1932

Abstract

Much progress has been made in the identification of specific human gene variants that contribute to enhanced susceptibility or resistance to viral diseases. Herein we review multiple discoveries made with genome-wide or candidate gene approaches that have revealed significant insights into virus–host interactions. Genetic factors that have been identified include genes encoding virus receptors, receptor-modifying enzymes, and a wide variety of innate and adaptive immunity-related proteins. We discuss a range of pathogenic viruses, including influenza virus, respiratory syncytial virus, human immunodeficiency virus, human T cell leukemia virus, human papilloma virus, hepatitis B and C viruses, herpes simplex virus, norovirus, rotavirus, parvovirus, and Epstein-Barr virus. Understanding the genetic underpinnings that affect infectious disease outcomes should allow tailored treatment and prevention approaches in the future.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-genet-120116-023425
2017-11-27
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/genet/51/1/annurev-genet-120116-023425.html?itemId=/content/journals/10.1146/annurev-genet-120116-023425&mimeType=html&fmt=ahah

Literature Cited

  1. Alter G, Heckerman D, Schneidewind A, Fadda L, Kadie CM. 1.  et al. 2011. HIV-1 adaptation to NK-cell-mediated immune pressure. Nature 476:96–100 [Google Scholar]
  2. Altfeld M, Addo MM, Rosenberg ES, Hecht FM, Lee PK. 2.  et al. 2003. Influence of HLA-B57 on clinical presentation and viral control during acute HIV-1 infection. AIDS 17:2581–91 [Google Scholar]
  3. An P, Bleiber G, Duggal P, Nelson G, May M. 3.  et al. 2004. APOBEC3G genetic variants and their influence on the progression to AIDS. J. Virol. 78:11070–76 [Google Scholar]
  4. Andersen LL, Mork N, Reinert LS, Kofod-Olsen E, Narita R. 4.  et al. 2015. Functional IRF3 deficiency in a patient with herpes simplex encephalitis. J. Exp. Med. 212:1371–79 [Google Scholar]
  5. Assone T, de Souza FV, Gaester KO, Fonseca LA, Luiz Odo C. 5.  et al. 2014. IL28B gene polymorphism SNP rs8099917 genotype GG is associated with HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) in HTLV-1 carriers. PLOS Negl. Trop. Dis. 8:e3199 [Google Scholar]
  6. Audry M, Ciancanelli M, Yang K, Cobat A, Chang H-H. 6.  et al. 2011. NEMO is a key component of NF-κB- and IRF-3-dependent TLR3-mediated immunity to herpes simplex virus. J. Allergy Clin. Immunol. 128:610–17.e4 [Google Scholar]
  7. Badano I, Stietz SM, Schurr TG, Picconi AM, Fekete D. 7.  et al. 2012. Analysis of TNFα promoter SNPs and the risk of cervical cancer in urban populations of Posadas (Misiones, Argentina). J. Clin. Virol. 53:54–59 [Google Scholar]
  8. Bibert S, Roger T, Calandra T, Bochud M, Cerny A. 8.  et al. 2013. IL28B expression depends on a novel TT/-G polymorphism which improves HCV clearance prediction. J. Exp. Med. 210:1109–16 [Google Scholar]
  9. Blackwell JM, Jamieson SE, Burgner D. 9.  2009. HLA and infectious diseases. Clin. Microbiol. Rev. 22:370–85 [Google Scholar]
  10. Boyoglu-Barnum S, Chirkova T, Todd SO, Barnum TR, Gaston KA. 10.  et al. 2014. Prophylaxis with a respiratory syncytial virus (RSV) anti-G protein monoclonal antibody shifts the adaptive immune response to RSV rA2-line19F infection from Th2 to Th1 in BALB/c mice. J. Virol. 88:10569–83 [Google Scholar]
  11. Brackenridge S, Evans EJ, Toebes M, Goonetilleke N, Liu MK. 11.  et al. 2011. An early HIV mutation within an HLA-B*57-restricted T cell epitope abrogates binding to the killer inhibitory receptor 3DL1. J. Virol. 85:5415–22 [Google Scholar]
  12. Bradley H, Markowitz LE, Gibson T, McQuillan GM. 12.  2014. Seroprevalence of herpes simplex virus types 1 and 2—United States, 1999–2010. J. Infect. Dis. 209:325–33 [Google Scholar]
  13. Brass AL, Huang IC, Benita Y, John SP, Krishnan MN. 13.  et al. 2009. The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Cell 139:1243–54 [Google Scholar]
  14. Brown KE, Anderson SM, Young NS. 14.  1993. Erythrocyte P antigen: cellular receptor for B19 parvovirus. Science 262:114–17 [Google Scholar]
  15. Brown KE, Hibbs JR, Gallinella G, Anderson SM, Lehman ED. 15.  et al. 1994. Resistance to parvovirus B19 infection due to lack of virus receptor (erythrocyte P antigen). New Engl. J. Med. 330:1192–96 [Google Scholar]
  16. Carneiro-Proietti AB, Amaranto-Damasio MS, Leal-Horiguchi CF, Bastos RH, Seabra-Freitas G. 16.  et al. 2014. Mother-to-child transmission of human T-cell lymphotropic viruses-1/2: what we know, and what are the gaps in understanding and preventing this route of infection. J. Pediatr. Infect. Dis. Soc. 3:Suppl. 1S24–29 [Google Scholar]
  17. Carrington M, Nelson GW, Martin MP, Kissner T, Vlahov D. 17.  et al. 1999. HLA and HIV-1: heterozygote advantage and B*35-Cw*04 disadvantage. Science 283:1748–52 [Google Scholar]
  18. Casrouge A, Zhang SY, Eidenschenk C, Jouanguy E, Puel A. 18.  et al. 2006. Herpes simplex virus encephalitis in human UNC-93B deficiency. Science 314:308–12 [Google Scholar]
