1887

Abstract

Chikungunya virus (CHIKV) has caused large-scale epidemics of fever, rash and arthritis since 2004. This unprecedented re-emergence has been associated with mutations in genes encoding structural envelope proteins, providing increased fitness in the secondary vector . In the 2008–2013 CHIKV outbreaks across Southeast Asia, an R82S mutation in non-structural protein 4 (nsP4) emerged early in Malaysia or Singapore and quickly became predominant. To determine whether this nsP4-R82S mutation provides a selective advantage in host cells, which may have contributed to the epidemic, the fitness of infectious clone-derived CHIKV with wild-type nsP4-82R and mutant nsP4-82S were compared in and human cell lines. Viral infectivity, dissemination and transmission in were not affected by the mutation when the two variants were tested separately. In competition, the nsP4-82R variant showed an advantage over nsP4-82S in dissemination to the salivary glands, but only in late infection (10 days). In human rhabdomyosarcoma (RD) and embryonic kidney (HEK-293T) cell lines coinfected at a 1 : 1 ratio, wild-type nsP4-82R virus was rapidly outcompeted by nsP4-82S virus as early as one passage (3 days). In conclusion, the nsP4-R82S mutation provides a greater selective advantage in human cells than in , which may explain its apparent natural selection during CHIKV spread in Southeast Asia. This is an unusual example of a naturally occurring mutation in a non-structural protein, which may have facilitated epidemic transmission of CHIKV.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/jgv.0.001338
2019-11-01
2019-11-22
Loading full text...

Full text loading...

References

  1. Weaver SC, Forrester NL. Chikungunya: evolutionary history and recent epidemic spread. Antiviral Res 2015;120:32–39 [CrossRef]
    [Google Scholar]
  2. Simizu B, Yamamoto K, Hashimoto K, Ogata T. Structural proteins of chikungunya virus. J Virol 1984;51:254–258
    [Google Scholar]
  3. Strauss JH, Strauss EG. The alphaviruses: gene expression, replication, and evolution. Microbiol Rev 1994;58:491–562
    [Google Scholar]
  4. Malet H, Coutard B, Jamal S, Dutartre H, Papageorgiou N et al. The crystal structures of chikungunya and venezuelan equine encephalitis virus NSP3 macro domains define a conserved adenosine binding pocket. J Virol 2009;83:6534–6545 [CrossRef]
    [Google Scholar]
  5. Hyde JL, Chen R, Trobaugh DW, Diamond MS, Weaver SC et al. The 5' and 3' ends of alphavirus RNAs-Non-coding is not non-functional. Virus Res 2015;206:99–107 [CrossRef]
    [Google Scholar]
  6. Chen R, Wang E, Tsetsarkin KA, Weaver SC. Chikungunya virus 3' untranslated region: adaptation to mosquitoes and a population bottleneck as major evolutionary forces. PLoS Pathog 2013;9:e1003591 [CrossRef]
    [Google Scholar]
  7. Powers AM, Brault AC, Tesh RB, Weaver SC. Re-emergence of chikungunya and O'nyong-nyong viruses: evidence for distinct geographical lineages and distant evolutionary relationships. J Gen Virol 2000;81:471–479 [CrossRef]
    [Google Scholar]
  8. Pialoux G, Gauzere BA, Jaureguiberry S, Chikungunya SM. An epidemic arbovirosis. Lancet Infect Dis 2007;7:319–327
    [Google Scholar]
  9. Powers AM, Logue CH. Changing patterns of chikungunya virus: re-emergence of a zoonotic arbovirus. J Gen Virol 2007;88:2363–2377 [CrossRef]
    [Google Scholar]
  10. The HS. Chikungunya epidemic in the Indian Ocean. Vector Borne Zoonotic Dis 2005-2006;2006:115–116
    [Google Scholar]
