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The phylogenomics of evolving virus virulence


How virulence evolves after a virus jumps to a new host species is central to disease emergence. Our current understanding of virulence evolution is based on insights drawn from two perspectives that have developed largely independently: long-standing evolutionary theory based on limited real data examples that often lack a genomic basis, and experimental studies of virulence-determining mutations using cell culture or animal models. A more comprehensive understanding of virulence mutations and their evolution can be achieved by bridging the gap between these two research pathways through the phylogenomic analysis of virus genome sequence data as a guide to experimental study.

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  1. 1.

    Bull, J. J. & Lauring, A. S. Theory and empiricism in virulence evolution. PLOS Pathog. 10, e1004387 (2014). This review provides insight into how virulence theory might be united with empirical data and what is needed to better understand the relationship between virulence and transmissibility.

  2. 2.

    McMahon, D. P. et al. Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Proc. Biol. Sci. 283, 20160811 (2016).

  3. 3.

    Power, R. A., Parkhill, J. & de Oliveira, T. Microbial genome-wide association studies: lessons from human GWAS. Nat. Rev. Genet 18, 41–50 (2017).

  4. 4.

    Ansari, M. A. et al. Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus. Nat. Genet. 49, 666 (2017).

  5. 5.

    Yang, J. et al. Unbiased parallel detection of viral pathogens in clinical samples by use of a metagenomic approach. J. Clin. Microbiol. 49, 3463–3469 (2011).

  6. 6.

    Shi, M. et al. Redefining the invertebrate virosphere. Nature 540, 539–543 (2016).

  7. 7.

    Shi, M. et al. The evolutionary history of vertebrate RNA viruses. Nature 556, 197–202 (2018).

  8. 8.

    Stern, A. et al. The evolutionary pathway to virulence of an RNA virus. Cell 169, 35–46 (2017). This study is a powerful example of the analytical approach outlined here. The authors use phylogenetics and experimental study to describe the evolutionary pathways by which OPV strains become pathogenic and propose a framework for vaccine design.

  9. 9.

    Rossi, S. L., Ebel, G. D., Shan, C., Shi, P.-Y. & Vasilakis, N. Did Zika virus mutate to cause severe outbreaks? Trends Microbiol. (2018).

  10. 10.

    Alizon, S. & Lion, S. Within-host parasite cooperation and the evolution of virulence. Proc. Biol. Sci. 278, 3738–3747 (2011).

  11. 11.

    Kerr, P. J. et al. Myxoma virus and the leporipoxviruses: an evolutionary paradigm. Viruses 7, 1029–1061 (2015).

  12. 12.

    Ebihara, H. et al. Molecular determinants of Ebola virus virulence in mice. PLOS Pathog. 2, e73 (2006).

  13. 13.

    Jimenez-Guardeño, J. M. et al. The PDZ-binding motif of severe acute respiratory syndrome coronavirus envelope protein is a determinant of viral pathogenesis. PLOS Pathog. 10, e1004320 (2014).

  14. 14.

    Kataoka, C. et al. The role of VP1 amino acid residue 145 of enterovirus 71 in viral fitness and pathogenesis in a cynomolgus monkey model. PLOS Pathog. 11, e1005033 (2015).

  15. 15.

    Song, H., Santi, N., Evensen, O. & Vakharia, V. N. Molecular determinants of infectious pancreatic necrosis virus virulence and cell culture adaptation. J. Virol. 79, 10289–10299 (2005).

  16. 16.

    Uraki, R. et al. Virulence determinants of pandemic A(H1N1)2009 influenza virus in a mouse model. J. Virol. 87, 2226–2233 (2013).

  17. 17.

    Liu, J. et al. Reverse engineering field isolates of myxoma virus demonstrates that some gene disruptions or loss of function do not explain virulence changes observed in the field. J. Virol. 91, e01289–17 (2017).

  18. 18.

    Oh, D. Y. & Hurt, A. C. Using ferrets as an animal model for investigating influenza antiviral effectiveness. Front. Microbiol. 7, 80 (2016).

  19. 19.

    Dudas, G. et al. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature 544, 309–315 (2017).

  20. 20.

    Faria, N. R. et al. Epidemic establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature 546, 406–410 (2017).

  21. 21.

    Holmes, E. C., Dudas, G., Rambaut, A. & Andersen, K. G. The evolution of Ebola virus: insights from the 2013–2016 epidemic. Nature 358, 193–200 (2016).

  22. 22.