  19. Chaigne-Delalande B, Li FY, O'Connor GM, Lukacs MJ, Jiang P. 19.  et al. 2013. Mg2+ regulates cytotoxic functions of NK and CD8 T cells in chronic EBV infection through NKG2D. Science 341:186–91 [Google Scholar]
  20. Chapgier A, Kong XF, Boisson-Dupuis S, Jouanguy E, Averbuch D. 20.  et al. 2009. A partial form of recessive STAT1 deficiency in humans. J. Clin. Investig. 119:1502–14 [Google Scholar]
  21. Chen Y, Mizuguchi H, Yao D, Ide M, Kuroda Y. 21.  et al. 2005. Thermolabile phenotype of carnitine palmitoyltransferase II variations as a predisposing factor for influenza-associated encephalopathy. FEBS Lett 579:2040–44 [Google Scholar]
  22. Chesarino NM, McMichael TM, Hach JC, Yount JS. 22.  2014. Phosphorylation of the antiviral protein interferon-inducible transmembrane protein 3 (IFITM3) dually regulates its endocytosis and ubiquitination. J. Biol. Chem. 289:11986–92 [Google Scholar]
  23. Chesarino NM, McMichael TM, Yount JS. 23.  2014. Regulation of the trafficking and antiviral activity of IFITM3 by post-translational modifications. Future Microbiol 9:1151–63 [Google Scholar]
  24. Chesarino NM, McMichael TM, Yount JS. 24.  2015. E3 ubiquitin ligase NEDD4 promotes influenza virus infection by decreasing levels of the antiviral protein IFITM3. PLOS Pathog 11:e1005095 [Google Scholar]
  25. Choi EH, Lee HJ, Chanock SJ. 25.  2013. Human genetics and respiratory syncytial virus disease: current findings and future approaches. Curr. Top. Microbiol. Immunol. 372:121–37 [Google Scholar]
  26. Choi EH, Lee HJ, Yoo T, Chanock SJ. 26.  2002. A common haplotype of interleukin-4 gene IL4 is associated with severe respiratory syncytial virus disease in Korean children. J. Infect. Dis. 186:1207–11 [Google Scholar]
  27. Ciancanelli MJ, Huang SXL, Luthra P, Garner H, Itan Y. 27.  et al. 2015. Life-threatening influenza and impaired interferon amplification in human IRF7 deficiency. Science 348:448–53 [Google Scholar]
  28. Cohen JI. 28.  2000. Epstein-Barr virus infection. N. Engl. J. Med. 343:481–92 [Google Scholar]
  29. Compton AA, Roy N, Porrot F, Billet A, Casartelli N. 29.  et al. 2016. Natural mutations in IFITM3 modulate post-translational regulation and toggle antiviral specificity. EMBO Rep 17:1657–71 [Google Scholar]
  30. Coon S, Wang D, Wu L. 30.  2012. Polymorphisms of the SAMHD1 gene are not associated with the infection and natural control of HIV type 1 in Europeans and African-Americans. AIDS Res. Hum. Retroviruses 28:1565–73 [Google Scholar]
  31. Currier RL, Payne DC, Staat MA, Selvarangan R, Shirley SH. 31.  et al. 2015. Innate susceptibility to norovirus infections influenced by FUT2 genotype in a United States pediatric population. Clin. Infect. Dis. 60:1631–38 [Google Scholar]
  32. Custer B, Sullivan SD, Hazlet TK, Iloeje U, Veenstra DL, Kowdley KV. 32.  2004. Global epidemiology of hepatitis B virus. J. Clin. Gastroenterol. 38:S158–68 [Google Scholar]
  33. Dean M, Carrington M, Winkler C, Huttley GA, Smith MW. 33.  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]
  34. Deshpande A, Nolan JP, White PS, Valdez YE, Hunt WC. 34.  et al. 2005. TNF-α promoter polymorphisms and susceptibility to human papillomavirus 16-associated cervical cancer. J. Infect. Dis. 191:969–76 [Google Scholar]
  35. Duarte I, Santos A, Sousa H, Catarino R, Pinto D. 35.  et al. 2005. G-308A TNF-α polymorphism is associated with an increased risk of invasive cervical cancer. Biochem. Biophys. Res. Commun. 334:588–92 [Google Scholar]
  36. Dunne EF, Unger ER, Sternberg M, McQuillan G, Swan DC. 36.  et al. 2007. Prevalence of HPV infection among females in the United States. JAMA 297:813–19 [Google Scholar]
  37. Dupuis S, Jouanguy E, Al-Hajjar S, Fieschi C, Al-Mohsen IZ. 37.  et al. 2003. Impaired response to interferon-α/β and lethal viral disease in human STAT1 deficiency. Nat. Genet. 33:388–91 [Google Scholar]
  38. Enard D, Cai L, Gwennap C, Petrov DA. 38.  2016. Viruses are a dominant driver of protein adaptation in mammals. eLife 5:e12469 [Google Scholar]
  39. Everitt AR, Clare S, Pertel T, John SP, Wash RS. 39.  et al. 2012. IFITM3 restricts the morbidity and mortality associated with influenza. Nature 484:519–23 [Google Scholar]
  40. Fellay J, Shianna KV, Ge D, Colombo S, Ledergerber B. 40.  et al. 2007. A whole-genome association study of major determinants for host control of HIV-1. Science 317:944–47 [Google Scholar]
  41. Ferrer-Admetlla A, Sikora M, Laayouni H, Esteve A, Roubinet F. 41.  et al. 2009. A natural history of FUT2 polymorphism in humans. Mol. Biol. Evol. 26:1993–2003 [Google Scholar]
  42. Gaiotti D, Chung J, Iglesias M, Nees M, Baker PD. 42.  et al. 2000. Tumor necrosis factor-α promotes human papillomavirus (HPV) E6/E7 RNA expression and cyclin-dependent kinase activity in HPV-immortalized keratinocytes by a ras-dependent pathway. Mol. Carcinog. 27:97–109 [Google Scholar]
  43. Ge D, Fellay J, Thompson AJ, Simon JS, Shianna KV. 43.  et al. 2009. Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance. Nature 461:399–401 [Google Scholar]
