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Leading Edge

Commentary
A Global Effort to Define the Human Genetics
of Protective Immunity to SARS-CoV-2 Infection
Jean-Laurent Casanova1,2,3,4,5,*, Helen C. Su6, and the COVID Human Genetic Effort
1St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller Unversity, New York, NY, USA
2Howard Hughes Medical Institute, New York, NY, USA
3Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France
4University of Paris, Imagine Institute, Paris, France
5Pediatric Hematology and Immunology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
6Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases,

National Institutes of Health, Bethesda, MD, USA


*Correspondence: casanova@rockefeller.edu
https://doi.org/10.1016/j.cell.2020.05.016

SARS-CoV-2 infection displays immense inter-individual clinical variability, ranging from silent infection to le-
thal disease. The role of human genetics in determining clinical response to the virus remains unclear. Studies
of outliers—individuals remaining uninfected despite viral exposure and healthy young patients with life-
threatening disease—present a unique opportunity to reveal human genetic determinants of infection and
disease.

There are seven known human-tropic co- identification of advanced age and co- than dizygotic twins. Adoption studies
ronaviruses (CoV), three of which have morbidities as major risk factors is clini- have shown that early death from any
caused severe epidemics. These three cally important and suggests that the type of infection is paradoxically corre-
RNA viruses—SARS-CoV-1 (discovered decline of the body weakens immunity, lated with early death from infection of
in 2002), MERS-CoV (2012), and SARS- which may be difficult to translate into the biological but not the foster parents.
CoV-2 (2019)—are much more virulent molecular, cellular, and immunolog- Finally, susceptibility to various infectious
than the other four (HCoV-229E, HCoV- ical terms. diseases has been shown, particularly by
NL63, HCoV-OC43, HCoV-HKU1), which However, there is also a more perplex- segregation studies, to be heritable and to
cause common colds and only rare cases ing, but perhaps less difficult, problem. reflect the impact of a major gene.
of severe disease, including pneumonia. Why are previously healthy children, ado- Since 1950, genetic and molecular
In 2002, SARS-CoV-1 caused an lescents, young, or middle-aged adults studies have provided an immunological
epidemic limited to China. In 2012, being admitted to intensive care for respi- basis for inherited predispositions to in-
MERS-CoV caused an epidemic that ratory failure, encephalitis, or Kawasaki fectious diseases. Patient- and family-
began in Saudi Arabia, subsequently disease, due to COVID-19? Why would a based studies led to the discovery of
spreading primarily in the Middle East 40-year-old man who completed a mara- autosomal recessive neutropenia and X-
before containment. SARS-CoV-2 was thon in October 2019 find himself intu- linked recessive agammaglobulinemia.
first detected in China in 2019, but has bated and ventilated for COVID-19 respi- These two seminal inborn errors of immu-
since become a devastating ongoing ratory failure in April 2020? The COVID nity appeared to be Mendelian, and the
global pandemic. Most SARS-CoV-2 in- Human Genetic Effort (https://www. pathophysiological mechanism of each
fections are asymptomatic or benign, covidhge.com/) proposes that previously was elucidated, providing proof of princi-
but SARS-CoV-2 infectious disease healthy, young patients with severe ple for genetic predisposition to human in-
2019 (COVID-19) can cause life-threat- COVID-19 carry causal genetic variants. fectious diseases. These and many other
ening disease, which typically begins This hypothesis is not yet supported by inborn errors of immunity are individually
with pneumonia. Severe COVID-19 oc- specific genetic epidemiological studies rare and underlie multiple, recurrent, and
curs much more frequently in patients of COVID-19, but it follows a long line of often unusual infections in individual pa-
over the age of 50 years and/or with co- classical genetic studies since 1905, tients. Since 1985, molecular genetics
morbid conditions such as pulmonary, relating to diverse infections in plants studies have confirmed these disorders
cardiovascular, and metabolic disorders and animals, including humans (Casa- to be Mendelian (monogenic with com-
(Figure 1). Life-threatening disease prob- nova and Abel, 2020). Three types of hu- plete clinical penetrance).
ably strikes less than 1 in 1,000 infected man genetic epidemiological studies These studies launched a painstaking
individuals below the age of 50 without merit specific comment. Twin studies mission to decipher the genetic basis of
underlying conditions but more than 1 in have shown that concordance rates for susceptibility to infections in humans,
10 infected patients over the age of 80 some infectious diseases, such as tuber- from the individual to whole-population
years with multiple comorbidities. The culosis, are much higher for monozygotic levels. This genetic patient-by-patient,