    Hadfield, J. et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics (2018).

  23. 23.

    Lässig, M. & Łuksza, M. Can we read the future from a tree? eLife 3, e05060 (2014).

  24. 24.

    Neher, R. A., Russell, C. A. & Shraiman, B. I. Predicting evolution from the shape of genealogical trees. eLife 3, e03568 (2014).

  25. 25.

    Longdon, B. et al. The causes and consequences of changes in virulence following pathogen host shifts. PLOS Pathog. 11, e1004728 (2015). This study combines experimental cross-species transmission and phylogenetics to reveal the nature of virulence evolution in a Drosophila virus. The results show that virulence levels were predictable from the host phylogeny.

  26. 26.

    Walter, S. et al. Differential infection patterns and recent evolutionary origins of equine hepaciviruses in donkeys. J. Virol. 91, e01711–e01716 (2016).

  27. 27.

    Leroy, E. M. et al. Fruit bats as reservoirs of Ebola virus. Nature 438, 575–566 (2005).

  28. 28.

    Allocati, N. et al. Bat-man disease transmission: zoonotic pathogens from wildlife reservoirs to human populations. Cell Death Dis. 2, 16048 (2016).

  29. 29.

    Truyen, U., Evermann, J. F., Vieler, E. & Parrish, C. R. Evolution of canine parvovirus involved loss and gain of feline host range. Virology 215, 186–189 (1996).

  30. 30.

    Allison, A. B. et al. Host-specific parvovirus evolution in nature is recapitulated by in vitro adaptation to different carnivore species. PLOS Pathog. 10, e1004475 (2014).

  31. 31.

    Geoghegan, J. L., Senior, A. M., Di Giallonardo, F. & Holmes, E. C. Virological factors that increase the transmissibility of emerging human viruses. Proc. Natl Acad. Sci. USA 113, 4170–4175 (2016).

  32. 32.

    Anderson, R. M. & May, R. M. Coevolution of hosts and parasites. Parasitology 85, 411–426 (1982).

  33. 33.

    Bull, J. J. Virulence. Evolution 48, 1423–1437 (1994).

  34. 34.

    Ebert, D. in Evolution in Health and Disease (ed. Stearns, S. C.) 161–172 (Oxford Univ. Press, Oxford, 1999).

  35. 35.

    Ebert, D. & Bull, J. J. Challenging the trade-off model for the evolution of virulence: is virulence management feasible? Trends Microbiol. 11, 15–20 (2003).

  36. 36.

    Ewald, P. W. Evolution of Infectious Diseases. (Oxford Univ. Press, Oxford, 1994).

  37. 37.

    Read, A. F. The evolution of virulence. Trends Microbiol. 2, 73–76 (1994).

  38. 38.

    Furió, V. et al. Relationship between within-host fitness and virulence in the vesicular stomatitis virus: correlation with partial decoupling. J. Virol. 86, 12228–12236 (2012).

  39. 39.

    Lion, S. & Metz, J. A. J. Beyond R0 maximisation: on pathogen evolution and environmental dimensions. Trends Ecol. Evol. 33, 458–473 (2018). This article argues that current formulations of R 0 are too simplistic to understand pathogen evolution and that a more complex, multidimensional approach is needed.

  40. 40.

    Fraser, C., Hollingsworth, T. D., Chapman, R., de Wolf, F. & Hanage, W. P. Variation in HIV-1 set-point viral load: epidemiological analysis and an evolutionary hypothesis. Proc. Natl Acad. Sci. USA 104, 17441–17446 (2007).

  41. 41.

    Alizon, S., Hurford, A., Mideo, N. & Van Baalen, M. Virulence evolution and the trade-off hypothesis: history, current state of affairs & the future. J. Evol. Biol. 22, 245–259 (2009). This paper provides an overview of the theory that there is a trade-off between virulence and transmissibility, highlighting areas in which the theory has been challenged and extended over the past 20 years.

  42. 42.

    Alizon, S. & Michalakis, Y. Adaptive virulence evolution: the good old fitness-based approach. Trends Ecol. Evol. 30, 248–254 (2015).

  43. 43.

    Lipsitch, M. & Moxon, E. R. Virulence and transmissibility of pathogens: what is the relationship? Trends Microbiol. 5, 31–37 (1997).

  44. 44.

    Novella, I. S., Elena, S. F., Moya, A., Domingo, E. & Holland, J. J. Size of genetic bottlenecks leading to virus fitness loss is determined by mean initial population fitness. J. Virol. 69, 2869–2872 (1995).