  44. Gentile DA, Doyle WJ, Zeevi A, Piltcher O, Skoner DP. 44.  2003. Cytokine gene polymorphisms moderate responses to respiratory syncytial virus in adults. Hum. Immunol. 64:93–98 [Google Scholar]
  45. Gessain A, Barin F, Vernant JC, Gout O, Maurs L. 45.  et al. 1985. Antibodies to human T-lymphotropic virus type-I in patients with tropical spastic paraparesis. Lancet 2:407–10 [Google Scholar]
  46. Halperin T, Vennema H, Koopmans M, Kahila Bar-Gal G, Kayouf R. 46.  et al. 2008. No association between histo-blood group antigens and susceptibility to clinical infections with genogroup II norovirus. J. Infect. Dis. 197:63–65 [Google Scholar]
  47. Hartshorn KL. 47.  2010. Role of surfactant protein A and D (SP-A and SP-D) in human antiviral host defense. Front. Biosci. (Schol. Ed.) 2:527–46 [Google Scholar]
  48. Hellberg A, Poole J, Olsson ML. 48.  2002. Molecular basis of the globoside-deficient Pk blood group phenotype. Identification of four inactivating mutations in the UDP-N-acetylgalactosamine: globotriaosylceramide 3-β-N-acetylgalactosaminyltransferase gene. J. Biol. Chem. 277:29455–59 [Google Scholar]
  49. Helminen ME, Kilpinen S, Virta M, Hurme M. 49.  2001. Susceptibility to primary Epstein-Barr virus infection is associated with interleukin-10 gene promoter polymorphism. J. Infect. Dis. 184:777–80 [Google Scholar]
  50. Helminen ME, Lahdenpohja N, Hurme M. 50.  1999. Polymorphism of the interleukin-10 gene is associated with susceptibility to Epstein-Barr virus infection. J. Infect. Dis. 180:496–99 [Google Scholar]
  51. Herman M, Ciancanelli M, Ou YH, Lorenzo L, Klaudel-Dreszler M. 51.  et al. 2012. Heterozygous TBK1 mutations impair TLR3 immunity and underlie herpes simplex encephalitis of childhood. J. Exp. Med. 209:1567–82 [Google Scholar]
  52. Herndon CN, Jennings RG. 52.  1951. A twin-family study of susceptibility to poliomyelitis. Am. J. Hum. Genet. 3:17–46 [Google Scholar]
  53. Herrera-Ramos E, López-Rodríguez M, Ruiz-Hernández JJ, Horcajada JP, Borderías L. 53.  et al. 2014. Surfactant protein A genetic variants associate with severe respiratory insufficiency in pandemic influenza A virus infection. Crit. Care 18:R127 [Google Scholar]
  54. Hislop AD, Palendira U, Leese AM, Arkwright PD, Rohrlich PS. 54.  et al. 2010. Impaired Epstein-Barr virus-specific CD8+ T-cell function in X-linked lymphoproliferative disease is restricted to SLAM family-positive B-cell targets. Blood 116:3249–57 [Google Scholar]
  55. Hobbs MR, Jones BB, Otterud BE, Leppert M, Kriesel JD. 55.  2008. Identification of a herpes simplex labialis susceptibility region on human chromosome 21. J. Infect. Dis. 197:340–46 [Google Scholar]
  56. Hoebee B, Rietveld E, Bont L, Oosten M, Hodemaekers HM. 56.  et al. 2003. Association of severe respiratory syncytial virus bronchiolitis with interleukin-4 and interleukin-4 receptor α polymorphisms. J. Infect. Dis. 187:2–11 [Google Scholar]
  57. Honda M, Sakai A, Yamashita T, Nakamoto Y, Mizukoshi E. 57.  et al. 2010. Hepatic ISG expression is associated with genetic variation in interleukin 28B and the outcome of IFN therapy for chronic hepatitis C. Gastroenterology 139:499–509 [Google Scholar]
  58. Honegger JR, Tedesco D, Kohout JA, Prasad MR, Price AA. 58.  et al. 2016. Influence of IFNL3 and HLA-DPB1 genotype on postpartum control of hepatitis C virus replication and T-cell recovery. PNAS 113:10684–89 [Google Scholar]
  59. Hrecka K, Hao C, Gierszewska M, Swanson SK, Kesik-Brodacka M. 59.  et al. 2011. Vpx relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein. Nature 474:658–61 [Google Scholar]
  60. Huck K, Feyen O, Niehues T, Ruschendorf F, Hübner N. 60.  et al. 2009. Girls homozygous for an IL-2-inducible T cell kinase mutation that leads to protein deficiency develop fatal EBV-associated lymphoproliferation. J. Clin. Investig. 119:1350–58 [Google Scholar]
  61. Hull J, Thomson A, Kwiatkowski D. 61.  2000. Association of respiratory syncytial virus bronchiolitis with the interleukin 8 gene region in UK families. Thorax 55:1023–27 [Google Scholar]
  62. Hurme M, Helminen ME. 62.  1998. Polymorphism of the IL-1 gene complex in Epstein-Barr virus seronegative and seropositive adult blood donors. Scand. J. Immunol. 48:219–22 [Google Scholar]
  63. Hutson AM, Atmar RL, Graham DY, Estes MK. 63.  2002. Norwalk virus infection and disease is associated with ABO histo-blood group type. J. Infect. Dis. 185:1335–37 [Google Scholar]
  64. Inoue Y, Shimojo N, Suzuki Y, Campos Alberto EJ, Yamaide A. 64.  et al. 2007. CD14-550 C/T, which is related to the serum level of soluble CD14, is associated with the development of respiratory syncytial virus bronchiolitis in the Japanese population. J. Infect. Dis. 195:1618–24 [Google Scholar]
  65. Pereyra F, Jia X, McLaren PJ, Telenti A. 65. International HIV Controllers Study Writing Team, et al. 2010. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science 330:1551–57 [Google Scholar]
  66. Ishitsuka K, Tamura K. 66.  2014. Human T-cell leukaemia virus type I and adult T-cell leukaemia-lymphoma. Lancet Oncol 15:e517–26 [Google Scholar]