  11. Tsetsarkin KA, Vanlandingham DL, McGee CE, Higgs S. A single mutation in chikungunya virus affects vector specificity and epidemic potential. PLoS Pathog 2007;3:e201 [CrossRef]
    [Google Scholar]
  12. de Lamballerie X, Leroy E, Charrel RN, Ttsetsarkin K, Higgs S et al. Chikungunya virus adapts to tiger mosquito via evolutionary convergence: a sign of things to come?. Virol J 2008;5:33 [CrossRef]
    [Google Scholar]
  13. Tsetsarkin KA, Chen R, Sherman MB, Weaver SC. Chikungunya virus: evolution and genetic determinants of emergence. Curr Opin Virol 2011;1:310–317 [CrossRef]
    [Google Scholar]
  14. Tsetsarkin KA, Weaver SC. Sequential adaptive mutations enhance efficient vector switching by chikungunya virus and its epidemic emergence. PLoS Pathog 2011;7:e1002412 [CrossRef]
    [Google Scholar]
  15. Sam IC, Chan YF, Chan SY, Loong SK, Chin HK et al. Chikungunya virus of Asian and Central/East African genotypes in Malaysia. J Clin Virol 2009;46:180–183 [CrossRef]
    [Google Scholar]
  16. Rozilawati H, Faudzi AY, Rahidah AAS, Azlina AHN, Abdullah AG et al. Entomological study of chikungunya infections in the state of Kelantan, Malaysia. Indian J Med Res 2011;133:670–673
    [Google Scholar]
  17. Sam IC, Loong SK, Michael JC, Chua CL, Wan Sulaiman WY et al. Genotypic and phenotypic characterization of Chikungunya virus of different genotypes from Malaysia. PLoS One 2012;7:e50476 [CrossRef]
    [Google Scholar]
  18. Hapuarachchi HC, Bandara KBAT, Sumanadasa SDM, Hapugoda MD, Lai YL et al. Re-emergence of chikungunya virus in south-east Asia: virological evidence from Sri Lanka and Singapore. J Gen Virol 2010;91:1067–1076 [CrossRef]
    [Google Scholar]
  19. Coffey LL, Beeharry Y, Bordería AV, Blanc H, Vignuzzi M. Arbovirus high fidelity variant loses fitness in mosquitoes and mice. Proc Natl Acad Sci USA 2011;108:16038–16043 [CrossRef]
    [Google Scholar]
  20. Rozen-Gagnon K, Stapleford KA, Mongelli V, Blanc H, Failloux AB et al. Alphavirus mutator variants present host-specific defects and attenuation in mammalian and insect models. PLoS Pathog 2014;10:e1003877 [CrossRef]
    [Google Scholar]
  21. Fata CL, Sawicki SG, Sawicki DL. Alphavirus minus-strand RNA synthesis: identification of a role for Arg183 of the NSP4 polymerase. J Virol 2002;76:8632–8640 [CrossRef]
    [Google Scholar]
  22. Rupp JC, Jundt N, Hardy RW. Requirement for the amino-terminal domain of Sindbis virus NSP4 during virus infection. J Virol 2011;85:3449–3460 [CrossRef]
    [Google Scholar]
  23. Agarwal A, Sharma AK, Sukumaran D, Parida M, Dash PK. Two novel epistatic mutations (E1:K211E and E2:V264A) in structural proteins of chikungunya virus enhance fitness in Aedes aegypti. Virology 2016;497:59–68 [CrossRef]
    [Google Scholar]
  24. Zouache K, Failloux AB. Insect-pathogen interactions: contribution of viral adaptation to the emergence of vector-borne diseases, the example of chikungunya. Curr Opin Insect Sci 2015;10:14–21 [CrossRef]
    [Google Scholar]
  25. Stapleford KA, Moratorio G, Henningsson R, Chen R, Matheus S et al. Whole-genome sequencing analysis from the chikungunya virus Caribbean outbreak reveals novel evolutionary genomic elements. PLoS Negl Trop Dis 2016;10:e0004402 [CrossRef]
    [Google Scholar]
  26. Coffey LL, Forrester N, Tsetsarkin K, Vasilakis N, Weaver SC. Factors shaping the adaptive landscape for arboviruses: implications for the emergence of disease. Future Microbiol 2013;8:155–176 [CrossRef]
