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

• DOI: 10.3201/eid2606.190928
• Publication Date: 2020-04-29T13:00:14Z
• Authors: Oumar Faye; Maria de Lourdes ...; Bram Vrancken; Matthieu Prot; Sebastian Lequime; Maryam Diarra; Oumar Ndiaye; Tomas Valdez; Sandra Tavarez; Jessica Ramos; Silvânia da Veiga...; Cecilio Pires; Antonio Moreira; Maria Filomena Ta...; Linete Fernandes; Jorge Noel Barreto; Maria do Céu Teix...; Maria da Luz de L...; Carolina Cardoso ...; Mariano Salazar C...; Laurence Ma; Frédéric Lemoine; Fabiana Gámbaro-R...; Déborah Delaune; Gamou Fall; Ibrahima Socé Fall; Mamadou Diop; Anavaj Sakuntabhai; Cheikh Loucoubar; Philippe Lemey; Edward C. Holmes; Ousmane Faye; Amadou Alpha Sall; Etienne Simon-Lor...
• Keywords: 0301 basic medicine; vector-borne infections; serology; Infectious and parasitic diseases; RC109-216; phylogeography; Asian lineage; Zika virus; Disease Outbreaks; 03 medical and health sciences; West Africa; epidemiologic studies; genomics; Cabo Verde; Humans; [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology; viruses; microcephaly; Western Africa; Cape Verde; [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]; outbreak; Zika Virus Infection; R; Genomics; Zika Virus; [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]; 3. Good health; Africa, Western; [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics; [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology; disease outbreaks; Synopsis; Microcephaly; Medicine; [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie; epidemiology; [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]; Brazil

During 2015-2016, Cape Verde, an island nation off the coast of West Africa, experienced a Zika virus (ZIKV) outbreak involving 7,580 suspected Zika cases and 18 microcephaly cases. Analysis of the complete genomes of 3 ZIKV isolates from the outbreak indicated the strain was of the Asian (not African) lineage. The Cape Verde ZIKV sequences formed a distinct monophylogenetic group and possessed 1-2 (T659A, I756V) unique amino acid changes in the envelope protein. Phylogeographic and serologic evidence support earlier introduction of this lineage into Cape Verde, possibly from northeast Brazil, between June 2014 and August 2015, suggesting cryptic circulation of the virus before the initial wave of cases were detected in October 2015. These findings underscore the utility of genomic-scale epidemiology for outbreak investigations.