  45. 45.

    Betancourt, M., Escriu, F., Fraile, A. & García-Arenal, F. Virulence evolution of a generalist plant virus in a heterogeneous host system. Evol. Appl. 6, 875–890 (2013).

  46. 46.

    Di Giallonardo, F. & Holmes, E. C. Virus biocontrol: grand experiments in disease emergence and evolution. Trends Microbiol. 23, 83–90 (2015).

  47. 47.

    Willemsen, A., Zwart, M. P. & Elena, S. F. High virulence does not necessarily impede viral adaptation to a new host: a case study using a plant RNA virus. BMC Evol. Biol 17, 25 (2017).

  48. 48.

    De Roode, J. C. et al. Virulence and competitive ability in genetically diverse malaria infections. Proc. Natl Acad. Sci. USA 102, 7624–7628 (2005).

  49. 49.

    Levin, B. R. & Bull, J. J. Short-sighted evolution and the virulence of pathogenic microorganisms. Trends Microbiol. 2, 76–81 (1994).

  50. 50.

    Lloyd-Smith, J. O. et al. Epidemic dynamics at the human-animal interface. Science 326, 1362–1367 (2009).

  51. 51.

    Bergstrom, C. T., McElhany, P. & Real, L. A. Transmission bottlenecks as determinants of virulence in rapidly evolving pathogens. Proc. Natl Acad. Sci. USA 96, 5095–5100 (1999).

  52. 52.

    Bolker, B. M., Nanda, A. & Shah, D. Transient virulence of emerging pathogens. J. R. Soc. Interface 7, 811–822 (2010).

  53. 53.

    Brown, S. P., Cornforth, D. M. & Mideo, N. Evolution of virulence in opportunistic pathogens: generalism, plasticity, and control. Trends Microbiol. 20, 336–342 (2012).

  54. 54.

    Dolan, P. T., Whitfield, Z. J. & Andino, R. Mapping the evolutionary potential of RNA viruses. Cell Host Microbe 23, 435–446 (2018). This article discusses what aspects of virus evolution might be predictable, including virulence, and how this can be tested and highlights the importance of parallel evolution as a marker of adaptation.

  55. 55.

    Sackman, A. M. et al. Mutation driven parallel evolution during viral adaptation. Mol. Biol. Evol. 34, 3243–3253 (2017).

  56. 56.

    Stewart, C.-B., Schilling, J. W. & Wilson, A. C. Convergent evolution of lysozyme sequences? Nature 332, 788 (1988).

  57. 57.

    Frickel, J., Feulner, P. G. D., Karakoc, E. & Becks, L. Population size changes and selection drive patterns of parallel evolution in a host-virus system. Nat. Commun. 9, 1706 (2018).

  58. 58.

    Brault, A. C. et al. A single positively selected West Nile viral mutation confers increased avian virogenesis in American crows. Nat. Genet. 39, 1162–1166 (2007). This study demonstrates that positive selection on a single amino acid substitution within the genome of WNV was responsible for increased virulence in the American crow.

  59. 59.

    Longdon, B. et al. Host shifts result in parallel genetic changes when viruses evolve in closely related species. PLOS Pathog. 14, e1006951 (2018).

  60. 60.

    Weaver, S. et al. Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes. Mol. Biol. Evol. 35, 773–777 (2018).

  61. 61.

    Kryazhimskiy, S. & Plotkin, J. B. The population genetics of dN/dS. PLOS Genet. 4, e1000304 (2008).

  62. 62.

    Pybus, O. G. et al. Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution. Mol. Biol. Evol. 24, 845–852 (2007).

  63. 63.

    Bhatt, S., Holmes, E. C. & Pybus, O. G. The genomic rate of molecular adaptation of the human influenza A virus. Mol. Biol. Evol. 28, 2443–2451 (2011).

  64. 64.

    Geoghegan, J. L., Senior, A. M. & Holmes, E. C. Pathogen population bottlenecks and adaptive landscapes: overcoming the barriers to disease emergence. Proc. Biol. Sci. 283, 1837 (2016).

  65. 65.

    Morley, V. J. & Turner, P. E. Dynamics of molecular evolution in RNA virus populations depend on sudden versus gradual environmental change. Evolution 71, 872–883 (2017).

  66. 66.

    Taubenberger, J. K. et al. Characterization of the 1918 influenza virus polymerase genes. Nature 437, 889–893 (2005).

