Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 26, Number 6—June 2020
Synopsis

Genomic Epidemiology of 2015–2016 Zika Virus Outbreak in Cape Verde

Oumar Faye1, Maria de Lourdes Monteiro1, Bram Vrancken1, Matthieu Prot1, Sebastian Lequime, Maryam Diarra, Oumar Ndiaye, Tomas Valdez, Sandra Tavarez, Jessica Ramos, Silvânia da Veiga Leal, Cecilio Pires, Antonio Moreira, Maria Filomena Tavares, Linete Fernandes, Jorge Noel Barreto, Maria do Céu Teixeira, Maria da Luz de Lima Mendonça, Carolina Cardoso da Silva Leite Gomes, Mariano Salazar Castellon, Laurence Ma, Frédéric Lemoine, Fabiana Gámbaro-Roglia, Déborah Delaune, Gamou Fall, Ibrahima Socé Fall, Mamadou Diop, Anavaj Sakuntabhai, Cheikh Loucoubar, Philippe Lemey, Edward C. Holmes, Ousmane Faye, Amadou Alpha Sall2, and Etienne Simon-Loriere2Comments to Author 
Author affiliations: Institut Pasteur, Dakar, Senegal (Oumar Faye, M. Diarra, O. Ndiaye, G. Fall, M. Diop, C. Loucoubar, Ousmane Faye, A.A. Sall); Ministerio da Saude, Praia, Cape Verde (M. de Lourdes Monteiro, T. Valdez, S. Tavarez, J. Ramos, S. da Veiga Leal, C. Pires, A. Moreira, M.F. Tavares, L. Fernandes, J.N. Barreto, M. do Céu Teixeira, M.L. de Lima Mendonça); Katholieke Universiteit Leuven, Leuven, Belgium (B. Vrancken, S. Lequime, P. Lemey); Institut Pasteur, Paris, France (M. Prot, L. Ma, F. Gámbaro-Roglia, D. Delaune, E. Simon-Loriere); World Health Organization, Praia (C.C. da Silva Leite Gomes, M.S. Castellon, I.S. Fall); CNRS USR 3756, Paris (F. Lemoine); Université de Paris, Sorbonne Paris Cité, Paris (F. Gámbaro-Roglia); Université Paris-Sud/Paris-Saclay, Orsay, France (D. Delaune); Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France (D. Delaune); CNRS UMR 2000, Paris (A. Sakuntabhai); The University of Sydney, Sydney, New South Wales, Australia (E.C. Holmes)

Main Article

Figure 3

Maximum clade credibility phylogenetic tree demonstrating migration history of Zika virus (ZIKV) Asian lineage, 2014–2018. A) Phylogeny of 459 ZIKV isolates. The tree base was removed for ease of presentation. Tips of tree are colored according to their sampling location and branches according to their most probable geographic location. Note that sequences from the 2016 Angola outbreak (23) were published during the later stages of preparation of this manuscript and therefore were not included i

Figure 3. Maximum clade credibility phylogenetic tree demonstrating migration history of Zika virus (ZIKV) Asian lineage, 2014–2018. A) Phylogeny of 459 ZIKV isolates. The tree base was removed for ease of presentation. Tips of tree are colored according to their sampling location and branches according to their most probable geographic location. Note that sequences from the 2016 Angola outbreak (23) were published during the later stages of preparation of this manuscript and therefore were not included in this Bayesian analysis. Scale bar indicates years. See Appendix Figure 1 for fully annotated tree. B) Expansion of tree containing Cape Verde ZIKV sequences (bold). Clade posterior probabilities are shown at well-supported nodes (>0.9). GenBank accession number, country of origin, and sampling date are provided for each ZIKV sequence.