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Commentary

Figure 1. Monogenic Causes of Susceptibility or Resistance to SARS-CoV-2 Infection


In the naive general population (black), a proportion of people become symptomatic (purple) when infected. Severe cases (red) tend to occur in the elderly or in
those patients having co-morbidities. However, rare ‘‘idiopathic’’ severe cases can occur in the young without co-morbidities, and these are hypothesized to
represent patients with monogenic causes. A proportion of people remain asymptomatic (blue) when infected. In some instances, these may be people who
remain resistant to infection (orange), who can be identified by their remaining seronegative despite heavy or repeated exposures to the virus. Created with
BioRender.

family-by-family, disorder-by-disorder Plasmodium falciparum malaria. With to clear hepatitis C virus spontaneously
approach was highly productive in the hindsight, this discovery told us more during primary infection.
few patients studied but seemed unlikely about the selective pressure imposed by We can hope that genome-wide
to deliver results of great significance for malaria on the Homo sapiens genome association studies for COVID-19 will
the general population. First, the pheno- than the mechanism by which individual generate results of similar or greater
type of multiple and familial infections is human genomes predispose to malaria. importance. Nevertheless, this approach
not observed in most people, who typi- It provided no significant explanation of is intrinsically limited by genetic and
cally display isolated and sporadic infec- malaria at the individual level, as it failed phenotypic heterogeneity and by the
tions. Second, populations consist of to explain why about 1 in 1,000 infected need for multiple testing corrections.
huge numbers of individuals, so defining children develops severe malaria, or 1 More importantly, statistical association
the population genetic architecture of in- in 10,000 sickle cell trait carriers. Further- studies do not provide mechanisms.
fectious diseases through causal ana- more, despite this initial breakthrough, the Without determining the chain of cause
lyses and genetics of individual cases is biometric approach fell short of its prom- and consequence, causality between
a Herculean task. A more tenable ise. Other association studies, whether a candidate genotype and a clinical
pathway from the population to the indi- genome-wide or candidate gene based, phenotype remains uncertain, no matter
vidual was proposed, based on associa- have not matched Allison’s discovery, how statistically probable. In human
tions and biometrics. in terms of effect size or proportion of medicine, establishing causality be-
The ambitious population-based bio- the variance explained. However, this tween genotype and phenotype requires
metrics approach to studying infectious approach did yield two important results the rigorous validation of mechanisms
diseases, initiated in the 1950s, highlights concerning viruses. Some HLA class I at the molecular, cellular, tissue, and
the persistent divide between Mendelian alleles are strongly associated with lower whole-organism levels. The genome of
geneticists and Galtonian biometricians. viral loads in the blood and slower disease the individual must explain the mecha-
The biometric approach began with a progression in individuals infected with nisms underlying severe COVID-19,
spectacular discovery when Anthony Alli- human immunodeficiency virus (HIV), and this requires in-depth biochemical
son found that the sickle cell trait provided and homozygotes for a type III IFN and immunological studies. Investigators
10-fold protection against severe forms of (IFNL3-IFNL4) haplotype are more likely have thus long been faced with the cruel