  67. 67.

    Sawyer, S. L., Emerman, M. & Malik, H. S. Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G. PLOS Biol. 2, e275 (2004).

  68. 68.

    Sawyer, S. L., Wu, L. I., Emerman, M. & Malik, H. S. Positive selection of primate TRIM5alpha identifies a critical species-specific retroviral restriction domain. Proc. Natl Acad. Sci. USA 102, 2832–2837 (2005).

  69. 69.

    Bedhomme, S., Hillung, J. & Elena, S. F. Emerging viruses: why they are not jacks of all trades? Curr. Opin. Virol. 10, 1–6 (2015).

  70. 70.

    Urbanowicz, R. A. et al. Human adaptation of Ebola virus during the West African outbreak. Cell 167, 1079–1087 (2016).

  71. 71.

    Simon-Loriere, E. & Holmes, E. C. Why do RNA viruses recombine? Nat. Rev. Microbiol. 9, 617–626 (2011).

  72. 72.

    Di Giallonardo, F. et al. Fluid spatial dynamics of West Nile virus in the USA: rapid spread in a permissive host environment. J. Virol. 90, 862–872 (2016).

  73. 73.

    LaDeau, S. L., Kilpatrick, A. M. & Marra, P. P. West Nile virus emergence and large-scale declines of North American bird populations. Nature 447, 710–713 (2007).

  74. 74.

    Kilpatrick, A. M. Globalization, land use, and the invasion of West Nile virus. Science 334, 323–327 (2011).

  75. 75.

    Guan, Y. et al. H5N1 influenza: a protean pandemic threat. Proc. Natl Acad. Sci. USA 101, 8156–8161 (2004).

  76. 76.

    Webby, R. J. & Webster, R. G. Are we ready for pandemic influenza? Science 302, 1519–1522 (2003).

  77. 77.

    Lam, T. T.-Y. et al. Dissemination, divergence and establishment of H7N9 influenza viruses in China. Nature 522, 102–105 (2015).

  78. 78.

    Yang, L. et al. Genesis and spread of newly emerged highly pathogenic H7N9 avian viruses in mainland China. J. Virol. 91, e01277–e01217 (2017).

  79. 79.

    Qi, W. et al. Emergence and adaptation of a novel highly pathogenic H7N9 influenza virus in birds and humans from a 2013 human-infecting low pathogenic ancestor. J. Virol. 92, e00921–17 (2018).

  80. 80.

    Lipsitch, M. et al. Viral factors in influenza pandemic risk assessment. eLife 5, e18491 (2016).

  81. 81.

    Baigent, S. J. & McCauley, J. W. Influenza type A in humans, mammals and birds: determinants of virus virulence, host-range and interspecies transmission. Bioessays 25, 657–671 (2003).

  82. 82.

    Horimoto, T. & Kawaoka, Y. Influenza: lessons from past pandemics, warnings from current incidents. Nat. Rev. Microbiol. 3, 591–600 (2005).

  83. 83.

    Monne, I. et al. Emergence of a highly pathogenic avian influenza virus from a low pathogenic progenitor. J. Virol. 88, 4375–4388 (2014).

  84. 84.

    Russell, C. A. et al. The potential for respiratory droplet-transmissible A/H5N1 influenza virus to evolve in a mammalian host. Science 336, 1541–1547 (2012).

  85. 85.

    Hatta, M., Gao, P., Halfmann, P. & Kawaoka, Y. Molecular basis for high virulence of Hong Kong H5N1 influenza A viruses. Science 293, 1840–1842 (2001).

  86. 86.

    Pearce, M. B. et al. Enhanced virulence of clade highly pathogenic avian influenza A H5N1 viruses in ferrets. Virology 502, 114–122 (2017).

  87. 87.

    Nogales, A., Martinez-Sobrido, L., Topham, D. J. & DeDiego, M. L. NS1 protein amino acid changes D189N and V194I affect interferon responses, thermosensitivity, and virulence of circulating H3N2 human influenza A viruses. J.Virol. 91, e01930–16 (2017).

  88. 88.

    Jackson, D., Hossain, M. J., Hickman, D., Perez, D. R. & Lamb, R. A. A new influenza virus virulence determinant: the NS1 protein four C-terminal residues modulate pathogenicity. Proc. Natl Acad. Sci. USA 105, 4381–4386 (2008).

  89. 89.

