1932
0
  1. Home
  2. A-Z Publications
  3. Annual Review of Genetics
  4. Volume 56, 2022
  5. Article

Annual Review of Genetics

Volume 56, 2022

The Awesome Power of Human Genetics of Infectious Disease

Abstract

Since the identification of sickle cell trait as a heritable form of resistance to malaria, candidate gene studies, linkage analysis paired with sequencing, and genome-wide association (GWA) studies have revealed many examples of genetic resistance and susceptibility to infectious diseases. GWA studies enabled the identification of many common variants associated with small shifts in susceptibility to infectious diseases. This is exemplified by multiple loci associated with leprosy, malaria, HIV, tuberculosis, and coronavirus disease 2019 (COVID-19), which illuminate genetic architecture and implicate pathways underlying pathophysiology. Despite these successes, most of the heritability of infectious diseases remains to be explained. As the field advances, current limitations may be overcome by applying methodological innovations such as cellular GWA studies and phenome-wide association (PheWA) studies as well as by improving methodological rigor with more precise case definitions, deeper phenotyping, increased cohort diversity, and functional validation of candidate loci in the laboratory or human challenge studies.

Keyword(s): cytokines, eQTL, genetic association, GWAS, heritability, inborn errors of immunity, natural selection
Loading

Article metrics loading...

/content/journals/10.1146/annurev-genet-080320-010449
2022-11-30
2024-05-08
Loading full text...

Full text loading...

/deliver/fulltext/genet/56/1/annurev-genet-080320-010449.html?itemId=/content/journals/10.1146/annurev-genet-080320-010449&mimeType=html&fmt=ahah

