140, XL-130, Gevokizumab, Can-04, a DOM4-130-201 antibody, DOM4- 130-202 antibody and Canakinumab.

[0011] In some embodiments of the methods of the disclosure, the inflammation inhibitor is an IL-6 inhibitor. In some embodiments, the IL-6 inhibitor comprises Sarilumab, Tocilizumab, Siltuximab, Olokizumab, Elsilimomab, Sirukimab, Levilimab, ALX-0061, Gerilimzumab, FE301 or FM101.

[0012] In some embodiments of the methods of the disclosure, the inflammation inhibitor comprises a Granulocyte-macrophage colony-stimulating factor (GM-CSF) inhibitor. In some embodiments, the GM-CSF inhibitor comprises Namilumab, Lenzilumab, MOR103, MORab002, Mavrilimumab, or Otilimab.

[0013] In some embodiments of the methods of the disclosure, the inflammation inhibitor comprises a Janus Kinase (JAK) inhibitor. In some embodiments, the JAK kinase inhibitor comprises Tofacitinib or Baricitinib.

[0014] In some embodiments of the methods of the disclosure, the COVID-19 therapy comprises an antibody therapy. In some embodiments, the antibody therapy comprises a C5 or C5a antagonist. In some embodiments, the antibody comprises Ravulizumab, Ravulizumab- cwvz, Eculizumab, or Vilobelimab. In some embodiments, the antibody therapy comprises an antibody to a SARS-CoV-2 viral protein. In some embodiments, the antibody comprises Casirivimab, Imdevimab, Bamlanivimab, or Etesevimab.

[0015] In some embodiments of the methods of the disclosure, the inflammation inhibitor prevents a sign or a symptom of COVID-19. In some embodiments, the inflammation inhibitor reduces a sign or a symptom of the COVID-19. In some embodiments of the methods of the disclosure, the inflammation inhibitor prevents a sign or a symptom of the CRS. In some embodiments, the inflammation inhibitor reduces a sign or a symptom of the CRS. In some embodiments, the sign or symptom of CRS comprises fever, tachycardia, tachypnea, hypoxia, hypotension, coagulopathy, hypoalbuminemia, hypoproteinemia, respiratory failure, refractory shock, multi-organ failure, two cytokine max fold changes of at least 75, one cytokine max fold change of at least 250, a C-reactive protein level of greater than or equal to 200 mg/L or a combination thereof. In some embodiments, the cytokine comprises IL-1, IL-2, IL-2R, IFNy, IL- 5, IL-6, IL-10, TNFa, MCP-1, gpl30, Flt3L, CX3CL1 or CSF. In some embodiments, the cytokine comprises IL-2, IL-6, IL-10 or TNFa.

[0016] In some embodiments of the methods of the disclosure, the inflammation inhibitor prevents a sign or a symptom of the CRS. In some embodiments, the inflammation inhibitor reduces a sign or a symptom of the CRS.

[0017] In some embodiments of the methods of the disclosure, the inflammation inhibitor reduces a level of one or more biomarkers selected from the group consisting of CCL20, PGE2, IL-1, IL-2, IL-2R, PTNGg, IL-5, IL-6, IL-10, TNFa, MCP-1, gpl30, Flt3L, CX3CL1) CSF, alanine aminotransferase, lactate dehydrogenase, C-reactive protein (CRP), ferritin, and D-dimer, in the subject.

[0018] In some embodiments of the methods of the disclosure, the inflammation inhibitor reduces a level of a pro-inflammatory cytokine in the subject. In some embodiments, the pro- inflammatory cytokine is IL-la, IL-Ib or IL-6 or TNF alpha.

[0019] The disclosure also provides an inflammation inhibitor as disclosed herein for use in any of the methods disclosed herein.

BRIEF DESCRIPTION OF THE DRAWINGS [0020] FIG. 1 is a plot showing IL-Ib haplotype frequency over population baseline in an African heritage population with COVID-19 critical illness. The y-axis shows the frequency of the indicated IL-Ib haplotypes (x-axis) in African heritage (AH) patients as percent of normal population frequency of the haplotype (the line at 1, indicated with the arrow).

[0021] FIG. 2 is a plot showing IL-Ib haplotype frequency in African heritage patients with cytokine release syndrome (sometimes called cytokine storm syndrome, or CSS), in African heritage patients presenting to the Hospital with major COVID-19 symptoms. Rear bars: % of African heritage patients who developed CSS carrying the indicated haplotype; front bars: total African heritage patients in the study cohort of COVID-19 patients carrying the indicated haplotype. Numbers indicated in white boxes show the frequency of the indicated haplotype in the population as a whole, and were calculated from the Atherosclerosis Risk in Communities (ARIC) study database, which had 227 individuals identified as African heritgate using NIH criteria. One sample that had a genetic pattern that was not a standard haplotype pair but most likely a B1/B2 with 1 haplotype mutation. This patient was African heritage, and developed CSS.

DETAILED DESCRIPTION OF THE INVENTION [0022] Cytokine release syndrome (CRS) is associated with, and caused by, elevated levels of pro-inflammatory cytokines. These cytokines include interleukin 1 (IL-1) family cytokines, interleukin 2 (IL-2), interleukin 6 (IL-6), interleukin 10 (IL-10), tumor necrosis factor alpha (TNFa), interferon gamma (IFNy), monocyte chemoattractant protein- 1 (MCP-1) and interleukin 6 signal transducer (gpl30). Thus, increased inflammation, such as that caused by an overproduction of IL-1, is associated with an increased risk of developing cytokine release syndrome. The present invention is based on the discovery that specific IL-1 genotype patterns stratify subjects into groups relating to their member’s likelihood of over-producing IL-1 following cellular challenge. It is thus possible to specifically target subjects who have high levels of inflammation and who are at risk of developing, or who have developed CRS, for treatment with IL-1 inhibitors and other therapies.

[0023] The sudden global spread of coronavirus disease of 2019 (COVID-19), the disease associated with severe acute respiratory infection syndrome coronavirus 2 (SARS-CoV-2) viral infection, has spurred a need for new methods of diagnosis, treatment, and risk assessment. Over 1 million cases in over 200 countries have been reported as of April 2020, less than 6 months following the original outbreak reported in Wuhan, China. While symptoms are mild for many COVID-19 patients, severe disease occurs in up to 20% of cases and the fatality rate is estimated to be between 3-4%. With no validated antiviral treatments currently available, there exists a desperate need for new compositions and methods for diagnosis, treatment, and risk assessment of COVID-19 (Zhang 2020).

[0024] Inflammatory response and cytokine release plays a critical role in cases of respiratory illness, for example those caused by influenzas and coronaviruses. Severe Acute Respiratory Syndrome (SARS) caused by the SARS-CoV coronavirus induced a significant hyper innate inflammatory response, causing a marked elevation of Thl cytokine interferon (IFN)-gamma, inflammatory cytokines interleukin (IL)-l, IL-6 and IL-12 for at least 2 weeks after disease onset, but there was no significant elevation of inflammatory cytokine tumor necrosis factor (TNF)-alpha, anti-inflammatory cytokine IL-10, Thl cytokine IL-2 and Th2 cytokine IL-4 (Wong 2004). This elevated cytokine release is associated with pulmonary inflammation and lung damage in SARS patients (Wong 2004). Similarly, severe cases of the Middle East Respiratory Syndrome (MERS) caused by the MERS-CoV coronavirus was also shown to cause significant but delayed IFN and pro-inflammatory cytokine (IL-Ib, IL-6, and IL- 8) responses (Lau 2013).

[0025] Early results in COVID-19 patients suggest a similar elevated cytokine release with SARS and MERS. Following infection by SARS-CoV-2, the upper and lower respiratory tracts are afflicted with mild or highly acute respiratory syndrome followed by release of pro- inflammatory cytokines, including IL-Ib and IL-6 (Conti 2020). In COVID-19 patients, interleukin IL-6, IL-10 and TNFa surge during illness and declines during recovery (Pederson 2020). Furthermore, it has been observed that plasma concentration of IL-2, IL-7, IL-10, GCSF, IP- 10, C-C motif chemokine ligand 2 (MCP1), C-C motif chemokine ligand 3 (MIP1A), and tumor necrosis factor (TNFa) were higher in ICU patients than non-ICU patients (Huang, 2020). Another study found that COVID-19 patients admitted to the ICU had high levels of IL-6, TNFa, IL-Ib, IL-8, and IL-2R (Zhang 2020).

[0026] Targeting cytokines for the treatment of severe COVID-19 has shown promising results. Tocilizumab is a monoclonal antibody targeting IL-6 receptor and mediates the inflammatory response. It has been approved in the United States for severe life-threatening cytokine release syndrome caused by CAR-T immunotherapy. A retrospective study observed efficacy of Tocilizumab in treating severe or critical COVID-19 patients. Following administration symptoms improved dramatically, including reduced fever, improved oxygenation, and a return to normal levels of lymphocytes (Zhang 2020). Later studies have been inconclusive regarding the efficacy of IL-6 inhibitors, although several observational studies have suggested a mortality benefit (www.idsociety.org/covid-19-real-time-learning- network/therapeutics-and-interventions/Tocilizumab-IL-6-Inhibitors/).

[0027] The present invention is based upon the discovery that inflammation, such as that caused by an overproduction of IL-1, is associated with an increased risk of developing CRS, and that specific IL-1 genotype patterns stratify subjects into groups relating to their member’s likelihood of over-producing IL-1. It is thus possible to specifically target subjects who have high levels of inflammation and who are at risk of developing, or who have developed CRS, for treatment with IL-1 inhibitors and other therapies.

[0028] The observed inflammatory response in COVID-19 patients shows that CRS can be used as a measurement to perform risk management and optimize treatment plans. Identification of COVID-19 patients more likely to have severe symptoms, and an excessive inflammatory response such as CRS, can be assessed using the IL-1 genotype patterns described herein, optionally in combination with additional markers. These methods can determine which patients are likely to have a severe or life-threatening response to SARS-CoV-2 infection. Further, IL-1 genotyping will allow primary care providers to optimize planning, and to include use of inflammation inhibitors with IL-1 positive subjects.

[0029] Accordingly, the disclosure provides methods to reduce the severity of, or prevent symptoms of viral respiratory illnesses.

[0030] The disclosure provides methods to reduce the severity of, or prevent symptoms of COVID-19 by treating patients with inflammation inhibitors, such as interleukin-6 targeting antibodies. The disclosure also provides methods of predicting a risk of or predisposition to developing cytokine release syndrome (CRS) associated with COVID-19 in a subject. Subjects known to be at risk of developing CRS can be targeted with additional medical interventions, or a higher degree of monitoring. Further, because the severity of symptoms and inflammatory response due to COVID-19 varies greatly from subject to subject, the disclosure provides methods of identifying those subjects that are likely to benefit from anti-inflammatory agents by determining predisposition to increased inflammation and CRS upon SARS-CoV-2 infection.

Stratification by IL-1 Genotype

[0031] Subjects can be stratified into one of two IL-1 genotype patterns, i.e., positive or negative, based upon their complex IL-1 genotype for three or five single nucleotide polymorphisms (SNPs) in the IL-1 locus. IL-1 positive and IL-1 negative genotypes of the disclosure are listed in Table 1 and Table 2 below. Table 1:

Table 2:

Table 3:

[0032] In Tables 1-3, “*” is G or C; “†” is C or T; and “J” is G or T.

[0033] A subject having an uncommon complex IL-1 genotype not exemplified in Tables 1-3 is considered herein as having an IL-1 genotype pattern of “Negative”.

[0034] A subject may be stratified into an IL-1 genotype pattern by the SNP loci listed in Tables 1-3 and/or SNP loci in linkage disequilibrium (LD), e.g., 80% LD, with the SNP loci listed in Tables 1-3.

[0035] A subject of certain racial/ethnic groups may be stratified into an IL-1 genotype pattern based upon five SNP loci listed in Table 1. Differences in the frequencies or even the absence of a specific SNP in certain racial/ethnic groups may require the inclusion of additional informative SNPs. For example, the three SNPs disclosed in Table 2 are able to stratify Caucasian populations but may fail to accurately stratify Asian populations.

[0036] Accordingly, the disclosure provides methods of diagnosing a subject as being IL-1 positive or negative based on IL-1 positive or negative genotype patterns.

[0037] The methods comprise obtaining information regarding the subject’s single nucleotide polymorphism (SNP) alleles for: (i) each of the rsl7561 polymorphic locus, the rsl6944 polymorphic locus and the rsl 143634 polymorphic locus; (ii) each of the rsl6944 polymorphic locus, the rsl 143623 polymorphic locus and the rs4848306 polymorphic locus; or (iii) each of the rsl7561 polymorphic locus, the rsl6944 polymorphic locus the rsl 143634 polymorphic locus, the rsl 143623 polymorphic locus and the rs4848306 polymorphic locus. [0038] In those embodiments comprising the SNPs at rsl7561, rsl6944 and rsl 143634, a subject can be diagnosed as IL-1 positive if the subject has an IL-1 genotype pattern that is the same as any of: T/T or T/G at rsl7561, C/C at rsl6944 and T/T/ or T/C at rsl 143634; G/G at rsl7561, C/C at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; G/G, T/T, G/T or T/G at rsl7561, C/C at rsl6944 and C/C at rsl 143634; and T/T or T/G at rsl7561, C/T at rsl6944 and T/T or T/C at rsl 143634. [0039] In those embodiments comprising the SNPs at rsl6944, rsl 143623 and rs4848306, a subject can be diagnosed as IL-1 positive if the subject has an IL-1 genotype pattern that is the same as any of: C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl6944; C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl 6944; C/C at rs4848306, C/G at rsl 143623, C/T at rsl6944; or C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944.

[0040] In those embodiments comprising the SNPs at rsl7561, rsl6944 rsl 143634, rsl 143623 and rs4848306, a subject can be diagnosed as IL-1 positive if the subject has an IL-1 genotype pattern that is the same as any of: (i) T/T or T/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl6944 and T/T or T/C at rsl 143634; (ii) G/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; (iii) G/G, T/T, G/T or T/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl6944 and C/C at rsl 143634; (iv) T/T or T/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl6944 and T/T or T/C at rsl 143634; (v) G/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl 6944 and C/C, T/T, C/T or T/C at rsl 143634; (vi) G/G, T/T, G/T or T/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl 6944 and C/C at rsl 143634;(vii) T/T or T/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl6944 and T/T or T/C at rsl 143634; (viii) G/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; (ix) G/G, T/T, G/T or T/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl6944 and C/C at rsl 143634; (x) T/T or T/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944 and T/T or T/C at rsl 143634; (xi) G/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl 6944 and C/C, T/T, C/T or T/C at rsl 143634; or (xii) G/G, T/T, G/T or T/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944 and C/C at rsl 143634.

[0041] In some embodiments, particularly those embodiments where the subject is African heritage, the subject is diagnosed as IL-1 positive if the subject has an IL-1 genotype pattern that is the same as any of: (xxi) any allele at rsl7561, C/C at rs4848306, G/G at rsl 143623, C/T at rsl6944, and any allele at rsl 143634; (xxii) any allele at rsl7561, C/T at rs4848306, G/G at rsl 143623, C/C at rsl6944, and any allele at rsl 143634; (xxii) any allele at rsl7561, C/C at rs4848306, G/C at rsl 143623, C/T at rsl6944, and any allele at rsl 143634; (xxiii) any allele at rsl7561, C/C at rs4848306, G/G at rsl 143623, C/C at rsl6944, and any allele at rsl 143634; (xxiv) T/G o r T/T at rsl7561, C/T at rs4848306, G/G at rsl 143623, C/T at rsl6944, and T/C or T/T at rsl 143634; (xxv) T/G o r T/T at rsl7561, C/C at rs4848306, C/G at rsl 143623, T/T at rsl 6944, and T/C or T/T at rsl 143634; or (xxvi) T/G o r T/T at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944, and T/C or T/T at rsl 143634.

[0042] The combinations of 3 and 5 polymorphic loci, and the haplotype pairs identified as IL-1 positive and IL-1 negative by the instant disclosure, provide superior methods of stratifying populations according to IL-1 genotype for the reasons outlined below.

[0043] First, the disclosure provides methods to unambiguously identify a subject as IL-1 positive or IL-1 negative using haplotype pairs determined from a survey of naturally occurring haplotypes. The methods of the instant disclosure are able to determine whether a subject is IL-1 positive or IL-1 negative without recourse to statistical models that may not be applicable to all populations.

[0044] Second, the 5 SNP -based haplotype pairs of the instant disclosure have been analyzed relative to actual tissue fluid levels of IL-Ib protein for more than 900 subjects carrying all of the 10 possible haplotype pairs. Additional populations have been analyzed for specific diseases.

This allows the 5 SNP haplotype pairs of the instant disclosure to identify a subject’s specific IL- 1 haplotype pair and define that subject as one who will produce high or lower levels of IL-Ib when challenged. For example, the inventors have identified 3 haplotype pairs that are predictably high producers of IL-1 b and 3 pairs that are predictably lower producers of IL-1 b and 4 pairs that are somewhere in the middle. The high IL-1 producing haplotype pairs chronically produce approximately 30% higher tissue levels than the 3 lower producers. Particularly in African heritage populations, there is a strong correlation between carriage of the B4 haplotype and the development of severe COVID-19 symptoms requiring hospitalization and cytokine storm. Association with carriage of B4, the haplotype that causes the highest IL-Ib expression levels with in vitro promoter assays, is particular strong (see Examples).