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Table 1. Monogenic Defects Underlying Narrow Susceptibility to Human Viral Diseases would encounter in the wild, but elucida-
tion of the underlying genotypes and
Outcome Pathogen (condition) Gene
mechanisms confirmed that the corre-
Susceptibility Influenza virus (severe pneumonia) IRF7
sponding gene products were probably
IRF9 essential for immunity to only a few infec-
TLR3 tious agents. Prior to these results, human
Rhinovirus (severe pneumonia) IFIH1 monogenic inborn errors of immunity
Herpes simplex virus 1 (encephalitis) UNC93B1 were considered to be rare, Mendelian
TLR3 disorders underlying recurrent, multiple,
TRIF and often unusual infections in individual
patients. After, the search for the molecu-
TRAF3
lar and cellular basis of human genetic
TBK1
susceptibility to isolated infections, rare
IRF3 or common, began in earnest.
SNORA31 Rare human ‘‘Mendelian infections’’
Herpes simplex virus 1, influenza virus, DBR1 had been recognized since the descrip-
norovirus (brainstem encephalitis) tion in 1946 of epidermodysplasia verruci-
Beta-papillomavirus (skin warts and cancer) TMC6 formis, an autosomal recessive predispo-
TMC8 sition to viral warts and cancer. However,
CIB1 they remained largely neglected until
Epstein-Barr virus (hemophagocytosis, SH2D1A
1996, when the first inborn error of immu-
lympho-proliferation, lymphoma, nity selectively underlying infectious dis-
XIAP
hypogammaglobulinemia) ease segregating in families as a Mende-
ITK
lian trait was molecularly deciphered
MAGT1 (Table 1). The first and best studied of
CD27 these conditions is Mendelian susceptibil-
CD70 ity to mycobacterial disease (MSMD),
Varicella-zoster virus (disseminated POLR3A caused by inborn errors of type II inter-
disease) POLR3C feron (IFN-g). Additionally, both Epstein-
Human herpes virus-8 (Kaposi sarcoma) TNFRSF4
Barr virus (EBV) and beta human papillo-
maviruses (beta HPV) are usually benign
Cytomegalovirus (disseminated disease) NOS2
but can cause a lethal disease that is
Hepatitis A virus (fulminant hepatitis) IL18BP
strictly Mendelian. Severe EBV-induced
Live-attenuated measles or yellow fever IFNAR1 disease can be caused by inborn errors
vaccine (disseminated disease) IFNAR2 that disrupt the killing of EBV-infected B
STAT2 cells by cytotoxic T and natural killer
IRF9 (NK) cells. These deficiencies affect the
Resistance Human immunodeficiency virus CCR5 collaboration between two major arms of
Norovirus FUT2
adaptive immunity. By contrast, epider-
modysplasia verruciformis results from
disruption of the EVER-CIB1-dependent
control of beta HPV in keratinocytes, a
dilemma of deeply understanding a sin- inbred mice. The protein encoded by deficiency of non-hematopoietic, cell-
gle patient through genetics or attempts Mx, a gene cloned by cell complementa- intrinsic immunity. Together with MSMD
at understanding the entire population tion, protects mice from influenza virus and two other fungal infections, these dis-
through biometrics. (Staeheli et al., 1986) and is potentially orders define the five known Mendelian
After 1996, the horizons of the field of relevant to COVID-19. Studies of infections.
inborn errors of immunity broadened, mycobacteria led to the first positional These studies paved the way for inves-
with discoveries of both Mendelian and cloning of a mouse gene, with the demon- tigation of other sporadic infectious dis-
non-Mendelian monogenic bases of in- stration that Nramp1 mutations render an- eases, testing the hypothesis that they
fectious diseases striking previously imals susceptible to mycobacteria (Vidal might be monogenic but not Mendelian.
healthy, seemingly immune competent et al., 1993). This hypothesis has been confirmed by
patients. This paradigm shift was inspired Unlike specific gene-targeting ap- molecular genetic studies, beginning
by two spectacular forward genetics proaches, these two studies focused on with viral diseases in 2007 (Zhang et al.,
studies in which the genetic bases of sus- mouse phenotypes suggestive of a nar- 2007). The first and best example is
ceptibility to influenza virus (Mx locus, row pattern of infection susceptibility. that of herpes simplex virus 1 (HSV-1) en-
1962) or Mycobacterium bovis BCG These laboratory mice were not chal- cephalitis, a sporadic disease caused, in
(Bcg locus, 1975) were characterized in lenged with as many microbes as they 5%–10% of cases, by mutations