Literature Cited

  1. 1.
    Akkaya M, Kwak K, Pierce SK. 2020. B cell memory: building two walls of protection against pathogens. Nat. Rev. Immunol. 20:229–38
     [Google Scholar]
  2. 2.
    Alkhatib G, Combadiere C, Broder CC, Feng Y, Kennedy PE et al. 1996. CC CKR5: a RANTES, MIP-1α, MIP-1β receptor as a fusion cofactor for macrophage-tropic HIV-1. Science 272:1955–58
     [Google Scholar]
  3. 3.
    Allison AC. 1954. Protection afforded by sickle-cell trait against subtertian malarial infection. Br. Med. J. 1:290–94
     [Google Scholar]
  4. 4.
    Altare F, Durandy A, Lammas D, Emile JF, Lamhamedi S et al. 1998. Impairment of mycobacterial immunity in human interleukin-12 receptor deficiency. Science 280:1432–35
     [Google Scholar]
  5. 5.
    Altare F, Lammas D, Revy P, Jouanguy E, Doffinger R et al. 1998. Inherited interleukin 12 deficiency in a child with bacille Calmette-Guérin and Salmonella enteritidis disseminated infection. J. Clin. Invest. 102:2035–40
     [Google Scholar]
  6. 6.
    Altshuler D, Daly MJ, Lander ES. 2008. Genetic mapping in human disease. Science 322:881–88
     [Google Scholar]
  7. 7.
    Alvarez MI, Glover LC, Luo P, Wang L, Theusch E et al. 2017. Human genetic variation in VAC14 regulates Salmonella invasion and typhoid fever through modulation of cholesterol. PNAS 114:E7746–55
     [Google Scholar]
  8. 8.
    Andreakos E, Abel L, Vinh DC, Kaja E, Drolet BA et al. 2022. A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection. Nat. Immunol. 23:159–64
     [Google Scholar]
  9. 9.
    Ardlie KG, Deluca DS, Segré AV, Sullivan TJ, Young TR et al. (GTEx Consort.) 2015. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348:648–60
     [Google Scholar]
  10. 10.
    Atmar RL, Bernstein DI, Harro CD, Al-Ibrahim MS, Chen WH et al. 2011. Norovirus vaccine against experimental human Norwalk virus illness. N. Engl. J. Med. 365:2178–87
     [Google Scholar]
  11. 11.
    Band G, Leffler EM, Jallow M, Sisay-Joof F, Ndila CM et al. 2021. Malaria protection due to sickle haemoglobin depends on parasite genotype. Nature 602:106–11
     [Google Scholar]
  12. 12.
    Banin E, Hughes D, Kuipers OP. 2017. Editorial: bacterial pathogens, antibiotics and antibiotic resistance. FEMS Microbiol. Rev. 41:450–52
     [Google Scholar]
  13. 13.
    Barbieri R, Signoli M, Chevé D, Costedoat C, Tzortzis S et al. 2020. Yersinia pestis: the natural history of plague. Clin. Microbiol. Rev. 34:e00044–19
     [Google Scholar]
  14. 14.
    Barreiro LB, Tailleux L, Pai AA, Gicquel B, Marioni JC, Gilad Y. 2012. Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection. PNAS 109:1204–9
     [Google Scholar]
  15. 15.
    Bastard P, Gervais A, Le Voyer T, Rosain J, Philippot Q et al. 2021. Autoantibodies neutralizing type I IFNs are present in ∼4% of uninfected individuals over 70 years old and account for ∼20% of COVID-19 deaths. Sci. Immunol. 6:eabl4340
     [Google Scholar]
  16. 16.
    Bastard P, Rosen LB, Zhang Q, Michailidis E, Hoffmann HH et al. 2020. Autoantibodies against type I IFNs in patients with life-threatening COVID-19. Science 370:eabd4585
     [Google Scholar]
  17. 17.
    Becattini S, Taur Y, Pamer EG. 2016. Antibiotic-induced changes in the intestinal microbiota and disease. Trends Mol. Med. 22:458–78
     [Google Scholar]
  18. 18.
    Bedford T, Riley S, Barr IG, Broor S, Chadha M et al. 2015. Global circulation patterns of seasonal influenza viruses vary with antigenic drift. Nature 523:217–20
     [Google Scholar]
  19. 19.
    Borrell S, Trauner A, Brites D, Rigouts L, Loiseau C et al. 2019. Reference set of Mycobacterium tuberculosis clinical strains: A tool for research and product development. PLOS ONE 14:e0214088
     [Google Scholar]
  20. 20.
    Bourgeois JS, Smith CM, Ko DC. 2020. These are the genes you're looking for: finding host resistance genes. Trends Microbiol. 29:346–62
     [Google Scholar]
  21. 21.
    Boyle EA, Li YI, Pritchard JK. 2017. An expanded view of complex traits: from polygenic to omnigenic. Cell 169:1177–86
     [Google Scholar]
  22. 22.
    Brodin P, Jojic V, Gao T, Bhattacharya S, Angel CJ et al. 2015. Variation in the human immune system is largely driven by non-heritable influences. Cell 160:37–47
     [Google Scholar]
  23. 23.
    Buniello A, MacArthur JAL, Cerezo M, Harris LW, Hayhurst J et al. 2019. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res. 47:D1005–12