[0045] Third, haplotype context is required for the different functional SNPs working together to regulate transcription of the IL-1B gene in response to complex activation of transcription. This occurs if the functional SNPs have different activities depending on the specific context of the functional SNPs within the pattern. Transcription factors binding to one or more SNPs in the pattern bring together 3 -dimensional nucleic acid structures to influence initiation of transcription and define the transcription rate.

[0046] Contrary to the routine mathematical projections of what haplotypes a subject may have at a specific genetic locus, the haplotypes of the instant disclosure are unambiguously determined from the composite genotype of the subject. Routine mathematical projections used in genotyping are based upon certain assumptions about the general population that may be influenced in the individual due to ancestry of the population from which they come. That means that for almost any place in North America, South America, and Europe, the admixture must be considered and therefore modifies the accuracy of the projection.

[0047] The ability to unambiguously define the two haplotypes carried by a specific subject provides greater precision in identifying which two haplotypes are carried by that subject. That capability exists because out of 8 possible haplotypes from 3 functional SNPs assayed, only 4 of the 8 are actually observed in nature across all major racial populations. However, these haplotypes are observed in different frequencies in different populations. For example, one haplotype, termed B4 (Rogus et al., 2008), accounts for 6% of Caucasian haplotypes in the IL-1 promoter, while the B4 haplotype accounts for 46% of haplotypes carried by subjects of African ancestry. Once the functional haplotypes have been unambiguously determined for a subject, the other two SNPs add further information about the biologic activity of the subject’s IL-1 transcription rates when cells are activated. That provides, in some racial populations, a substantially different assessment of the subject’s IL-1 biologic activity than one may derive from nonfunctional patterns that may be generated using standard mathematical formula.

[0048] Fourth, the inventors have determined that non-functional SNPs, rsl7561 and rsl 143634 are also associated with inflammatory biomarkers. In Caucasian populations, carriage of both minor alleles at rsl7561 and rsl 143634 is found in only approximately 35% of the population. However, the minor alleles are found in 84% of the pro-inflammatory haplotype pairs B1/B3, B3/B3, B2/B3, and B3/B4 identified in Rogus et al. (2008). Adding genotype information from rsl7561 and rsl 143634 to genotyping at rs4848306, rsl 143623 and rsl6944, and classifying the 5 SNP haplotype pairs of the instant invention, as shown in Table 1 allows, for the first time, for the successful stratification of IL-1 haplotype pairs that are common in populations beyond those that are predominantly Caucasian, such as African-American populations. [0049] Lastly, the 5 SNP haplotype patterns of the instant disclosure account for differences in ancestry to a greater degree than previous studies. The set of patterns that include 5 SNPs of the instant disclosure represent additional ancestry context that goes beyond the IL-Ib haplotype. As a result, when the 5 SNPs of the instant disclosure were used to assess large databases, there were clear situations where subjects of African or Chinese ancestries have very different frequencies of 5 SNP patterns based on ancestry factors that go beyond the IL-Ib haplotypes. [0050] The 5 SNP test of the instant invention provides more refined information about how IL- 1 haplotype pairs translate into higher or lower IL-Ib production across all major racial populations. If one used the Rogus et al. (2008) 3 SNP patterns on subjects with an African ancestry several patterns would produce false negative results compared to the 5-SNP patterns. This example would result in approximately 18% of subjects of African ancestry receiving a false negative IL-1 gene test if the Rogus 3 SNP test were used instead of the 5 SNP test of the instant invention.

[0051] A subject at risk of CRS, for example a subject who is infected with SARS-CoV-2, or with suspected exposure to SARS-CoV-2, will provide or has provided a biological sample comprising a nucleic acid. Single nucleotide polymorphism (SNP) alleles in the isolated nucleic acid for each of the, at least 3, or 5 polymorphic loci identified in Tables 1-3, or polymorphic loci in linkage disequilibrium to the polymorphic loci identified in Tables 1-3 will be detected by any method known in the art and a composite IL-1 genotype will be determined. From the determined composite IL-1 genotype, a positive or negative IL-1 genotype pattern will be determined based on the information disclosed in Tables 1-3.

Severe COVID-19 and Cytokine Release Syndrome

[0052] The disclosure provides methods of predicting a risk of, reducing a risk of, preventing, or treating severe COVID-19 symptoms, including cytokine release syndrome (CRS). The disclosure further provides methods of treating CRS associated with viral respiratory illnesses. The viral respiratory illnesses can be caused, for example, by influenza viruses ( e.g ., seasonal or pandemic influenza) or coronaviruses (e.g., SARS-CoV-2 or other related viruses). In some embodiments, the methods comprise (a) obtaining information regarding the subject’s single nucleotide polymorphism (SNP) alleles for: (i) each of the rsl7561 polymorphic locus, the rsl6944 polymorphic locus and the rsl 143634 polymorphic locus; (ii) each of the rsl6944 polymorphic locus, the rsl 143623 polymorphic locus and the rs4848306 polymorphic locus; or (iii) each of the rsl7561 polymorphic locus, the rsl6944 polymorphic locus, the rsl 143634 polymorphic locus, the rsl 143623 polymorphic locus and the rs4848306 polymorphic locus; and (b) diagnosing the subject as having a positive IL-1 genotype pattern obtained in (b) if the IL-1 genotype of the subject is the same as any of those disclosed in Tables 1-3, depending upon which SNPs alleles are obtained.

[0053] In some embodiments, the viral respiratory illness comprises COVID-19, and the methods comprise (a) identifying a subject at risk of developing COVID-19; (b) obtaining information regarding the subject’s single nucleotide polymorphism (SNP) alleles for: (i) each of the rsl7561 polymorphic locus, the rsl6944 polymorphic locus and the rsl 143634 polymorphic locus; (ii) each of the rsl 6944 polymorphic locus, the rsl 143623 polymorphic locus and the rs4848306 polymorphic locus; or (iii) each of the rsl7561 polymorphic locus, the rsl6944 polymorphic locus the rsl 143634 polymorphic locus, the rsl 143623 polymorphic locus and the rs4848306 polymorphic locus; and (c) diagnosing the subject as having a positive IL-1 genotype pattern obtained in (b) if the IL-1 genotype of the subject is the same as any of those disclosed in Tables 1-3, depending upon which SNPs alleles are obtained. In some embodiments, the methods further comprise (d) administering an inflammation inhibitor to the subject diagnosed with a positive IL-1 genotype pattern in step (c), thereby reducing the risk of the subject for developing CRS in a subject that has not yet developed CRS, preventing the development of CRS in the subject, or treating CRS in a subject who has developed CRS. Accordingly, the disclosure provides methods of reducing the risk of developing CRS induced by SARS-CoV-2 infection, preventing the development of CRS in subjects with COVID-19 who have not developed CRS, treating CRS in subjects with COVID-19, or reducing a sign or a symptom of CRS in subjects with COVID-19, the methods comprising administering inflammation inhibitors to subjects diagnosed as IL-1 positive using the compositions and methods described herein. In some embodiments, the inflammation inhibitor is an IL-1 inhibitor. In some embodiments, the inflammation inhibitor is an IL-6 inhibitor.

[0054] As used herein the term "symptom" is defined as an indication of disease, illness, injury, or that something is not right in the body. Symptoms are felt or noticed by the subject experiencing the symptom, but may not easily be noticed by others. Others are defined as non- health-care professionals.

[0055] Severe symptoms, for example severe COVID-19 symptoms, refer to symptoms sufficient to cause hospitalization. Severe COVID-19 symptoms include trouble breathing, persistent pain or pressure in the chest, new confusion, inability to wake or stay awake, pale, gray or blue-colored skin, lips or nailbeds, or a combination thereof.

[0056] As used herein the term "sign" is also defined as an indication that something is not right in the body. But signs are defined as things that can be seen by a doctor, nurse, or other health care professional.

[0057] CRS is a potentially life-threatening condition(s) that can occur after infection with the SARS-CoV-2 virus. While many people infected with SARS-CoV-2 are asymptomic, others can develop moderate to severe cases of the respiratory illness COVID-19. Symptoms are thought to develop between 2 and 14 days following SARS-CoV-2 exposure. Initial symptoms of COVID-19 include fever, cough, fatigue and myalgia. These symptoms can be followed by pneumonia, shortness of breath, and acute respiratory distress syndrome. Additional symptoms also include sputum production, diarrhea, headache and hemoptysis. CRS is caused by a large, rapid release of cytokines into the blood by immune cells. CRS can be detected by measuring levels of serum cytokines such as IL-1, IL-2R, IL-6, IL-10 and TNFa. Increased levels of these cytokines are associated with increased severity of COVID-19 symptoms.

[0058] Symptoms of cytokine release syndrome include, but are not limited to, fever, nausea, headache, rash, rapid heartbeat (tachycardia), low blood pressure, trouble breathing, tachypnea (fast, shallow breathing), hypoxia (inadequate oxygen supply to one or more regions of the body, or the whole body), hypotension (low blood pressure), coagulopathy (impaired clotting), hypoalbuminemia (abnormally low blood albumin), hypoproteinemia (abnormally low blood protein), respiratory failure (low blood oxygen, high blood CO2), refractory shock (lethal cardiovascular failure) and multi-organ failure. CRS can be mild (e.g., mild fever and rash), or severe and life threatening.

[0059] Any one or more of the symptoms of CRS can be reduced or prevented by the methods described herein. In some embodiments, the methods of the disclosure can reduce or prevent fever, nausea, headache, rash, tachycardia, low blood pressure, trouble breathing, tachypnea, hypoxia, hypotension, coagulopathy, hypoalbuminemia, hypoproteinemia, respiratory failure, refractory shock, multi-organ failure, or a combination thereof, associated with COVID- 19 associated CRS in a subject.

[0060] In some cases, subjects with COVID-19 will develop neurological complications, such as neurotoxicity. In some embodiments, the neurotoxicity is associated with CRS. Neurotoxicity frequently manifests as encephalopathy. The encephalopathy can occur with expressive or receptive aphasia, i.e. loss of ability to produce and/or understand language. Signs and symptoms of neurotoxicity include, but are not limited to encephalopathy, aphasia, delirium, tremor, seizure activity, status epilepticus, obtundation, increased intracranial pressure, cerebral edema, brain hernia or a combination thereof.

[0061] Methods of measuring signs and symptoms of neurotoxicity will be apparent to the person of ordinary skill in the art. Methods include screening to assess the degree of aphasia and obtundation, inserting a pressure sensitive probe through the skull to measure intracranial pressure, cranial computed tomography to visualize cerebral edema, cerebral magnetic resonance imaging and electroencephalograms to measure seizure activity.

[0062] Signs of CRS and/or neurotoxicity include, but are not limited to, elevated levels of one or more cytokines in the blood. Cytokines are small proteins that are secreted by cells into the circulatory system, and act through receptors to modulate cellular behavior. Cytokines include pro-inflammatory cytokines secreted by cells of the immune system, for example IL-la, IL-Ib, TNFa and IL-6. When large numbers of white blood cells are activated and release pro- inflammatory cytokines, this cytokine release can lead to CRS. In some embodiments, the one or more cytokines comprises interleukin 1 (IL-1), interleukin 2 (IL-2), IL-2R, interferon gamma (IFNy), interleukin 5 (IL-5), interleukin 6 (IL-6), interleukin 10 (IL-10), tumor necrosis factor alpha (TNFa), monocyte chemoattractant protein-1 (MCP-1), interleukin 6 signal transducer (gpl30), Fms-related tyrosine kinase 3 ligand (Flt3L), C-X3-C motif chemokine ligand 1 (CX3CL1) or colony stimulating factor 2 (CSF). In some cases, the IL-1 cytokine is IL-la or IL- ⁱp·

[0063] In some embodiments, the methods further comprise measuring at least one biomarker. Biomarkers can indicate that a subject is undergoing a broad release of cytokines, or otherwise provide an indication of the severity of COVID-19. In some embodiments, the at least on biomarker is selected from the group consisting of C-C motif chemokine ligand 20 (CCL20), Prostaglandin E2 (PGE2), interleukin 1 (IL-1), interleukin 2 (IL-2), IL-2R, interferon gamma (IFNy), interleukin 5 (IL-5), interleukin 6 (IL-6), interleukin 10 (IL-10), tumor necrosis factor alpha (TNFa), monocyte chemoattractant protein-1 (MCP-1), interleukin 6 signal transducer (gpl30), Fms-related tyrosine kinase 3 ligand (Flt3L), C-X3-C motif chemokine ligand 1 (CX3CL1), colony stimulating factor 2 (CSF), alanine aminotransferase (ALT), aspartate aminotransferase (ART), lactate dehydrogenase (LDH), C-reactive protein (CRP), ferritin, and D-dimer. In some embodiments, the at least on biomarker is selected from the group consisting of IL-2, IL-2R, IL-6, IL-10, TNFa, ALT, ART, LDH, CRP, ferritin, and D-dimer.

[0064] In some embodiments, a sign, or biomarker, of CRS comprises an elevated level of at least one cytokine. In some embodiments, the at least one cytokine is elevated at least 50X, at least 100X, at least 150X, at least 200X, at least 250X or at least 350X compared to the level of the at least one cytokine in a subject who does not have CRS. In some embodiments, the sign of CRS comprises an elevated level of at least two cytokines. In some embodiments, the at least two cytokines are elevated at least 25X, at least 50X, at least 75X, at least 100X, at least 125X, at least 150X, at least 175X or at least 200X compared to the level of the at least two cytokines in a subject who does not have CRS a. In some embodiments, the sign of CRS comprises an elevated level of at least one cytokine, at least two cytokines, at least three cytokines, at least 4 cytokines, at least 5 cytokines, at least 6 cytokines, at least 7 cytokines, at least 8 cytokines, at least 9 cytokines or at least 10 cytokines. Levels of cytokines in the subject with CRS can be compared to levels of cytokines in a subject, e.g. in the same subject before the onset of symptoms of CRS associated with COVID-19. Alternatively, or in addition, levels of cytokines in the subject with CRS can be compared to levels of cytokines in a healthy subject without CRS, or without COVID-19, or to reference levels of cytokines known in the art to be within the normal range for a healthy subject without CRS.

[0065] In some embodiments, administering an inflammation inhibitor to a subject who is IL-1 positive and has CRS reduces a level of a cytokine in the subject. In some embodiments, the level of the pro-inflammatory cytokine is reduced at least about IX, 2X, 3X, 4X, 5X, 10X, 20X,

3 OX, 40X, 5 OX, 60X, 70X, 80X, 90X, 100X, 125X, 150X, 175X, 200X, 225X, 250X, 275X or 300X. In some embodiments, administering an inflammation inhibitor to the subject reduces a level of at least one cytokine, at least two cytokines, at least three cytokines, at least 4 cytokines, at least 5 cytokines, at least 6 cytokines, at least 7 cytokines, at least 8 cytokines, at least 9 cytokines or at least 10 cytokines. In some embodiments, the cytokine or cytokines are selected from the group consisting of interleukin 1 (IL-la and IL-Ib), IL-2, IL-2R, IFNy, IL-5, IL-6, IL- 10, TNFa, MCP-1, gpl30, Flt3L, CX3CL1 and CSF.

[0066] Methods of measuring levels of cytokines will be apparent to the person of ordinary skill in the art. Levels of cytokines can be measured, for example by enzyme-linked immunosorbent assay (ELISA), bead based systems (e.g. Luminex), the Cytokine Bead Array (Pharmingen) and array-based systems (e.g., EMD Biosciences’ ProteoPlex).

[0067] Signs, or biomarkers, of CRS include, but are not limited elevated levels of C reactive protein (CRP). CRP is a blood protein marker of inflammation. In subjects without inflammation, CRP is typically below about 3 mg/L. In some embodiments, a level of CRP in the blood is greater than or equal to 10 mg/L, 20 mg/L, 30 mg/L, 40 mg/L, 50 mg/L, 60 mg/L, 70 mg/L, 80 mg/L, 90 mg/L, 100 mg/L, 110 mg/L, 120 mg/L, 130 mg/L, 140 mg/L, 150 mg/L, 160 mg/L, 170 mg/L, 180 mg/L, 190 mg/L, 200 mg/L, 210 mg/L, 220 mg/L, 230 mg/L, 240 mg/dL, 250 mg/L, 260 mg/L, 270 mg/L, 280 mg/L, 290 mg/L, 300 mg/L, 350 mg/L, 400 mg/L, 450 mg/L, 500 mg/L or 550 mg/L. Levels of CRP in the subject with CRS can be compared to levels of CRP in a subject, e.g. in the same subject before the manifestation of symptoms of CRS associated with COVID-19. In some embodiments, a level of CRP in the blood is greater than or equal to 200 mg/L. Alternatively, or in addition, levels of CRP in the subject with CRS can be compared to levels of CRP in a healthy subject without COVID-19, or to reference levels of CRP known in the art to be within the normal range for a healthy subject without CRS.

[0068] In some embodiments, administering an inflammation inhibitor to a subject who is IL-1 positive and has CRS reduces a level of CRP. In some embodiments, the level of CRP is reduced at least about IX, 2X, 3X, 4X, 5X, 10X, 20X, 30X, 40X or 50X.