  67. Jackson M, Scott R. 67.  1996. Different patterns of cytokine induction in cultures of respiratory syncytial (RS) virus-specific human TH cell lines following stimulation with RS virus and RS virus proteins. J. Med. Virol 49161–69 [Google Scholar]
  68. Janssen R, Bont L, Siezen CL, Hodemaekers HM, Ermers MJ. 68.  et al. 2007. Genetic susceptibility to respiratory syncytial virus bronchiolitis is predominantly associated with innate immune genes. J. Infect. Dis. 196:826–34 [Google Scholar]
  69. Jiang D-K, Ma X-P, Wu X, Peng L, Yin J. 69.  et al. 2015. Genetic variations in STAT4, C2, HLA-DRB1 and HLA-DQ associated with risk of hepatitis B virus-related liver cirrhosis. Sci. Rep. 5:16278 [Google Scholar]
  70. Jiang D-K, Sun J, Cao G, Liu Y, Lin D. 70.  et al. 2013. Genetic variants in STAT4 and HLA-DQ genes confer risk of hepatitis B virus–related hepatocellular carcinoma. Nat. Genet. 45:72–75 [Google Scholar]
  71. Jiang X, Su K, Tao J, Fan R, Xu Y. 71.  et al. 2016. Association of STAT4 polymorphisms with hepatitis B virus infection and clearance in Chinese Han population. Amino Acids 48:2589–98 [Google Scholar]
  72. Johnson PC, Mathewson JJ, DuPont HL, Greenberg HB. 72.  1990. Multiple-challenge study of host susceptibility to Norwalk gastroenteritis in US adults. J. Infect. Dis. 161:18–21 [Google Scholar]
  73. Johnson TR, Parker RA, Johnson JE, Graham BS. 73.  2003. IL-13 is sufficient for respiratory syncytial virus G glycoprotein-induced eosinophilia after respiratory syncytial virus challenge. J. Immunol. 170:2037–45 [Google Scholar]
  74. Kaslow RA, Carrington M, Apple R, Park L, Munoz A. 74.  et al. 1996. Influence of combinations of human major histocompatibility complex genes on the course of HIV-1 infection. Nat. Med. 2:405–11 [Google Scholar]
  75. Key FM, Peter B, Dennis MY, Huerta-Sánchez E, Tang W. 75.  et al. 2014. Selection on a variant associated with improved viral clearance drives local, adaptive pseudogenization of interferon lambda 4 (IFNL4). PLOS Genet 10:e1004681 [Google Scholar]
  76. Kim LH, Cheong HS, Namgoong S, Kim JO, Kim J-H. 76.  et al. 2015. Replication of genome wide association studies on hepatocellular carcinoma susceptibility loci of STAT4 and HLA-DQ in a Korean population. Infect. Genet. Evol. 33:72–76 [Google Scholar]
  77. Kirkpatrick A, Bidwell J, van den Brule AJC, Meijer CJLM, Pawade J, Glew S. 77.  2004. TNFα polymorphism frequencies in HPV-associated cervical dysplasia. Gynecol. Oncol. 92:675–79 [Google Scholar]
  78. Kodama D, Saito M, Matsumoto W, Sabouri AH, Izumo S. 78.  et al. 2004. Longer dinucleotide repeat polymorphism in matrix metalloproteinase-9 (MMP-9) gene promoter which correlates with higher HTLV-I Tax mediated transcriptional activity influences the risk of HTLV-I associated myelopathy/tropical spastic paraparesis (HAM/TSP). J. Neuroimmunol. 156:188–94 [Google Scholar]
  79. Kohaar I, Thakur N, Salhan S, Batra S, Singh V. 79.  et al. 2007. TNFα-308G/A polymorphism as a risk factor for HPV associated cervical cancer in Indian population. Cell Oncol 29:249–56 [Google Scholar]
  80. Kresfelder TL, Janssen R, Bont L, Pretorius M, Venter M. 80.  2011. Confirmation of an association between single nucleotide polymorphisms in the VDR gene with respiratory syncytial virus related disease in South African children. J. Med. Virol 831834–40 [Google Scholar]
  81. Kriesel JD, Jones BB, Matsunami N, Patel MK, St. Pierre CA. 81.  et al. 2011. C21orf91 genotypes correlate with herpes simplex labialis (cold sore) frequency: description of a cold sore susceptibility gene. J. Infect. Dis. 204:1654–62 [Google Scholar]
  82. Laguette N, Sobhian B, Casartelli N, Ringeard M, Chable-Bessia C. 82.  et al. 2011. SAMHD1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by Vpx. Nature 474:654–57 [Google Scholar]
  83. Lahti M, Lofgren J, Marttila R, Renko M, Klaavuniemi T. 83.  et al. 2002. Surfactant protein D gene polymorphism associated with severe respiratory syncytial virus infection. Pediatr. Res. 51:696–99 [Google Scholar]
  84. Lavanchy D. 84.  2004. Hepatitis B virus epidemiology, disease burden, treatment, and current and emerging prevention and control measures. J. Viral Hepatol. 11:97–107 [Google Scholar]
  85. Lazarczyk M, Pons C, Mendoza JA, Cassonnet P, Jacob Y, Favre M. 85.  2008. Regulation of cellular zinc balance as a potential mechanism of EVER-mediated protection against pathogenesis by cutaneous oncogenic human papillomaviruses. J. Exp. Med. 205:35–42 [Google Scholar]
  86. Li FY, Chaigne-Delalande B, Kanellopoulou C, Davis JC, Matthews HF. 86.  et al. 2011. Second messenger role for Mg2+ revealed by human T-cell immunodeficiency. Nature 475:471–76 [Google Scholar]
  87. Li Y, Si L, Zhai Y, Hu Y, Hu Z. 87.  et al. 2016. Genome-wide association study identifies 8p21.3 associated with persistent hepatitis B virus infection among Chinese. Nat. Commun. 7:11664 [Google Scholar]
  88. Lindesmith L, Moe C, Marionneau S, Ruvoen N, Jiang X. 88.  et al. 2003. Human susceptibility and resistance to Norwalk virus infection. Nat. Med. 9:548–53 [Google Scholar]
