Influence of Zika virus 3′-end sequence and nonstructural protein evolution on the viral replication competence and virulence

References

• Oehler E, Watrin L, Larre P, et al. Zika virus infection complicated by Guillain-Barre syndrome - case report, French Polynesia, December 2013. Euro Surveill. 2014;19(9):4–6.
   Google Scholar
• Fauci AS, Morens DM. Zika virus in the Americas - yet another Arbovirus threat. N Engl J Med. 2016;374(7):601–604.
   PubMed Web of Science ®Google Scholar
• Dick GWA, Haddow AJ, Uganda S. Virus. A hitherto unrecorded virus isolated from mosquitoes in Ugnada. (I). Isolation and pathogenicity. Trans R Soc Trop Med Hyg. 1952;46(6):600–618.
   PubMed Web of Science ®Google Scholar
• Boorman JP, Draper CC. Isolations of arboviruses in the Lagos area of Nigeria, and a survey of antibodies to them in man and animals. Trans R Soc Trop Med Hyg. 1968;62(2):269–277.
   PubMed Web of Science ®Google Scholar
• Wikan N, Smith DR. First published report of Zika virus infection in people: Simpson, not MacNamara. Lancet Infect Dis. 2017;17(1):15–17.
   PubMed Web of Science ®Google Scholar
• Simpson DI. Zika virus infection in man. Trans R Soc Trop Med Hyg. 1964;58:335–338.
   PubMedGoogle Scholar
• MacNamara FN. Zika virus: a report on three cases of human infection during an epidemic of jaundice in Nigeria. Trans R Soc Trop Med Hyg. 1954;48(2):139–145.
   PubMed Web of Science ®Google Scholar
• Marchette NJ, Garcia R, Rudnick A. Isolation of Zika virus from Aedes aegypti mosquitoes in Malaysia. Am J Trop Med Hyg. 1969;18(3):411–415.
   PubMed Web of Science ®Google Scholar
• Olson JG, Ksiazek TG, Suhandiman, et al. Zika virus, a cause of fever in Central Java, Indonesia. Trans R Soc Trop Med Hyg. 1981;75(3):389–393.
   PubMed Web of Science ®Google Scholar
• Chan JFW, Choi GKY, Yip CCY, et al. Zika fever and congenital Zika syndrome: an unexpected emerging arboviral disease. J Infection. 2016;72(5):507–524.
   PubMed Web of Science ®Google Scholar
• Duffy MR, Chen TH, Hancock WT, et al. Zika virus outbreak on Yap Island, Federated States of Micronesia. N Engl J Med. 2009;360(24):2536–2543.
   PubMed Web of Science ®Google Scholar
• Musso D. Zika virus transmission from French Polynesia to Brazil. Emerg Infect Dis. 2015;21(10):1887.
   PubMed Web of Science ®Google Scholar
• Cao-Lormeau VM, Roche C, Teissier A, et al. Zika virus, French Polynesia, South Pacific, 2013. Emerg Infect Dis. 2014;20(6):1085–1086.
   PubMed Web of Science ®Google Scholar
• Teixeira MG, Costa MDN, de Oliveira WK, et al. The epidemic of Zika virus-related microcephaly in Brazil: detection, control, etiology, and future scenarios. Am J Public Health. 2016;106(4):601–605.
   PubMed Web of Science ®Google Scholar
• Wang L, Valderramos SG, Wu AP, et al. From mosquitos to humans: genetic evolution of Zika virus. Cell Host Microbe. 2016;19(5):561–565.
   PubMed Web of Science ®Google Scholar
• Rusanov T, Kent T, Saeed M, et al. Identification of a small interface between the methyltransferase and RNA polymerase of NS5 that is essential for Zika virus replication. Sci Rep. 2018;8(1):17384.
   PubMedGoogle Scholar
• Kim Y-G, Yoo J-S, Kim J-H, et al. Biochemical characterization of a recombinant Japanese encephalitis virus RNA-dependent RNA polymerase. BMC Mol Biol. 2007;8(1):59.
   PubMedGoogle Scholar
• Pettersson JHO, Eldholm V, Seligman SJ, et al. How did Zika virus emerge in the Pacific Islands and Latin America? mBio. 2016;7(5):e01239–16.
   PubMed Web of Science ®Google Scholar
• Marzi A, Emanuel J, Callison J, et al. Lethal Zika virus disease models in young and older interferon alpha/beta receptor knock out mice. Front Cell Infect Microbiol. 2018;8:117.
   PubMed Web of Science ®Google Scholar
• Anfasa F, Siegers JY, van der Kroeg M, et al. Phenotypic differences between Asian and African lineage Zika viruses in human neural progenitor cells. mSphere. 2017;2(4):e00292–17.
