Abstract
Phylogenetic studies with Zika virus (ZIKV) have been conducted in Brazil. In this study, we sequenced 8 new sequences of the ZIKV envelope (E) gene from strains of cases from the Paraná and Mato Grosso do Sul states in 2016. A low phylogenetic signal was observed, with more than 40% of unresolved quartets, and the Maximum Likelihood Tree grouped all sequences in the Brazilian branches within the Asian genotype. In addition, a Shannon entropy analysis was conducted, showing a high stability in the E protein through the ZIKV polyprotein. Taken together, these results suggest a high degree of conservation in the ZIKV E gene from the recent American outbreaks.
References
Campos GS, Bandeira AC, Sardi SI (2015) Zika virus outbreak, Bahia, Brazil. Emerg Infect Dis 21:1885–1886
Pessoa R, Patriota JV, Lourdes de Souza M et al (2016) Investigation into an outbreak of dengue-like illness in Pernambuco, Brazil, revealed a cocirculation of Zika, chikungunya, and dengue virus type 1. Medicine (Baltimore) 95:e3201. https://doi.org/10.1097/MD.0000000000003201
Zanluca C, de Melo VCA, Mosimann ALP et al (2015) First report of autochthonous transmission of Zika virus in Brazil. Mem Inst Oswaldo Cruz 110:569–572. https://doi.org/10.1590/0074-02760150192
Cao-Lormeau V-M, Blake A, Mons S, Lastère S, Roche C, Vanhomwegen J, Dub T, Baudouin L, Teissier A, Larre P, Vial AL, Decam C, Choumet V, Halstead SK, Willison HJ, Musset L, Manuguerra JC, Despres P, Fournier E, Mallet HP, Musso D, Fontanet A, Neil J, Ghawché F (2016) Guillain-Barré syndrome outbreak associated with Zika virus infection in French Polynesia: a case-control study. Lancet 387:1531–1539. https://doi.org/10.1016/S0140-6736(16)00562-6
Brasil. Ministério da Saúde. Secretaria de Vigilância em Saúde. Monitoramento dos casos de arboviroses urbanas transmitidas pelo Aedes (dengue, chikungunya e Zika), Semanas Epidemiológicas 01 a 52. Brasília, v51, n.2, Jan. 2020
Haddow AD, Schuh AJ, Yasuda CY, Kasper MR, Heang V, Huy R, Guzman H, Tesh RB, Weaver SC (2012) Genetic characterization of Zika virus strains: geographic expansion of the Asian lineage. PLoS Negl Trop Dis 6:e1477. https://doi.org/10.1371/journal.pntd.0001477
Lanciotti RS, Kosoy OL, Laven JJ, Velez JO, Lambert AJ, Johnson AJ, Stanfield SM, Duffy MR (2008) Genetic and serologic properties of Zika virus associated with an epidemic, Yap State, Micronesia, 2007. Emerg Infect Dis 14:1232–1239. https://doi.org/10.3201/eid1408.080287
Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175–185
Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. https://doi.org/10.1093/nar/gkh340
Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772
Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502–504
Strimmer K, von Haeseler A (1997) Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc Natl Acad Sci U S A 94:6815–6819
Galtier N, Gouy M, Gautier C (1996) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12:543–548
Efron B, Halloran E, Holmes S (1996) Bootstrap confidence levels for phylogenetic trees. Proc Natl Acad Sci U S A 93:13429–13434
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In: Nucleic acids symposium series, vol c1979-c2000. Information Retrieval Ltd., London, pp 95–98
Faye O, Freire CCM, Iamarino A, Faye O, de Oliveira JVC, Diallo M, Zanotto PMA, Sall AA (2014) Molecular evolution of Zika virus during its emergence in the 20(th) century. PLoS Negl Trop Dis 8:e2636. https://doi.org/10.1371/journal.pntd.0002636