  89. Liu P, Wang X, Lee J-C, Teunis P, Hu S. 89.  et al. 2014. Genetic susceptibility to norovirus GII.3 and GII.4 infections in Chinese pediatric diarrheal disease. Pediatr. Infect. Dis. J. 33:e305–9 [Google Scholar]
  90. Liu R, Paxton WA, Choe S, Ceradini D, Martin SR. 90.  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]
  91. Löfgren J, Marttila R, Renko M, Rämet M, Hallman M. 91.  2010. Toll-like receptor 4 Asp299Gly polymorphism in respiratory syncytial virus epidemics. Pediatr. Pulmonol. 45:687–92 [Google Scholar]
  92. Löfgren J, Rämet M, Renko M, Marttila R, Hallman M. 92.  2002. Association between surfactant protein A gene locus and severe respiratory syncytial virus infection in infants. J. Infect. Dis. 185:283–89 [Google Scholar]
  93. Lopman BA, Trivedi T, Vicuna Y, Costantini V, Collins N. 93.  et al. 2015. Norovirus infection and disease in an Ecuadorian birth cohort: association of certain norovirus genotypes with host FUT2 secretor status. J. Infect. Dis. 211:1813–21 [Google Scholar]
  94. Mak CM, Lam C-W, Fong N-C, Siu W-K, Lee H-C. 94.  et al. 2011. Fatal viral infection-associated encephalopathy in two Chinese boys: a genetically determined risk factor of thermolabile carnitine palmitoyltransferase II variants. J. Hum. Genet. 56:617–21 [Google Scholar]
  95. Mansouri D, Mahdaviani SA, Khalilzadeh S, Mohajerani SA, Hasanzad M. 95.  et al. 2012. IL-2-inducible T-cell kinase deficiency with pulmonary manifestations due to disseminated Epstein-Barr virus infection. Int. Arch. Allergy Immunol. 158:418–22 [Google Scholar]
  96. Marionneau S, Airaud F, Bovin NV, Le Pendu J, Ruvoën-Clouet N. 96.  2005. Influence of the combined ABO, FUT2 and FUT3 polymorphism on susceptibility to Norwalk virus attachment. J. Infect. Dis. 192:1071–77 [Google Scholar]
  97. Marionneau S, Ruvoën N, Le Moullac-Vaidye B, Clement M, Cailleau-Thomas A. 97.  et al. 2002. Norwalk virus binds to histo-blood group antigens present on gastroduodenal epithelial cells of secretor individuals. Gastroenterology 122:1967–77 [Google Scholar]
  98. Martin MP, Gao X, Lee JH, Nelson GW, Detels R. 98.  et al. 2002. Epistatic interaction between KIR3DS1 and HLA-B delays the progression to AIDS. Nat. Genet. 31:429–34 [Google Scholar]
  99. Matsuura K, Isogawa M, Tanaka Y. 99.  2016. Host genetic variants influencing the clinical course of hepatitis B virus infection. J. Med. Virol 88371–79 [Google Scholar]
  100. McFarland AP, Horner SM, Jarret A, Joslyn RC, Bindewald E. 100.  et al. 2014. The favorable IFNL3 genotype escapes mRNA decay mediated by AU-rich elements and hepatitis C virus-induced microRNAs. Nat. Immunol. 15:72–79 [Google Scholar]
  101. McLaughlin RN Jr., Malik HS. 101.  2017. Genetic conflicts: the usual suspects and beyond. J. Exp. Biol. 220:6–17 [Google Scholar]
  102. McNally JD, Sampson M, Matheson LA, Hutton B, Little J. 102.  2014. Vitamin D receptor (VDR) polymorphisms and severe RSV bronchiolitis: a systematic review and meta-analysis. Pediatr. Pulmonol. 49:790–99 [Google Scholar]
  103. Migueles SA, Sabbaghian MS, Shupert WL, Bettinotti MP, Marincola FM. 103.  et al. 2000. HLA B*5701 is highly associated with restriction of virus replication in a subgroup of HIV-infected long term nonprogressors. PNAS 97:2709–14 [Google Scholar]
  104. Molinari NA, Ortega-Sanchez IR, Messonnier ML, Thompson WW, Wortley PM. 104.  et al. 2007. The annual impact of seasonal influenza in the US: measuring disease burden and costs. Vaccine 25:5086–96 [Google Scholar]
  105. Nair H, Nokes DJ, Gessner BD, Dherani M, Madhi SA. 105.  et al. 2010. Global burden of acute lower respiratory infections due to respiratory syncytial virus in young children: a systematic review and meta-analysis. Lancet 375:1545–55 [Google Scholar]
  106. Nakahata S, Saito Y, Hamasaki M, Hidaka T, Arai Y. 106.  et al. 2009. Alteration of enhancer of polycomb 1 at 10p11.2 is one of the genetic events leading to development of adult T-cell leukemia/lymphoma. Genes Chromosomes Cancer 48:768–76 [Google Scholar]
  107. Nordgren J, Nitiema LW, Ouermi D, Simpore J, Svensson L. 107.  2013. Host genetic factors affect susceptibility to norovirus infections in Burkina Faso. PLOS ONE 8:e69557 [Google Scholar]
  108. O'Brien TR, Pfeiffer RM, Paquin A, Lang Kuhs KA, Chen S. 108.  et al. 2015. Comparison of functional variants in IFNL4 and IFNL3 for association with HCV clearance. J. Hepatol. 63:1103–10 [Google Scholar]
  109. O'Brien TR, Prokunina-Olsson L, Donnelly RP. 109.  2014. IFN-λ4: the paradoxical new member of the interferon lambda family. J. Interferon. Cytokine Res. 34:829–38 [Google Scholar]
  110. Palendira U, Low C, Chan A, Hislop AD, Ho E. 110.  et al. 2011. Molecular pathogenesis of EBV susceptibility in XLP as revealed by analysis of female carriers with heterozygous expression of SAP. PLOS Biol 9:e1001187 [Google Scholar]
  111. Pan W, Song IS, Shin HJ, Kim MH, Choi YL. 111.  et al. 2011. Genetic polymorphisms in Na+-taurocholate co-transporting polypeptide (NTCP) and ileal apical sodium-dependent bile acid transporter (ASBT) and ethnic comparisons of functional variants of NTCP among Asian populations. Xenobiotica 41:501–10 [Google Scholar]