     [Google Scholar]
  24. 24.
    Busslinger M, Tarakhovsky A. 2014. Epigenetic control of immunity. Cold Spring Harb. Perspect. Biol. 6:a019307
     [Google Scholar]
  25. 25.
    Bycroft C, Freeman C, Petkova D, Band G, Elliott LT et al. 2018. The UK Biobank resource with deep phenotyping and genomic data. Nature 562:203–9
     [Google Scholar]
  26. 26.
    Casadevall A, Pirofski L-A. 1999. Host-pathogen interactions: redefining the basic concepts of virulence and pathogenicity. Infect. Immun. 67:3703–13
     [Google Scholar]
  27. 27.
    Casanova JL, Abel L. 2013. The genetic theory of infectious diseases: a brief history and selected illustrations. Annu. Rev. Genom. Hum. Genet. 14:215–43
     [Google Scholar]
  28. 28.
    Cheng Y, Cheng G, Chui CH, Lau FY, Chan PK et al. 2005. ABO blood group and susceptibility to severe acute respiratory syndrome. JAMA 293:1447–51
     [Google Scholar]
  29. 29.
    Chimusa ER, Zaitlen N, Daya M, Moller M, van Helden PD et al. 2014. Genome-wide association study of ancestry-specific TB risk in the South African Coloured population. Hum. Mol. Genet. 23:796–809
     [Google Scholar]
  30. 30.
    Choe H, Farzan M, Sun Y, Sullivan N, Rollins B et al. 1996. The β-chemokine receptors CCR3 and CCR5 facilitate infection by primary HIV-1 isolates. Cell 85:1135–48
     [Google Scholar]
  31. 31.
    Ciancanelli MJ, Huang SX, Luthra P, Garner H, Itan Y et al. 2015. Life-threatening influenza and impaired interferon amplification in human IRF7 deficiency. Science 348:448–53
     [Google Scholar]
  32. 32.
    Clark PJ, Muir AJ. 2012. Lost in translation? IL28B's discovery and the journey back to the patient. Hepatology 56:5–8
     [Google Scholar]
  33. 33.
    COVID-19 Host Genet. Initiat 2021. Mapping the human genetic architecture of COVID-19. Nature 600:472–77
     [Google Scholar]
  34. 34.
    Crosse KM, Monson EA, Beard MR, Helbig KJ. 2018. Interferon-stimulated genes as enhancers of antiviral innate immune signaling. J. Innate Immun. 10:85–93
     [Google Scholar]
  35. 35.
    Curtis J, Luo Y, Zenner HL, Cuchet-Lourenco D, Wu C et al. 2015. Susceptibility to tuberculosis is associated with variants in the ASAP1 gene encoding a regulator of dendritic cell migration. Nat. Genet. 47:523–27
     [Google Scholar]
  36. 36.
    Darton TC, Blohmke CJ, Moorthy VS, Altmann DM, Hayden FG et al. 2015. Design, recruitment, and microbiological considerations in human challenge studies. Lancet Infect. Dis. 15:840–51
     [Google Scholar]
  37. 37.
    Darton TC, Blohmke CJ, Pollard AJ. 2014. Typhoid epidemiology, diagnostics and the human challenge model. Curr. Opin. Gastroenterol. 30:7–17
     [Google Scholar]
  38. 38.
    de Jong R, Altare F, Haagen IA, Elferink DG, Boer T et al. 1998. Severe mycobacterial and Salmonella infections in interleukin-12 receptor-deficient patients. Science 280:1435–38
     [Google Scholar]
  39. 39.
    Dean M, Carrington M, Winkler C, Huttley GA, Smith MW et al. 1996. Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Science 273:1856–62
     [Google Scholar]
  40. 40.
    Deng H, Liu R, Ellmeier W, Choe S, Unutmaz D et al. 1996. Identification of a major co-receptor for primary isolates of HIV-1. Nature 381:661–66
     [Google Scholar]
  41. 41.
    Ding J, Liu Y, Lai Y. 2021. Knowledge from London and Berlin: finding threads to a functional HIV cure. Front. Immunol. 12:688747
     [Google Scholar]
  42. 42.
    Ding K, de Andrade M, Manolio TA, Crawford DC, Rasmussen-Torvik LJ et al. 2013. Genetic variants that confer resistance to malaria are associated with red blood cell traits in African-Americans: an electronic medical record-based genome-wide association study. G3 3:1061–68
     [Google Scholar]
  43. 43.
    Doranz BJ, Rucker J, Yi Y, Smyth RJ, Samson M et al. 1996. A dual-tropic primary HIV-1 isolate that uses fusin and the β-chemokine receptors CKR-5, CKR-3, and CKR-2b as fusion cofactors. Cell 85:1149–58
     [Google Scholar]
  44. 44.
    Dragic T, Litwin V, Allaway GP, Martin SR, Huang Y et al. 1996. HIV-1 entry into CD4+ cells is mediated by the chemokine receptor CC-CKR-5. Nature 381:667–73
     [Google Scholar]
  45. 45.
    Dupuis S, Dargemont C, Fieschi C, Thomassin N, Rosenzweig S et al. 2001. Impairment of mycobacterial but not viral immunity by a germline human STAT1 mutation. Science 293:300–3