    [Google Scholar]
  27. Vignuzzi M, Higgs S. The bridges and blockades to evolutionary convergence on the road to predicting chikungunya virus evolution. Annu Rev Virol 2017;4:181–200 [CrossRef]
    [Google Scholar]
  28. Arankalle VA, Shrivastava S, Cherian S, Gunjikar RS, Walimbe AM et al. Genetic divergence of chikungunya viruses in India (1963-2006) with special reference to the 2005-2006 explosive epidemic. J Gen Virol 2007;88:1967–1976 [CrossRef]
    [Google Scholar]
  29. Schuffenecker I, Iteman I, Michault A, Murri S, Frangeul L et al. Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak. PLoS Med 2006;3:e263 [CrossRef]
    [Google Scholar]
  30. Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 2012;9:772 [CrossRef]
    [Google Scholar]
  31. Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH et al. Beast 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 2014;10:e1003537 [CrossRef]
    [Google Scholar]
  32. Rambaut A. 2014; FigTree v1.4.2, a graphical viewer of phylogenetic trees. http://tree.bio.ed.ac.uk/software/figtree/
  33. Condreay LD, Brown DT. Exclusion of superinfecting homologous virus by Sindbis virus-infected Aedes albopictus (mosquito) cells. J Virol 1986;58:81–86
    [Google Scholar]
  34. Pohjala L, Utt A, Varjak M, Lulla A, Merits A et al. Inhibitors of alphavirus entry and replication identified with a stable chikungunya replicon cell line and virus-based assays. PLoS One 2011;6:e28923 [CrossRef]
    [Google Scholar]
  35. Tsetsarkin K, Higgs S, McGee CE, De Lamballerie X, Charrel RN et al. Infectious clones of chikungunya virus (La Réunion isolate) for vector competence studies. Vector Borne Zoonotic Dis 2006;6:325–337 [CrossRef]
    [Google Scholar]
  36. Wong HV, Vythilingam I, Sulaiman WYW, Lulla A, Merits A et al. Detection of persistent chikungunya virus RNA but not infectious virus in experimental vertical transmission in Aedes aegypti from Malaysia. Am J Trop Med Hyg 2016;94:182–186 [CrossRef]
    [Google Scholar]
  37. Wong HV, Chan YF, Sam IC, Wan Sulaiman WY, Vythilingam I. Chikungunya virus infection of Aedes mosquitoes In JJH Chu, Ang SK. (editors) Chikungunya Virus: Methods and Protocols, 1426. Methods in Molecular Biology. Springer Nature; 2016; pp119–128
    [Google Scholar]
  38. Zheng K, Li J, Zhang Q, Liang M, Li C et al. Genetic analysis of chikungunya viruses imported to mainland China in 2008. Virol J 2010;7:8 [CrossRef]
    [Google Scholar]
  39. Tsetsarkin KA, Chen R, Yun R, Rossi SL, Plante KS et al. Multi-peaked adaptive landscape for chikungunya virus evolution predicts continued fitness optimization in Aedes albopictus mosquitoes. Nat Commun 2014;5:4084 [CrossRef]
    [Google Scholar]
  40. Coffey LL, Vignuzzi M. Host alternation of chikungunya virus increases fitness while restricting population diversity and adaptability to novel selective pressures. J Virol 2011;85:1025–1035 [CrossRef]
    [Google Scholar]
  41. Quiñones-Mateu ME, Ball SC, Marozsan AJ, Torre VS, Albright JL et al. A dual infection/competition assay shows a correlation between ex vivo human immunodeficiency virus type 1 fitness and disease progression. J Virol 2000;74:9222–9233 [CrossRef]
    [Google Scholar]
  42. Ball SC, Abraha A, Collins KR, Marozsan AJ, Baird H et al. Comparing the ex vivo fitness of CCR5-tropic human immunodeficiency virus type 1 isolates of subtypes B and C. J Virol 2003;77:1021–1038 [CrossRef]
    [Google Scholar]