   PubMed Web of Science ®Google Scholar
• Dowall SD, Graham VA, Rayner E, et al. Lineage-dependent differences in the disease progression of Zika virus infection in type-I interferon receptor knockout (A129) mice. PLoS Negl Trop Dis. 2017;11(7):e0005704.
   PubMed Web of Science ®Google Scholar
• Duggal NK, Ritter JM, McDonald EM, et al. Differential neurovirulence of African and Asian genotype Zika virus isolates in outbred immunocompetent mice. Am J Trop Med Hyg. 2017;97(5):1410–1417.
   PubMed Web of Science ®Google Scholar
• Nunes BTD, Fontes-Garfias CR, Shan C, et al. Zika structural genes determine the virulence of African and Asian lineages. Emerg Microbes Infect. 2020;9(1):1023–1033.
   PubMed Web of Science ®Google Scholar
• Nakayama E, Kato F, Tajima S, et al. Neuroinvasiveness of the MR766 strain of Zika virus in IFNAR−/− mice maps to prM residues conserved amongst African genotype viruses. PLoS Pathog. 2021;17(7):e1009788.
   PubMed Web of Science ®Google Scholar
• Yuan L, Huang XY, Liu ZY, et al. A single mutation in the prM protein of Zika virus contributes to fetal microcephaly. Science. 2017;358(6365):933–936.
   PubMed Web of Science ®Google Scholar
• Nomaguchi M, Ackermann M, Yon CS, et al. De novo synthesis of negative-strand RNA by dengue virus RNA-dependent RNA polymerase in vitro: nucleotide, primer, and template parameters. J Virol. 2003;77(19):8831–8842.
   PubMed Web of Science ®Google Scholar
• Khromykh AA, Kondratieva N, Sgro JY, et al. Significance in replication of the terminal nucleotides of the Flavivirus genome. J Virol. 2003;77(19):10623–10629.
   PubMed Web of Science ®Google Scholar
• Schurer H, Lang K, Schuster J, et al. A universal method to produce in vitro transcripts with homogeneous 3′ ends. Nucleic Acids Res. 2002;30(12):e56.
   PubMed Web of Science ®Google Scholar
• Ahn DG, Lee W, Choi JK, et al. Interference of ribosomal frameshifting by antisense peptide nucleic acids suppresses SARS coronavirus replication. Antiviral Res. 2011;91(1):1–10.
   PubMed Web of Science ®Google Scholar
• Li JQ, Deng CL, Gu DY, et al. Development of a replicon cell line-based high throughput antiviral assay for screening inhibitors of Zika virus. Antiviral Res. 2018;150:148–54.
   PubMed Web of Science ®Google Scholar
• Tsetsarkin KA, Kenney H, Chen RB, et al. A full-length infectious cDNA clone of Zika virus from the 2015 epidemic in Brazil as a genetic platform for studies of virus-host interactions and vaccine development. mBio. 2016;7(4):e01114–16.
   PubMed Web of Science ®Google Scholar
• Baer A, Kehn-Hall K. Viral concentration determination through plaque assays: using traditional and novel overlay systems. J Vis Exp. 2014;93:e52065.
   Google Scholar
• Sardi Silvia I, Somasekar S, Naccache Samia N, et al. Coinfections of Zika and Chikungunya viruses in Bahia, Brazil, identified by metagenomic next-generation sequencing. J Clin Microbiol. 2016;54(9):2348–2353.
   PubMed Web of Science ®Google Scholar
• Aubry F, Jacobs S, Darmuzey M, et al. Recent African strains of Zika virus display higher transmissibility and fetal pathogenicity than Asian strains. Nat Commun. 2021;12(1):916.
   PubMed Web of Science ®Google Scholar
• Kim M, Cho H, Ahn D-G, et al. In vitro replication inhibitory activity of xanthorrhizol against severe acute respiratory syndrome coronavirus 2. Biomedicines. 2021;9(11):1725.
   PubMed Web of Science ®Google Scholar
• Cho H, Lee W, Kim GW, et al. Regulation of La/SSB-dependent viral gene expression by pre-tRNA 3’ trailer-derived tRNA fragments. Nucleic Acids Res. 2019;47(18):9888–9901.
   PubMed Web of Science ®Google Scholar
• Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26(5):589–595.
   PubMed Web of Science ®Google Scholar
• Rana J, Campos JLS, Leccese G, et al. Role of capsid anchor in the morphogenesis of Zika virus. J Virol. 2018;92(22):e01174-18.
   PubMed Web of Science ®Google Scholar
• Xie X, Zou J, Shan C, et al. Zika virus replicons for drug discovery. EBioMedicine. 2016;12:156–160.
   PubMed Web of Science ®Google Scholar
• Eyer L, Nencka R, Huvarová I, et al. Nucleoside inhibitors of Zika virus. J Infect Dis. 2016;214(5):707–711.