[0069] Methods of measuring concentrations of CRP will be known to the person of ordinary skill in the art and include ELISA, radial immunodiffusion (RID), electroimmunoassay (EIA), rapid immunodiffusion, visual agglutination, immunoturbidimetry (IT), and laser nephelometry (LN). SARS-CoV-2 and COVID-19

[0070] The disclosure provides methods of reducing the risk of developing severe COVID- 19 symptoms, including with CRS, reducing a symptom of COVID-19 or CRS, or treating symptoms of COVID-19 or CRS associated with COVID-19 in a subject. The disclosure further provides methods of targeting subjects who are at risk of developing severe COVID-19 symptoms, including CRS, for additional treatments, such, as inflammation inhibitors and/or antibody treatments for COVID-19. In some embodiments, the subject has tested positive for SARS-CoV-2. In some embodiments, the subject is known to have been exposed, or is suspected of having been exposed to SARS-CoV-2.

[0071] Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), previously known by the provisional name 2019 novel coronavirus (2019-nCoV) is a positive-sense single-stranded RNA virus, and a strain of Severe acute respiratory syndrome-related coronavirus (SARS-CoV). SARS-CoV-2 causes the respiratory illness known as coronavirus disease 2019 (COVID-19). [0072] SARS-CoV-2 is thought to spread between humans through droplets and fomites generated by coughing and sneezing. Symptoms of COVID-19 are thought to develop between 1 and 14 days after exposure to the SARS-CoV-2 virus. Without intervention such as social distancing, it is thought that COVID-19 has an R0 of between 2 and 2.5, i.e. that each infected person infects between 2 and 2.5 other people. Thus, subjects who have had contact with SARS- CoV-2 positive people or surfaces touched by SARS-CoV-2 positive people are suspected, or known, to have exposure to the virus. Certain groups are particularly at risk of exposure, including health care workers, first responders, and those in crowded environments such as hospitals, nursing homes and cruise ships.

[0073] In some embodiments, the subject has tested positive for SARS-CoV-2. Any suitable test can be used to determine if a subject is positive for SARS-CoV-2. A number of tests for SARS-CoV-2 are known in the art, and include inter alia, PCR based methods to detect viral RNA, and methods for detecting antibodies to the virus. Exemplary SARS-CoV-2 tests include the cobas® SARS-CoV-2 Test (Roche) that detects viral RNA in a nose or throat swab, Xpert® Xpress SARS-CoV-2 (Cepheid), and the ID NOW™ COVID-19 (Abbott). Inflammation Inhibitors

[0074] The present invention allows for optimal treatment for a subject based upon his/her IL-1 genotype pattern. For subjects with high levels of inflammation, for example subjects diagnosed as IL-1 positive using the methods of the instant disclosure, this treatment can include an inflammation inhibitor to lower levels of inflammation. The inflammation inhibitor can be, for example, an IL-1 or IL-6 inhibitor.

[0075] The disclosure features methods for treating, reducing the severity of, COVID-19 symptoms, including CRS, in a subject who has tested positive for SARS-CoV-2, or is suspected of having SARS-CoV-2, the methods comprising diagnosing a subject as IL-1 positive using the SNP genotypes described herein and administering an inflammation inhibitor to the subject. [0076] In some embodiments, the inflammation inhibitor is an IL-1 inhibitor. Due to the possibility of side effects and adverse events, the ability to predict which subjects that could derive a clinical benefit from IL-1 inhibitors from those that will not is critical for the success of this class of drugs. IL-1 inhibitors, such as IL-Ib inhibitors, in general suppress the IL-1 mediated innate immune response and increase the risk of fatal infection. Thus, in IL-1 negative subjects without higher IL-1 driven levels of inflammation, treatment with an IL-1 inhibitor is more likely to result in immunosuppression and infection. In contrast, subjects with higher IL-1 driven inflammation are more likely to benefit from anti -IL-1 treatment, and less likely to experience suppression of innate immunity with the associated risk of infection.

[0077] Accordingly, the disclosure features methods for predicting the risk of and preventing CRS in response toSARS-CovV-2 infection in a human subject comprising diagnosing a subject as IL-1 positive using the SNP genotypes described herein, and optionally administering an IL-1 inhibitor if the subject is diagnosed as IL-1 positive to reduce inflammation and thereby reduce the risk of developing CRS.

[0078] The present invention, in view of the disclosures of Tables 1-3, allows a skilled artisan to identify: subjects likely to derive more benefit from an inflammation inhibitor, such as an IL-1 inhibitor, IL-1 a, IL-1 b inhibitor, IL-6 inhibitor or GM-CSF inhibitor; subjects with a positive IL-1 genotype pattern who may respond favorably to lower levels of an IL-1 inhibitor, PMa,PMb inhibitor, IL-6 inhibitor or GM-CSF inhibitor than subjects of a negative IL-1 genotype pattern; subjects who should be on an IL-1 inhibitor, IL-1 a, IL-1 b inhibitor, IL-6 inhibitor or GM-CSF inhibitor earlier than others because their genotype pattern is more aggressive; and subjects with a IL-1 dominant CRS predictably responsive to an IL-1 inhibitor, IL-1 a, IL-1 b inhibitor, IL-6 inhibitor or GM-CSF inhibitor but not other agents which have different modes of action.

[0079] Modulators of IL-1 biological activity (e.g., IL-la, IL-Ib, or IL-1 receptor antagonists) or a protein encoded by a gene that is in linkage disequilibrium with an IL-1 gene, can comprise any type of compound, including a protein, peptide, peptidomimetic, lipid, small molecule, or nucleic acid. A modulator may be a botanical, or an extract of a botanical.

[0080] A modulator may indirectly act upon an IL-1 gene in that the modulator activates or represses a gene or protein that, in turn or ultimately, acts upon the IL-1 gene. As used herein, the term “ultimately” is meant that the modulator acts upon a first gene or protein and the first gene or protein directly acts upon the IL-1 gene or the first gene or protein acts upon a second gene or protein which directly (or indirectly) acts upon the IL-1 gene. Such indirect gene regulation is well known in the art. A modulator that acts upstream to the IL-1 gene is useful in the present invention. An example of a modulator that acts upstream of the IL-1 gene is Aldeyra’s NS2 compound which traps excess free aldehydes, which are known to activate a number of intracellular inflammatory factors including NF-kB, a prominent protein in the inflammatory response. Another example of that acts upstream of the IL-1 gene is Ionis Pharmaceutical’s IONIS-APO(a)-L_RX and Arrowhead’s ARC-LPA which reduces Lp(a) levels that would be expected to activate arterial wall macrophages to produce IL-Ib.

[0081] Alternately, a modulator may act downstream of the IL-1 gene by directly or indirectly affecting a gene or protein that operates in parallel to IL-1 in an inflammatory cascade. [0082] An agonist can be a protein or derivative thereof having at least one bioactivity of the wild-type protein, e.g., receptor binding activity. An agonist can also be a compound that upregulates expression of a gene or which increases at least one bioactivity of a protein. An agonist can also be a compound which increases the interaction of a polypeptide with another molecule, e.g., a receptor.

[0083] An inhibitor (sometimes referred to as an antagonist) can be a compound which inhibits or decreases the interaction between a protein and another molecule, e.g., blocking the binding to receptor, blocking signal transduction, and preventing post-translation processing (e.g., IL-1 converting enzyme (ICE) inhibitor). The IL-Ib converting enzymes, such as caspase 1, which are produced within inflammasomes to cleave the IL-Ib pro peptide produce the mature cell-secreted IL-Ib protein. An inhibitor can also be a compound that downregulates expression of a gene or which reduces the amount of a protein present. The inhibitor can be a dominant negative form of a polypeptide, e.g., a form of a polypeptide which is capable of interacting with a target. Inhibitors include nucleic acids (e.g., single (antisense) or double stranded (triplex)

DNA or PNA and ribozymes), protein (e.g., antibodies) and small molecules that act to suppress or inhibit IL-1 transcription and/or protein activity.

[0084] An anti-inflammatory drug refers to any agent or therapeutic regimen (including a pharmaceutical, biologic, nutraceutical, and botanical) that prevents or postpones the development of or alleviates a symptom of the particular disease, disorder, or condition that involved an inflammatory process in the subject. The drug can be a polypeptide, peptidomimetic, nucleic acid or other inorganic or organic molecule, a “small molecule,” vitamin, mineral, or other nutrient. The drug modulates the production of the active IL-Ib or IL-1 a polypeptides, or at least one activity of an IL-1 polypeptide, e.g., interaction with a receptor, by mimicking or potentiating (agonizing) or inhibiting (antagonizing) the effects of a naturally-occurring polypeptide. An anti-inflammatory drug also includes, but is not limited to, anti-cholesterol drugs (e.g., statins), diabetes mellitus drugs, drugs that treat acute syndromes of the heart and vascular system (e.g., a cardiovascular disease), and arthritis.

[0085] Non-limiting examples of anti-inflammatory agents that modulate or inhibit IL-1 biological activity useful in the present invention are listed in Table 4. These agents generally have a mode of action that includes modulation of IL-1 gene expression, modulation of inflammasomes, IL-1 receptor blocking agents, and agents that bind IL-Ib or IL-1 a to inhibit attachment to the active receptor. IL-1 blocking agents may also indirectly target IL-1 by blocking key activators of IL-1 gene expression.

[0086] Table 4. IL-1 inhibitors

[0087] IL-1 inhibitors of the disclosure can inhibit IL-Ib, IL-la, or both IL-Ib and IL-la.

[0088] Exemplary IL-Ib inhibitors include ABT-981, Anakinra, Anakinra Biosimilar, APX-

002, binimetinib, CAN-04, Diacerein, DLX-2681, Givinostat, Isunakinra, Rilonacept, SER-140, XL-130, Gevokizumab, Can-04, Canakinumab, a DOM4-130-201 and DOM4- 130-202 antibody. In some embodiments, the IL-Ib inhibitor is Canakinumab or a derivative thereof.

[0089] Exemplary IL-la inhibitors include Bermekimab, ABT-981, Isunakinra, AC-701, Sairei-To, Can-04, XL-130, a MABpl antibody and Givinostat. In some embodiments, the IL-la inhibitor is Bermekimab or a derivative thereof.

[0090] In some embodiments, the IL-1 inhibitor comprises an inflammasome modulator. In some embodiments, the inflammasome modulator can cross the blood brain barrier. In some embodiments, the inflammasome modulator comprises Diacerein, Sarei-To, Binimetinib, Can- 04, Rilonacept, XL-130, Givinostat or Ammonium trichloro-tellurate.

[0091] In some embodiments, the inflammation inhibitor is an interleukin 6 (IL-6) inhibitor. IL-6 is a multifunctional cytokine that mediates cytokine release syndrome. IL-6 inhibitors include inhibitors that target IL-6 and the interleukin 6 receptor (IL6R), for example antibodies, biologies or small molecules that bind to IL-6 or IL6R. Exemplary IL-6 inhibitors are shown in Table 5 below:

[0092] Table 5. IL-6 inhibitors

[0093] In some embodiments, the inflammation inhibitor is a Granulocyte-macrophage colony-stimulating factor (GM-CSF) inhibitor. GM-CSF is a monomeric glycoprotein secreted by immune cells such as macrophages, T cells, mast cells and natural killer (NK) cells that functions as a cytokine and growth factor. GM-CSF has been considered as a therapeutic target for the treatment of autoimmune and inflammatory disorders, such as rheumatoid arthritis. Recently, an anti-GM-CSF antibody, Lenzilumab, was shown to result in clinical improvement in oxygenation and mean CRP and IL-6 values in COVID-19 patients treated with the antibody. Similarly, non-ventilated patients treated with mavrilimumab showed improved outcomes, and were less likely to need ventilation. Tofacitinib, a Janus Kinase (JAK) inhibitor, also inhibits IL- 1b synthesis from GM-CSF stimulated neutrophils, and so may be used to block GM-CSF mediated inflammatory responses.

[0094] Representative GM-CSF therapies are described in Table 6, below.

[0095] Table 6. GM-CSF inhibitors

[0096] Additional inflammatory inhibitors may be useful in treating COVID-19 symptoms and CRS. Additional inflammatory inhibitors, which target various parts of the inflammatory response, are presented in Table 7 below.

[0097] Table 7. Additional inhibitors of the inflammatory response

[0098] Any of the agents listed in Tables 4-7 may be used in the present invention. The subject may be administered one or more agents of Tables 4-6, or Table 7 at a higher dose or at a lower dose (e.g., the dose of a single treatment and/or a daily dose comprising one or more single treatments) depending on his/her IL-1 genotype.

[0099] In some embodiments, one or more clinical indicators (biomarkers) may also be measured, such as levels of C-reactive protein (CRP) or cytokines. For example, CRP levels greater than or equal to 2.0 mg/L are associated with increased risk of cardiovascular disease. In some embodiments, the cytokines comprise one or more cytokines selected from the group consisting of interleukin 1 (IL-1), interleukin-2 (IL-2), interferon gamma (IFNy), interleukin 5 (IL-5), interleukin 6 (IL-6), interleukin 10 (IL-10), tumor necrosis factor alpha (TNFa), monocyte chemoattractant protein-1 (MCP-1), interleukin 6 signal transducer (gpl30), Fms- related tyrosine kinase 3 ligand (Flt3L), C-X3-C motif chemokine ligand 1 (CX3CL1) and colony stimulating factor 2 (CSF). In some embodiments, the cytokines comprise one or more cytokines selected from the group consisting of IL-2, IL-6, IL-10 and TNFa. Alternately, the subject may be not given the particular agent depending on his/her IL-1 genotype pattern and optionally, status of one or more clinical indicators, and instead may be administered a different agent.

[00100] Additionally, agents other than those listed in Tables 4-7 may be used in the present invention. For this, an alternate agent having a mode of action (MO A) similar to or identical to a drug listed in Tables 4-7 may be provided instead of or in addition to the agents listed in Tables 4-7. One skilled in the art is able to determine alternate agents that are useful in the present invention.

[00101] A subject may be administered one or more agents from Tables 4-7, or one or more alternate agents having a MOA similar to or identical to an agent listed in Tables 4-7 at the standard therapeutic dose. An agent may be given at a dose lower than the standard therapeutic dose, e.g., 99%, 95%, 90%, 85%, 80%, 75%, 70%, 60%, 50%, 40%, 30%, 20%, 15%, 10%, or 5%, and any percentage in between lower than the standard therapeutic dose. A agent may be given at a dose higher than the standard therapeutic dose, e.g., 5%, 10%, 15%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 125%, 150%, 175%, 200%, 300%, 400%, 500%, 600%, 700%, 800%, 900%, 1000%, 2000%, or more, and any percentage in between higher than the standard therapeutic dose. For example, if a standard therapeutic dose is 10 mg per day, a subject may be given 7 mg per day as a lower than standard therapeutic dose or 13 mg per day as a higher than standard therapeutic dose.

[00102] In some embodiments, the inflammation inhibitor is formulated as an aerosol. Aerosols can be inhaled into the lungs, and are thus able to target inflammation inhibitors to inflamed lung tissues. In some embodiments, the aerosol is administered as a nasal spray.

[00103] In some embodiments, the IL-Ib inhibitor is Canakinumab or a derivative thereof. In some embodiments, Canakinumab is administered to the subject at a dose of 25 mg to 300 mg. In some embodiments, the subject weighs less than 40 kg and the Canakinumab is administered to the subject at a dose of 2 mg/kg or 4 mg/kg. Alternatively, when the subject weighs more than 40 kg, the Canakinumab can be administered to the subject at a dose of 150 mg or 300 mg. In some cases, Canakinumab is administered parenterally. Parenteral administration includes intravenous injection, intravenous infusion, intramuscularly, via intrapulmonary administration or subcutaneously.

[00104] In some embodiments, the IL-la inhibitor is Bermekimab. In some cases, the Bermekimab is administered at between 3 mg/kg to 20 mg/kg. In some cases, the Bermekimab is administered at 7.5 mg/kg. Parenteral administration includes intravenous injection, intravenous infusion, intramuscularly, via intrapulmonary administration or subcutaneously.

[00105] In some embodiments, administering the IL-1 inhibitor to a subject who is IL-1 positive reduces the risk of developing, or prevents the development of, a severe case to COVID- 19 resulting from SARS-CoV-2 infection. For example, diagnosing subjects as IL-1 positive and administering IL-1 inhibitors prior to the development of COVID-19 can reduce the risk of developing COVID-19 induced CRS.

[00106] In some embodiments, the inflammation inhibitor is a GM-CSF inhibitor. In some embodiments, administering the GM-SCF inhibitor to a subject who is IL-1 positive reduces the risk of developing, or prevents the development of, a severe case of COVID-19 resulting from SARS-CoV-2 infection. For example, diagnosing subjects as IL-1 positive and administering GM-CSF inhibitors prior to the development of COVID-19 can reduce the risk of developing severe COVID-19 symptoms, or COVID-19 induced CRS. In some embodiments, the GM-CSF inhibitor comprises Namilumab, Lenzilumab, MOR103, MORab002, Mavrilimumab or Otilimab. In some embodiments, the GM-CSF inhibitor comprises Namilumab, Lenzilumab, Mavrilimumab or Otilimab. In some embodiments, the inhibitor may inhibit GM-CSF indirectly. Indirect inhibitors of GM-CSF mediated inflammation response include, for example, Tofacitinib.