  112. Parrino TA, Schreiber DS, Trier JS, Kapikian AZ, Blacklow NR. 112.  1977. Clinical immunity in acute gastroenteritis caused by Norwalk agent. N. Engl. J. Med. 297:86–89 [Google Scholar]
  113. Patel AS, Karagas MR, Pawlita M, Waterboer T, Nelson HH. 113.  2008. Cutaneous human papillomavirus infection, the EVER2 gene and incidence of squamous cell carcinoma: a case-control study. Int. J. Cancer 122:2377–79 [Google Scholar]
  114. Payne DC, Currier RL, Staat MA, Sahni LC, Selvarangan R. 114.  et al. 2015. Epidemiologic association between FUT2 secretor status and severe rotavirus gastroenteritis in children in the United States. JAMA Pediatr 169:1040–45 [Google Scholar]
  115. Pelak K, Need AC, Fellay J, Shianna KV, Feng S. 115.  et al. 2011. Copy number variation of KIR genes influences HIV-1 control. PLOS Biol 9:e1001208 [Google Scholar]
  116. Peng L, Zhao Q, Li Q, Li M, Li C. 116.  et al. 2015. The p.Ser267Phe variant in SLC10A1 is associated with resistance to chronic hepatitis B. Hepatology 61:1251–60 [Google Scholar]
  117. Percher A, Ramakrishnan S, Thinon E, Yuan X, Yount JS, Hang HC. 117.  2016. Mass-tag labeling reveals site-specific and endogenous levels of protein S-fatty acylation. PNAS 113:4302–7 [Google Scholar]
  118. Pérez de Diego R, Sancho-Shimizu V, Lorenzo L, Puel A, Plancoulaine S. 118.  et al. 2010. Human TRAF3 adaptor molecule deficiency leads to impaired Toll-like receptor 3 response and susceptibility to herpes simplex encephalitis. Immunity 33:400–11 [Google Scholar]
  119. Plancoulaine S, Gessain A, Tortevoye P, Boland-Auge A, Vasilescu A. 119.  et al. 2006. A major susceptibility locus for HTLV-1 infection in childhood maps to chromosome 6q27. Hum. Mol. Genet. 15:3306–12 [Google Scholar]
  120. Poiesz BJ, Ruscetti FW, Gazdar AF, Bunn PA, Minna JD, Gallo RC. 120.  1980. Detection and isolation of type C retrovirus particles from fresh and cultured lymphocytes of a patient with cutaneous T-cell lymphoma. PNAS 77:7415–19 [Google Scholar]
  121. Prokunina-Olsson L, Muchmore B, Tang W, Pfeiffer RM, Park H. 121.  et al. 2013. A variant upstream of IFNL3 (IL28B) creating a new interferon gene IFNL4 is associated with impaired clearance of hepatitis C virus. Nat. Genet. 45:164–71 [Google Scholar]
  122. Puel A, Reichenbach J, Bustamante J, Ku CL, Feinberg J. 122.  et al. 2006. The NEMO mutation creating the most-upstream premature stop codon is hypomorphic because of a reinitiation of translation. Am. J. Hum. Genet. 78:691–701 [Google Scholar]
  123. Puthothu B, Forster J, Heinzmann A, Krueger M. 123.  2006. TLR-4 and CD14 polymorphisms in respiratory syncytial virus associated disease. Dis. Markers 22:303–8 [Google Scholar]
  124. Puthothu B, Krueger M, Forster J, Heinzmann A. 124.  2006. Association between severe respiratory syncytial virus infection and IL13/IL4 haplotypes. J. Infect. Dis. 193:438–41 [Google Scholar]
  125. Ramoz N, Rueda LA, Bouadjar B, Montoya LS, Orth G, Favre M. 125.  2002. Mutations in two adjacent novel genes are associated with epidermodysplasia verruciformis. Nat. Genet. 32:579–81 [Google Scholar]
  126. Rauch A, Kutalik Z, Descombes P, Cai T, Di Iulio J. 126.  et al. 2010. Genetic variation in IL28B is associated with chronic hepatitis C and treatment failure: a genome-wide association study. Gastroenterology 138:1338–45.e7 [Google Scholar]
  127. Rocha-Júnior MC, Haddad R, Cilião Alves DC, de Deus Wagatsuma VM, Mendes-Junior CT. 127.  et al. 2012. Interleukin-18 and interferon-gamma polymorphisms are implicated on proviral load and susceptibility to human T-lymphotropic virus type 1 infection. Tissue Antigens 80:143–50 [Google Scholar]
  128. Sabouri AH, Saito M, Lloyd AL, Vine AM, Witkover AW. 128.  et al. 2004. Polymorphism in the interleukin-10 promoter affects both provirus load and the risk of human T lymphotropic virus type I-associated myelopathy/tropical spastic paraparesis. J. Infect. Dis. 190:1279–85 [Google Scholar]
  129. Samson M, Libert F, Doranz BJ, Rucker J, Liesnard C. 129.  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]
  130. Sancho-Shimizu V, Pérez de Diego R, Lorenzo L, Halwani R, Alangari A. 130.  et al. 2011. Herpes simplex encephalitis in children with autosomal recessive and dominant TRIF deficiency. J. Clin. Investig. 121:4889–902 [Google Scholar]
  131. Sarasin-Filipowicz M, Oakeley EJ, Duong FH, Christen V, Terracciano L. 131.  et al. 2008. Interferon signaling and treatment outcome in chronic hepatitis C. PNAS 105:7034–39 [Google Scholar]
  132. Scheffner M, Werness BA, Huibregtse JM, Levine AJ, Howley PM. 132.  1990. The E6 oncoprotein encoded by human papillomavirus types 16 and 18 promotes the degradation of p53. Cell 63:1129–36 [Google Scholar]
  133. Schweitzer A, Horn J, Mikolajczyk RT, Krause G, Ott JJ. 133.  2015. Estimations of worldwide prevalence of chronic hepatitis B virus infection: a systematic review of data published between 1965 and 2013. Lancet 386:1546–55 [Google Scholar]