     [Google Scholar]
  46. 46.
    Ellinghaus D, Degenhardt F, Bujanda L, Buti M, Albillos A et al. Severe Covid-19 GWAS Group). 2020. Genomewide association study of severe Covid-19 with respiratory failure. N. Engl. J. Med. 383:1522–34
     [Google Scholar]
  47. 47.
    Fairfax BP, Humburg P, Makino S, Naranbhai V, Wong D et al. 2014. Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science 343:1246949
     [Google Scholar]
  48. 48.
    Filipe-Santos O, Bustamante J, Haverkamp MH, Vinolo E, Ku C-L et al. 2006. X-linked susceptibility to mycobacteria is caused by mutations in NEMO impairing CD40-dependent IL-12 production. J. Exp. Med. 203:1745–59
     [Google Scholar]
  49. 49.
    Ge D, Fellay J, Thompson AJ, Simon JS, Shianna KV et al. 2009. Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance. Nature 461:399–401
     [Google Scholar]
  50. 50.
    Gilchrist JJ, Mentzer AJ, Rautanen A, Pirinen M, Mwarumba S et al. 2018. Genetic variation in VAC14 is associated with bacteremia secondary to diverse pathogens in African children. PNAS 115:E3601–3
     [Google Scholar]
  51. 51.
    Hathi P, Haque S, Pant L, Coffey D, Spears D. 2017. Place and child health: the interaction of population density and sanitation in developing countries. Demography 54:337–60
     [Google Scholar]
  52. 52.
    Hawn TR, Misch EA, Dunstan SJ, Thwaites GE, Lan NT et al. 2007. A common human TLR1 polymorphism regulates the innate immune response to lipopeptides. Eur. J. Immunol. 37:2280–89
     [Google Scholar]
  53. 53.
    He J, Guo Y, Mao R, Zhang J. 2021. Proportion of asymptomatic coronavirus disease 2019: a systematic review and meta-analysis. J. Med. Virol. 93:820–30
     [Google Scholar]
  54. 54.
    Hernandez N, Melki I, Jing H, Habib T, Huang SSY et al. 2018. Life-threatening influenza pneumonitis in a child with inherited IRF9 deficiency. J. Exp. Med. 215:2567–85
     [Google Scholar]
  55. 55.
    Herndon CN, Jennings RG. 1951. A twin-family study of susceptibility to poliomyelitis. Am. J. Hum. Genet. 3:17–46
     [Google Scholar]
  56. 56.
    Herzog H. 1998. History of tuberculosis. Respiration 65:5–15
     [Google Scholar]
  57. 57.
    Hill AVS. 2006. Aspects of genetic susceptibility to human infectious diseases. Annu. Rev. Genet. 40:469–86
     [Google Scholar]
  58. 58.
    Hill AVS. 2012. Evolution, revolution and heresy in the genetics of infectious disease susceptibility. Philos. Trans. R. Soc. B 367:840–49
     [Google Scholar]
  59. 59.
    Houwen RH, Baharloo S, Blankenship K, Raeymaekers P, Juyn J et al. 1994. Genome screening by searching for shared segments: mapping a gene for benign recurrent intrahepatic cholestasis. Nat. Genet. 8:380–86
     [Google Scholar]
  60. 60.
    Huang QQ, Ritchie SC, Brozynska M, Inouye M. 2018. Power, false discovery rate and Winner's Curse in eQTL studies. Nucleic Acids Res. 46:e133
     [Google Scholar]
  61. 61.
    Huang Y, Paxton WA, Wolinsky SM, Neumann AU, Zhang L et al. 1996. The role of a mutant CCR5 allele in HIV-1 transmission and disease progression. Nat. Med. 2:1240–43
     [Google Scholar]
  62. 62.
    Huffman JE, Butler-Laporte G, Khan A, Pairo-Castineira E, Drivas TG et al. 2022. Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19. Nat. Genet. 54:125–27
     [Google Scholar]
  63. 63.
    Hui KPY, Ho JCW, Cheung M-C, Ng K-C, Ching RHH et al. 2022. SARS-CoV-2 Omicron variant replication in human bronchus and lung ex vivo. Nature 603:715–20
     [Google Scholar]
  64. 64.
    Internat. HapMap Consort 2005. A haplotype map of the human genome. Nature 437:1299–320
     [Google Scholar]
  65. 65.
    Ito K, Piantham C, Nishiura H. 2022. Relative instantaneous reproduction number of Omicron SARS-CoV-2 variant with respect to the Delta variant in Denmark. J. Med. Virol. 5:2265–68
     [Google Scholar]
  66. 66.
    Jallow M, Teo YY, Small KS, Rockett KA, Deloukas P et al. 2009. Genome-wide and fine-resolution association analysis of malaria in West Africa. Nat. Genet. 41:657–65
     [Google Scholar]
  67. 67.
    Jameson SC, Masopust D. 2018. Understanding subset diversity in T cell memory. Immunity 48:214–26
     [Google Scholar]
  68. 68.
    Kariuki SN, Williams TN. 2020. Human genetics and malaria resistance. Hum. Genet. 139:801–11
     [Google Scholar]
  69. 69.