[00107] In some cases, the inflammation inhibitor is administered prior to the onset of COVID-19 symptoms. For example, an inflammation inhibitor is administered after a subject as a known SARS-CoV-2 exposure, or tests positive for SARS-CoV-2, but the inflammation inhibitor is administered 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 days prior to the onset of COVID-19 symptoms.

[00108] In some cases, the IL-1 inhibitor is administered after the onset of COVID-19 symptoms, but prior to the onset of CRS. For example, inflammation inhibitors can be administered after the manifestation of initial symptoms such as fever, cough, fatigue and myalgia, but prior to the development of cytokine release syndrome and the symptoms associated therewith. In some cases, a dose of the IL-1 inhibitor is administered 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 days after the onset of initial symptoms. In some embodiments, the inflammation inhibitor is administered concurrently with symptoms of cytokine release syndrome.

[00109] In some embodiments, administering an IL-1 inhibitor to a subject who is IL-1 positive and has CRS reduces the severity of CRS. In some embodiments, administering an IL-1 inhibitor to a subject who is IL-1 positive and has CRS reduces a sign or a symptom of CRS.

Therapies

[00110] The methods of treating, preventing or reducing the severity of COVID-19 or CRS associated with COVID-19 described herein are combinable with any standard of care for the disease.

[00111] In some embodiments, the methods described herein are combined with supportive, or palliative treatment. For example, the methods described herein can be combined with intravenous fluids to prevent dehydration, medications to manage COVID-19 symptoms and additional supportive methods such as pronation or ventilators to aid in respiration. Medications to manage symptoms include morphine or other pain medications to treat pain, dyspnea, cough or shortness of breath, antidepressants such as Haloperidol or Lorazepam to treat nausea, restlessness, anxiety, or agitation, anti-nausea drugs such as Metaclopromide, and drugs to treat diarrhea or constipation.

[00112] In some cases, antiviral drugs may be used to treat COVID-19. For example, the antiviral Favipiravir (Avigan) was recently approved as an experimental treatment, and remdesivir (developed by Gilead) has been approved for compassionate use. Without wishing to be bound by theory, it is thought that some hypertension drugs may also be effective for treating COVID-19, possibly by blocking the receptors that SARS-CoV-2 needs to infect cells. Exemplary hypertension drugs include angiotensin-converting enzyme 2 (ACE2) inhibitors, renin-angiotensin-aldosterone system (RAAS) inhibitors, angiotensin-converting enzyme inhibitors (ACEI), and angiotensin II receptor blocker (ARB) therapy.

[00113] COVID-19 treatment regimens including steroids such as dexamethasone, prednisolone, or other corticosteroids have also been found to be effective. [00114] Monoclonal antibodies specific to COVID-19 have been successfully used to reduce the severity and duration of COVID-19 symptoms, and reduce the likelihood that a subject with COVID-19 will need hospitalization. Complement targeted therapies, such as C5 and C5a targeted inhibition, has shown efficacy in treating COVID-19. Antibody therapies currently in development, or in use for treating COVID-19, are shown in Table 8 below.

[00115] Table 8. COVID-19 antibody therapies

[00116] In some embodiments, the inflammation inhibitors described herein are used as a monotherapy. In alternative embodiments, the inflammation inhibitors are part of a combination therapy. As used herein, "monotherapy" refers to the administration of a single active or therapeutic compound to a subject in need thereof. Preferably, monotherapy will involve administration of a therapeutically effective amount of an active compound. Monotherapy may be contrasted with combination therapy, in which a combination of multiple active compounds is administered, preferably with each component of the combination present in a therapeutically effective amount.

[00117] As used herein, the terms “prevent,” “preventing,” “prevention,” “prophylactic treatment” and the like refer to reducing the probability of developing a disorder, condition or symptom in a subject, who does not have, but is at risk of or susceptible to developing a disorder, condition or symptom.

[00118] As used herein, the terms “treat,” treating,” “treatment,” and the like refer to reducing or ameliorating a disorder and/or a symptom associated therewith. It will be appreciated that, although not precluded, treating a disorder or condition does not require that the disorder, condition or symptoms associated therewith be completely eliminated. Treating may include a health care professional or diagnostic scientist making a recommendation to a subject for a desired course of action or treatment regimen, e.g., a prescription. It should be noted that “Treating” or “treat” describes the management and care of a patient for the purpose of combating a disease, condition, or disorder and includes the administration of a composition of the present disclosure or a pharmaceutically acceptable salt, polymorph or solvate thereof, to alleviate one or more symptoms or complications of a disease, condition or disorder, or to eliminate the disease, condition or disorder. The term "treat" can also include treatment of a cell in vitro or an animal model.

[00119] A composition of the present invention, or a pharmaceutically acceptable salt, polymorph or solvate thereof, can also be used to prevent a disease, condition or disorder, or used to identify suitable candidates for such purposes. As used herein, “preventing” or “prevent” describes reducing or eliminating the onset of the symptoms or complications of the disease, condition or disorder. “Prevent” or “preventing” also describes reducing the probability, or risk, of developing a sign or a symptom of a disease of the disclosure.

[00120] As used herein, the term “alleviate” is meant to describe a process by which the severity of a sign or symptom of a disorder is decreased. Importantly, a sign or symptom can be alleviated without being eliminated. In a preferred embodiment, the administration of pharmaceutical compositions of the invention leads to the elimination of a sign or symptom, however, elimination is not required. Effective dosages are expected to decrease the severity of a sign or symptom. For instance, a sign or symptom of a disorder such as COVID-19, which can occur in multiple locations, is alleviated if the severity of the sign or symptom is decreased within at least one of multiple locations.

[00121] As used herein, the term "severity" is meant to describe the strength of symptoms and the potential of the disease to lead to symptoms that require long term recovery, hospitalization, or death. An estimated 80% of people experience mild to moderate COVID-19, and recover without hospitalization. Symptoms of mild to moderate COVID-19 include symptoms such as fever, cough, fatigue and myalgia. About 15% of people develop severe cases of COVID-19, and about 5% become critically ill. Symptoms of severe COVID-19 include difficulty breathing or shortness of breath, persistent pain or pressure in the chest, confusion or inability to arouse, and bluish lips or face. Further signs and symptoms of severe COVID-19 include development of pneumonia and/or severe acute respiratory syndrome, symptoms of CRS and neurological symptoms (such as confusion, stroke and seizures).

Formulations

[00122] The disclosure provides formulations of the inflammation inhibitors disclosed herein. [00123] A drug is prepared depending in its route of drug administration. Examples of drug administration routes that are useful in the present invention are described on the U.S. Food and Drug Administration’s website at the World Wide Web

(www. fda.gov/Drugs/DevelopmentApprovalProcess/FormsSubmissionRequirements/ElectronicS ubmissions/DataStandardsManualmonographs/ucm071667.htm).

[00124] Preparations for oral administration generally contain inert excipients in addition to the active pharmaceutical ingredient. Oral preparations may be enclosed in gelatin capsules or compressed into tablets. Common excipients used in such preparations include pharmaceutically compatible fillers/diluents such as microcrystalline cellulose, hydroxypropyl methylcellulose, starch, lactose, sucrose, glucose, mannitol, sorbitol, dibasic calcium phosphate, or calcium carbonate; binding agents such as alginic acid, carboxymethylcellulose, microcrystalline cellulose, gelatin, gum tragacanth, or polyvinylpyrrolidone; disintegrating agents such as alginic acid, cellulose, starch, or polyvinylpyrrolidone; lubricants such as calcium stearate, magnesium stearate, talc, silica, or sodium stearyl fumarate; glidants such as colloidal silicon dioxide; sweetening agents such as sucrose or saccharin; flavoring agents such as peppermint, methyl salicylate, or citrus flavoring; coloring agents; and preservatives such as antioxidants (e.g., vitamin A, vitamin C, vitamin E, or retinyl palmitate), citric acid, or sodium citrate. Oral preparations may also be administered as aqueous suspensions, elixirs, or syrups. For these, the active ingredient may be combined with various sweetening or flavoring agents, coloring agents, and, if so desired, emulsifying and/or suspending agents, as well as diluents such as water, ethanol, glycerin, and combinations thereof.

[00125] For parenteral administration (including subcutaneous, intradermal, intravenous, intramuscular, and intraperitoneal), the preparation may be an aqueous or an oil-based solution. Aqueous solutions may include a sterile diluent such as water, saline solution, a pharmaceutically acceptable polyol such as glycerol, propylene glycol, or other synthetic solvents; an antibacterial and/or antifungal agent such as benzyl alcohol, methyl paraben, chlorobutanol, phenol, thimerosal, and the like; an antioxidant such as ascorbic acid or sodium bisulfite; a chelating agent such as ethylenediaminetetraacetic acid (EDTA); a buffer such as acetate, citrate, or phosphate; and/or an agent for the adjustment of tonicity such as sodium chloride, dextrose, or a polyalcohol such as mannitol or sorbitol. The pH of the aqueous solution may be adjusted with acids or bases such as hydrochloric acid or sodium hydroxide. Oil-based solutions or suspensions may further comprise sesame, peanut, olive oil, or mineral oil.

[00126] For topical (e.g., transdermal or transmucosal) administration, penetrants appropriate to the barrier to be permeated are generally included in the preparation. Transmucosal administration may be accomplished through the use of nasal sprays, aerosol sprays, tablets, or suppositories, and transdermal administration may be via ointments, salves, gels, patches, or creams as generally known in the art. Topical ocular formulations, e.g., eye drops and eye ointments, are considered.

[00127] The amount of agent that is administered to the subject can and will vary depending upon the type of agent, the subject, and the particular mode of administration. Those skilled in the art will appreciate that dosages may also be determined with guidance from Goodman & Gilman’s The Pharmacological Basis of Therapeutics, Twelfth Edition (2011), Appendix II, pp. 1891-1991, and the Physicians’ Desk Reference 70^th Edition, 2016.

Pharmacogenomics

[00128] Pharmacogenomics is the methodology which associates genetic variability with physiological and clinical responses to a drug. Pharmacogenetics is a subset of pharmacogenomics and is defined as “the study of variations in DNA sequence as related to drug response” (ICH El 5; see the World Wide Web www.fda.gov/downloads/RegulatoryInformation/Guidances/ucml29296.pdf). Pharmacogenetics often focuses on genetic polymorphisms in genes related to drug metabolism, drug mechanism of action, underlying disease type, and drug associated side effects. Pharmacogenetics is the cornerstone of Personalized Medicine which allows the development and the targeted use of drug therapies to obtain effective and safe treatment, as well as to adjust existing treatment regimens to further optimize the efficacy and safety profile for the individual patient.

[00129] Pharmacogenetics has become a core component of many drug development programs, being used to explain variability in drug response among subjects in clinical trials, to address unexpected emerging clinical issues, such as adverse events, to determine eligibility for a clinical trial (pre-screening) to optimize trial yield, to develop drug companion diagnostic tests to identify patients who are more likely or less likely to benefit from treatment or who may be at risk of adverse events, to provide information in drug labels to guide physician treatment decisions, to better understand the mechanism of action or metabolism of new and existing drugs, and to provide better understanding of disease mechanisms as associated with treatment response.

[00130] Generally, pharmacogenetics analyses are often performed using the candidate genes research technique, which is a hypothesis-driven approach, based on the detection of polymorphisms in candidate genes pre-selected using knowledge of the disease, the drug’s mode of action, toxicology, or metabolism of the drug.

Ex vivo diagnostics

[00131] In aspects of the present invention, IL-1 levels can be measured ex vivo and in response to treatment with a therapeutic compound. For this, lymphocytes will be obtained from a subject. The lymphocytes will be treated with an IL-1 activator and then IL-1 levels (protein and/or mRNA) will be measured. If the lymphocytes produce increased IL-1 and to a critical level, then a diagnosis of the subject can be made and a prediction regarding an optimal treatment can be determined.

Isolated Nucleic Acid Molecules

[00132] As used herein, an “isolated nucleic acid molecule” generally is one that contains one or more of the SNPs disclosed herein or one that hybridizes to such molecule such as a nucleic acid with a complementary sequence, and is separated from most other nucleic acids present in the natural source of the nucleic acid molecule. As used herein, “a non-naturally occurring nucleic acid molecule” generally is one that contains one or more of the SNPs disclosed herein or one that hybridizes to such a molecule, such as a nucleic acid with a complementary sequence, but which does not correspond to a naturally occurring molecule, e.g., it can be a molecule prepared by recombinant nucleic acid technology, chemical synthesis, or other synthetic means such as polymerase chain reaction (PCR), and/or a nucleic acid which comprises one or more synthetic components such as a non-natural nucleotide or an added tag/motif.

[00133] The isolated nucleic acid may be obtained from any bodily fluid (such as blood, serum, plasma, urine, saliva, phlegm, gastric juices, semen, tears, sweat, etc.), skin, hair, cell (especially nucleated cells), biopsy, buccal swab, tissue, or tumor specimen. Alternately, the isolated nucleic acid may be amplified or synthesized from a nucleic acid obtained from any bodily fluid, skin, hair, cell, biopsy, buccal swab, tissue, or tumor specimen.

[00134] Generally, an isolated SNP-containing nucleic acid molecule includes one or more of SNPs and/or one or more SNPs in linkage disequilibrium with one or more SNPs. The isolated SNP-containing nucleic acid molecule may include flanking nucleotide sequences on either side of the SNP position. A flanking sequence can include nucleotide residues that are naturally associated with the SNP site and/or heterologous nucleotide sequences. Preferably, the flanking sequence is up to about 10,000, 1,000, 500, 300, 100, 60, 50, 30, 25, 20, 15, 10, 8, or 4 nucleotides (or any other length in-between) on either side of a SNP position, or as long as the full-length gene, entire protein-coding sequence (or any portion thereof such as an exon), entire enhancer/promoter region or portion thereof, or entire intron or portion thereof.

[00135] An isolated SNP-containing nucleic acid molecule can include, for example, a full- length gene or transcript, such as a gene isolated from genomic DNA (e.g., by cloning or PCR amplification), a cDNA molecule, or an mRNA transcript molecule.

[00136] An isolated nucleic acid molecule of the disclosed subject matter further encompasses a SNP-containing polynucleotide that is the product of any one of a variety of nucleic acid amplification methods, which are used to increase the copy numbers of a polynucleotide of interest in a nucleic acid sample. Such amplification methods are well known in the art, and they include but are not limited to, polymerase chain reaction (PCR) (U.S. Pat. Nos. 4,683,195 and 4,683,202; PCR Technology: Principles and Applications for DNA Amplification, ed. H. A. Erlich, Freeman Press, NY, N.Y. (1992)), ligase chain reaction (LCR) (Wu and Wallace, Genomics 4:560 (1989); Landegren et al ., Science 241:1077 (1988)), strand displacement amplification (SDA) (U.S. Pat. Nos. 5,270,184 and 5,422,252), transcription-mediated amplification (TMA) (U.S. Pat. No. 5,399,491), linked linear amplification (LLA) (U.S. Pat. No. 6,027,923) and the like, and isothermal amplification methods such as nucleic acid sequence based amplification (NASBA) and self-sustained sequence replication (Guatelli el a/., Proc Natl Acad Sci USA 87:1874 (1990)). Based on such methodologies, a person skilled in the art can readily design primers in any suitable regions 5' and 3' to a SNP disclosed herein. Such primers may be used to amplify DNA of any length so long that it contains the SNP of interest in its sequence. [00137] The isolated nucleic acid molecules that include, consist of, or consist essentially of one or more polynucleotide sequences that contain one or more SNPs disclosed herein, complements thereof, SNPs in linkage disequilibrium with the SNPs disclosed herein, and/or SNP-containing fragments thereof. Non-limiting examples of SNPs in linkage disequilibrium with the SNPs disclosed herein include those listed in Table 9 below.

Table 9

[00138] Isolated nucleic acid molecules can be in the form of RNA, such as mRNA, or in the form DNA, including cDNA and genomic DNA, which may be obtained, for example, by molecular cloning or produced by chemical synthetic techniques or by a combination thereof. Sambrook and Russell, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press,

N. Y. (2000). Furthermore, isolated nucleic acid molecules, particularly SNP detection reagents such as probes and primers, can also be partially or completely in the form of one or more types of nucleic acid analogs, such as peptide nucleic acid (PNA). U.S. Pat. Nos. 5,539,082; 5,527,675; 5,623,049; and 5,714,331. The nucleic acid, especially DNA, can be double-stranded or single- stranded. Single-stranded nucleic acid can be the coding strand (sense strand) or the complementary non-coding strand (anti-sense strand). DNA, RNA, or PNA segments can be assembled, for example, from fragments of the human genome (in the case of DNA or RNA) or single nucleotides, short oligonucleotide linkers, or from a series of oligonucleotides, to provide a synthetic nucleic acid molecule. Nucleic acid molecules can be readily synthesized using the sequences provided herein as a reference; oligonucleotide and PNA oligomer synthesis techniques are well known in the art. See, e.g., Corey, “Peptide nucleic acids: expanding the scope of nucleic acid recognition,” Trends Biotechnol 15 (6):224-9 (June 1997), and Hyrup et al ., “Peptide nucleic acids (PNA): synthesis, properties and potential applications,” Bioorg Med Chem 4 (l):5-23 (January 1996). Furthermore, large-scale automated oligonucleotide/PNA synthesis (including synthesis on an array or bead surface or other solid support) can readily be accomplished using commercially available nucleic acid synthesizers, such as the Applied Biosystems (Foster City, Calif.) 3900 High-Throughput DNA Synthesizer or Expedite 8909 Nucleic Acid Synthesis System and the sequence information provided herein. [00139] The isolated SNP-containing nucleic acid molecule may comprise modified, synthetic, or non-naturally occurring nucleotides or structural elements or other alternative/modified nucleic acid chemistries known in the art. Such nucleic acid analogs are useful, for example, as detection reagents (e.g., primers/probes) for detecting the SNPs identified herein. Furthermore, kits/systems (such as beads, arrays, etc.) that include these analogs are also encompassed herein.

