Inter- and intra-lineage genetic diversity of wild-type Zika viruses reveals both common and distinctive nucleotide variants and clusters of genomic diversity

References

• Dick GW, Kitchen S, Haddow A. Zika virus (I). Isolations and serological specificity. Trans R Soc Trop Med Hyg. 1952;46:509–520. doi: 10.1016/0035-9203(52)90042-4
   PubMed Web of Science ®Google Scholar
• Musso D, Gubler DJ. Zika virus. Clin Microbiol Rev. 2016;29:487–524. doi: 10.1128/CMR.00072-15
   PubMed Web of Science ®Google Scholar
• Duffy M, Chen T, Hancock W, et al. Zika virus outbreak on Yap island, Federated States of Micronesia. N Engl J Med. 2009;360:2536–2543. doi: 10.1056/NEJMoa0805715
   PubMed Web of Science ®Google Scholar
• Weaver SC, Costa F, Garcia-Blanco MA, et al. Zika virus: history, emergence, biology, and prospects for control. Antiviral Res. 2016;130:69–80. doi: 10.1016/j.antiviral.2016.03.010
   PubMed Web of Science ®Google Scholar
• Cao-Lormeau V-M, Blake A, Mons S, et al. Guillain-Barré syndrome outbreak associated with Zika virus infection in French Polynesia: a case-control study. Lancet. 2016;387:1531–1539. doi: 10.1016/S0140-6736(16)00562-6
   PubMed Web of Science ®Google Scholar
• Costello A, Dua T, Duran P, et al. Defining the syndrome associated with congenital Zika virus infection. Bull World Health Organ. 2016;94:406–406A. doi: 10.2471/BLT.16.176990
   PubMed Web of Science ®Google Scholar
• Faye O, Freire CCM, Iamarino A, et al. Molecular evolution of Zika virus during its emergence in the 20th Century. PLoS Negl Trop Dis. 2014;8:e2636. doi: 10.1371/journal.pntd.0002636
   PubMed Web of Science ®Google Scholar
• Lanciotti RS, Lambert AJ, Holodniy M, et al. Phylogeny of Zika virus in Western Hemisphere, 2015. Emerg Infect Dis J. 2016;22:933–935. doi: 10.3201/eid2205.160065
   PubMed Web of Science ®Google Scholar
• Ye Q, Liu Z-Y, Han J-F, et al. Genomic characterization and phylogenetic analysis of Zika virus circulating in the Americas. Infect Genet Evol. 2016;43:43–49. doi: 10.1016/j.meegid.2016.05.004
   PubMed Web of Science ®Google Scholar
• Kochakarn T, Kotanan N, Kümpornsin K, et al. Comparative genome analysis between Southeast Asian and South American Zika viruses. Asian Pac J Trop Med. 2016;9:1048–1054. doi: 10.1016/j.apjtm.2016.10.002
   PubMed Web of Science ®Google Scholar
• Pettersson JH, Eldholm V, Seligman SJ, et al. How did Zika virus emerge in the Pacific islands and Latin America. MBio. 2016;7:e01239–6. doi: 10.1128/mBio.01239-16
   PubMed Web of Science ®Google Scholar
• Kuno G, Chang GJ, Tsuchiya KR, et al. Phylogeny of the genus flavivirus. J Virol. 1998;72:73–83.
   PubMed Web of Science ®Google Scholar
• Heinz FX, Allison SL. Flavivirus structure and membrane fusion. Adv Virus Res. 2003;59:63–97. doi: 10.1016/S0065-3527(03)59003-0
   PubMed Web of Science ®Google Scholar
• Lindenbach BD, Rice C. Molecular biology of flaviviruses. Adv Virus Res. 2003;59:23–61. doi: 10.1016/S0065-3527(03)59002-9
   PubMed Web of Science ®Google Scholar
• Chambers TJ, Hahn CS, Galler R, et al. Flavivirus genome organization, expression, and replication. Annu Rev Microbiol. 1990;44:649–688. doi: 10.1146/annurev.mi.44.100190.003245
   PubMed Web of Science ®Google Scholar
• Bray M, Men R, Tokimatsu I, et al. Genetic determinants responsible for acquisition of dengue type 2 virus mouse neurovirulence. J Virol. 1998;72:1647–1651.
   PubMed Web of Science ®Google Scholar
• de Borba L, Strottmann DM, de Noronha L, et al. Synergistic interactions between the NS3 hel and E proteins contribute to the virulence of dengue virus type 1. PLoS Negl Trop Dis. 2012;6:e1624.