  43. Pulmanausahakul R, Roytrakul S, Auewarakul P, Smith DR. Chikungunya in Southeast Asia: understanding the emergence and finding solutions. Int J Infect Dis 2011;15:e671–e676 [CrossRef]
    [Google Scholar]
  44. Sreekumar E, Issac A, Nair S, Hariharan R, Janki MB et al. Genetic characterization of 2006-2008 isolates of chikungunya virus from Kerala, South India, by whole genome sequence analysis. Virus Genes 2010;40:14–27 [CrossRef]
    [Google Scholar]
  45. Ng KW, Chow A, Win MK, Dimatatac F, Neo HY et al. Clinical features and epidemiology of chikungunya infection in Singapore. Singapore Med J 2009;50:785–790
    [Google Scholar]
  46. Thavara U, Tawatsin A, Pengsakul T, Bhakdeenuan P, Chanama S et al. Outbreak of chikungunya fever in Thailand and virus detection in field population of vector mosquitoes, Aedes aegypti (L.) and Aedes albopictus Skuse (Diptera: Culicidae). Southeast Asian J Trop Med Public Health 2009;40:951–962
    [Google Scholar]
  47. Qiaoli Z, Jianfeng H, De W, Zijun W, Xinguang Z et al. Maiden outbreak of chikungunya in Dongguan City, Guangdong Province, China: epidemiological characteristics. PLoS One 2012;7:e42830 [CrossRef]
    [Google Scholar]
  48. Tun MMN, Thant KZ, Inoue S, Nabeshima T, Aoki K et al. Detection of east/central/south African genotype of chikungunya virus in Myanmar, 2010. Emerg Infect Dis 2014;20:1378–1381 [CrossRef]
    [Google Scholar]
  49. Auksornkitti V, Pongsiri P, Theamboonlers A, Rianthavorn P, Poovorawan Y et al. Whole-genome characterisation of chikungunya virus from Aedes albopictus collected in Thailand. Ann Trop Med Parasitol 2010;104:265–269 [CrossRef]
    [Google Scholar]
  50. Leslie A, Kavanagh D, Honeyborne I, Pfafferott K, Edwards C et al. Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA. J Exp Med 2005;201:891–902 [CrossRef]
    [Google Scholar]
  51. Wanlapakorn N, Thongmee T, Linsuwanon P, Chattakul P, Vongpunsawad S et al. Chikungunya outbreak in bueng kan province, Thailand, 2013. Emerg Infect Dis 2014;20:1404–1406 [CrossRef]
    [Google Scholar]
  52. Weaver SC, Winegar R, Manger ID, Forrester NL. Alphaviruses: population genetics and determinants of emergence. Antiviral Res 2012;94:242–257 [CrossRef]
    [Google Scholar]
  53. Anishchenko M, Bowen RA, Paessler S, Austgen L, Greene IP et al. Venezuelan encephalitis emergence mediated by a phylogenetically predicted viral mutation. Proc Natl Acad Sci USA 2006;103:4994–4999 [CrossRef]
    [Google Scholar]
  54. Vashishtha M, Phalen T, Marquardt MT, Ryu JS, Ng AC et al. A single point mutation controls the cholesterol dependence of Semliki Forest virus entry and exit. J Cell Biol 1998;140:91–99 [CrossRef]
    [Google Scholar]
  55. Lu YE, Cassese T, Kielian M. The cholesterol requirement for Sindbis virus entry and exit and characterization of a spike protein region involved in cholesterol dependence. J Virol 1999;73:4272–4278
    [Google Scholar]
  56. Ahn A, Schoepp RJ, Sternberg D, Kielian M. Growth and stability of a cholesterol-independent Semliki Forest virus mutant in mosquitoes. Virology 1999;262:452–456 [CrossRef]
    [Google Scholar]
  57. Berry IM, Eyase F, Pollett S, Konongoi LS, Figuero K et al. Recent outbreaks of chikungunya virus (CHIKV) in Africa and Asia are driven by a variant carrying mutations associated with increased fitness for Aedes aegypti. bioRxiv 2018
    [Google Scholar]
  58. Arias-Goeta C, Mousson L, Rougeon F, Failloux AB. Dissemination and transmission of the E1-226V variant of chikungunya virus in Aedes albopictus are controlled at the midgut barrier level. PLoS One 2013;8:e57548 [CrossRef]