[00140] The practice of the present methods will employ, unless otherwise indicated, conventional techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature. See, for example, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory (2001); DNA Cloning, Volumes I and II (P. N. Glover ed., 1985); Oligonucleotide Synthesis (M. J. Gait ed., 1984); Mullis et al. U.S. Pat.

No. 4,683,195; Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. 1984); Transcription And Translation (B. Q. Hames & S. J. Higgins eds. 1984); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc., 1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide To Molecular Cloning (1984); the treatise, Methods In Enzymology (Academic Press, Inc., N. Y.); Gene Transfer Vectors For Mammalian Cells (J. H. Miller and M. P. Calos eds., 1987, Cold Spring Harbor Laboratory); Methods In Enzymology, Vols. 154 and 155 (Wu at al. eds.), Immunochemical Methods In Cell And Molecular Biology (Mayer and Walker, eds., Academic Press, London, 1987); Handbook Of Experimental Immunology, Volumes I-IV (D. M. Weir and C. C. Blackwell, eds., 1986); Manipulating the Mouse Embryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986).

SNP Detection Reagents

[00141] In aspects of the present invention, each of the one or more of the SNPs disclosed herein can be used for the design of SNP detection reagents. As used herein, a “SNP detection reagent” is a reagent that specifically detects a specific target SNP position disclosed herein, and that is preferably specific for a particular nucleotide (allele) of the target SNP position (i.e., the detection reagent preferably can differentiate between different alternative nucleotides at a target SNP position, thereby allowing the identity of the nucleotide present at the target SNP position to be determined). Typically, such detection reagent hybridizes to a target SNP-containing nucleic acid molecule by complementary base-pairing in a sequence specific manner and discriminates the target variant sequence from other nucleic acid sequences such as an art-known form in a test sample. An example of a detection reagent is a non-naturally occurring nucleic acid probe that hybridizes to a target nucleic acid containing one of the SNPs disclosed herein. In a preferred embodiment, such a probe can differentiate between nucleic acids having a particular nucleotide (allele) at the target SNP position from other nucleic acids that have a different nucleotide at the same target SNP position. In addition, a detection reagent may hybridize to a specific region 5' and/or 3' to the SNP position.

[00142] Another example of a detection reagent is a non-naturally occurring nucleic acid primer that acts as an initiation point of nucleotide extension along a complementary strand of a target polynucleotide. The SNP sequence information provided herein is also useful for designing primers, e.g., allele-specific primers, to amplify (e.g., using PCR) the SNP of the disclosed subject matter.

[00143] A SNP detection reagent may be an isolated or synthetic DNA or RNA polynucleotide probe or primer or PNA oligomer, or a combination of DNA, RNA and/or PNA that hybridizes to a segment of a target nucleic acid molecule containing one of the SNPs disclosed herein. A detection reagent in the form of a non-naturally occurring polynucleotide may optionally contain modified base analogs, intercalators, or minor groove binders. Multiple detection reagents such as probes may be, for example, affixed to a solid support (e.g., an array and bead) or supplied in solution (e.g., probe/primer sets for enzymatic reactions such as PCR, RT-PCR, TaqMan® assays, and primer-extension reactions) to form a SNP detection kit.

[00144] For analyzing SNPs, it can be appropriate to use oligonucleotides specific for alternative SNP alleles. Such oligonucleotides that detect single nucleotide variations in target sequences may be referred to by such terms as “allele-specific oligonucleotides,” “allele-specific probes,” or “allele-specific primers.” The design and use of allele-specific probes for analyzing polymorphisms is described in, e.g., Mutation Detection: A Practical Approach, Cotton et al ., eds., Oxford University Press (1998); Saiki et al ., Nature 324:163-166 (1986); Dattagupta, EP235,726; and Saiki, WO 89/11548.

[00145] In another embodiment, a probe or primer may be designed to hybridize to a segment of target DNA such that the SNP aligns with either the 5 '-most end or the 3 '-most end of the probe or primer. When using an oligonucleotide ligation assay (U.S. Pat. No. 4,988,617), the 3' most nucleotide of the probe aligns with the SNP position in the target sequence.

[00146] Allele-specific probes are often used in pairs (or, less commonly, in sets of 3 or 4), and such pairs may be identical except for a one nucleotide mismatch that represents the allelic variants at the SNP position. Typically, one member of a probe pair perfectly matches a reference form of a target sequence that has a more common SNP allele (i.e., the allele that is more frequent in the target population) and the other member of the pair perfectly matches a form of the target sequence that has a less common SNP allele (i.e., the allele that is rarer in the target population). In the case of an array, multiple pairs of probes can be immobilized on the same support for simultaneous analysis of multiple different polymorphisms.

[00147] In one type of PCR-based assay, an allele-specific primer hybridizes to a region on a target nucleic acid molecule that overlaps a SNP position and only primes amplification of an allelic form to which the primer exhibits perfect complementarity. Gibbs, Nucleic Acid Res 17:2427-2448 (1989). Typically, the primer’s 3'-most nucleotide is aligned with and complementary to the SNP position of the target nucleic acid molecule. This primer is used in conjunction with a second primer that hybridizes at a distal site. Amplification proceeds from the two primers, producing a detectable product that indicates which allelic form is present in the test sample. A control is usually performed with a second pair of primers, one of which shows a single base mismatch at the polymorphic site and the other of which exhibits perfect complementarity to a distal site. The single-base mismatch prevents amplification or substantially reduces amplification efficiency, so that either no detectable product is formed or it is formed in lower amounts or at a slower pace. The method generally works most effectively when the mismatch is at the 3 '-most position of the oligonucleotide (i.e., the 3 '-most position of the oligonucleotide aligns with the target SNP position) because this position is most destabilizing to elongation from the primer (see, e.g., WO 93/22456). This PCR-based assay can be utilized as part of the TaqMan® assay, described below.

[00148] A primer may contain a sequence substantially complementary to a segment of a target SNP-containing nucleic acid molecule except that the primer has a mismatched nucleotide in one of the three nucleotide positions at the 3 '-most end of the primer, such that the mismatched nucleotide does not base pair with a particular allele at the SNP site. In a preferred embodiment, the mismatched nucleotide in the primer is the second from the last nucleotide at the 3 '-most position of the primer. In a more preferred embodiment, the mismatched nucleotide in the primer is the last nucleotide at the 3 '-most position of the primer.

[00149] A SNP detection reagent may be labeled with a fluorogenic reporter dye that emits a detectable signal. While the preferred reporter dye is a fluorescent dye, any reporter dye that can be attached to a detection reagent such as an oligonucleotide probe or primer is suitable for use in the disclosed subject matter. Such dyes include, but are not limited to, Acridine, AMCA, BODIPY, Cascade Blue, Cy2, Cy3, Cy5, Cy7, Dabcyl, Edans, Eosin, Erythrosin, Fluorescein, 6- Fam, Tet, Joe, Hex, Oregon Green, Rhodamine, Rhodol Green, Tamra, Rox, and Texas Red. [00150] In yet another embodiment, the detection reagent may be further labeled with a quencher dye such as TAMRA, especially when the reagent is used as a self-quenching probe such as a TaqMan® (U.S. Pat. Nos. 5,210,015 and 5,538,848) or Molecular Beacon probe (U.S. Pat. Nos. 5,118,801 and 5,312,728), or other stemless or linear beacon probe (Livak et al ., PCR Method Appl 4:357-362 (1995); Tyagi et al., Nature Biotechnology 14:303-308 (1996); Nazarenko etal, Nuc’ Acids Res 25:2516-2521 (1997); U.S. Pat. Nos. 5,866,336 and 6,117,635. [00151] Detection reagents may also contain other labels, including but not limited to, biotin for streptavidin binding, hapten for antibody binding, and an oligonucleotide for binding to another complementary oligonucleotide. [00152] Reagents may not contain (or be complementary to) a SNP nucleotide as describe herein but that are used to assay one or more SNPs disclosed herein. For example, primers that flank, but do not hybridize directly to a target SNP position provided herein are useful in primer extension reactions in which the primers hybridize to a region adjacent to the target SNP position (i.e., within one or more nucleotides from the target SNP site). During the primer extension reaction, a primer is typically not able to extend past a target SNP site if a particular nucleotide (allele) is present at that target SNP site, and the primer extension product can be detected in order to determine which SNP allele is present at the target SNP site. For example, particular ddNTPs are typically used in the primer extension reaction to terminate primer extension once a ddNTP is incorporated into the extension product (a primer extension product which includes a ddNTP at the Y-most end of the primer extension product, and in which the ddNTP is a nucleotide of a SNP disclosed herein, is a composition that is specifically herein). Thus, reagents that bind to a nucleic acid molecule in a region adjacent to a SNP site and that are used for assaying the SNP site, even though the bound sequences do not necessarily include the SNP site itself, are also contemplated by the disclosed subject matter.

[00153] For example, the SNP may be identified using single-base extension (SBE). SBE determines the identity of a nucleotide base at a specific position along a nucleic acid. In the method, an oligonucleotide primer hybridizes to a complementary region along the nucleic acid, to form a duplex, with the primer’ s terminal 3' end directly adjacent to the nucleotide base to be identified. The oligonucleotide primer is enzymatically extended by a single base in the presence of all four nucleotide terminators; the nucleotide terminator complementary to the base in the template being interrogated is incorporated and identified. The presence of all four terminators ensures that no further extension occurs beyond the single incorporated base. Many approaches can be taken for determining the identity of a terminator, including fluorescence labeling, mass labeling for mass spectrometry, measuring enzyme activity using a protein moiety, and isotope labeling.

[00154] Reagents and techniques described herein may be directed to performance of “Next Generation Sequencing.” (See, e.g., Srivatsan et al ., PLoS Genet 4: el00139 (2008);

Rasmussen et al., Nature 463:757-762 (2010); Li et al., Nature 463: 311-317 (2010); Pelak et al., PLoS Genet 6: elOOllll (2010); Ram et al, Syst Biol Reprod Med (57(3): 117-118 (2011); McEllistrem, Future Microbiol 4: 857-865 (2009); Lo et al., Clin Chem 55: 607-608 (2009); Robinson, Genome Biol 11 : 144 (2010); and Araya et al. , Trends Biotechnology doilO. 1016j.tibtech.2011.04.003 (2011)). For example, such techniques may involve the fragmentation of a genomic nucleic acid sample followed by parallel sequencing of those fragments and the alignment of the sequenced fragments to reconstruct the original sequence. Here, the genomic nucleic acid of interest is sheared into fragments and “adapters” (short nucleic acids of known sequence) are ligated to the fragments. Adaptor-modified fragments can be enriched via PCR.

An adaptor-modified fragment (and amplified copies thereof, if present) may be flowed across a flow cell where the fragments are allowed to hybridize to primers immobilized on the surface of the cell. The fragments are then amplified by isothermal bridge amplification into a cluster consisting of thousands of molecules identical to the original. Sequencing primers can then be hybridized to the ends of one strand of the clusters, reversibly blocked, and labeled nucleotides added. The addition of each particular nucleotide can be identified by the label, then the label can be removed and the nucleotide un-blocked so that another blocked and labeled nucleotide can be added to identify the next position in the nucleic acid sequence. Once the desired number of rounds of addition, detection, and unblocking occur, the resulting sequences can be aligned. [00155] It will be apparent to one of skill in the art that such primers and probes are directly useful as reagents for detecting the SNPs of the disclosed subject matter, and can be incorporated into any kit/system format.

SNP Genotyping Methods

[00156] SNP genotyping includes, for example, collecting a biological sample from a human subject (e.g., sample of tissues, cells, fluids, secretions, etc.), isolating nucleic acids (e.g., genomic DNA, mRNA or both) from the cells of the sample, contacting the nucleic acids with one or more primers which specifically hybridize to a region of the isolated nucleic acid containing a target SNP under conditions such that hybridization and amplification of the target nucleic acid region occurs, and determining the nucleotide present at the SNP position of interest, or, in some assays, detecting the presence or absence of an amplification product (assays can be designed so that hybridization and/or amplification will only occur if a particular SNP allele is present or absent). In some assays, the size of the amplification product is detected and compared to the length of a control sample; for example, deletions and insertions can be detected by a change in size of the amplified product compared to a normal genotype.

[00157] SNP genotyping is useful for numerous practical applications, as described herein. Examples of such applications include, but are not limited to, SNP-disease association analysis, disease predisposition screening, disease diagnosis, disease prognosis, disease progression monitoring, determining therapeutic strategies based on a subject’s genotype (“pharmacogenomics”), developing therapeutic agents based on SNP genotypes associated with a disease or likelihood of responding to a drug, stratifying patient populations for clinical trials of a therapeutic, preventive, or diagnostic agent, and human identification applications such as forensics.

[00158] Nucleic acid samples can be genotyped to determine which allele is present at any given SNP position of interest by methods well known in the art. The neighboring sequence can be used to design SNP detection reagents such as oligonucleotide probes, which may optionally be implemented in a kit format. Exemplary SNP genotyping methods are described in Chen etal ., “Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput,” Pharmacogenomics J 3 (2):77-96 (2003); Kwok etal., “Detection of single nucleotide polymorphisms,” Curr Issues Mol Biol 5 (2):43-60 (April 2003); Shi, “Technologies for individual genotyping: detection of genetic polymorphisms in drug targets and disease genes,” Am J Pharmacogenomics 2 (3): 197-205 (2002); and Kwok, “Methods for genotyping single nucleotide polymorphisms,” Annu Rev Genom Hum Genet 2:235-58 (2001). Techniques for high-throughput SNP genotyping are described in Mamellos, “High-throughput SNP analysis for genetic association studies,” Curr Opin Drug Disc Devel 6 (3):317-21 (May 2003).

[00159] SNP genotyping methods include, but are not limited to, TaqMan^® assays, molecular beacon assays, nucleic acid arrays, allele-specific primer extension, allele-specific PCR, arrayed primer extension, homogeneous primer extension assays, primer extension with detection by mass spectrometry, pyrosequencing, multiplex primer extension sorted on genetic arrays, ligation with rolling circle amplification, homogeneous ligation, Oligonucleotide Ligation Assay (OLA: U.S. Pat. No. 4,988,167), multiplex ligation reaction sorted on genetic arrays, restriction- fragment length polymorphism, single base extension-tag assays, denaturing gradient gel electrophoresis, and the Invader assay. Such methods may be used in combination with detection mechanisms such as, for example, luminescence or chemiluminescence detection, fluorescence detection, time-resolved fluorescence detection, fluorescence resonance energy transfer, fluorescence polarization, mass spectrometry, and electrical detection.

[00160] In one embodiment, SNP genotyping is performed using the TaqMan® assay, which is also known as the 5' nuclease assay (U.S. Pat. Nos. 5,210,015 and 5,538,848). The TaqMan® assay detects the accumulation of a specific amplified product during PCR. The TaqMan® assay utilizes an oligonucleotide probe labeled with a fluorescent reporter dye and a quencher dye. The reporter dye is excited by irradiation at an appropriate wavelength, it transfers energy to the quencher dye in the same probe via a process called fluorescence resonance energy transfer (FRET). When attached to the probe, the excited reporter dye does not emit a signal. The proximity of the quencher dye to the reporter dye in the intact probe maintains a reduced fluorescence for the reporter. The reporter dye and quencher dye may be at the 5' most and the 3' most ends, respectively, or vice versa. Alternatively, the reporter dye may be at the 5' or 3' most end while the quencher dye is attached to an internal nucleotide, or vice versa. In yet another embodiment, both the reporter and the quencher may be attached to internal nucleotides at a distance from each other such that fluorescence of the reporter is reduced.

[00161] During PCR, the 5' nuclease activity of DNA polymerase cleaves the probe, thereby separating the reporter dye and the quencher dye and resulting in increased fluorescence of the reporter. Accumulation of PCR product is detected directly by monitoring the increase in fluorescence of the reporter dye. The DNA polymerase cleaves the probe between the reporter dye and the quencher dye only if the probe hybridizes to the target SNP-containing template which is amplified during PCR, and the probe is designed to hybridize to the target SNP site only if a particular SNP allele is present.

[00162] Preferred TaqMan® primer and probe sequences can readily be determined using the SNP and associated nucleic acid sequence information provided herein. A number of computer programs, such as Primer Express (Applied Biosystems, Foster City, Calif.), can be used to rapidly obtain optimal primer/probe sets. These probes and primers can be readily incorporated into a kit format. The disclosed subject matter also includes modifications of the TaqMan® assay well known in the art such as the use of Molecular Beacon probes (U.S. Pat. Nos. 5,118,801 and 5,312,728) and other variant formats (U.S. Pat. Nos. 5,866,336 and 6,117,635). [00163] Another method for genotyping the SNPs can be the use of two oligonucleotide probes in an OLA (see, e.g., U.S. Pat. No. 4,988,617). In this method, one probe hybridizes to a segment of a target nucleic acid with its 3' most end aligned with the SNP site. A second probe hybridizes to an adjacent segment of the target nucleic acid molecule directly 3' to the first probe. The two juxtaposed probes hybridize to the target nucleic acid molecule and are ligated in the presence of a linking agent such as a ligase if there is perfect complementarity between the 3' most nucleotide of the first probe with the SNP site. If there is a mismatch, ligation would not occur. After the reaction, the ligated probes are separated from the target nucleic acid molecule and detected as indicators of the presence of a SNP.