   Web of Science ®Google Scholar
• Davis CT, Galbraith SE, Zhang S, et al. A combination of Naturally Occurring mutations in North American West Nile virus nonstructural protein genes and in the 3’ Untranslated region Alters virus phenotype. J Virol. 2007;81:6111–6116. doi: 10.1128/JVI.02387-06
   PubMed Web of Science ®Google Scholar
• Yu Y. Phenotypic and genotypic characteristics of Japanese encephalitis attenuated live vaccine virus SA14-14-2 and their stabilities. Vaccine. 2010;28:3635–3641. doi: 10.1016/j.vaccine.2010.02.105
   PubMed Web of Science ®Google Scholar
• Beck A, Tesh RB, Wood TG, et al. Comparison of the live attenuated yellow fever vaccine 17D-204 strain to its virulent parental strain Asibi by deep sequencing. J Infect Dis. 2014;209:334–344. doi: 10.1093/infdis/jit546
   PubMed Web of Science ®Google Scholar
• Collins ND, Beck AS, Widen SG, et al. Structural and nonstructural genes contribute to the genetic diversity of RNA Viruses. MBio. 2018;9:1–13. doi: 10.1128/mBio.01871-18
   Web of Science ®Google Scholar
• Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–1797. doi: 10.1093/nar/gkh340
   PubMed Web of Science ®Google Scholar
• Stamatakis A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–1313. doi: 10.1093/bioinformatics/btu033
   PubMed Web of Science ®Google Scholar
• Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. 2010 Gateway Computing Environments Workshop; 2010 Nov 14; New Orleans, LA; 2010.
   Google Scholar
• Piccolo SR, Frampton MB. Tools and techniques for computational reproducibility. Gigascience. 2016;5:1–13. doi: 10.1186/s13742-016-0135-4
   Web of Science ®Google Scholar
• Fishman SL, Branch AD. The quasispecies nature and biological implications of the hepatitis C virus. Infect Genet Evol. 2009;9:1158–1167. doi: 10.1016/j.meegid.2009.07.011
   PubMed Web of Science ®Google Scholar
• Nasu A, Marusawa H, Ueda Y, et al. Genetic heterogeneity of hepatitis C virus in association with antiviral therapy determined by ultra-deep sequencing. PLoS One. 2011;6:e24907. doi: 10.1371/journal.pone.0024907
   PubMed Web of Science ®Google Scholar
• Nishijima N, Marusawa H, Ueda Y, et al. Dynamics of hepatitis B virus quasispecies in association with nucleos(t)ide analogue treatment determined by ultra-deep sequencing. PLoS One. 2012;7:e35052. doi: 10.1371/journal.pone.0035052
   PubMed Web of Science ®Google Scholar
• Heang V, Yasuda CY, Sovann L, et al. Zika virus infection, Cambodia, 2010. Emerg Infect Dis. 2012;18:349–351. doi: 10.3201/eid1802.111224
   PubMed Web of Science ®Google Scholar
• Metsky HC, Matranga CB, Wohl S, et al. Zika virus evolution and spread in the Americas. Nature. 2017;546:411–415. doi: 10.1038/nature22402
   PubMed Web of Science ®Google Scholar
• Faria NR, Quick J, Claro IM, et al. Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature. 2017;546:406–410. doi: 10.1038/nature22401
   PubMed Web of Science ®Google Scholar
• Xia H, Luo H, Shan C, et al. An evolutionary NS1 mutation enhances Zika virus evasion of host interferon induction. Nat Commun. 2018;9:414. doi: 10.1038/s41467-017-02816-2
   PubMed Web of Science ®Google Scholar
• Yuan L, Huang X-Y, Liu Z-Y, et al. Single mutation in the prM protein of Zika virus contributes to microcephaly. Science. 2017;358:933–936. doi: 10.1126/science.aam7120
   PubMed Web of Science ®Google Scholar
• Liu Y, Liu J, Du S, et al. Evolutionary enhancement of Zika virus infectivity in Aedes aegypti mosquitoes. Nature. 2017;545:482–486. doi: 10.1038/nature22365
   PubMed Web of Science ®Google Scholar
• Wang L, Valderramos SG, Wu A, et al. From Mosquitos to humans: genetic evolution of Zika virus. Cell Host Microbe. 2016;19:561–565. doi: 10.1016/j.chom.2016.04.006
   PubMed Web of Science ®Google Scholar
• Dudley DM, Aliota MT, Mohr EL, et al. A rhesus macaque model of Asian-lineage Zika virus infection. Nat Commun. 2016;7:12204. doi: 10.1038/ncomms12204
   PubMed Web of Science ®Google Scholar
• Weger-Lucarelli J, Al E. Development and Characterization of recombinant virus generated from a New World Zika virus Infectious Clone. J Virol. 2017;91:1–10.