    Killingley B, Enstone JE, Greatorex J, Gilbert AS, Lambkin-Williams R et al. 2012. Use of a human influenza challenge model to assess person-to-person transmission: proof-of-concept study. J Infect. Dis. 205:35–43
     [Google Scholar]
  70. 70.
    Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS et al. 2005. Complement factor H polymorphism in age-related macular degeneration. Science 308:385–89
     [Google Scholar]
  71. 71.
    Ko DC, Gamazon ER, Shukla KP, Pfuetzner RA, Whittington D et al. 2012. Functional genetic screen of human diversity reveals that a methionine salvage enzyme regulates inflammatory cell death. PNAS 109:E2343–52
     [Google Scholar]
  72. 72.
    Ko DC, Shukla KP, Fong C, Wasnick M, Brittnacher MJ et al. 2009. A genome-wide in vitro bacterial-infection screen reveals human variation in the host response associated with inflammatory disease. Am. J. Hum. Genet. 85:214–27
     [Google Scholar]
  73. 73.
    Kosmicki JA, Horowitz JE, Banerjee N, Lanche R, Marcketta A et al. 2021. Pan-ancestry exome-wide association analyses of COVID-19 outcomes in 586,157 individuals. Am. J. Hum. Genet. 108:1350–55
     [Google Scholar]
  74. 74.
    Ku CL, Dupuis-Girod S, Dittrich AM, Bustamante J, Santos OF et al. 2005. NEMO mutations in 2 unrelated boys with severe infections and conical teeth. Pediatrics 115:e615–19
     [Google Scholar]
  75. 75.
    Lander ES, Botstein D. 1986. Mapping complex genetic traits in humans: new methods using a complete RFLP linkage map. Cold Spring Harb. Symp. Quant. Biol. 51:49–62
     [Google Scholar]
  76. 76.
    Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PAC, Monlong J et al. 2013. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501:506–11
     [Google Scholar]
  77. 77.
    Latinovic OS, Reitz M, Heredia A. 2019. CCR5 inhibitors and HIV-1 infection. J AIDS HIV Treat 1:1–5
     [Google Scholar]
  78. 78.
    Lau CM, Adams NM, Geary CD, Weizman OE, Rapp M et al. 2018. Epigenetic control of innate and adaptive immune memory. Nat. Immunol. 19:963–72
     [Google Scholar]
  79. 79.
    Lederberg J. 1999. J. B. S. Haldane (1949) on infectious disease and evolution. Genetics 153:1–3
     [Google Scholar]
  80. 80.
    Lederer SE. 2014. The challenges of challenge experiments. N. Engl. J. Med. 371:695–97
     [Google Scholar]
  81. 81.
    Lee MN, Ye C, Villani A-C, Raj T, Li W et al. 2014. Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science 343:1246980
     [Google Scholar]
  82. 82.
    Li Y, Oosting M, Smeekens SP, Jaeger M, Aguirre-Gamboa R et al. 2016. A functional genomics approach to understand variation in cytokine production in humans. Cell 167:1099–110.e14
     [Google Scholar]
  83. 83.
    Lim HK, Huang SXL, Chen J, Kerner G, Gilliaux O et al. 2019. Severe influenza pneumonitis in children with inherited TLR3 deficiency. J. Exp. Med. 216:2038–56
     [Google Scholar]
  84. 84.
    Lindesmith L, Moe C, Marionneau S, Ruvoen N, Jiang X et al. 2003. Human susceptibility and resistance to Norwalk virus infection. Nat. Med. 9:548–53
     [Google Scholar]
  85. 85.
    Liu H, Irwanto A, Fu X, Yu G, Yu Y et al. 2015. Discovery of six new susceptibility loci and analysis of pleiotropic effects in leprosy. Nat. Genet. 47:267–71
     [Google Scholar]
  86. 86.
    Liu R, Paxton WA, Choe S, Ceradini D, Martin SR et al. 1996. Homozygous defect in HIV-1 coreceptor accounts for resistance of some multiply-exposed individuals to HIV-1 infection. Cell 86:367–77
     [Google Scholar]
  87. 87.
    Luo Y, Suliman S, Asgari S, Amariuta T, Baglaenko Y et al. 2019. Early progression to active tuberculosis is a highly heritable trait driven by 3q23 in Peruvians. Nat. Commun. 10:3765
     [Google Scholar]
  88. 88.
    Lyon SM, Rossman MD. 2017. Pulmonary tuberculosis. Microbiol. Spectr. 5: https://doi.org/10.1128/microbiolspec.TNMI7-0032-2016
    [Crossref] [Google Scholar]
  89. 89.
    Mackinnon MJ, Mwangi TW, Snow RW, Marsh K, Williams TN. 2005. Heritability of malaria in Africa. PLOS Med. 2:e340
     [Google Scholar]
  90. 90.
    Malar. Genom. Epidemiol. Netw 2014. Reappraisal of known malaria resistance loci in a large multicenter study. Nat. Genet. 46:1197–204
     [Google Scholar]
  91. 91.
    Malar. Genom. Epidemiol. Netw 2015. A novel locus of resistance to severe malaria in a region of ancient balancing selection. Nature 526:253–57
     [Google Scholar]
  92. 92.