Main Article

References
  1. Baud  D, Gubler  DJ, Schaub  B, Lanteri  MC, Musso  D. An update on Zika virus infection. Lancet. 2017;390:2099109. DOIPubMed
  2. Faye  O, Freire  CC, Iamarino  A, Faye  O, de Oliveira  JV, Diallo  M, et al. Molecular evolution of Zika virus during its emergence in the 20(th) century. PLoS Negl Trop Dis. 2014;8:e2636. DOIPubMed
  3. Posen  HJ, Keystone  JS, Gubbay  JB, Morris  SK. Epidemiology of Zika virus, 1947-2007. BMJ Glob Health. 2016;1:e000087. DOIPubMed
  4. Cao-Lormeau  VM, Blake  A, Mons  S, Lastère  S, Roche  C, Vanhomwegen  J, et al. Guillain-Barré Syndrome outbreak associated with Zika virus infection in French Polynesia: a case-control study. Lancet. 2016;387:15319. DOIPubMed
  5. Pan American Health Organization; World Health Organization. Zika cases and congenital syndrome associated with Zika virus reported by countries and territories in the Americas, 2015–2018, cumulative cases. 2018 Jan 4 [cited 2019 Oct 15]. https://www.paho.org/hq/index.php?option=com_docman&task=doc_download&gid=43296
  6. de Araújo  TVB, Ximenes  RAA, Miranda-Filho  DB, Souza  WV, Montarroyos  UR, de Melo  APL, et al.; investigators from the Microcephaly Epidemic Research Group; Brazilian Ministry of Health; Pan American Health Organization; Instituto de Medicina Integral Professor Fernando Figueira; State Health Department of Pernambuco. Association between microcephaly, Zika virus infection, and other risk factors in Brazil: final report of a case-control study. Lancet Infect Dis. 2018;18:32836. DOIPubMed
  7. Mlakar  J, Korva  M, Tul  N, Popović  M, Poljšak-Prijatelj  M, Mraz  J, et al. Zika virus associated with microcephaly. N Engl J Med. 2016;374:9518. DOIPubMed
  8. Lourenço  J, de Lourdes Monteiro  M, Valdez  T, Monteiro Rodrigues  J, Pybus  O, Rodrigues Faria  N. Epidemiology of the Zika Virus Outbreak in the Cabo Verde Islands, West Africa. PLoS Curr. 2018;10:10. DOIPubMed
  9. Serviço de Vigilância Integrada e Resposta a Epidemias, Ministério da Saúde e da Segurança Social. Boletim informativo seminal, infeção por vírus Zika (ZIKV), ano 2016, (semanas 1 a 21). 2016 [cited 2019 Jul 1]. http://www.minsaude.gov.cv/index.php/documentosite/zika-1/341-boletim-informativo-semanal-da-infecao-por-virus-zika-semana-21-ano-2016/file
  10. Faria  NR, Azevedo  RDSDS, Kraemer  MUG, Souza  R, Cunha  MS, Hill  SC, et al. Zika virus in the Americas: Early epidemiological and genetic findings. Science. 2016;352:3459. DOIPubMed
  11. De Madrid  AT, Porterfield  JS. A simple micro-culture method for the study of group B arboviruses. Bull World Health Organ. 1969;40:11321.PubMed
  12. Quick  J, Grubaugh  ND, Pullan  ST, Claro  IM, Smith  AD, Gangavarapu  K, et al. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat Protoc. 2017;12:126176. DOIPubMed
  13. Katoh  K, Standley  DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:77280. DOIPubMed
  14. Larsson  A. AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics. 2014;30:32768. DOIPubMed
  15. Suchard  MA, Lemey  P, Baele  G, Ayres  DL, Drummond  AJ, Rambaut  A. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 2018;4:vey016. DOIPubMed
  16. Drummond  AJ, Ho  SY, Phillips  MJ, Rambaut  A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006;4:e88. DOIPubMed
  17. Gill  MS, Lemey  P, Faria  NR, Rambaut  A, Shapiro  B, Suchard  MA. Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Mol Biol Evol. 2013;30:71324. DOIPubMed
  18. Shapiro  B, Rambaut  A, Drummond  AJ. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol. 2006;23:79. DOIPubMed
  19. Lemey  P, Rambaut  A, Drummond  AJ, Suchard  MA. Bayesian phylogeography finds its roots. PLOS Comput Biol. 2009;5:e1000520. DOIPubMed
  20. Rambaut  A, Drummond  AJ, Xie  D, Baele  G, Suchard  MA. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst Biol. 2018;67:9014. DOIPubMed
  21. Duffy  MR, Chen  TH, Hancock  WT, Powers  AM, Kool  JL, Lanciotti  RS, et al. Zika virus outbreak on Yap Island, Federated States of Micronesia. N Engl J Med. 2009;360:253643. DOIPubMed
  22. Sow  A, Loucoubar  C, Diallo  D, Faye  O, Ndiaye  Y, Senghor  CS, et al. Concurrent malaria and arbovirus infections in Kedougou, southeastern Senegal. Malar J. 2016;15:47. DOIPubMed
  23. Hill  SC, Vasconcelos  J, Neto  Z, Jandondo  D, Zé-Zé  L, Aguiar  RS, et al. Emergence of the Asian lineage of Zika virus in Angola: an outbreak investigation. Lancet Infect Dis. 2019;19:113847. DOIPubMed
  24. Sassetti  M, Zé-Zé  L, Franco  J, Cunha  JD, Gomes  A, Tomé  A, et al. First case of confirmed congenital Zika syndrome in continental Africa. Trans R Soc Trop Med Hyg. 2018;112:45862. DOIPubMed
  25. Faria  NR, Quick  J, Claro  IM, Thézé  J, de Jesus  JG, Giovanetti  M, et al. Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature. 2017;546:40610. DOIPubMed
  26. Thézé  J, Li  T, du Plessis  L, Bouquet  J, Kraemer  MUG, Somasekar  S, et al. Genomic epidemiology reconstructs the introduction and spread of Zika virus in Central America and Mexico. Cell Host Microbe. 2018;23:855864.e7. DOIPubMed

Main Article

1These first authors contributed equally to this article.

2These senior authors contributed equally to this article.

Page created: May 18, 2020
Page updated: May 18, 2020
Page reviewed: May 18, 2020
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external