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

Oumar Faye (1) , Maria de Lourdes Monteiro (2) , Bram Vrancken (3) , Matthieu Prot (4) , Sebastian Lequime (3) , Maryam Diarra (1) , Oumar Hamady Ndiaye (1) , Tomas Valdez (2) , Sandra Tavarez (2) , Jessica Ramos (2) , Silvânia da Veiga Leal (2) , Cecilio Pires (2) , António Moreira (2) , Maria Filomena Tavares (2) , Linete Fernandes (2) , Jorge Noel Barreto (2) , Maria Do Céu Teixeira (2) , Maria da Luz de Lima Mendonça (2) , Carolina Cardoso da Silva Leite Gomes (5) , Mariano Salazar Castellon (5) , Laurence Ma (4) , Fréderic Lemoine (6) , Fabiana Gámbaro-Roglia (4, 7) , Deborah Delaune (4, 8, 9) , Gamou Fall (1) , Ibrahima Socé Fall (5) , Mamadou Diop (1) , Anavaj Sakuntabhai (10) , Cheikh Loucoubar (1) , Philippe Lemey (3) , Edward C Holmes (11) , Ousmane Faye (1) , Amadou Alpha Sall (1) , Etienne Simon-Loriere (4)

1 Institut Pasteur de Dakar
2 Ministry of Health [Cape Verde]
3 KU Leuven - Catholic University of Leuven - Katholieke Universiteit Leuven
4 IP - Institut Pasteur [Paris]
5 WHO - World Health Organisation
6 Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB
7 SU - Sorbonne Université
8 UP11 - Université Paris-Sud - Paris 11
9 IRBA - Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge]
10 Génétique fonctionnelle des maladies infectieuses - Functional Genetics of Infectious Diseases
11 The University of Sydney

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.

Keywords: epidemiology; genomics; microcephaly; outbreak; phylogeography; serology; Asian lineage; vector-borne infections; Brazil; viruses; Cabo Verde; Cape Verde; West Africa; Zika virus; disease outbreaks; epidemiologic studies

Domains: Bioinformatics [q-bio.QM]; Quantitative Methods [q-bio.QM]; Human genetics; Populations and Evolution [q-bio.PE]; Virology; Parasitology; Santé publique et épidémiologie

Oumar Faye, Maria de Lourdes Monteiro, Bram Vrancken, Matthieu Prot, Sebastian Lequime, et al.. Genomic Epidemiology of 2015–2016 Zika Virus Outbreak in Cape Verde. Emerging Infectious Diseases, 2020, 26 (6), pp.1084-1090. ⟨10.3201/eid2606.190928⟩. ⟨pasteur-02862296⟩