    Kash, J. C. et al. Genomic analysis of increased host immune and cell death responses induced by 1918 influenza virus. Nature 443, 578–581 (2006). This paper presents a comprehensive study of the virulence of the 1918 influenza virus in a mouse model, revealing the importance of virus–host interactions involving a wide set of interacting virus genes.

  90. 90.

    Bae, J.-Y. et al. A single amino acid in the polymerase acidic protein determines the pathogenicity of influenza B viruses. J. Virol. 92, e00259–e00218 (2018).

  91. 91.

    Fenner, F. Biological control as exemplified by smallpox eradication and myxomatosis. Proc. R. Soc. B. 218, 259–285 (1983).

  92. 92.

    Fenner, F. & Marshall, I. D. A comparison of the virulence for European rabbits (Oryctolagus cuniculus) of strains of myxoma virus recovered in the field in Australia, Europe and America. J. Hyg. 55, 149–191 (1957).

  93. 93.

    Fenner, F. & Ratcliffe, F. N. Myxomatosis (Cambridge Univ. Press, Cambridge, 1965).

  94. 94.

    Kerr, P. J. et al. Evolutionary history and attenuation of myxoma virus on two continents. PLOS Pathog. 8, e1002950 (2012). This article presents the first large-scale phylogenomic analysis of MYXV and shows that, despite parallel evolution at the phenotypic (that is, virulence grade) level, different virus mutations were responsible for evolution of virulence in both Australia and Europe.

  95. 95.

    Kerr, P. J. et al. Genome scale evolution of myxoma virus (MYXV) reveals host-pathogen adaptation and rapid geographic spread. J. Virol. 87, 12900–12915 (2013).

  96. 96.

    Elena, S. F., Carrasco, P., Daròs, J. A. & Sanjuán, R. Mechanisms of genetic robustness in RNA viruses. EMBO Rep. 7, 168–173 (2006).

  97. 97.

    Gandon, S., Mackinnon, M. J., Nee, S. & Read, A. F. Imperfect vaccines and the evolution of pathogen virulence. Nature 414, 751–756 (2001).

  98. 98.

    Smith, T. Imperfect vaccines and imperfect models. Trends Ecol. Evol. 17, 154–156 (2002).

  99. 99.

    Read, A. F. et al. Imperfect vaccination can enhance the transmission of highly virulent pathogens. PLOS Biol. 13, e1002198 (2015). This paper presents a clear demonstration that imperfect vaccination was responsible for increased virulence in the case of the MDV of chickens and considers the evolutionary implications of imperfect vaccination in general.

  100. 100.

    Kamil, J. P. et al. vLIP, a viral lipase homologue, is a virulence factor of Marek’s disease virus. J. Virol. 79, 6984–6996 (2005).

  101. 101.

    Trimpert, J. et al. A phylogenomic analysis of Marek’s disease virus reveals independent paths to virulence in Eurasia and North America. Evol. Appl. 10, 1091–1101 (2017).

  102. 102.

    Mackinnon, M. J. & Read, A. F. Immunity promotes virulence evolution in a malaria model. PLOS Biol. 2, e230 (2004).

  103. 103.

    Carre, N. et al. Has the rate of progression to AIDS changed in recent years? AIDS 11, 1611–1618 (1997).

  104. 104.

    Fraser, C. et al. Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective. Science 343, 1243727 (2014). This key study of the evolution of HIV virulence focuses on the factors that determine the SPVL and shows the importance of virus genetic traits in shaping SPVL and hence disease severity.

  105. 105.

    Galai, N. et al. Temporal trends of initial CD4 cell counts following human immunodeficiency virus seroconversion in Italy, 1985-1992. The human immunodeficiency virus Italian seroconversion study. Am. J. Epidemiol. 143, 278–282 (1996).

  106. 106.

    Herbeck, J. T. et al. Is the virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease progression and transmission. AIDS 26, 193–205 (2012).

  107. 107.

    Vanhems, P., Lambert, J., Guerra, M., Hirschel, B. & Allard, R. Association between the rate of CD4+ T cell decrease and the year of human immunodeficeny virus (HIV) type 1 seroconversion among persons enrolled in the Swiss HIV cohort study. J. Infect. Dis. 180, 1803–1808 (1999).

  108. 108.

    Arien, K. K., Vanham, G. & Arts, E. J. Is HIV-1 evolving to a less virulent form in humans? Nat. Rev. Microbiol. 5, 141–151 (2007).

  109. 109.