[00164] The following patents, patent applications, and published international patent applications, which are all hereby incorporated by reference, provide additional information pertaining to techniques for carrying out various types of Oligonucleotide Ligation Assay (OLA). The following U.S. patents describe OLA strategies for performing SNP detection: U.S. Pat. Nos. 6,027,889; 6,268,148; 5,494,810; 5,830,711 and 6,054,564. WO 97/31256 and WO 00/56927 describe OLA strategies for performing SNP detection using universal arrays, where a zipcode sequence can be introduced into one of the hybridization probes, and the resulting product, or amplified product, hybridized to a universal zip code array. U.S. application Ser. No. 01/17,329 (and Ser. No. 09/584,905) describes OLA (or LDR) followed by PCR, where zipcodes are incorporated into OLA probes, and amplified PCR products are determined by electrophoretic or universal zipcode array readout. U.S. applications 60/427,818, 60/445,636, and 60/445,494 describe SNPIex methods and software for multiplexed SNP detection using OLA followed by PCR, where zipcodes are incorporated into OLA probes, and amplified PCR products are hybridized with a zipchute reagent, and the identity of the SNP determined from electrophoretic readout of the zipchute. In some embodiments, OLA is carried out prior to PCR (or another method of nucleic acid amplification). In other embodiments, PCR (or another method of nucleic acid amplification) is carried out prior to OLA.

[00165] Another method for SNP genotyping is based on mass spectrometry. Mass spectrometry takes advantage of the unique mass of each of the four nucleotides of DNA. SNPs can be unambiguously genotyped by mass spectrometry by measuring the differences in the mass of nucleic acids having alternative SNP alleles. MALDI-TOF (Matrix Assisted Laser Desorption Ionization-Time of Flight) mass spectrometry technology is preferred for extremely precise determinations of molecular mass, such as SNPs. Numerous approaches to SNP analysis have been developed based on mass spectrometry. Preferred mass spectrometry-based methods of SNP genotyping include primer extension assays, which can also be utilized in combination with other approaches, such as traditional gel-based formats and microarrays.

[00166] Typically, a mass spectrometry with primer extension assay involves designing and annealing a primer to a template PCR amplicon upstream (5') from a target SNP position. A mix of dideoxy nucleotide triphosphates (ddNTPs) and/or deoxynucleotide triphosphates (dNTPs) are added to a reaction mixture containing template (e.g., a SNP-containing nucleic acid molecule which has typically been amplified, such as by PCR), primer, and DNA polymerase. Extension of the primer terminates at the first position in the template where a nucleotide complementary to one of the ddNTPs in the mix occurs. The primer can be either immediately adjacent (i.e., the nucleotide at the 3' end of the primer hybridizes to the nucleotide next to the target SNP site) or two or more nucleotides removed from the SNP position. If the primer is several nucleotides removed from the target SNP position, the only limitation is that the template sequence between the 3' end of the primer and the SNP position cannot contain a nucleotide of the same type as the one to be detected, or this will cause premature termination of the extension primer.

Alternatively, if all four ddNTPs alone, with no dNTPs, are added to the reaction mixture, the primer will always be extended by only one nucleotide, corresponding to the target SNP position. In this instance, primers are designed to bind one nucleotide upstream from the SNP position (i.e., the nucleotide at the 3' end of the primer hybridizes to the nucleotide that is immediately adjacent to the target SNP site on the 5' side of the target SNP site). Extension by only one nucleotide is preferable, as it minimizes the overall mass of the extended primer, thereby increasing the resolution of mass differences between alternative SNP nucleotides. Furthermore, mass-tagged ddNTPs can be employed in the primer extension reactions in place of unmodified ddNTPs. This increases the mass difference between primers extended with these ddNTPs, thereby providing increased sensitivity and accuracy, and is particularly useful for typing heterozygous base positions.

[00167] Primer extension assays may be used in conjunction with MALDI-TOF mass spectrometry for SNP genotyping, see, e.g., Wise et al ., “A standard protocol for single nucleotide primer extension in the human genome using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry,” Rapid Comm. Mass Spect. 17 (11): 1195-202 (2003).

[00168] SNPs can also be scored by direct DNA sequencing. A variety of automated sequencing procedures can be utilized (e.g., Biotechniques 19:448 (1995)), including sequencing by mass spectrometry. See, e.g., PCT International Publication No. WO 94/16101; Cohen etal ., Adv Chromatogr 36:127-162 (1996); and Griffin et al, Appl Biochem Biotechnol 38:147-159 (1993). The nucleic acid sequences of the disclosed subject matter enable one of ordinary skill in the art to readily design sequencing primers for such automated sequencing procedures. Commercial instrumentation, such as the Applied Biosystems 377, 3100, 3700, 3730, and 3730x1 DNA Analyzers (Foster City, Calif.), is commonly used in the art for automated sequencing.

[00169] Other methods that can be used to genotype the SNPs of the disclosed subject matter include single-strand conformational polymorphism (SSCP) and denaturing gradient gel electrophoresis (DGGE). Myers etal., Nature 313:495 (1985). SSCP identifies base differences by alteration in electrophoretic migration of single stranded PCR products, as described in Orita et al. , Proc. Nat. Acad. Single-stranded PCR products can be generated by heating or otherwise denaturing double stranded PCR products. Single-stranded nucleic acids may refold or form secondary structures that are partially dependent on the base sequence. The different electrophoretic mobilities of single-stranded amplification products are related to base-sequence differences at SNP positions. DGGE differentiates SNP alleles based on the different sequence- dependent stabilities and melting properties inherent in polymorphic DNA and the corresponding differences in electrophoretic migration patterns in a denaturing gradient gel. PCR Technology: Principles and Applications for DNA Amplification Chapter 7, Erlich, ed., W.H. Freeman and Co, N.Y. (1992).

[00170] Sequence-specific ribozymes (U.S. Pat. No. 5,498,531) can also be used to score SNPs based on the development or loss of a ribozyme cleavage site. Perfectly matched sequences can be distinguished from mismatched sequences by nuclease cleavage digestion assays or by differences in melting temperature. If the SNP affects a restriction enzyme cleavage site, the SNP can be identified by alterations in restriction enzyme digestion patterns, and the corresponding changes in nucleic acid fragment lengths determined by gel electrophoresis.

SNP Detection Kits and Systems

[00171] A person skilled in the art will recognize that, based on the SNP and associated sequence information disclosed herein, detection reagents can be developed and used to assay the SNP of the disclosed subject matter individually or in combination with other SNPs, and such detection reagents can be readily incorporated into one of the established kit or system formats which are well known in the art.

[00172] The terms “kits” and “systems,” as used herein in the context of SNP detection reagents, are intended to refer to such things as combinations of multiple SNP detection reagents, or one or more SNP detection reagents in combination with one or more other types of elements or components (e.g., other types of biochemical reagents, containers, packages such as packaging intended for commercial sale, substrates to which SNP detection reagents are attached, electronic hardware components, and software recorded on a non-transitory processor-readable medium). Accordingly, the disclosed subject matter further provides SNP detection kits and systems, including but not limited to, packaged probe and primer sets (e.g., TaqMan® probe/primer sets), arrays/microarrays of nucleic acid molecules, and beads that contain one or more probes, primers, or other detection reagents for detecting one or more SNPs of the disclosed subject matter.

[00173] The kits/systems can optionally include various electronic hardware components; for example, arrays (“DNA chips”) and microfluidic systems (“lab-on-a-chip” systems) provided by various manufacturers typically include hardware components. Other kits/systems (e.g., probe/primer sets) may not include electronic hardware components, but may include, for example, one or more SNP detection reagents (along with, optionally, other biochemical reagents) packaged in one or more containers.

[00174] In some embodiments, a SNP detection kit typically contains one or more detection reagents and other components (e.g., a buffer, enzymes such as DNA polymerases or ligases, chain extension nucleotides such as deoxynucleotide triphosphates, and in the case of Sanger- type DNA sequencing reactions, chain terminating nucleotides, positive control sequences, negative control sequences, and the like) necessary to carry out an assay or reaction, such as amplification and/or detection of a SNP-containing nucleic acid molecule.

[00175] A kit may further contain instructions for using the kit to detect the SNP-containing nucleic acid molecule of interest.

[00176] The instructions may include information which allows a user to identify whether a subject having or suspected of having an CRS has genotype-specific differential expression of IL-1, i.e., is a “high” or “low” producer of IL-1, based upon the composite IL-1 genotype or IL-1 genotype patterns disclosed in Tables 1-3. The instructions may include information which allows a user to decide on an appropriate inflammation inhibitor (e.g., as disclosed in Tables 4-7, and/or an alternate inhibitor having a similar or identical mode of action as an agent disclosed in Tables 4-7) and at an appropriate dose.

[00177] In one embodiment, kits are provided which contain the necessary reagents to carry out one or more assays to detect one or more SNPs disclosed herein. In another embodiment,

SNP detection kits/sy stems are in the form of nucleic acid arrays, or compartmentalized kits, including microfluidic/lab-on-a-chip systems.

[00178] SNP detection kits/systems may contain, for example, one or more probes, or pairs of probes, that hybridize to a nucleic acid molecule at or near each target SNP position. Multiple pairs of allele-specific probes may be included in the kit/system to simultaneously assay large numbers of SNPs, at least one of which is the SNP of the disclosed subject matter. In some kits/systems, the allele-specific probes are immobilized to a substrate such as an array or bead. [00179] The terms “arrays,” “microarrays,” and “DNA chips” are used herein interchangeably to refer to an array of distinct polynucleotides affixed to a substrate, such as glass, plastic, paper, nylon or other type of membrane, filter, chip, or any other suitable solid support. The polynucleotides can be synthesized directly on the substrate or synthesized separate from the substrate and then affixed to the substrate.

[00180] Any number of probes, such as allele-specific probes, may be implemented in an array, and each probe or pair of probes can hybridize to a different SNP position. In the case of polynucleotide probes, they can be synthesized at designated areas (or synthesized separately and then affixed to designated areas) on a substrate using a light-directed chemical process. Each DNA chip can contain, for example, thousands to millions of individual synthetic polynucleotide probes arranged in a grid-like pattern and miniaturized (e.g., to the size of a dime). Preferably, probes are attached to a solid support in an ordered, addressable array.

[00181] A SNP detection kit/system can include components that are used to prepare nucleic acids from a test sample for the subsequent amplification and/or detection of a SNP-containing nucleic acid molecule. Such sample preparation components can be used to produce nucleic acid extracts (including DNA and/or RNA), proteins or membrane extracts from any bodily fluids (such as blood, serum, plasma, urine, saliva, phlegm, gastric juices, semen, tears, sweat, etc.), skin, hair, cells (especially nucleated cells), biopsies, buccal swabs or tissue or tumor specimens. Methods of preparing nucleic acids, proteins, and cell extracts are well known in the art and can be readily adapted to obtain a sample that is compatible with the system utilized. Automated sample preparation systems for extracting nucleic acids from a test sample are commercially available, and examples are Qiagen’s BioRobot 9600, Applied Biosystems’ PRISM 6700 sample preparation system, and Roche Molecular Systems’ COBAS AmpliPrep System.

[00182] For genotyping SNPs, an exemplary microfluidic system may integrate, for example, nucleic acid amplification, primer extension, capillary electrophoresis, and a detection method such as laser induced fluorescence detection. In an exemplary process for using such an exemplary system, nucleic acid samples are amplified, preferably by PCR. Then, the amplification products are subjected to automated primer extension reactions using ddNTPs (specific fluorescence for each ddNTP) and the appropriate oligonucleotide primers to carry out primer extension reactions which hybridize just upstream of the targeted SNP. Once the extension at the 3' end is completed, the primers are separated from the unincorporated fluorescent ddNTPs by capillary electrophoresis. The separation medium used in capillary electrophoresis can be, for example, polyacrylamide, polyethyleneglycol or dextran. The incorporated ddNTPs in the single nucleotide primer extension products are identified by laser- induced fluorescence detection. Such an exemplary microchip can be used to process, for example, at least 96 to 384 samples, or more, in parallel.

[00183] An exemplary kit allows a user to determine whether a subject has genotype-specific differential expression of IL-1, i.e., is a “high” or “low” producer of IL-1, based upon the composite IL-1 genotype or IL-1 genotype patterns disclosed in Tables 1-3. The exemplary kit may include instructions having information which allows a user to decide on an appropriate agent or agents for inflammation based treatment (e.g., as disclosed in Tables 4 -7, and/or an alternate agents(s) having a similar or identical mode of action as those disclosed in Tables 4-7) and at an appropriate dose.

Reports, Programmed Computers, and Systems

[00184] The results of a test provide an identification of a composite IL-1 genotype or IL-1 genotype pattern, as disclosed in Tables 1-3, which determine whether or not a subject should be administered IL-1 inhibiting agent (e.g., a response to an agent disclosed in Tables 4-7, and/or an alternate agent having a mode of action similar to or identical to an agent from Tables 4-7) prior to immunotherapy or the onset of CRS, or for the treatment of immunotherapy induced CRS a. The results may be referred to herein as a “report”. The report may include other information based on assaying the SNPs disclosed herein, alone or in combination with other SNPs, and/or a subject’s allele/genotype at the SNPs disclosed herein, alone or in combination with other SNPs, etc.), and/or any other information pertaining to a test.

[00185] A tangible report can optionally be generated as part of a testing process (which may be interchangeably referred to herein as “reporting”, or as “providing” a report, “producing” a report, or “generating” a report).

[00186] Examples of tangible reports may include, but are not limited to, reports in paper (such as computer-generated printouts of test results or hand written reports) or equivalent formats and reports stored on computer readable medium (such as a CD, USB flash drive or other removable storage device, computer hard drive, or computer network server, etc.). Reports, particularly those stored on computer readable medium, can be part of a database, which may optionally be accessible via the internet (such as a database of patient records or genetic information stored on a computer network server, which may be a “secure database” that has security features that limit access to the report, such as to allow only the patient and the patient’s medical practitioners to view the report while preventing other unauthorized subjects from viewing the report, for example). In addition to, or as an alternative to, generating a tangible report, reports can also be displayed on a computer screen (or the display of another electronic device or instrument). [00187] In addition to, or as an alternative to, the report may be “intangible” in that it is orally presented to another.

[00188] A tangible report may be hand written or may be prepared using a computer.

[00189] A report may be provided to the subject who can then implement the information and/or instructions contained therein.

[00190] A report may be provided to a health care professional who can then implement the information and/or instructions contained therein and/or instruct the subject (e.g., prescribe and make a recommendation).

[00191] A report can include, for example, a recommendation of whether or not a subject should be administered an IL-1 inhibitor either prophylactically or as a treatment for CRS. For example, the report can recommend administering an agent disclosed in Table 4, 5 or 6 , and/or an alternate agent having a mode of action similar to or identical to an agent from Table 4, 5, or 6 based upon his/her composite IL-1 genotype or IL-1 genotype pattern, as disclosed in Tables 1-3, as disclosed herein; the allele/genotype that a subject carries at the SNP locations disclosed herein; the status of his/her clinical indicators such as cytokine or CRP level; and/or his/her composite IL-1 genotype or IL-1 genotype pattern. Thus, for example, the report can include information of medical/biological significance (e.g., drug responsiveness, suggested treatment, and prophylactic methods). The report may just include allele/genotype information and/or a composite IL-1 genotype or IL-1 genotype pattern and status of one or more clinical indicators but without including disease risk or other medical/biological significance; thus, the subject viewing the report can use the allele/genotype information and/or composite IL-1 genotype or IL-1 genotype pattern and status of one or more clinical indicators to determine the associated disease risk or other medical/biological significance from a source outside of the report itself, such as from a medical practitioner, publication, website, etc., which may optionally be linked to the report such as by a hyperlink.

[00192] A report can further be “transmitted” or “communicated” (these terms may be used herein interchangeably), such as to the subject who was tested, a medical practitioner (e.g., a doctor, nurse, clinical laboratory practitioner, genetic counselor, etc.), a healthcare organization, a clinical laboratory, and/or any other party or requester intended to view or possess the report. The act of “transmitting” or “communicating” a report can be by any means known in the art, based on the format of the report. Furthermore, “transmitting” or “communicating” a report can include delivering a report (“pushing”) and/or retrieving (“pulling”) a report. For example, reports can be transmitted/communicated by various means, including being physically transferred between parties (such as for reports in paper format) such as by being physically delivered from one party to another, or by being transmitted electronically or in signal form (e.g., via e-mail or over the internet, by facsimile, and/or by any wired or wireless communication methods known in the art) such as by being retrieved from a database stored on a computer network server.