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affecting the TLR3 or snoRNA31 path- brain, as for HSV-1 in patients with TLR3 heterogeneity (one causal locus per
ways (forebrain infection) or DBR1 (brain- mutations. kindred) and genetic homogeneity (a
stem infection) (Zhang et al., 2018). These COVID-19 is a completely new disease, causal locus in two or more kindreds)
mutations impair neuron-intrinsic immu- and the current pandemic dwarfs previ- are being tested in parallel. The large
nity to HSV-1 in the CNS. Other examples ous SARS-CoV-1 and MERS-CoV out- number of patients may facilitate the
more closely related to COVID-19 include breaks. We can, therefore, study newly in- detection of promising candidate geno-
influenza virus pneumonia, which can be fected patients on a massive scale, with types in single patients or families,
caused by inborn errors impairing antiviral minimal interference from vaccines, previ- including variants of known viral suscepti-
type I and III IFN immunity (IFN-a/b and ous related infections, and herd immunity, bility genes.
-l), including IRF7, IRF9, and TLR3 defi- in sharp distinction to influenza. COVID- More importantly, this initiative will also
ciencies, in circulating plasmacytoid den- 19 provides us with a tragic but unparal- detect genetic homogeneity, if the same
dritic cells and/or pulmonary epithelial leled opportunity to define precisely the gene is mutated in geographically distant
cells (Ciancanelli et al., 2015; Hernandez genetic requirements for the control of patients. The analysis and comparison of
et al., 2018; Lim et al., 2019), and rhino- an emerging, virulent, viral infection. The genetic variants from a large number of in-
virus pneumonia, which can be caused body makes use of the pleiotropic func- dividuals from diverse backgrounds will
by a deficiency of IFN-inducing MDA5 tions of many cells to control infection, be crucial, as we cannot solely rely on cur-
(Asgari et al., 2017; Lamborn et al., including subsets of pulmonary cells and rent databases of data for ‘‘healthy’’ indi-
2017). These disorders underlie severe leukocytes. Many genes are also pleio- viduals to identify rare variants, which
viral disease through the impairment of tropic. Genome-wide searches for candi- include individuals never before exposed
antiviral type I and/or III IFN immunity. date monogenic, or digenic, disorders to SARS-CoV-2. A large sample of ge-
Similar immunological scenarios, and should therefore be immunologically nomes may also facilitate the detection
even some of the same inborn errors, agnostic, testing diverse genetic hypothe- of a polygenic background for monogenic
could underlie severe pulmonary COVID- ses. Approaches should include search- mutations or the testing of polygenic sig-
19 in previously healthy young patients ing not only for highly penetrant rare vari- nals detected by other studies. Finally,
with monogenic disorders. In the absence ants but also for common variants that the inclusion of patients of diverse ances-
of known human genetic determinants of can be highly penetrant in specific infec- tries will make it possible to detect candi-
susceptibility to other coronaviruses, tions, as recently shown for a common date genotypes specific or common to
influenza is likely to provide the best com- monogenic etiology of tuberculosis (Ker- ancestries and to consider the evolu-
parison. The threshold levels of type I and/ ner et al., 2019). Moreover, highly pene- tionary forces driving variation at these