  134. Shea PR, Shianna KV, Carrington M, Goldstein DB. 134.  2013. Host genetics of HIV acquisition and viral control. Annu. Rev. Med. 64:203–17 [Google Scholar]
  135. Sorensen TI, Nielsen GG, Andersen PK, Teasdale TW. 135.  1988. Genetic and environmental influences on premature death in adult adoptees. N. Engl. J. Med. 318:727–32 [Google Scholar]
  136. Speelmon EC, Livingston-Rosanoff D, Li SS, Vu Q, Bui J. 136.  et al. 2006. Genetic association of the antiviral restriction factor TRIM5α with human immunodeficiency virus type 1 infection. J. Virol. 80:2463–71 [Google Scholar]
  137. St. Gelais C, Wu L. 137.  2011. SAMHD1: a new insight into HIV-1 restriction in myeloid cells. Retrovirology 8:55 [Google Scholar]
  138. Steffensen R, Carlier K, Wiels J, Levery SB, Stroud M. 138.  et al. 2000. Cloning and expression of the histo-blood group PkUDP-galactose: Galβ1-4Glcβ1-cer α1,4-galactosyltransferase. Molecular genetic basis of the p phenotype. J. Biol. Chem. 275:16723–29 [Google Scholar]
  139. Steininger C, Popow-Kraupp T, Laferl H, Seiser A, Godl I. 139.  et al. 2003. Acute encephalopathy associated with influenza A virus infection. Clin. Infect. Dis. 36:567–74 [Google Scholar]
  140. Stepensky P, Weintraub M, Yanir A, Revel-Vilk S, Krux F. 140.  et al. 2011. IL-2-inducible T-cell kinase deficiency: clinical presentation and therapeutic approach. Haematologica 96:472–76 [Google Scholar]
  141. Stoppelenburg AJ, von Hegedus JH, Huis in't Veld R, Bont L, Boes M. 141.  2014. Defective control of vitamin D receptor-mediated epithelial STAT1 signalling predisposes to severe respiratory syncytial virus bronchiolitis. J. Pathol. 232:57–64 [Google Scholar]
  142. Storey A, Thomas M, Kalita A, Harwood C, Gardiol D. 142.  et al. 1998. Role of a p53 polymorphism in the development of human papillomavirus-associated cancer. Nature 393:229–34 [Google Scholar]
  143. Sumegi J, Huang D, Lanyi A, Davis JD, Seemayer TA. 143.  et al. 2000. Correlation of mutations of the SH2D1A gene and Epstein-Barr virus infection with clinical phenotype and outcome in X-linked lymphoproliferative disease. Blood 96:3118–25 [Google Scholar]
  144. Sun Y, López CB. 144.  2017. The innate immune response to RSV: advances in our understanding of critical viral and host factors. Vaccine 35:481–88 [Google Scholar]
  145. Suppiah V, Moldovan M, Ahlenstiel G, Berg T, Weltman M. 145.  et al. 2009. IL28B is associated with response to chronic hepatitis C interferon-α and ribavirin therapy. Nat. Genet. 41:1100–4 [Google Scholar]
  146. Svensson A, Bergin AM, Lowhagen GB, Tunback P, Bellner L. 146.  et al. 2008. A 3′-untranslated region polymorphism in the TBX21 gene encoding T-bet is a risk factor for genital herpes simplex virus type 2 infection in humans. J. Gen. Virol. 89:2262–68 [Google Scholar]
  147. Tabeta K, Hoebe K, Janssen EM, Du X, Georgel P. 147.  et al. 2006. The Unc93b1 mutation 3d disrupts exogenous antigen presentation and signaling via Toll-like receptors 3, 7 and 9. Nat. Immunol. 7:156–64 [Google Scholar]
  148. Tanaka Y, Nishida N, Sugiyama M, Kurosaki M, Matsuura K. 148.  et al. 2009. Genome-wide association of IL28B with response to pegylated interferon-α and ribavirin therapy for chronic hepatitis C. Nat. Genet. 41:1105–9 [Google Scholar]
  149. Tapia LI, Ampuero S, Palomino MA, Luchsinger V, Aguilar N. 149.  et al. 2013. Respiratory syncytial virus infection and recurrent wheezing in Chilean infants: a genetic background?. Infect. Genet. Evol. 16:54–61 [Google Scholar]
  150. Tate G, Suzuki T, Kishimoto K, Mitsuya T. 150.  2004. Novel mutations of EVER1/TMC6 gene in a Japanese patient with epidermodysplasia verruciformis. J. Hum. Genet. 49:223–25 [Google Scholar]
  151. Terczyńska-Dyla E, Bibert S, Duong FH, Krol I, Jørgensen S. 151.  et al. 2014. Reduced IFNλ4 activity is associated with improved HCV clearance and reduced expression of interferon-stimulated genes. Nat. Commun. 5:5699 [Google Scholar]
  152. Thomas DL, Thio CL, Martin MP, Qi Y, Ge D. 152.  et al. 2009. Genetic variation in IL28B and spontaneous clearance of hepatitis C virus. Nature 461:798–801 [Google Scholar]
  153. Thomas NJ, DiAngelo S, Hess JC, Fan R, Ball MW. 153.  et al. 2009. Transmission of surfactant protein variants and haplotypes in children hospitalized with respiratory syncytial virus. Pediatr. Res. 66:70–73 [Google Scholar]
  154. Thrift AP, El-Serag HB, Kanwal F. 154.  2017. Global epidemiology and burden of HCV infection and HCV-related disease. Nat. Rev. Gastroenterol. Hepatol. 14:122–32 [Google Scholar]
  155. To KKW, Zhou J, Song Y-Q, Hung IFN, Ip WCT. 155.  et al. 2014. Surfactant protein B gene polymorphism is associated with severe influenza. Chest 145:1237–43 [Google Scholar]
  156. Trowsdale J, Knight JC. 156.  2013. Major histocompatibility complex genomics and human disease. Annu. Rev. Genom. Hum. Genet. 14:301–23 [Google Scholar]
  157. Tsukasaki K, Miller CW, Kubota T, Takeuchi S, Fujimoto T. 157.  et al. 2001. Tumor necrosis factor α polymorphism associated with increased susceptibility to development of adult T-cell leukemia/lymphoma in human T-lymphotropic virus type 1 carriers. Cancer Res 61:3770–74 [Google Scholar]