   Web of Science ®Google Scholar
• Grubaugh ND, Ladner JT, Kraemer MUG, et al. Genomic epidemiology reveals multiple introductions of Zika virus into the United States. Nature. 2017;546:401–405. doi: 10.1038/nature22400
   PubMed Web of Science ®Google Scholar
• Shrivastava S, Puri V, Dilley KA, et al. Whole genome sequencing, variant analysis, phylogenetics, and deep sequencing of Zika virus strains. Sci Rep. 2018;8:1–11. doi: 10.1038/s41598-017-17765-5
   PubMed Web of Science ®Google Scholar
• Lazear HM, Govero J, Smith AM, et al. A mouse model of Zika virus Pathogenesis. Cell Host Microbe. 2016;19:1–11. doi: 10.1016/j.chom.2016.03.010
   PubMed Web of Science ®Google Scholar
• Rossi SL, Tesh RB, Azar SR, et al. Characterization of a Novel Murine model to study Zika virus. Am J Trop Med Hyg. 2016;94:1362–1369. doi: 10.4269/ajtmh.16-0111
   PubMed Web of Science ®Google Scholar
• Zmurko J, Marques RE, Schols D, et al. The viral polymerase inhibitor 7-deaza-2’-C-methyladenosine is a potent inhibitor of in vitro Zika virus replication and delays disease progression in a robust mouse infection model. PLoS Negl Trop Dis. 2016;10:1–15. doi: 10.1371/journal.pntd.0004695
   Web of Science ®Google Scholar
• Aliota MT, Dudley DM, Newman CM, et al. Heterologous protection against Asian Zika virus challenge in Rhesus macaques. PLoS Negl Trop Dis. 2016;10:1–22.
   Web of Science ®Google Scholar
• Adams Waldorf KM, Stencel-Baerenwald JE, Kapur RP, et al. Fetal brain lesions after subcutaneous inoculation of Zika virus in a pregnant nonhuman primate. Nat Med. 2016;22:1256–1259. doi: 10.1038/nm.4193
   PubMed Web of Science ®Google Scholar
• Azar SR, Rossi SL, Haller SH, et al. ZIKV demonstrates minimal pathologic effects and mosquito infectivity in viremic cynomolgus macaques. Viruses. 2018;10:1–20. doi: 10.3390/v10110661
   Web of Science ®Google Scholar
• Koide F, Goebel S, Snyder B, et al. Development of a zika virus infection model in cynomolgus macaques. Front Microbiol. 2016;7:1–8. doi: 10.3389/fmicb.2016.02028
   PubMed Web of Science ®Google Scholar
• Tai W, He L, Wang Y, et al. Critical neutralizing fragment of Zika virus EDIII elicits cross-neutralization and protection against divergent Zika viruses article. Emerg Microbes Infect. 2018;7:1–8. doi: 10.1038/s41426-017-0007-8
   PubMed Web of Science ®Google Scholar
• Moser LA, Boylan BT, Moreira FR, et al. Growth and adaptation of Zika virus in mammalian and mosquito cells. PLoS Negl Trop Dis. 2018;12:1–19.
   Web of Science ®Google Scholar
• Ojha CR, Rodriguez M, Karuppan MKM, et al. Toll-like receptor 3 regulates Zika virus infection and associated host inflammatory response in primary human astrocytes. PLoS One. 2019;14:1–26. doi: 10.1371/journal.pone.0208543
   Web of Science ®Google Scholar
• Bowen JR, Quicke KM, Maddur MS, et al. Zika virus Antagonizes type I Interferon Responses during infection of human dendritic cells. PLoS Pathog. 2017;13:1–30. doi: 10.1371/journal.ppat.1006164
   Web of Science ®Google Scholar
• Li G, Bos S, Tsetsarkin KA, et al. The roles of prM-E proteins in historical and epidemic zika virus-mediated infection and neurocytotoxicity. Viruses. 2019;11:E157. doi: 10.3390/v11020157
   PubMed Web of Science ®Google Scholar
• Guo Q, Chan JFW, Poon VKM, et al. Immunization with a novel human type 5 adenovirus-vectored vaccine expressing the premembrane and envelope proteins of zika virus provides consistent and sterilizing protection in multiple immunocompetent and immunocompromised animal models. J Infect Dis. 2018;218:365–377. doi: 10.1093/infdis/jiy187
   PubMed Web of Science ®Google Scholar
• Liu X, Qu L, Ye X, et al. Incorporation of NS1 and prM/M are important to confer effective protection of adenovirus-vectored Zika virus vaccine carrying E protein. npj Vaccines. 2018;3:1–8. doi: 10.1038/s41541-017-0041-5
   PubMed Web of Science ®Google Scholar
• Li A, Yu J, Lu M, et al. A Zika virus vaccine expressing premembrane-envelope-NS1 polyprotein. Nat Commun. 2018;9:3067. doi: 10.1038/s41467-018-05276-4
   PubMed Web of Science ®Google Scholar
• Duggal NK, McDonald EM, Weger-Lucarelli J, et al. Mutations present in a low-passage Zika virus isolate result in attenuated pathogenesis in mice. Virology. 2019;530:19–26. doi: 10.1016/j.virol.2019.02.004
   PubMed Web of Science ®Google Scholar
• Yang Y, Shan C, Zou J, et al. A cDNA Clone-Launched platform for high-yield Production of Inactivated Zika vaccine. EBioMedicine. 2017;17:145–156. doi: 10.1016/j.ebiom.2017.02.003
   PubMed Web of Science ®Google Scholar