    Malar. Genom. Epidemiol. Netw 2019. Insights into malaria susceptibility using genome-wide data on 17,000 individuals from Africa, Asia and Oceania. Nat. Commun. 10:5732
     [Google Scholar]
  93. 93.
    Martin AR, Kanai M, Kamatani Y, Okada Y, Neale BM, Daly MJ. 2019. Clinical use of current polygenic risk scores may exacerbate health disparities. Nat. Genet. 51:584–91
     [Google Scholar]
  94. 94.
    Mason WP. 1909.. “ Typhoid Mary. .” Science 30:117–18
     [Google Scholar]
  95. 95.
    McLaren PJ, Coulonges C, Bartha I, Lenz TL, Deutsch AJ et al. 2015. Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load. PNAS 112:14658–63
     [Google Scholar]
  96. 96.
    McLaren PJ, Coulonges C, Ripke S, van den Berg L, Buchbinder S et al. 2013. Association study of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls. PLOS Pathog. 9:e1003515
     [Google Scholar]
  97. 97.
    Mikacenic C, Reiner AP, Holden TD, Nickerson DA, Wurfel MM. 2013. Variation in the TLR10/TLR1/TLR6 locus is the major genetic determinant of interindividual difference in TLR1/2-mediated responses. Genes Immun. 14:52–57
     [Google Scholar]
  98. 98.
    Miller LH, Mason SJ, Clyde DF, McGinniss MH. 1976. The resistance factor to Plasmodium vivax in blacks. The Duffy-blood-group genotype. FyFy. N. Engl. J. Med. 295:302–4
     [Google Scholar]
  99. 99.
    Minegishi Y, Saito M, Morio T, Watanabe K, Agematsu K et al. 2006. Human tyrosine kinase 2 deficiency reveals its requisite roles in multiple cytokine signals involved in innate and acquired immunity. Immunity 25:745–55
     [Google Scholar]
  100. 100.
    Mizrahi B, Shilo S, Rossman H, Kalkstein N, Marcus K et al. 2020. Longitudinal symptom dynamics of COVID-19 infection. Nat. Commun. 11:6208
     [Google Scholar]
  101. 101.
    Monot M, Honoré N, Garnier T, Araoz R, Coppée JY et al. 2005. On the origin of leprosy. Science 308:1040–42
     [Google Scholar]
  102. 102.
    Mozzi A, Pontremoli C, Sironi M. 2018. Genetic susceptibility to infectious diseases: current status and future perspectives from genome-wide approaches. Infect. Genet. Evol. 66:286–307
     [Google Scholar]
  103. 103.
    Ndila CM, Uyoga S, Macharia AW, Nyutu G, Peshu N et al. 2018. Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study. Lancet Haematol. 5:E333–45
     [Google Scholar]
  104. 104.
    Nedelec Y, Sanz J, Baharian G, Szpiech ZA, Pacis A et al. 2016. Genetic ancestry and natural selection drive population differences in immune responses to pathogens. Cell 167:657–69.e21
     [Google Scholar]
  105. 105.
    Newport MJ, Huxley CM, Huston S, Hawrylowicz CM, Oostra BA et al. 1996. A mutation in the interferon-γ-receptor gene and susceptibility to mycobacterial infection. N. Engl. J. Med. 335:1941–49
     [Google Scholar]
  106. 106.
    Novelli F, Casanova J-L. 2004. The role of IL-12, IL-23 and IFN-γ in immunity to viruses. Cytokine Growth Factor Rev. 15:367–77
     [Google Scholar]
  107. 107.
    Oidtman RJ, Arevalo P, Bi Q, McGough L, Russo CJ et al. 2021. Influenza immune escape under heterogeneous host immune histories. Trends Microbiol. 29:1072–82
     [Google Scholar]
  108. 108.
    Okondo MC, Johnson DC, Sridharan R, Go EB, Chui AJ et al. 2017. DPP8 and DPP9 inhibition induces pro-caspase-1-dependent monocyte and macrophage pyroptosis. Nat. Chem. Biol. 13:46–53
     [Google Scholar]
  109. 109.
    Oran DP, Topol EJ. 2020. Prevalence of asymptomatic SARS-CoV-2 infection: a narrative review. Ann. Intern. Med. 173:362–67
     [Google Scholar]
  110. 110.
    Pae M, Wu D. 2017. Nutritional modulation of age-related changes in the immune system and risk of infection. Nutr. Res. 41:14–35
     [Google Scholar]
  111. 111.
    Pairo-Castineira E, Clohisey S, Klaric L, Bretherick AD, Rawlik K et al. 2021. Genetic mechanisms of critical illness in COVID-19. Nature 591:92–98
     [Google Scholar]
  112. 112.
    Povysil G, Butler-Laporte G, Shang N, Wang C, Khan A et al. 2021. Rare loss-of-function variants in type I IFN immunity genes are not associated with severe COVID-19. J. Clin. Invest. 131:e147834
     [Google Scholar]
  113. 113.
    Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. 2006. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38:904–9
     [Google Scholar]
  114. 114.
    Qi H, Zhang YB, Sun L, Chen C, Xu B et al. 2017. Discovery of susceptibility loci associated with tuberculosis in Han Chinese. Hum. Mol. Genet. 26:4752–63
     [Google Scholar]