    [Google Scholar]
  59. Chen R, Puri V, Fedorova N, Lin D, Hari KL et al. Comprehensive genome scale phylogenetic study provides new insights on the global expansion of chikungunya virus. J Virol 2016;90:10600–10611 [CrossRef]
    [Google Scholar]
  60. Santhosh SR, Dash PK, Parida MM, Khan M, Tiwari M et al. Comparative full genome analysis revealed E1: A226V shift in 2007 Indian Chikungunya virus isolates. Virus Res 2008;135:36–41 [CrossRef]
    [Google Scholar]
  61. Tan KK, Sy AKD, Tandoc AO, Khoo JJ, Sulaiman S et al. Independent emergence of the cosmopolitan Asian chikungunya virus, Philippines 2012. Sci Rep 2015;5:12279 [CrossRef]
    [Google Scholar]
  62. Bui TT, Moi ML, Nabeshima T, Takemura T, Nguyen TT et al. A single amino acid substitution in the NS4B protein of dengue virus confers enhanced virus growth and fitness in human cells in vitro through IFN-dependent host response. J Gen Virol 2018;99:1044–1057 [CrossRef]
    [Google Scholar]
  63. Xia H, Luo H, Shan C, Muruato AE, Nunes BTD et al. An evolutionary NS1 mutation enhances Zika virus evasion of host interferon induction. Nat Commun 2018;9:414 [CrossRef]
    [Google Scholar]
  64. Liu Y, Liu J, Du S, Shan C, Nie K et al. Evolutionary enhancement of Zika virus infectivity in Aedes aegypti mosquitoes. Nature 2017;545:482–486 [CrossRef]
    [Google Scholar]
  65. Pietilä MK, Hellström K, Ahola T. Alphavirus polymerase and RNA replication. Virus Res 2017;234:44–57 [CrossRef]
    [Google Scholar]
  66. Weston J, Villoing S, Brémont M, Castric J, Pfeffer M et al. Comparison of two aquatic alphaviruses, salmon pancreas disease virus and sleeping disease virus, by using genome sequence analysis, monoclonal reactivity, and cross-infection. J Virol 2002;76:6155–6163 [CrossRef]
    [Google Scholar]
  67. Rupp JC, Sokoloski KJ, Gebhart NN, Hardy RW. Alphavirus RNA synthesis and non-structural protein functions. J Gen Virol 2015;96:2483–2500 [CrossRef]
    [Google Scholar]
  68. Rubach JK, Wasik BR, Rupp JC, Kuhn RJ, Hardy RW et al. Characterization of purified Sindbis virus nsP4 RNA-dependent RNA polymerase activity in vitro. Virology 2009;384:201–208 [CrossRef]
    [Google Scholar]
  69. Tomar S, Hardy RW, Smith JL, Kuhn RJ. Catalytic core of alphavirus nonstructural protein nsP4 possesses terminal adenylyltransferase activity. J Virol 2006;80:9962–9969 [CrossRef]
    [Google Scholar]
  70. Cristea IM, Carroll JWN, Rout MP, Rice CM, Chait BT et al. Tracking and elucidating alphavirus-host protein interactions. J Biol Chem 2006;281:30269–30278 [CrossRef]
    [Google Scholar]
  71. Cristea IM, Rozjabek H, Molloy KR, Karki S, White LL et al. Host factors associated with the Sindbis virus RNA-dependent RNA polymerase: role for G3BP1 and G3BP2 in virus replication. J Virol 2010;84:6720–6732 [CrossRef]
    [Google Scholar]
  72. Betts MJ, Russell RB. Amino acid properties and consequences of substitutions Bioinformatics for Geneticists Sons, Ltd: John Wiley; 2003; pp291–316
    [Google Scholar]
  73. Keck F, Ataey P, Amaya M, Bailey C, Narayanan A. Phosphorylation of single stranded RNA virus proteins and potential for novel therapeutic strategies. Viruses 2015;7:5257–5273 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/jgv.0.001338
Loading
/content/journal/jgv/10.1099/jgv.0.001338
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most Cited This Month

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