or III IFN for protection against SARS- trant monogenic disorders should not be loci (Quintana-Murci, 2019). Once candi-
CoV-2 might be similar to those for the considered only in children, as illustrated date genotypes have been identified, their
1918 influenza virus but higher than those by the death of a NOS2-deficient patient contribution to the pathogenicity of se-
for seasonal influenza. IFN-dependent over the age of 50 years from primary vere COVID-19 will be investigated with
control of the virus could be profoundly cytomegalovirus infection (Drutman in-depth molecular, cellular, and immuno-
impaired during initial infection in patients et al., 2020). Amid the uncertainties con- logical approaches. Studies of single pa-
with early-onset pneumonia, whereas cerning the genetic architecture of tients can be illuminating, but more
those whose condition deteriorates later COVID-19 suceptibility, only one thing is detailed mechanistic studies are required
could have milder IFN deficiency or almost certain: as for other infectious dis- for firm conclusions (Casanova et al.,
genetically determined excessive inflam- eases, there will be considerable genetic 2014). In these genetic studies, we aim
mation. For example, IL18BP mutations heterogeneity, reflecting the multiple to discover the pathogenesis of unex-
underlie fulminant viral hepatitis because layers of host defense that a virus must plained, severe COVID-19 in young, previ-
they unleash IL-18-dependent inflamma- overcome to lead to mortality. ously healthy patients.
tion in the liver, whereas SH2D1A To understand the genetic require- We anticipate that monogenic cases
mutations underlie hemophagocytosis ments for immune control of SARS-CoV- will provide insight into other types of
following B cell infection with EBV. Inborn 2, in February 2020, we began recruiting cases, such as severe COVID-19 in
errors could impair IFN immunity in leuko- COVID-19 patients from as many centers elderly patients with several comorbid
cytes or pulmonary cells or enhance local and countries as possible to the COVID conditions, suggesting novel therapeutic
or systemic inflammation. It will be inter- Human Genetic Effort. We target young possibilities for these patients. The patho-
esting to determine whether known inborn patients (<50 years) with life-threatening genesis may be similar in these patients,
errors of inflammation, such as defi- disease and no pre-existing medical with different causes converging on com-
ciencies of IL-1 or IL-6 immunity, protect conditions. Our initiative has been rapidly mon pathophysiological mechanisms. For
against severe forms of COVID-19. Inborn expanding, with a growing number of example, inborn errors of IFN-g and IL-
errors of cell-intrinsic immunity in the CNS centers that recruit patients, take clinical 17A/F immunity underlie mycobacteriosis
might be involved in the rarer neurological histories, and send blood samples to and candidiasis, respectively. The same
complications of COVID-19. The anosmia sequencing hubs. The exome and infections occur in patients with autoanti-
reported by some patients suggests that genome data are analyzed simulta- bodies against IFN-g and IL-17A/F, and in
SARS-CoV-2 may infect the olfactory neously locally at the hubs and centrally patients infected with HIV who have low
bulb, from which it may invade the fore- by the consortium. Hypotheses of genetic levels of IFN-g and IL-17A/F production