  115. 115.
    Quach H, Rotival M, Pothlichet J, Loh YE, Dannemann M et al. 2016. Genetic adaptation and Neandertal admixture shaped the immune system of human populations. Cell 167:643–56.e17
     [Google Scholar]
  116. 116.
    Randolph HE, Fiege JK, Thielen BK, Mickelson CK, Shiratori M et al. 2021. Genetic ancestry effects on the response to viral infection are pervasive but cell type specific. Science 374:1127–33
     [Google Scholar]
  117. 117.
    Rapeport G, Smith E, Gilbert A, Catchpole A, McShane H, Chiu C. 2021. SARS-CoV-2 human challenge studies—establishing the model during an evolving pandemic. N. Engl. J. Med. 385:961–64
     [Google Scholar]
  118. 118.
    Sakaue S, Kanai M, Tanigawa Y, Karjalainen J, Kurki M et al. 2021. A cross-population atlas of genetic associations for 220 human phenotypes. Nat. Genet. 53:1415–24
     [Google Scholar]
  119. 119.
    Samson M, Libert F, Doranz BJ, Rucker J, Liesnard C et al. 1996. Resistance to HIV-1 infection in Caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature 382:722–25
     [Google Scholar]
  120. 120.
    Sauerwein RW, Roestenberg M, Moorthy VS. 2011. Experimental human challenge infections can accelerate clinical malaria vaccine development. Nat. Rev. Immunol. 11:57–64
     [Google Scholar]
  121. 121.
    Schott BH, Wang L, Zhu X, Harding AT, Ko ER et al. 2022. Single-cell genome-wide association reveals a nonsynonymous variant in ERAP1 confers increased susceptibility to influenza virus. bioRxiv 2022.01.30.478319. https://doi.org/10.1101/2022.01.30.478319
    [Crossref]
  122. 122.
    Scriver CR. 2008. Garrod's Croonian Lectures (1908) and the charter ‘Inborn Errors of Metabolism’: albinism, alkaptonuria, cystinuria, and pentosuria at age 100 in 2008. J. Inherit. Metab. Dis. 31:580–98
     [Google Scholar]
  123. 123.
    Shtrichman R, Samuel CE. 2001. The role of gamma interferon in antimicrobial immunity. Curr. Opin. Microbiol. 4:251–59
     [Google Scholar]
  124. 124.
    Siena K. 2019. Rotten Bodies: Class and Contagion in 18th-Century Britain New Haven, CT: Yale Univ. Press
  125. 125.
    Smith CM, Baker RE, Proulx MK, Mishra BB, Long JE et al. 2022. Host-pathogen genetic interactions underlie tuberculosis susceptibility in genetically diverse mice. eLife 11:e74419
     [Google Scholar]
  126. 126.
    Sommer F, Anderson JM, Bharti R, Raes J, Rosenstiel P. 2017. The resilience of the intestinal microbiota influences health and disease. Nat. Rev. Microbiol. 15:630–38
     [Google Scholar]
  127. 127.
    Sorensen TI, Nielsen GG, Andersen PK, Teasdale TW. 1988. Genetic and environmental influences on premature death in adult adoptees. N. Engl. J. Med. 318:727–32
     [Google Scholar]
  128. 128.
    Steere-Williams J. 2016. The germ theory. A Companion to the History of American Science GM Montgomery, MA Largent 397–407 Hoboken, NJ: John Wiley & Sons
     [Google Scholar]
  129. 129.
    Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP et al. 2007. Population genomics of human gene expression. Nat. Genet. 39:1217–24
     [Google Scholar]
  130. 130.
    Sul JH, Martin LS, Eskin E. 2018. Population structure in genetic studies: confounding factors and mixed models. PLOS Genet. 14:e1007309
     [Google Scholar]
  131. 131.
    Tang KL, Rashid R, Godley J, Ghali WA. 2016. Association between subjective social status and cardiovascular disease and cardiovascular risk factors: a systematic review and meta-analysis. BMJ Open 6:e010137
     [Google Scholar]
  132. 132.
    Tangye SG, Al-Herz W, Bousfiha A, Chatila T, Cunningham-Rundles C et al. 2020. Human inborn errors of immunity: 2019 update on the classification from the International Union of Immunological Societies Expert Committee. J. Clin. Immunol. 40:24–64
     [Google Scholar]
  133. 133.
    Tebas P, Jadlowsky JK, Shaw PA, Tian L, Esparza E et al. 2021. CCR5-edited CD4+ T cells augment HIV-specific immunity to enable post-rebound control of HIV replication. J. Clin. Invest. 131:e144486
     [Google Scholar]
  134. 134.
    Tebas P, Stein D, Tang WW, Frank I, Wang SQ et al. 2014. Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV. N. Engl. J. Med. 370:901–10
     [Google Scholar]
  135. 135.
    Thye T, Owusu-Dabo E, Vannberg FO, van Crevel R, Curtis J et al. 2012. Common variants at 11p13 are associated with susceptibility to tuberculosis. Nat. Genet. 44:257–59
