Brazil has experienced an unprecedented epidemic of Zika virus (ZIKV), with ~30,000 cases reported to date. ZIKV was first detected in Brazil in May 2015, and cases of microcephaly potentially associated with ZIKV infection were identified in November 2015. We performed next-generation sequencing to generate seven Brazilian ZIKV genomes sampled from four self-limited cases, one blood donor, one fatal adult case, and one newborn with microcephaly and congenital malformations. Results of phylogenetic and molecular clock analyses show a single introduction of ZIKV into the Americas, which we estimated to have occurred between May and December 2013, more than 12 months before the detection of ZIKV in Brazil. The estimated date of origin coincides with an increase in air passengers to Brazil from ZIKV-endemic areas, as well as with reported outbreaks in the Pacific Islands. ZIKV genomes from Brazil are phylogenetically interspersed with those from other South American and Caribbean countries. Mapping mutations onto existing structural models revealed the context of viral amino acid changes present in the outbreak lineage; however, no shared amino acid changes were found among the three currently available virus genomes from microcephaly cases. Municipality-level incidence data indicate that reports of suspected microcephaly in Brazil best correlate with ZIKV incidence around week 17 of pregnancy, although this correlation does not demonstrate causation. Our genetic description and analysis of ZIKV isolates in Brazil provide a baseline for future studies of the evolution and molecular epidemiology of this emerging virus in the Americas.
Authors: Nuno Rodrigues Faria, Raimunda do Socorro da Silva Azevedo, Moritz U. G. Kraemer, Renato Souza, Mariana Sequetin Cunha, Sarah C. Hill, Julien Thézé, Michael B. Bonsall, Thomas A. Bowden, Ilona Rissanen, Iray Maria Rocco, Juliana Silva Nogueira, Adriana Yurika Maeda, Fernanda Giseli da Silva Vasami, Fernando Luiz de Lima Macedo, Akemi Suzuki, Sueli Guerreiro Rodrigues, Ana Cecilia Ribeiro Cruz, Bruno Tardeli Nunes, Daniele Barbosa de Almeida Medeiros, Daniela Sueli Guerreiro Rodrigues, Alice Louize Nunes Queiroz, Eliana Vieira Pinto da Silva, Daniele Freitas Henriques, Elisabeth Salbe Travassos da Rosa, Consuelo Silva de Oliveira, Livia Caricio Martins, Helena Baldez Vasconcelos, Livia Medeiros Neves Casseb, Darlene de Brito Simith, Jane P. Messina, Leandro Abade, José Lourenço, Luiz Carlos Junior Alcantara, Maricélia Maia de Lima, Marta Giovanetti, Simon I. Hay, Rodrigo Santos de Oliveira, Poliana da Silva Lemos, Layanna Freitas de Oliveira, Clayton Pereira Silva de Lima, Sandro Patroca da Silva, Janaina Mota de Vasconcelos, Luciano Franco, Jedson Ferreira Cardoso, João Lídio da Silva Gonçalves Vianez-Júnior, Daiana Mir, Gonzalo Bello, Edson Delatorre, Kamran Khan, Marisa Creatore, Giovanini Evelim Coelho, Wanderson Kleber de Oliveira, Robert Tesh, Oliver G. Pybus, Marcio R. T. Nunes, Pedro F. C. Vasconcelos