[00193] Additional teaching relevant to the present invention are described in one or more of the following: US 5,686,246, US 5,698,399, US 5,808,918, US 6,108,635, US 6,140,047,

US 6,210,877, US 6,251,598, US 6,268,142, US 6,383,775, US 6,437,216, US 6,524,795,

US 6,551,785, US 6,558,905, US 6,706,478, US 6,713,253, US 6,720,141, US 6,730,476,

US 6,733,967, US 6,746,839, US 7,723,028, US 7,820,383, US 8,101,360, US 8,105,775,

US 2002/0182612, US 2003/0100031, US 2003/0124524, US 2003/0152947, US 2003/0235890,

US 2004/0152124, US 2005/0032077, US 2005/0064453, US 2005/0171338, US 2005/0282198,

US 2006/0183161, US 2006/0252050, US 2007/0264645, US 2007/0275104, US 2008/0118920,

US 2008/0187920, US 2008/0199865, US 2008/0254476, US 2008/0254477, US 2008/0254478,

US 2008/0311581, US 2009/0023147, US 2009/0093396, US 2009/0163460, US 2009/0170105,

US 2009/0191564, US 2010/0028893, US 2010/0129798, US 2010/0255475, US 2010/0279280,

US 2011/0008906, US 2013/0011841, US 2003/0175764, US 2004/0110168, US 2010/0098775,

US 2010/0098809, US 2010/0105038, US 2010/0112570, US 2010/0136561, US 2012/0208187 and US 2013/0337448, each of which is incorporated herein by reference in their entireties. [00194] The term “single nucleotide polymorphisms” (SNPs) refers to a variation in the sequence of a gene in the genome of a population that arises as the result of a single base change, such as an insertion, deletion or, a change in a single base. A locus is the site at which divergence occurs. SNPs can result in modified amino acid sequences, altering structure and function of coded protein, and influence the splicing process when present at exon-intron transitions and modify gene transcription when part of promoters. This modification can lead to altered levels of protein expression.

[00195] As used herein the term subject is meant to include any human subject. [00196] As used herein, the terms “drug”, “medication”, “therapeutic”, “active agent”, “therapeutic compound”, “composition”, or “compound” are used interchangeably and refer to any chemical entity, pharmaceutical, drug, biological, botanical, and the like that can be used to treat or prevent a disease, illness, condition, or disorder of bodily function. A drug may comprise both known and potentially therapeutic compounds. A drug may be determined to be therapeutic by screening using the screening known to those having ordinary skill in the art. A “known therapeutic compound”, “drug”, or “medication” refers to a therapeutic compound that has been shown (e.g., through animal trials or prior experience with administration to humans) to be effective in such treatment. A “therapeutic regimen” relates to a treatment comprising a “drug”, “medication”, “therapeutic”, “active agent”, “therapeutic compound”, “composition”, or “compound” as disclosed herein and/or a treatment comprising behavioral modification by the subject and/or a treatment comprising a surgical means.

[00197] All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. The references cited herein are not admitted to be prior art to the claimed invention. In the case of conflict, the present Specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be limiting.

[00198] Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. The references cited herein are not admitted to be prior art to the claimed invention. In the case of conflict, the present Specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be limiting.

[00199] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this application belongs and as commonly used in the art to which this application belongs; such art is incorporated by reference in its entirety.

[00200] Any of the above aspects and embodiments can be combined with any other aspect or embodiment as disclosed in the Summary, and/or in the Detailed Description sections. REFERENCES

[00201] Rogus J, Beck JD, Offenbacher S, et al. IL1B gene promoter haplotype pairs predict clinical levels of interleukin-lbeta and C-reactive protein. Hum Genet 2008; 123:387-398. [00202] Tanaka et al. Targeting of Interleukin-6 for the Treatment of Rheumatoid Arthritis: A Review and Update. Rheumatol Curr Res 2013, S4 (DOI: 10.4172/2161-1149. S4-002). Zhang et al. he cytokine release syndrome (CRS) of severe COVID-19 and Interleukin-6 receptor (IL-6R) antagonist Tocilizumab may be the key to reduce the mortality. Int. J. Antimicrob. Agents 2020; doi: 10.1016/j.ijantimicag.2020.105954.

[00203] Pedersen, S. F. SARS-CoV-2:AStorm isRaging. J. Clin. Invest. (March 2020); doi.org/10.1172/JCI137647.

[00204] Conti, P. et al. Induction of pro-inflammatory cytokines (IL-1 and IL-6) and lung inflammation by Coronavirus-19 (COVI-19 or SARS-CoV-2): anti-inflammatory strategies. J Biol Regul Homeost Agents. 2020 Mar 14;34(2). pii: 1. doi: 10.23812/CONTI-E.

[00205] Chen, G. et al. Clinical and immunologic features in severe and moderate Coronavirus Disease 2019. J. Clin. Invest. (March 2020); doi.org/10.1172/JCI137244.

[00206] Wong, CK. et al. Plasma inflammatory cytokines and chemokines in severe acute respiratory syndrome. Clin Exp Immunol 2004; 136: 95-103.

[00207] Zhang, W. et al. The use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 2019 (COVID-19): The Perspectives of clinical immunologists from China. Clin Immunol. 2020 Mar 25;214: 108393.

[00208] Lau, SK. et al. Delayed induction of proinflammatory cytokines and suppression of innate antiviral response by the novel Middle East respiratory syndrome coronavirus: implications for pathogenesis and treatment. J Gen Virol. 2013;94(Pt 12):2679-2690.

[00209] Huang, C. et al. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020 Feb 15;395(10223):497-506.

[00210] Verit, R. et al. Estimates of the severity of coronavirus disease 2019: A model-based analysis. The Lancet (March 2020): doi.org/ 10.1016/S1473-3099(2)30243-7. EXAMPLES

Example 1: IL-Ib haplotype in an African heritage population with COVID-19 critical illness [00211] Patients presenting to the emergency room and admitted to the hospital with severe COVID-19 symptoms were genotyped for IL-Ib haplotype. The entire cohort consisted of 60 individuals. As the hospital was located in a predominantly African American community, 39 of these 60 individuals self-identified as African American (African heritage), 19 as Caucasian, and 2 as Asian.

[00212] FIG. 1 shows the frequency of L-Ib haplotype in the 39 African heritage individuals, as a percentage of the normal population frequency of the haplotype. Normal allele carriage frequencies in African heritage individuals were calculated from the Atherosclerosis Risk in Communities (ARIC) study database, which had 227 individuals self-identified as African American using NIH criteria. As shown in FIG. 1, African heritage patients with the B4 haplotype were expected to have a B4 population frequency at “1,” based on carriage of the allele in the ARIC population, which were not selected as having severe COVID-19. B4 is associated with the strongest IL-1 promoter in with vitro studies of promoter strength. Instead, patients admitted with COVID-19 had a B4 haplotype frequency above population frequency, which indicates that in these B4 individual COVID-19 signs and symptoms likely appeared earlier, and were more severe than in individuals carrying other IL-Ib haplotypes.

[00213] The B2, which is associated with the lowest levels IL-1 production in with vitro studies, also showed a strong negative correlation with severe COVID-19. As seen in FIG. 1, African heritage patients with severe COVID-19 had a B2 haplotype frequency that was substantially lower than the B2 haplotype frequency in the African heritage general population, as calculated using the ARIC study data.

[00214] Bl, B2 , B3 and B4 haplotypes are described, for example, in US Patent No.

9347090, and Rogus 2008. Example 2: IL-Ib haplotype in an African American population with Cytokine Release Syndrome

[00215] The initial cohort of 60 patients was tracked to see what proportion developed cytokine release syndrome (CRS, sometimes also referred to as cytokine storm syndrome, or CSS). The results are shown in FIG. 2 with respect to African heritage patients.

[00216] Of the 39 African heritage patients that presented with severe COVID-19, 30 of the 39 were B4 carriers. Of the B4 carriers, 80% went on to develop CRS. B4 carriers were both more likely to develop severe COVID-19 symptoms, i.e. symptoms severe enough to require hospitalization, and to develop cytokine release syndrome, than predicted by the carriage of the B4 allele in the general population. In contrast, B2 carriers developed cytokine storm less frequently than would be predicted by B2 allele carriage in the general population (0.211 in the population, versus 0.125 developing CSS, as seen in FIG. 2).

[00217] The 19 Caucasian individuals presenting with severe COVID-19 were also followed. Of these 19, 11 developed cytokine storm. Intriguingly, the only 2 Caucasian individuals carrying the B4 haplotype developed cytokine storm, which supports the link between high IL-1 production and severe COVID-19, and cytokine storm.

OTHER EMBODIMENTS

[00218] While the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.

Claims

CLAIMS What is claimed is:

1. A method of reducing a risk of developing severe COVID-19 symptoms or cytokine release syndrome (CRS) associated with COVID-19, comprising: a. identifying a subject who has or is at risk of developing COVID-19; b. obtaining information regarding the subject’s single nucleotide polymorphism (SNP) alleles for: i. each of the rsl7561 polymorphic locus, the rsl6944 polymorphic locus and the rsl 143634 polymorphic locus; ii. each of the rsl 6944 polymorphic locus, the rsl 143623 polymorphic locus and the rs4848306 polymorphic locus; or iii. each of the rsl7561 polymorphic locus, the rsl6944 polymorphic locus the rsl 143634 polymorphic locus, the rsl 143623 polymorphic locus and the rs4848306 polymorphic locus; c. diagnosing the subject as having a positive IL-1 genotype pattern obtained in (b) if the IL-1 genotype of the subject is selected from the group consisting of: i. T/T or T/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl6944 and T/T or T/C at rsl 143634; ii. G/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl 6944 and C/C, T/T, C/T or T/C at rsl 143634; iii. G/G, T/T, G/T or T/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl 6944 and C/C at rsl 143634; iv. T/T or T/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl 6944 and T/T or T/C at rsl 143634; v. G/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl 6944 and C/C, T/T, C/T or T/C at rsl 143634; vi. G/G, T/T, G/T or T/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl6944 and C/C at rsl 143634; vii. T/T or T/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl 6944 and T/T or T/C at rsl 143634; viii. G/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; ix. G/G, T/T, G/T or T/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl 6944 and C/C at rsl 143634; x. T/T or T/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl 6944 and T/T or T/C at rsl 143634; xi. G/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; xii. G/G, T/T, G/T or T/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl 6944 and C/C at rsl 143634; xiii. T/T or T/G at rsl7561, C/C at rsl6944 and T/T/ or T/C at rsl 143634; xiv. G/G at rsl7561, C/C at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; xv. G/G, T/T, G/T or T/G at rsl7561, C/C at rsl6944 and C/C at rsl 143634 xvi. T/T or T/G at rsl7561, C/T at rsl6944 and T/T or T/C at rsl 143634; xvii. C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl6944; xviii. C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl 6944; xix. C/C at rs4848306, C/G at rsl 143623, C/T at rsl 6944; and xx. C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944; and d. administering an inflammation inhibitor to the subject diagnosed with a positive

IL-1 genotype pattern in step (c), thereby reducing the risk of the subject for developing CRS associated with

COVID-19.

2. A method of reducing the severity of COVID-19 symptoms or cytokine release syndrome (CRS) induced by COVID-19, comprising: a. identifying a subject who has or is at risk of developing COVID-19; b. obtaining information regarding the subject’s single nucleotide polymorphism (SNP) alleles for: i. each of the rsl7561 polymorphic locus, the rsl6944 polymorphic locus and the rsl 143634 polymorphic locus; ii. each of the rs 16944 polymorphic locus, the rsl 143623 polymorphic locus and the rs4848306 polymorphic locus; or iii. each of the rsl7561 polymorphic locus, the rsl6944 polymorphic locus the rsl 143634 polymorphic locus, the rsl 143623 polymorphic locus and the rs4848306 polymorphic locus; c. diagnosing the subject as having a positive IL-1 genotype pattern obtained in (b) if the IL-1 genotype of the subject is selected from the group consisting of: i. T/T or T/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl6944 and T/T or T/C at rsl 143634; ii. G/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl 6944 and C/C, T/T, C/T or T/C at rsl 143634; iii. G/G, T/T, G/T or T/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl 6944 and C/C at rsl 143634; iv. T/T or T/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl 6944 and T/T or T/C at rsl 143634; v. G/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl 6944 and C/C, T/T, C/T or T/C at rsl 143634; vi. G/G, T/T, G/T or T/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl6944 and C/C at rsl 143634; vii. T/T or T/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl 6944 and T/T or T/C at rsl 143634; viii. G/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; ix. G/G, T/T, G/T or T/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl 6944 and C/C at rsl 143634; x. T/T or T/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl 6944 and T/T or T/C at rsl 143634; xi. G/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; xii. G/G, T/T, G/T or T/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl 6944 and C/C at rsl 143634; xiii. T/T or T/G at rsl7561, C/C at rsl6944 and T/T/ or T/C at rsl 143634; xiv. G/G at rsl7561, C/C at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; xv. G/G, T/T, G/T or T/G at rsl7561, C/C at rsl6944 and C/C at rsl 143634 xvi. T/T or T/G at rsl7561, C/T at rsl6944 and T/T or T/C at rsl 143634; xvii. C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl6944; xviii. C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl 6944; xix. C/C at rs4848306, C/G at rsl 143623, C/T at rsl 6944; and xx. C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944; and d. administering an inflammation inhibitor to the subject diagnosed with a positive IL-1 genotype pattern in step (c), thereby reducing the severity of the CRS in the subject.

3. A method of treating COVID-19 in a subject, comprising: a. identifying a subject who has or is at risk of developing COVID-19; b. obtaining information regarding the subject’s single nucleotide polymorphism (SNP) alleles for: i. each of the rsl7561 polymorphic locus, the rsl6944 polymorphic locus and the rsl 143634 polymorphic locus; ii. each of the rsl 6944 polymorphic locus, the rsl 143623 polymorphic locus and the rs4848306 polymorphic locus; or iii. each of the rsl7561 polymorphic locus, the rsl6944 polymorphic locus the rsl 143634 polymorphic locus, the rsl 143623 polymorphic locus and the rs4848306 polymorphic locus; c. diagnosing the subject as having a positive IL-1 genotype pattern obtained in (b) if the IL-1 genotype of the subject is selected from the group consisting of: i. T/T or T/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl6944 and T/T or T/C at rsl 143634; ii. G/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl 6944 and C/C, T/T, C/T or T/C at rsl 143634; iii. G/G, T/T, G/T or T/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl 6944 and C/C at rsl 143634; iv. T/T or T/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl 6944 and T/T or T/C at rsl 143634; v. G/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl 6944 and C/C, T/T, C/T or T/C at rsl 143634; vi. G/G, T/T, G/T or T/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl6944 and C/C at rsl 143634; vii. T/T or T/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl 6944 and T/T or T/C at rsl 143634; viii. G/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; ix. G/G, T/T, G/T or T/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl 6944 and C/C at rsl 143634; x. T/T or T/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl 6944 and T/T or T/C at rsl 143634; xi. G/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; xii. G/G, T/T, G/T or T/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl 6944 and C/C at rsl 143634; xiii. T/T or T/G at rsl7561, C/C at rsl6944 and T/T/ or T/C at rsl 143634; xiv. G/G at rsl7561, C/C at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; xv. G/G, T/T, G/T or T/G at rsl7561, C/C at rsl6944 and C/C at rsl 143634 xvi. T/T or T/G at rsl7561, C/T at rsl6944 and T/T or T/C at rsl 143634; xvii. C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl6944; xviii. C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl 6944; xix. C/C at rs4848306, C/G at rsl 143623, C/T at rsl 6944; and xx. C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944; and d. administering an inflammation inhibitor, a COVID-19 therapy or a combination thereof, to the subject diagnosed with a positive IL-1 genotype pattern in step (c), thereby treating the CRS from COVID-19.

4. The method of any one of claims 1-3, wherein step (c) comprises diagnosing the subject as having a positive IL-1 genotype pattern obtained in (b) if the IL-1 genotype of the subject is selected from the group consisting of: xxi. any allele at rsl7561, C/C at rs4848306, G/G at rsl 143623, C/T at rsl6944, and any allele at rsl 143634; xxii. any allele at rsl7561, C/T at rs4848306, G/G at rsl 143623, C/C at rsl6944, and any allele at rsl 143634; xxiii. any allele at rsl7561, C/C at rs4848306, G/C at rsl 143623, C/T at rsl6944, and any allele at rsl 143634; xxiiv. any allele at rsl7561, C/C at rs4848306, G/G at rsl 143623, C/C at rsl6944, and any allele at rsl 143634; xxv. T/G or T/T at rsl7561, C/T at rs4848306, G/G at rsl 143623, C/T at rsl6944, and T/C or T/T at rsl 143634; xxvi. T/G or T/T at rsl7561, C/C at rs4848306, C/G at rsl 143623, T/T at rsl6944, and T/C or T/T at rsl 143634; and xxvii. T/G or T/T at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944, and T/C or T/T at rsl 143634.

5. The method of any one of claims 1-4, wherein the subject has tested positive for severe acute respiratory syndrome coronavirus (SARS-CoV-2).

6. The method of any one of claims 1-4, wherein the subject is known, or is suspected, to have been exposed to SARS-CoV-2.

7. The method of any one of claims 1-6, further comprising measuring at least one biomarker associated with the development of CRS.