  158. Tu L-T, Liu F-P, Huang Y-C, Huang C-G, Yang S. 158.  et al. 2017. Genetic susceptibility to norovirus GII.4 Sydney strain infections in Taiwanese children. Pediatr. Infect. Dis. J. 36:353–57 [Google Scholar]
  159. Urban TJ, Thompson AJ, Bradrick SS, Fellay J, Schuppan D. 159.  et al. 2010. IL28B genotype is associated with differential expression of intrahepatic interferon-stimulated genes in patients with chronic hepatitis C. Hepatology 52:1888–96 [Google Scholar]
  160. Walboomers JMM, Jacobs MV, Manos MM, Bosch FX, Kummer JA. 160.  et al. 1999. Human papillomavirus is a necessary cause of invasive cervical cancer worldwide. J. Pathol. 189:12–19 [Google Scholar]
  161. Wang SS, Carreon JD, Hanchard B, Chanock S, Hisada M. 161.  2009. Common genetic variants and risk for non-Hodgkin lymphoma and adult T-cell lymphoma/leukemia in Jamaica. Int. J. Cancer 125:1479–82 [Google Scholar]
  162. Wang ZF, Zhang AL, Wan YM, Liu XN, Qiu C. 162.  et al. 2014. Early hypercytokinemia is associated with interferon-induced transmembrane protein-3 dysfunction and predictive of fatal H7N9 infection. PNAS 111:769–74 [Google Scholar]
  163. Weichert S, Koromyslova A, Singh BK, Hansman S, Jennewein S. 163.  et al. 2016. Structural basis for norovirus inhibition by human milk oligosaccharides. J. Virol. 90:4843–48 [Google Scholar]
  164. Werness BA, Levine AJ, Howley PM. 164.  1990. Association of human papillomavirus type-16 and type-18 E6 proteins with p53. Science 248:76–79 [Google Scholar]
  165. Westman JS, Benktander J, Storry JR, Peyrard T, Hult AK. 165.  et al. 2015. Identification of the molecular and genetic basis of PX2, a glycosphingolipid blood group antigen lacking on globoside-deficient erythrocytes. J. Biol. Chem. 290:18505–18 [Google Scholar]
  166. Westman JS, Hellberg A, Peyrard T, Hustinx H, Thuresson B, Olsson ML. 166.  2013. P1/P2 genotyping of known and novel null alleles in the P1PK and GLOB histo-blood group systems. Transfusion 53:2928–39 [Google Scholar]
  167. Whitley RJ, Kimberlin DW, Roizman B. 167.  1998. Herpes simplex viruses. Clin. Infect. Dis. 26:541–53 [Google Scholar]
  168. Wilson J, Rowlands K, Rockett K, Moore C, Lockhart E. 168.  et al. 2005. Genetic variation at the IL10 gene locus is associated with severity of respiratory syncytial virus bronchiolitis. J. Infect. Dis. 191:1705–9 [Google Scholar]
  169. Yan H, Zhong G, Xu G, He W, Jing Z. 169.  et al. 2012. Sodium taurocholate cotransporting polypeptide is a functional receptor for human hepatitis B and D virus. eLife 1:e00049 [Google Scholar]
  170. Yang JD, Roberts LR. 170.  2010. Hepatocellular carcinoma: a global view. Nat. Rev. Gastroenterol. Hepatol. 7:448–58 [Google Scholar]
  171. Yao D, Mizuguchi H, Yamaguchi M, Yamada H, Chida J. 171.  et al. 2008. Thermal instability of compound variants of carnitine palmitoyltransferase II and impaired mitochondrial fuel utilization in influenza-associated encephalopathy. Hum. Mutat. 29:718–27 [Google Scholar]
  172. Yount JS, Moltedo B, Yang Y-Y, Charron G, Moran TM. 172.  et al. 2010. Palmitoylome profiling reveals S-palmitoylation-dependent antiviral activity of IFITM3. Nat. Chem. Biol. 6:610–14 [Google Scholar]
  173. Zhang M, Lu Y, Zhang X, Lu A, Wang L, Chen C. 173.  2016. Interleukin-4 polymorphism is associated with severity of respiratory syncytial virus infection. J. Paediatr. Child Health 52:25–29 [Google Scholar]
  174. Zhang S-Y, Herman M, Ciancanelli MJ, Pérez de Diego R, Sancho-Shimizu V. 174.  et al. 2013. TLR3 immunity to infection in mice and humans. Curr. Opin. Immunol. 25:19–33 [Google Scholar]
  175. Zhang S-Y, Jouanguy E, Ugolini S, Smahi A, Elain G. 175.  et al. 2007. TLR3 deficiency in patients with herpes simplex encephalitis. Science 317:1522–27 [Google Scholar]
  176. Zhang Y-H, Makvandi-Nejad S, Qin L, Zhao Y, Zhang T. 176.  et al. 2015. Interferon-induced transmembrane protein-3 rs12252-C is associated with rapid progression of acute HIV-1 infection in Chinese MSM cohort. AIDS 29:889–94 [Google Scholar]
  177. Zhang Y-H, Zhao Y, Li N, Peng Y-C, Giannoulatou E. 177.  et al. 2013. Interferon-induced transmembrane protein-3 genetic variant rs12252-C is associated with severe influenza in Chinese individuals. Nat. Commun. 4:1418 [Google Scholar]
  178. Zhou J, Zhang X, Liu S, Wang Z, Chen Q. 178.  et al. 2016. Genetic association of TLR4 Asp299Gly, TLR4 Thr399Ile, and CD14 C-159T polymorphisms with the risk of severe RSV infection: a meta-analysis. Influenza Other Respir. Viruses 10:224–33 [Google Scholar]
  179. Zhu X, Petrovski S, Xie P, Ruzzo EK, Lu YF. 179.  et al. 2015. Whole-exome sequencing in undiagnosed genetic diseases: interpreting 119 trios. Genet. Med. 17:774–81 [Google Scholar]
/content/journals/10.1146/annurev-genet-120116-023425
Loading
/content/journals/10.1146/annurev-genet-120116-023425
Loading

Data & Media loading...

  • Article Type: Review Article
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