   PubMed Web of Science ®Google Scholar
• Pallarés HM, Navarro GSC, Villordo SM, et al. Zika virus subgenomic Flavivirus RNA generation requires cooperativity between duplicated RNA structures that are essential for productive infection in human cells. J Virol. 2020;94(18):e00343–20.
   PubMed Web of Science ®Google Scholar
• Sheehan KCF, Lai KS, Dunn GP, et al. Blocking monoclonal antibodies specific for mouse IFN-alpha/beta receptor subunit 1 (IFNAR-1) from mice immunized by in vivo hydrodynamic transfection. J Interf Cytok Res. 2006;26(11):804–819.
   PubMed Web of Science ®Google Scholar
• Grant A, Ponia SS, Tripathi S, et al. Zika virus targets human STAT2 to inhibit type I interferon signaling. Cell Host Microbe. 2016;19(6):882–890.
   PubMed Web of Science ®Google Scholar
• Emeny JM, Morgan MJ. Regulation of the interferon system: evidence that Vero cells have a genetic defect in interferon production. J Gen Virol. 1979;43(1):247–252.
   PubMed Web of Science ®Google Scholar
• Kim M, Cho H, Lee SH, et al. An infectious cDNA clone of a growth attenuated Korean isolate of MERS coronavirus KNIH002 in clade B. Emerg Microbes Infect. 2020;9(1):2714–2726.
   PubMed Web of Science ®Google Scholar
• Gadea G, Bos S, Krejbich-Trotot P, et al. A robust method for the rapid generation of recombinant Zika virus expressing the GFP reporter gene. Virology. 2016;497:157–162.
   PubMed Web of Science ®Google Scholar
• Munster M, Plaszczyca A, Cortese M, et al. A reverse genetics system for Zika virus based on a simple molecular cloning strategy. Viruses. 2018;10(7):368.
   PubMed Web of Science ®Google Scholar
• Schwarz MC, Sourisseau M, Espino MM, et al. Rescue of the 1947 Zika virus prototype strain with a cytomegalovirus promoter-driven cDNA clone. mSphere. 2016;1(5):e00246–16.
   PubMed Web of Science ®Google Scholar
• Shan C, Xie XP, Muruato AE, et al. An infectious cDNA clone of Zika virus to study viral virulence, mosquito transmission, and antiviral inhibitors. Cell Host Microbe. 2016;19(6):891–900.
   PubMed Web of Science ®Google Scholar
• Yang YJ, Shan C, Zou J, et al. A cDNA clone-launched platform for high-yield production of inactivated Zika vaccine. EBioMedicine. 2017;17:145–156.
   PubMed Web of Science ®Google Scholar
• Weger-Lucarelli J, Duggal NK, Bullard-Feibelman K, et al. Development and characterization of recombinant virus generated from a new world Zika virus infectious clone. J Virol. 2017;91(1):e01765–16.
   PubMed Web of Science ®Google Scholar
• Marquez-Jurado S, Nogales A, Avila-Perez G, et al. An alanine-to-valine substitution in the residue 175 of Zika virus NS2A protein affects viral RNA synthesis and attenuates the virus in vivo. Viruses. 2018;10(10):547.
   PubMed Web of Science ®Google Scholar
• Avila-Perez G, Nogales A, Park JG, et al. A natural polymorphism in Zika virus NS2A protein responsible of virulence in mice. Sci Rep. 2019;9(1):19968.
   PubMedGoogle Scholar
• Deng CL, Zhang QY, Chen DD, et al. Recovery of the Zika virus through an in vitro ligation approach. J Gen Virol. 2017;98(7):1739–1743.
   PubMed Web of Science ®Google Scholar
• Chen Y, Liu T, Zhang Z, et al. Novel genetically stable infectious clone for a Zika virus clinical isolate and identification of RNA elements essential for virus production. Virus Res. 2018;257:14–24.
   PubMed Web of Science ®Google Scholar
• Willard KA, Demakovsky L, Tesla B, et al. Zika virus exhibits lineage-specific phenotypes in cell culture, in Aedes aegypti mosquitoes, and in an embryo model. Viruses. 2017;9(12):383.
   PubMed Web of Science ®Google Scholar
• Wu YX, Liu QX, Zhou J, et al. Zika virus evades interferon-mediated antiviral response through the co-operation of multiple nonstructural proteins in vitro. Cell Discov. 2017;3:17006.
   PubMed Web of Science ®Google Scholar
• Xia HJ, Luo HL, Shan C, et al. An evolutionary NS1 mutation enhances Zika virus evasion of host interferon induction. Nat Commun. 2018;9(1):414.
   PubMed Web of Science ®Google Scholar
• Tan MJA, Chan KWK, Ng IHW, et al. The potential role of the ZIKV NS5 nuclear spherical-shell structures in cell type-specific host immune modulation during ZIKV infection. Cells-Basel. 2019;8(12):1519.
   PubMed Web of Science ®Google Scholar