    Claiborne, D. T. et al. Replicative fitness of transmitted HIV-1 drives acute immune activation, proviral load in memory CD4+ T cells, and disease progression. Proc. Natl Acad. Sci. USA 112, E1480–E1489 (2015).

  110. 110.

    Miura, T. et al. Impaired replication capacity of acute/early viruses in persons who become HIV controllers. J. Virol. 84, 7581–7591 (2010).

  111. 111.

    Blanquart, F. et al. Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe. PLOS Biol. 15, e2001855 (2017).

  112. 112.

    Fellay, J. et al. Common genetic variation and the control of HIV-1 in humans. PLOS Genet. 5, e1000791 (2009).

  113. 113.

    Alizon, S. et al. Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load. PLOS Pathog. 6, e1001123 (2010).

  114. 114.

    Blanquart, F. et al. A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda. eLife 5, e20492 (2016).

  115. 115.

    Sofonea, M. T., Aldakak, L., Boullosa, L. F. V. V. & Alizon, S. Can Ebola virus evolve to be less virulent in humans? J. Evol. Biol. 31, 382–392 (2018).

  116. 116.

    Diehl, W. E. et al. Ebola virus glycoprotein with increased infectivity dominated the 2013-2016 epidemic. Cell 167, 1088–1098 (2016). This study uses a combination of phylogenetics and experimental study to demonstrate the importance of the A82V substitution in the EBOV glycoprotein to viral infectivity and suggests that A82V has increased virus virulence.

  117. 117.

    Ng, M. et al. Filovirus receptor NPC1 contributes to species-specific patterns of ebolavirus susceptibility in bats. eLife 4, e11785 (2015).

  118. 118.

    Marzi, A. et al. Recently identified mutations in the Ebola virus-Makona genome do not alter pathogenicity in animal models. Cell Rep. 23, 1806–1816 (2018).

  119. 119.

    Chan, J. F., Choi, G. K., Yip, C. C., Cheng, V. C. & Yuen, K. Y. Zika fever and congenital Zika syndrome: an unexpected emerging arboviral disease. J. Infect. 72, 507–524 (2016).

  120. 120.

    Cao-Lormeau, V. M. et al. Guillain–Barré syndrome outbreak associated with Zika virus infection in French Polynesia: a case–control study. Lancet 387, 1531–1539 (2016).

  121. 121.

    Fauci, A. S. & Morens, D. M. Zika virus in the Americas — yet another arbovirus threat. N. Engl. J. Med. 374, 601–604 (2016).

  122. 122.

    Simonin, Y., van Riel, D., Van de Perre, P., Rockx, B. & Salinas, S. Differential virulence between Asian and African lineages of Zika virus. PLOS Negl. Trop. Dis. 11, e0005821 (2017).

  123. 123.

    Grubaugh, N. D., Faria, N. R., Andersen, K. G. & Pybus, O. G. Genomic insights into Zika virus emergence and spread. Cell 172, 1160–1162 (2018).

  124. 124.

    Liu, Y. et al. Evolutionary enhancement of Zika virus infectivity in Aedes aegypti mosquitoes. Nature 545, 482–486 (2017). The results of this study suggest that a mutation in the NS1 protein in the ZIKV associated with the recent outbreak in the Americas causes increased infectivity in Aedes aegypti mosquitoes, in turn elevating epidemic potential.

  125. 125.

    Yuan, L. et al. A single mutation in the prM protein of Zika virus contributes to fetal microcephaly. Science 358, 933–936 (2017).

  126. 126.

    Rosenfeld, A. B., Doobin, D. J., Warren, A. L., Racaniello, V. R. & Vallee, R. B. Replication of early and recent Zika virus isolates throughout mouse brain development. Proc. Natl Acad. Sci. USA 114, 12273–12278 (2017).

  127. 127.

    Firth, C. & Lipkin, W. I. The genomics of emerging pathogens. Annu. Rev. Genom. Hum. Genet. 14, 281–300 (2013).

  128. 128.

    Gardy, J. L. & Loman, N. J. Towards a genomics-informed, real-time, global pathogen surveillance system. Nat. Rev. Genet. 19, 9–20 (2018).

  129. 129.

    Shi, M., Zhang, Y.-Z. & Holmes, E. C. Meta-transcriptomics and the evolutionary biology of RNA viruses. Virus Res. 243, 83–90 (2018).

  130. 130.

    Geoghegan, J. L. & Holmes, E. C. Predicting virus emergence amidst evolutionary noise. Open Biol. 7, 170189 (2017).