     [Google Scholar]
  136. 136.
    Thye T, Vannberg FO, Wong SH, Owusu-Dabo E, Osei I et al. 2010. Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2. Nat. Genet. 42:739–41
     [Google Scholar]
  137. 137.
    Tian C, Hromatka BS, Kiefer AK, Eriksson N, Noble SM et al. 2017. Genome-wide association and HLA region fine-mapping studies identify susceptibility loci for multiple common infections. Nat. Commun. 8:599
     [Google Scholar]
  138. 138.
    Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C et al. 2022. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature 603:679–86
     [Google Scholar]
  139. 139.
    Wang L, Balmat TJ, Antonia AL, Constantine FJ, Henao R et al. 2021. An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility. Genome Med. 13:83
     [Google Scholar]
  140. 140.
    Wang L, Pittman KJ, Barker JR, Salinas RE, Stanaway IB et al. 2018. An atlas of genetic variation linking pathogen-induced cellular traits to human disease. Cell Host Microbe 24:308–23.e6
     [Google Scholar]
  141. 141.
    Wang Z, Sun Y, Fu X, Yu G, Wang C et al. 2016. A large-scale genome-wide association and meta-analysis identified four novel susceptibility loci for leprosy. Nat. Commun. 7:13760
     [Google Scholar]
  142. 142.
    Wickenhagen A, Sugrue E, Lytras S, Kuchi S, Noerenberg M et al. 2021. A prenylated dsRNA sensor protects against severe COVID-19. Science 374:eabj3624
     [Google Scholar]
  143. 143.
    Wijmenga C. 2021. From LD-based mapping to GWAS. Nat. Rev. Genet. 22:480–81
     [Google Scholar]
  144. 144.
    Wilkinson TM, Li CKF, Chui CSC, Huang AKY, Perkins M et al. 2012. Preexisting influenza-specific CD4+ T cells correlate with disease protection against influenza challenge in humans. Nat. Med. 18:274–80
     [Google Scholar]
  145. 145.
    Wong SH, Hill AV, Vannberg FO. 2010. Genomewide association study of leprosy. N. Engl. J. Med. 362:1446–47; author reply 1447–48
    [Google Scholar]
  146. 146.
    World Health Organ 2021. WHO coronavirus disease (COVID-19) dashboard. World Health Organization. https://covid19.who.int/
  147. 147.
    Wurfel MM, Gordon AC, Holden TD, Radella F, Strout J et al. 2008. Toll-like receptor 1 polymorphisms affect innate immune responses and outcomes in sepsis. Am. J. Respir. Crit. Care Med. 178:710–20
     [Google Scholar]
  148. 148.
    Yewdell JW, Santos JJS. 2021. Original antigenic sin: How original? How sinful? Cold Spring Harb. . Perspect. Med. 11:a038786
     [Google Scholar]
  149. 149.
    Yoshikawa TT. 2000. Epidemiology and unique aspects of aging and infectious diseases. Clin. Infect. Dis. 30:931–33
     [Google Scholar]
  150. 150.
    Zhang Q, Bastard P, Liu Z, Le Pen J, Moncada-Velez M et al. 2020. Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science 370:eabd4570
     [Google Scholar]
  151. 151.
    Zhang S-Y, Clark NE, Freije CA, Pauwels E, Taggart AJ et al. 2018. Inborn errors of RNA lariat metabolism in humans with brainstem viral infection. Cell 172:952–65.e18
     [Google Scholar]
  152. 152.
    Zhao J, Yang Y, Huang H, Li D, Gu D et al. 2020. Relationship between the ABO blood group and the COVID-19 susceptibility. medRxiv 2020.03.11.20031096. https://doi.org/10.1101/2020.03.11.20031096
    [Crossref]
  153. 153.
    Zhao J, Yang Y, Huang H, Li D, Gu D et al. 2021. Relationship between the ABO blood group and the coronavirus disease 2019 (COVID-19) susceptibility. Clin. Infect. Dis. 73:328–31
     [Google Scholar]
  154. 154.
    Zheng R, Li Z, He F, Liu H, Chen J et al. 2018. Genome-wide association study identifies two risk loci for tuberculosis in Han Chinese. Nat. Commun. 9:4072
     [Google Scholar]
  155. 155.
    Zhong FL, Robinson K, Teo DET, Tan KY, Lim C et al. 2018. Human DPP9 represses NLRP1 inflammasome and protects against autoinflammatory diseases via both peptidase activity and FIIND domain binding. J. Biol. Chem. 293:18864–78
     [Google Scholar]
/content/journals/10.1146/annurev-genet-080320-010449
Loading
The Awesome Power of Human Genetics of Infectious Disease
Annual Review of Genetics 56, 41 (2022); https://doi.org/10.1146/annurev-genet-080320-010449
/content/journals/10.1146/annurev-genet-080320-010449
/content/journals/10.1146/annurev-genet-080320-010449
Loading

Data & Media loading...

  • Article Type: Review Article

Most Cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error