8. The method of claim 7, wherein the at least one biomarker is selected from the group consisting of C-C motif chemokine ligand 20 (CCL20), Prostaglandin E2 (PGE2), interleukin 1 (IL-1), interleukin-2 (IL-2), IL-2R, interferon gamma (IFNy), interleukin 5 (IL-5), interleukin 6 (IL-6), interleukin 10 (IL-10), tumor necrosis factor alpha (TNFa), monocyte chemoattractant protein- 1 (MCP-1), interleukin 6 signal transducer (gpl30), Fms-related tyrosine kinase 3 ligand (Flt3L), C-X3-C motif chemokine ligand 1 (CX3CL1), colony stimulating factor 2 (CSF), alanine aminotransferase (ALT), aspartate aminotransferase (ART), lactate dehydrogenase (LDH), C-reactive protein (CRP), ferritin, and D-dimer.

9. The method of claim 7, wherein the at least one biomarker is selected from the group consisting of CCL20, PGE2, IL-2, IL-2R, IL-6, IL-10, TNFa, ALT, ART, LDH, CRP, ferritin, and D-dimer.

10. The method of any one of claims 7-9, wherein the at least one biomarker comprises a two-cytokine max fold change of at least 75 fold each, a one cytokine max fold change of at least 250, a C-reactive protein level of greater than or equal to 200 mg/L, or a combination thereof.

11. The method of claim 10, wherein the cytokine is selected from the group consisting of IL-1, IL-2, IL-2R, PTNGg, IL-5, IL-6, IL-10, TNFa, MCP-1, gpl30, Flt3L, CX3CL1 and CSF.

12. The method of any one of claims 1-11, wherein the inflammation inhibitor is administered prior to the manifestation of COVID-19 symptoms.

13. The method of any one of claims 1-11, wherein the inflammation inhibitor is administered after the manifestation of initial COVID-19 symptoms but prior to the onset of CRS.

14. The method of claim 13, wherein the initial COVID-19 symptoms comprise one or more of fever, cough, fatigue or myalgia.

15. The method of any one of claims 1-11, wherein the inflammation inhibitor is administered after or concurrent with the onset of CRS.

16. The method of any one of claims 1-15, wherein the inflammation inhibitor is an IL-1 inhibitor.

17. The method of claim 16, wherein the IL-1 inhibitor comprises an inflammasome modulator.

18. The method of claim 17, wherein the inflammasome modulator can cross the blood brain barrier.

19. The method of claim 17, wherein the inflammasome modulator comprises Diacerein, Sarei-To, Binimetinib, Can-04, Rilonacept, XL- 130, Givinostat or Ammonium trichloro- tellurate.

20. The method of claim 16, wherein the IL-1 inhibitor is an IL-la inhibitor or an IL-Ib inhibitor.

21. The method of claim 20, wherein the IL-la inhibitor is selected from the group consisting of Bermekimab, ABT-981, Isunakinra, AC-701, Sairei-To, Can-04, XL-130, a MABpl antibody and Givinostat.

22. The method of claim 20, wherein the IL-Ib inhibitor is selected from the group consisting of ABT-981, Anakinra, Anakinra Biosimilar, APX-002, binimetinib, CAN-04, Diacerein, DLX-2681, Givinostat, Isunakinra, Rilonacept, SER-140, XL-130, Gevokizumab, Can-04, a DOM4-130-201 antibody, DOM4-130-202 antibody and Canakinumab.

23. The method of any one of claims 1-15, wherein the inflammation inhibitor is an IL-6 inhibitor.

24. The method of claim 22, wherein the IL-6 inhibitor comprises Tocilizumab, Siltuximab, Sarilumab, Olokizumab, Elsilimomab, Sirukimab, Levilimab, ALX-0061, Gerilimzumab, FE301 or FM101.

25. The method of any one of claims 1-15, wherein the inflammation inhibitor comprises a Granulocyte-macrophage colony-stimulating factor (GM-CSF) inhibitor.

26. The method of claim 25, wherein the GM-CSF inhibitor comprises Namilumab, Lenzilumab, MOR103, MORab002, Mavrilimumab,or Otilimab.

27. The method of any one of claims 1-15, wherein the inflammation inhibitor comprises a Janus Kinase (JAK) inhibitor.

28. The method of claim 27, wherein the JAK kinase inhibitor comprises Tofacitinib or Baricitinib.

29. The method of any one of claims 3-28, wherein the COVID-19 therapy comprises an antibody therapy.

30. The method of claim 29, wherein the antibody therapy comprises a C5 or C5a antagonist.

31. The method of claim 30, wherein the antibody comprises Ravulizumab, Ravulizumab- cwvz, Eculizumab, or Vilobelimab.

32. The method of claim 29, wherein the antibody therapy comprises an antibody to a SARS- CoV-2 viral protein.

33. The method of claim 32, wherein the antibody comprises Casirivimab, Imdevimab, Bamlanivimab, or Etesevimab.

34. The method of any one of claims 1-33, wherein the inflammation inhibitor prevents a sign or a symptom of the CRS.

35. The method of any one of claims 1-33, wherein the inflammation inhibitor reduces a sign or a symptom of the CRS.

36. The method of any one of claims 1-35, wherein the inflammation inhibitor prevents a sign or a symptom of COVID-19.

37. The method of any one of claims 1-35, wherein the inflammation inhibitor reduces a sign or symptom of COVID-19.

38. The method of any one of claims 34-37, wherein the sign or symptom of CRS comprises fever, tachycardia, tachypnea, hypoxia, hypotension, coagulopathy, hypoalbuminemia, hypoproteinemia, respiratory failure, refractory shock, multi-organ failure, two cytokine max fold changes of at least 75, one cytokine max fold change of at least 250, a C- reactive protein level of greater than or equal to 200 mg/L or a combination thereof.

39. The method of claim 38, wherein the cytokine comprises IL-1, IL-2, IL-2R, IFNy, IL-5, IL-6, IL-10, TNFa, MCP-1, gpl30, Flt3L, CX3CL1 or CSF.

40. The method of claim 38, wherein the cytokine comprises IL-2, IL-6, IL-10 or TNFa.

41. The method of any one of claims 1-40, wherein the inflammation inhibitor reduces a level of one or more biomarkers selected from the group consisting of CCL20, PGE2, IL- 1, IL-2, IL-2R, PTNGg, IL-5, IL-6, IL-10, TNFa, MCP-1, gpl30, Flt3L, CX3CL1) CSF, alanine aminotransferase, lactate dehydrogenase, C-reactive protein (CRP), ferritin, and D-dimer, in the subject.

42. The method of any one of claims 1-41, wherein the inflammation inhibitor reduces a level of a pro-inflammatory cytokine in the subject.

43. The method of claim 42, wherein the pro-inflammatory cytokine is IL-la, IL-Ib or IL-6

44. A method of predicting a risk of, or predisposition to, hospitalization because of, or developing cytokine release syndrome (CRS) associated with COVID-19 in a subject, comprising: a. identifying a subject who has or is at risk of developing COVID-19; b. obtaining information regarding the subject’s single nucleotide polymorphism (SNP) alleles for: i. each of the rsl7561 polymorphic locus, the rsl6944 polymorphic locus and the rsl 143634 polymorphic locus; ii. each of the rsl 6944 polymorphic locus, the rsl 143623 polymorphic locus and the rs4848306 polymorphic locus; or iii. each of the rsl7561 polymorphic locus, the rsl6944 polymorphic locus the rsl 143634 polymorphic locus, the rsl 143623 polymorphic locus and the rs4848306 polymorphic locus; and c. diagnosing the subject as having a positive IL-1 genotype pattern obtained in (b) if the IL-1 genotype of the subject is selected from the group consisting of: i. T/T or T/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl6944 and T/T or T/C at rsl 143634; ii. G/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl 6944 and C/C, T/T, C/T or T/C at rsl 143634; iii. G/G, T/T, G/T or T/G at rsl7561, C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rs 16944 and C/C at rsl 143634; iv. T/T or T/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl 6944 and T/T or T/C at rsl 143634; v. G/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl 6944 and C/C, T/T, C/T or T/C at rsl 143634; vi. G/G, T/T, G/T or T/G at rsl7561, C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl6944 and C/C at rsl 143634; vii. T/T or T/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl 6944 and T/T or T/C at rsl 143634; viii. G/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; ix. G/G, T/T, G/T or T/G at rsl7561, C/C at rs4848306, C/G at rsl 143623, C/T at rsl 6944 and C/C at rsl 143634; x. T/T or T/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl 6944 and T/T or T/C at rsl 143634; xi. G/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; xii. G/G, T/T, G/T or T/G at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl 6944 and C/C at rsl 143634; xiii. T/T or T/G at rsl7561, C/C at rsl6944 and T/T/ or T/C at rsl 143634; xiv. G/G at rsl7561, C/C at rsl6944 and C/C, T/T, C/T or T/C at rsl 143634; xv. G/G, T/T, G/T or T/G at rsl7561, C/C at rsl6944 and C/C at rsl 143634; xvi. T/T or T/G at rsl7561, C/T at rsl6944 and T/T or T/C at rsl 143634; xvii. C/C, T/T, C/T or T/C at rs4848306, G/G at rsl 143623, C/C at rsl6944; xviii. C/C or C/T at rs4848306, G/G at rsl 143623, C/T at rsl 6944; xix. C/C at rs4848306, C/G at rsl 143623, C/T at rsl 6944; and xx. C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944; thereby predicting the risk of or predisposition to developing cytokine release syndrome (CRS) associated with COVID-19 in the subject.

45. The method of claim 44, wherein step (c) comprises diagnosing the subject as having a positive IL-1 genotype pattern obtained in (b) if the IL-1 genotype of the subject is selected from the group consisting of: xxi. any allele at rsl7561, C/C at rs4848306, G/G at rsl 143623, C/T at rsl6944, and any allele at rsl 143634; xxii. any allele at rsl7561, C/T at rs4848306, G/G at rsl 143623, C/C at rsl6944, and any allele at rsl 143634; xxiii. any allele at rsl7561, C/C at rs4848306, G/C at rsl 143623, C/T at rsl6944, and any allele at rsl 143634; xxiv. any allele at rsl7561, C/C at rs4848306, G/G at rsl 143623, C/C at rsl6944, and any allele at rsl 143634; xxv. T/G or T/T at rsl7561, C/T at rs4848306, G/G at rsl 143623, C/T at rsl6944, and T/C or T/T at rsl 143634; xxvi. T/G or T/T at rsl7561, C/C at rs4848306, C/G at rsl 143623, T/T at rsl6944, and T/C or T/T at rsl 143634; and xxvii. T/G or T/T at rsl7561, C/C at rs4848306, G/G at rsl 143623, T/T at rsl6944, and T/C or T/T at rsl 143634.

46. The method of claim 44 or 45, wherein the subject has tested positive for SARS-CoV-2.

47. The method of claim 44 or 45, wherein the subject is known, or is suspected, to have been exposed to SARS-CoV-2.

48. The method of any one of claims 44-47, further comprising measuring at least one biomarker associated with the development of CRS.

49. The method of claim 48, wherein the at least one biomarker is selected from the group consisting of C-C motif chemokine ligand 20 (CCL20), Prostaglandin E2 (PGE2), interleukin 1 (IL-1), interleukin-2 (IL-2), IL-2R, interferon gamma (IFNy), interleukin 5 (IL-5), interleukin 6 (IL-6), interleukin 10 (IL-10), tumor necrosis factor alpha (TNFa), monocyte chemoattractant protein- 1 (MCP-1), interleukin 6 signal transducer (gpl30), Fms-related tyrosine kinase 3 ligand (Flt3L), C-X3-C motif chemokine ligand 1 (CX3CL1), colony stimulating factor 2 (CSF), alanine aminotransferase (ALT), aspartate aminotransferase (ART), lactate dehydrogenase (LDH), C-reactive protein (CRP), ferritin, and D-dimer.

50. The method of claim 48, wherein the at least one biomarker is selected from the group consisting of CCL20, PGE2, IL-2, IL-2R, IL-6, IL-10, TNFa, ALT, ART, LDH, CRP, ferritin, and D-dimer.

51. The method of any one of claims 48-50, wherein the at least one biomarker comprises a two-cytokine max fold change of at least 75 fold each, a one cytokine max fold change of at least 250, a C-reactive protein level of greater than or equal to 200 mg/L, or a combination thereof.

52. The method of claim 51, wherein the cytokine is selected from the group consisting of IL-1, IL-2, IL-2R, PTNGg, IL-5, IL-6, IL-10, TNFa, MCP-1, gpl30, Flt3L, CX3CL1 and CSF.

53. The method of any one of claims 44-52, further comprising administering an inflammation inhibitor, a COVID-19 therapy, or a combination thereof.

54. The method of claim 53, wherein the inflammation inhibitor is administered prior to the manifestation of COVID-19 symptoms.

55. The method of claim 53, wherein the inflammation inhibitor is administered after the manifestation of initial COVID-19 symptoms but prior to the onset of CRS.

56. The method of claim 55, wherein the initial COVID-19 symptoms comprise one or more of fever, cough, fatigue or myalgia.

57. The method of claim 53, wherein the inflammation inhibitor is administered after or concurrent with the onset of CRS.

58. The method of any one of claims 53-57, wherein the inflammation inhibitor is an IL-1 inhibitor.

59. The method of claim 58, wherein the IL-1 inhibitor comprises an inflammasome modulator.

60. The method of claim 59, wherein the inflammasome modulator can cross the blood brain barrier.

61. The method of claim 59, wherein the inflammasome modulator comprises Diacerein, Sarei-To, Binimetinib, Can-04, Rilonacept, XL- 130, Givinostat or Ammonium trichloro- tellurate.

62. The method of claim 58, wherein the IL-1 inhibitor is an IL-la inhibitor or an IL-Ib inhibitor.

63. The method of claim 62, wherein the IL-la inhibitor is selected from the group consisting of Bermekimab, ABT-981, Isunakinra, AC-701, Sairei-To, Can-04, XL-130, a MABpl antibody and Givinostat.

64. The method of claim 62, wherein the L-Ib inhibitor is selected from the group consisting of ABT-981, Anakinra, Anakinra Biosimilar, APX-002, binimetinib, CAN-04, Diacerein, DLX-2681, Givinostat, Isunakinra, Rilonacept, SER-140, XL-130, Gevokizumab, Can- 04, a DOM4-130-201 antibody, DOM4-130-202 antibody and Canakinumab.

65. The method of any one of claims 53-57, wherein the inflammation inhibitor is an IL-6 inhibitor.

66. The method of claim 65, wherein the IL-6 inhibitor comprises Sarilumab Tocilizumab, Siltuximab, Olokizumab, Elsilimomab, Sirukimab, Levilimab, ALX-0061,

Gerilimzumab, FE301 or FMlOl.

67. The method of any one of claims 53-57, wherein the inflammation inhibitor comprises a Granulocyte-macrophage colony-stimulating factor (GM-CSF) inhibitor.

68. The method of claim 67, wherein the GM-CSF inhibitor comprises Namilumab, Lenzilumab, MOR103, MORab002, Mavrilimumab,or Otilimab.

69. The method of any one of claims 53-57, wherein the inflammation inhibitor comprises a Janus Kinase (JAK) inhibitor.

70. The method of claim 69, wherein the JAK kinase inhibitor comprises Tofacitinib or Baricitinib.

71. The method of any one of claims 53-70, wherein the COVID-19 therapy comprises an antibody therapy.

72. The method of claim 71, wherein the antibody therapy comprises a C5 or C5a antagonist.

73. The method of claim 72, wherein the antibody comprises Ravulizumab, Ravulizumab- cwvz, Eculizumab, or Vilobelimab.

74. The method of claim 71, wherein the antibody therapy comprises an antibody to a SARS- CoV-2 viral protein.

75. The method of claim 74, wherein the antibody comprises Casirivimab, Imdevimab, Bamlanivimab, or Etesevimab.

76. The method of any one of claims 44-75, wherein the inflammation inhibitor prevents a sign or a symptom of the CRS.

77. The method of any one of claims 44-76, wherein the inflammation inhibitor reduces a sign or a symptom of the CRS.

78. The method of any one of claims 44-77, wherein the inflammation inhibitor prevents a sign or a symptom of COVID-19.

79. The method of any one of claims 44-78, wherein the inflammation inhibitor reduces a sign or symptom of COVID-19.

80. The method of any one of claims 76-79, wherein the sign or symptom of CRS comprises fever, tachycardia, tachypnea, hypoxia, hypotension, coagulopathy, hypoalbuminemia, hypoproteinemia, respiratory failure, refractory shock, multi-organ failure, two cytokine max fold changes of at least 75, one cytokine max fold change of at least 250, a C- reactive protein level of greater than or equal to 200 mg/L or a combination thereof.

81. The method of claim 80, wherein the cytokine comprises IL-1, IL-2, IL-2R, IFNy, IL-5, IL-6, IL-10, TNFa, MCP-1, gpl30, Flt3L, CX3CL1 or CSF.

82. The method of claim 80, wherein the cytokine comprises IL-2, IL-6, IL-10 or TNFa.

83. The method of any one of claims 44-82, wherein the inflammation inhibitor reduces a level of one or more biomarkers selected from the group consisting of CCL20, PGE2, IL- 1, IL-2, IL-2R, PTNGg, IL-5, IL-6, IL-10, TNFa, MCP-1, gp!30, Flt3L, CX3CL1) CSF, alanine aminotransferase, lactate dehydrogenase, C-reactive protein (CRP), ferritin, and D-dimer, in the subject.

84. The method of any one of claims 44-83, wherein the inflammation inhibitor reduces a level of a pro-inflammatory cytokine in the subject.

85. The method of claim 84, wherein the pro-inflammatory cytokine is IL-la, IL-Ib or IL-6.