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Commentary

by CD4+ T cells, providing broader indica- countries with short memories. Infections Carrie Lucas, Davood Mansouri, Isabelle
tions for the therapeutic use of the corre- remain the only inevitable, unpredictable, Meyts, Joshua Milner, Trine Mogensen,
sponding cytokines. Thus, monogenic catastrophic medical threat to human- Tomohiro Morio, Lisa Ng, Luigi D. Notaran-
cases may clarify pathogenesis more kind. The idea that infections were a prob- gelo, Satoshi Okada, Tayfun Ozcelik, Pere
broadly for COVID-19 patients. Such clar- lem solved once and for all by Pasteur’s Soler Palacı́n, Anna Planas, Carolina
ification cannot easily be achieved by germ theory and the advances in hygiene, Prando, Anne Puel, Aurora Pujol, Claire
directly studying patients with acquired serotherapy, vaccination, aseptic sur- Redin, Laurent Renia, Jose Carlos Rodri-
immunodeficiencies, due to the many gery, and anti-infectious drug treatments guez Gallego, Lluis Quintana-Murci, Va-
confounding factors and difficulties in that followed, is incorrect, complacent, nessa Sancho-Shimizu, Vijay Sankaran,
determining whether immunological ab- and dangerous. Mikko R.J. Seppänen, Mohammad Shah-
normalities in patients are causes or con- The COVID-19 pandemic should make rooei, Andrew Snow, András Spaan, Stu-
sequences of infection. Genetics pro- us consider an alternative approach to art Tangye, Jordi Perez Tur, Stuart Turvey,
vides us with access to the root cause of studying infectious diseases. We have all Donald C. Vinh, Horst von Bernuth, Xiao-
phenomena. witnessed enormous interindividual clin- chuan Wang, Pawel Zawadzki, Qian
This project will also facilitate the ical variability in response to SARS-CoV- Zhang, and Shenying Zhang.
detection of individuals naturally resistant 2 exposure, ranging from resistance to
to SARS-CoV-2 infection. Why would the death, and everything in between. Similar SUPPLEMENTAL INFORMATION
spouse of a patient already ill for days variability is observed for all human-tropic
and now in intensive care remain not microbes, whether viruses, bacteria, Supplemental Information can be found online at
https://doi.org/10.1016/j.cell.2020.05.016.
only healthy but seronegative? How could fungi, or parasites. The proportion of life-
a health care worker treating contagious threatening cases varies among mi-
WEB RESOURCES
COVID-19 patients with insufficient pro- crobes, from less than one in a million to
tection remain healthy and seronegative? greater than one in ten. This clinical vari- COVID Human Genetic Effort, https://www.
If such individuals also test negative for ability during primary infection is the covidhge.com/
T cell responses to SARS-CoV-2, it is fundamental ‘‘infection enigma,’’ which
plausible that some are genetically resis- in 1955, led René Dubos to pen ‘‘Second ACKNOWLEDGMENTS
tant to the virus. The first example of thoughts on the germ theory’’ (Dubos,
such a situation was a regulatory DARC 1955). It is now time to test more compre- J.L.C. was supported by funding from the Howard
variant discovered in the 1970s and deci- hensively the hypothesis that the clinical Hughes Medical Institute, the Rockefeller Univer-
phered genetically in 1995. In the homo- manifestations of human infections, sity, the St. Giles Foundation, the National Insti-
tutes of Health (NIH) (UL1TR001866 and
zygous state, this variant confers resis- including those caused by SARS-CoV-2,
R01AI088364), the French National Research
tance to Plamodium vivax by abolishing can be governed by human genetics, at
Agency (ANR) ‘‘Investments for the Future’’ pro-
the expression of a parasite receptor on least in outliers resistant to infection or un- gram (ANR-10-IAHU-01), Laboratoire d’Excellence
erythrocytes. Two other known mono- usually prone to severe disease. This Integrative Biology of Emerging Infectious
genic forms of resistance are more paradigm shift would open up new ave- Diseases (ANR-10-LABX-62-IBEID), French
directly relevant to COVID-19. Homozy- nues for studying host-pathogen interac- Foundation for Medical Research (FRM)
gosity for CCR5 null mutations protects tions in the course of evolution, controlling (EQU201903007798), Institut National de la Santé
et de la Recherche Médicale (INSERM), and the
against CCR5-tropic HIV, and homozy- the current COVID-19 threat in the general
University of Paris. H.C.S. was supported by funds
gosity for null FUT2 alleles protects population, and developing the infrastruc- from the Division of Intramural Research in the Na-
against intestinal norovirus infection. ture required to thwart future emerging tional Institute of Allergy and Infections Diseases,
Similarly, we speculate that loss-of-func- threats. NIH. We thank Yelena Nemirovskaya for editorial
tion variants of ACE2, encoding a recep- assistance.
tor for SARS-CoV-2, might confer resis- CONSORTIUM
tance, while hypomorphic variants might DECLARATION OF INTERESTS
protect against severe disease in infected The members of the COVID Human Ge-
Helen Su holds Adjunct Faculty position in the
individuals. Identifying the genetic basis netic Effort include Laurent Abel, Alessan- Department of Pathology and Laboratory Medi-
of resistance to SARS-CoV-2 would pro- dro Aiuti, Saleh Almuhsen, Andres Au- cine, University of Pennsylvania.
vide a pharmacological target for prevent- gusto Arias, Paul Bastard, Catherine
ing or reducing viral infection in other indi- Biggs, Dusan Bogunovic, Bertrand Bois- REFERENCES
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