Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil
Marta Giovanetti, Francesco Pinotti, Camila Zanluca, Vagner Fonseca, Taishi Nakase, Andrea C. Koishi, Marcel Tscha, Guilherme Soares, Gisiane Gruber Dorl, Antônio Ernesto M.L Marques, Renato Sousa, Talita Emile Ribeiro Adelino, Joilson Xavier, Carla de Oliveira, Sandro Patroca, Natalia Rocha Guimaraes, Hegger Fritsch, Maria Angélica Mares-Guia, Flavia Levy, Pedro Henrique Passos, Vinicius Leme da Silva, Luiz Augusto Pereira, Ana Flávia Mendonça, Isabel Luana de Macêdo, Davi Emanuel Ribeiro de Sousa, Gabriela Rodrigues de Toledo Costa, Marcio Botelho de Castro, Miguel de Souza Andrade, Filipe Vieira Santos de Abreu, Fabrício Souza Campos, Felipe Campos de Melo Iani, Maira Alves Pereira, Karina Ribeiro Leite Jardim Cavalcante, Andre Ricardo Ribas de Freitas, Carlos Frederico Campelo de Albuquerque, Eduardo Marques Macário, Marlei Pickler Debiasi dos Anjos, Rosane Campanher Ramos, Aline Alves Scarpellini Campos, Adriano Pinter, Marcia Chame, Livia Abdalla, Irina Nastassja Riediger, Sérvio Pontes Ribeiro, Ana I. Bento, Tulio de Oliveira, Carla Freitas, Noely Fabiana Oliveira de Moura, Allison Fabri, Cintia Damasceno dos Santos Rodrigues, Carolina Cardoso Dos Santos, Marco Antonio Barreto de Almeida, Edmilson dos Santos, Jader Cardoso, Douglas Adriano Augusto, Eduardo Krempser, Luís Filipe Mucci, Renata Rispoli Gatti, Sabrina Fernandes Cardoso, João Augusto Brancher Fuck, Maria Goretti David Lopes, Ivana Lucia Belmonte, Gabriela Mayoral Pedroso da Silva, Maiane Regina Ferreira Soares, Marilia de Melo Santos de Castilhos, Joseana Cardoso de Souza e Silva, Alceu Bisetto Junior, Emanuelle Gemin Pouzato, Laurina Setsuko Tanabe, Daniele Akemi Arita, Ricardo Matsuo, Josiane dos Santos Raymundo, Paula Cristina Linder Silva, Ana Santana Araújo Ferreira Silva, Sandra Samila, Glauco Carvalho, Rodrigo Stabeli, Wildo Navegantes, Luciano Andrade Moreira, Alvaro Gil A. Ferreira, Guilherme Garcia Pinheiro, Bruno Tardelli Diniz Nunes, Daniele Barbosa de Almeida Medeiros, Ana Cecília Ribeiro Cruz, Rivaldo Venâncio da Cunha, Wes Van Voorhis, Ana Maria Bispo de Filippis, Maria Almiron, Edward C. Holmes, Daniel Garkauskas Ramos, Alessandro Romano, José Lourenço, Luiz Carlos Junior Alcantara, Claudia Nunes Duarte dos Santos- Multidisciplinary
Despite the considerable morbidity and mortality of yellow fever virus (YFV) infections in Brazil, our understanding of disease outbreaks is hampered by limited viral genomic data. Here, through a combination of phylogenetic and epidemiological models, we reconstructed the recent transmission history of YFV within different epidemic seasons in Brazil. A suitability index based on the highly domesticated Aedes aegypti was able to capture the seasonality of reported human infections. Spatial modeling revealed spatial hotspots with both past reporting and low vaccination coverage, which coincided with many of the largest urban centers in the Southeast. Phylodynamic analysis unraveled the circulation of three distinct lineages and provided proof of the directionality of a known spatial corridor that connects the endemic North with the extra-Amazonian basin. This study illustrates that genomics linked with eco-epidemiology can provide new insights into the landscape of YFV transmission, augmenting traditional approaches to infectious disease surveillance and control.