Marta Giovanetti, Nuno Rodrigues Faria, Jose ́Lourenco, Jaqueline Goes de Jesus, Joilson Xavier, Ingra Morales Claro, Moritz U.G. Kraemer, Vagner Fonseca, Simon Dellicour, Julien Theze, Flavia da Silva Salles, Tiago Graf, Paola Paz Silveira, Valdinete Alves do Nascimento, Victor Costa de Souza, Felipe Campos de Melo Iani, Emerson Augusto Castilho-Martins, Laura Nogueira Cruz, Gabriel Wallau, Allison Fabri, Flavia Levy, Joshua Quick, Vasco de Azevedo, Renato Santana Aguiar, Tulio de Oliveira, Camila Botto de Menezes, Marcia da Costa Castilho, Tirza Matos Terra, Marineide Souza da Silva, Ana Maria Bispo de Filippis, Andre ́Luiz de Abreu, Wanderson Kleber Oliveira, Julio Croda, Carlos F. Campelo de Albuquerque, Marcio R.T. Nunes, Ester Cerdeira Sabino, Nicholas Loman, Felipe Gomes Naveca, Oliver G. Pybus, and Luiz Carlos Alcantara
Zika virus (ZIKV) has caused an explosive epidemic linked to severe clinical outcomes in the Americas. As of June 2018, 4,929 ZIKV suspected infections and 46 congenital syndrome cases had been reported in Manaus, Amazonas, Brazil. Although Manaus is a key demographic hub in the Amazon region, little is known about the ZIKV epidemic there, in terms of both transmission and viral genetic diversity. Using portable virus genome sequencing, we generated 59 ZIKV genomes in Manaus. Phylogenetic analyses indicated multiple introductions of ZIKV from northeastern Brazil to Manaus. Spatial genomic analysis of virus movement among six areas in Manaus suggested that populous northern neighborhoods acted as sources of virus transmission to other neighborhoods. Our study revealed how the ZIKV epidemic was ignited and maintained within the largest urban metropolis in the Amazon. These results might contribute to improving the public health response to outbreaks in Brazil.