  131. 131.

    Lighten, J. & van Oosterhout, C. Biocontrol of common carp in Australia poses risks to biosecurity. Nat. Ecol. Evol. 1, 87 (2017).

  132. 132.

    Marshall, J. et al. Biocontrol of invasive carp: risks abound. Science 359, 877 (2018).

  133. 133.

    McColl, K. A., Sheppard, A. W. & Barwick, M. Safe and effective biocontrol of common carp. Nat. Ecol. Evol. 1, 134 (2017).

  134. 134.

    McColl, K. A., Sunarto, A. & Holmes, E. C. Cyprinid herpesvirus 3 and its evolutionary future as a biological control agent for carp in Australia. Virol. J. 13, 206 (2016).

  135. 135.

    Andre, J. B. & Hochberg, M. E. Virulence evolution in emerging infectious diseases. Evolution 59, 1406–1412 (2005).

  136. 136.

    Chahroudi, A., Bosinger, S. E., Vanderford, T. H., Paiardini, M. & Silvestri, G. Natural SIV hosts: Showing AIDS the door. Science 335, 1188–1193 (2012).

  137. 137.

    Silvestri, G., Paiardini, M., Pandrea, I., Lederman, M. M. & Sodora, D. L. Understanding the benign nature of SIV infection in natural hosts. J. Clin. Invest. 117, 3148–3154 (2007).

  138. 138.

    Keele, B. F. et al. Increased mortality and AIDS-like immunopathology in wild chimpanzees infected with SIVcpz. Nature 460, 515–519 (2009). The results of this study suggest that simian immunodeficiency virus in chimpanzees, which is the ancestor of HIV, increases mortality in these animals, although with less overt disease than in humans.

  139. 139.

    Crawford, P. C. et al. Transmission of equine influenza virus to dogs. Science 310, 482–485 (2005).

  140. 140.

    Parrish, C. R., Murcia, P. R. & Holmes, E. C. Influenza virus reservoirs and intermediate hosts: dogs, horses, and new possibilities for influenza virus exposure of humans. J. Virol. 89, 2990–2994 (2015).

  141. 141.

    Feng, K. H. et al. Equine and canine influenza viruses H3N8 viruses show minimal biological differences despite phylogenetic divergence. J. Virol. 89, 6860–6873 (2015).

  142. 142.

    Bourhy, H., Dautry-Varsat, A., Hotez, P. J. & Salomon, J. Rabies, still neglected after 125 years of vaccination. PLOS Negl Trop. Dis. 4, e839 (2010).

  143. 143.

    Garver, K. A., Batts, W. N. & Kurath, G. Virulence comparisons of infectious hematopoietic necrosis virus U and M genogroups in sockeye slamon and rainbow trout. J. Aquat. Anim. Health 18, 232–243 (2006).

  144. 144.

    Penaranda, M. M., Purcell, M. K. & Kurath, G. Differential virulence mechanisms of infectious hematopoietic necrosis virus in rainbow trout (Oncorhynchus mykiss) include host entry and virus replication kinetics. Gen. J. Virol. 90, 2172–2182 (2009).

  145. 145.

    Kerr, P. J. et al. The evolution of myxoma virus: genomic and phenotypic characterization of isolates from Great Britain reveals multiple successful evolutionary pathways distinct from those in Australia. PLOS Pathog. 13, e1006252 (2017).

  146. 146.

    Kerr, P. J. et al. Next step in the ongoing arms race between myxoma virus and wild rabbits in Australia is a novel disease phenotype. Proc. Natl Acad. Sci. USA 114, 9397–9402 (2017).

  147. 147.

    Jiao, P. et al. A single-amino-acid substitution in the NS1 protein changes the pathogenicity of H5N1 avian influenza viruses in mice. J. Virol. 82, 1146–1154 (2008).

  148. 148.

    Cotter, C. R., Jin, H. & Chen, Z. A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity. PLOS Pathog. 10, e1003831 (2014).

  149. 149.

    Gromowski, G. D., Firestone, C. Y. & Whitehead, S. S. Genetic determinants of Japanese encephalitis virus vaccine strain SA14-14-2 that govern attenuation of virulence in mice. J. Virol. 89, 6328–6337 (2015).

  150. 150.

    He, W. et al. Effect of an 88-amino-acid deletion in nsp2 of porcine reproductive and respiratory syndrome virus on virus replication and cytokine responses in vitro. Arch. Virol. 163, 1489–1501 (2018).