Faria NR, Quick J, Claro IM, Thézé J, de Jesus JG, Giovanetti M, Kraemer MUG, Hill SC, Black A, da Costa AC, Franco LC, Silva SP, Wu CH, Raghwani J, Cauchemez S, du Plessis L, Verotti MP, de Oliveira WK, Carmo EH, Coelho GE, Santelli ACFS, Vinhal LC, Henriques CM, Simpson JT, Loose M, Andersen KG, Grubaugh ND, Somasekar S, Chiu CY, Muñoz-Medina JE, Gonzalez-Bonilla CR, Arias CF, Lewis-Ximenez LL, Baylis SA, Chieppe AO, Aguiar SF, Fernandes CA, Lemos PS, Nascimento BLS, Monteiro HAO, Siqueira IC, de Queiroz MG, de Souza TR, Bezerra JF, Lemos MR, Pereira GF, Loudal D, Moura LC, Dhalia R, França RF, Magalhães T, Marques ET Jr, Jaenisch T, Wallau GL, de Lima MC, Nascimento V, de Cerqueira EM, de Lima MM, Mascarenhas DL, Neto JPM, Levin AS, Tozetto-Mendoza TR, Fonseca SN, Mendes-Correa MC, Milagres FP, Segurado A, Holmes EC, Rambaut A, Bedford T, Nunes MRT, Sabino EC, Alcantara LCJ, Loman NJ, Pybus OG (2017) Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature 546:406–410. https://doi.org/10.1038/nature22401
Metsky HC, Matranga CB, Wohl S, Schaffner SF, Freije CA, Winnicki SM, West K, Qu J, Baniecki ML, Gladden-Young A, Lin AE, Tomkins-Tinch CH, Ye SH, Park DJ, Luo CY, Barnes KG, Shah RR, Chak B, Barbosa-Lima G, Delatorre E, Vieira YR, Paul LM, Tan AL, Barcellona CM, Porcelli MC, Vasquez C, Cannons AC, Cone MR, Hogan KN, Kopp EW, Anzinger JJ, Garcia KF, Parham LA, Ramírez RMG, Montoya MCM, Rojas DP, Brown CM, Hennigan S, Sabina B, Scotland S, Gangavarapu K, Grubaugh ND, Oliveira G, Robles-Sikisaka R, Rambaut A, Gehrke L, Smole S, Halloran ME, Villar L, Mattar S, Lorenzana I, Cerbino-Neto J, Valim C, Degrave W, Bozza PT, Gnirke A, Andersen KG, Isern S, Michael SF, Bozza FA, Souza TML, Bosch I, Yozwiak NL, MacInnis BL, Sabeti PC (2017) Zika virus evolution and spread in the Americas. Nature 546:411–415. https://doi.org/10.1038/nature22402
Angeletti S, Lo Presti A, Giovanetti M et al (2016) Nonstructural proteins are preferential positive selection targets in Zika virus and related flaviviruses. Pathog Glob Health 10:269–274. https://doi.org/10.1371/journal.pntd.0004978
Liang D, Leung RKK, Lee SS, Kam KM (2017) Insights into intercontinental spread of Zika virus. PLoS One 12:e0176710. https://doi.org/10.1371/journal.pone.0176710
Holmes EC (2003) Patterns of intra- and Interhost nonsynonymous variation reveal strong purifying selection in dengue virus. J Virol 77:11296 LP–11211298. https://doi.org/10.1128/JVI.77.20.11296-11298.2003
Kivisild T (2013) Founder effect. Brenner's encyclopedia of genetics, second edn. Academic press, San Diego, pp 100–101
Rai MA, Nerurkar VR, Khoja S, Khan S, Yanagihara R, Rehman A, Kazmi SU, Ali SH (2010) Evidence for a “founder effect” among HIV-infected injection drug users (IDUs) in Pakistan. BMC Infect Dis 10:7. https://doi.org/10.1186/1471-2334-10-7
Acknowledgments
We thank the Laboratório Central do Estado do Paraná, Brazil, for supplying the samples used in this study.
Funding
This work was supported by Fundação Araucária de Apoio ao Desenvolvimento Científico e Tecnológico do Estado do Paraná, Brazil (Grant. no. 040/2016).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
On behalf of all authors, the corresponding author states that there is no conflict of interest.
Ethical approval
The use of human samples was approved by the Permanent Research Ethics Committee of the State University of Maringá (Protocol no. 1.751.311).
Additional information
Responsible Editor: Mauricio Nogueira.
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Thomazella, M.V., Lima Neto, Q.A., Duarte Junior, F.F. et al. Insights on Zika virus envelope gene conservation in American outbreaks. Braz J Microbiol 51, 1601–1605 (2020). https://doi.org/10.1007/s42770-020-00349-3
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s42770-020-00349-3