  151. 151.

    Yu, X. et al. The glutamic residue at position 402 in the C-terminus of Newcastle disease virus nucleoprotein is critical for the virus. Sci. Rep. 7, 17471 (2017).

  152. 152.

    Panzarin, V. et al. Low evolutionary rate of infectious pancreatic necrosis virus (IPNV) in Italy is associated with reduced virulence in trout. Virus Evol. 4, vey019 (2018).

  153. 153.

    Dietzschold, B. et al. Characterization of an antigenic determinant of the glycoprotein that correlates with pathogenicity of rabies virus. Proc. Natl Acad. Sci. USA 80, 70–74 (1983).

  154. 154.

    Blanie, S., Mortier, J., Delverdier, M., Bertagnoli, S. & Camus-Bouclainville, C. M148R and M149R are two virulence factors for myxoma virus pathogenesis in the European rabbit. Vet. Res. 40, 11 (2009).

  155. 155.

    Bauer, P. H. et al. Genetic and structural analysis of a virulence determinant in polyomavirus VP1. J. Virol. 69, 7925–7931 (1995).

  156. 156.

    Balinsky, C. A. et al. Sheeppox virus kelch-like gene SPPV-019 affects virus virulence. J. Virol. 81, 11392–11401 (2007).

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E.C.H. is funded by an Australian Research Council Australian Laureate Fellowship (FL170100022). The authors thank J. Bull for helpful discussions.

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Nature Reviews Genetics thanks S. Alizon and the other, anonymous reviewer(s) for their contribution to the peer review of this work.

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Correspondence to Edward C. Holmes.

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Although virulence can be defined in a range of case-specific ways, the simplest definition is the severity or harmfulness of a pathogen.


The study of genetic material recovered from microbial (including viral) communities in which genome sequence data are simultaneously generated for all the microorganisms present.

Biological control

The reduction in numbers or elimination of pest organisms through the introduction of a pathogen.

Virulence determinants

Mutations in pathogen genomes that directly affect virulence.

Reverse genetics

Experimental method used to identify gene function by modifying the sequence of a target gene and analysing its phenotypic consequences.


The inference of evolutionary patterns and/or processes through the comparison of whole-genome sequences.


Depiction of the evolutionary history of a genetically related group of organisms. Contains branches and nodes.

Emerging infectious diseases

Infectious diseases that have recently appeared in populations or known diseases that are rapidly increasing in incidence or geographic range.

Basic reproductive number

(R0). Represents the number of secondary infections caused by an infectious host in an entirely susceptible population.

Evolutionary trade-off

Occurs when a change in one trait increases fitness but simultaneously reduces fitness because of its impact on another trait, thereby preventing the organism from optimizing both traits.


The initial and sometimes transient appearance of a pathogen in a new species following a host jump.

Population bottlenecks

Reductions, sometimes drastic, in the size of populations. They often accompany inter-host virus transmission.

Cross-species transmission

The transmission of a pathogen from one host species to another. Also called host-jumping or host-switching.

Parallel evolution

An evolutionary process by which two or more separate lineages develop identical characteristics independently.

Convergent evolution

The descendants of unrelated ancestors that have evolved similar traits independently.

Positive selection

Natural selection that leads to advantageous mutations spreading through a population. Mutations in coding regions can be either synonymous (which do not change the amino acid; measured as dS) or non-synonymous (which change the amino acid; measured as dN). The dN/dS ratio >1 is sometimes used to infer the occurrence of positive selection, although the accuracy of this measure depends on various factors, including the timescale of sampling.

Purifying selection

Natural selection that acts to remove low-fitness (including deleterious) mutations from populations. It is the most common form of natural selection and gives a dN/dS < 1. Also called negative selection.


The interaction among genes at different loci. The function and evolution of one gene may be dependent on the presence of one or more other genes.

Subtype of influenza virus

Influenza A viruses are categorized into subtypes on the basis of the diversity in two proteins present in the viral envelope: haemagglutinin (H or HA) and neuraminidase (N or NA).


The amount of phenotypic variation in a population that is attributable to individual genetic differences.

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Further reading

Fig. 1: Phylogenomics of virulence evolution.
Fig. 2: Example of how phylogenomics can guide the experimental analysis of virulence determinants.
Fig. 3: Evolution of virulence in the context of imperfect vaccination.
Fig. 4: The relationship between host adaptation and the evolution of virulence in Ebola virus.