Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil
Authors: Giovanetti Marta , Pinotti Francesco , Zanluca Camila , Fonseca Vagner , Nakase Taishi , Koishi Andrea C. , Tscha Marcel , Soares Guilherme , Dorl Gisiane Gruber , Marques Antônio Ernesto M.L , Sousa Renato , Adelino Talita Emile Ribeiro , Xavier Joilson , de Oliveira Carla , Patroca Sandro , Guimaraes Natalia Rocha , Fritsch Hegger , Mares-Guia Maria Angélica , Levy Flavia , Passos Pedro Henrique , da Silva Vinicius Leme , Pereira Luiz Augusto , Mendonça Ana Flávia , de Macêdo Isabel Luana , Ribeiro de Sousa Davi Emanuel , Rodrigues de Toledo Costa Gabriela , Botelho de Castro Marcio , de Souza Andrade Miguel , de Abreu Filipe Vieira Santos , Campos Fabrício Souza , Iani Felipe Campos de Melo , Pereira Maira Alves , Cavalcante Karina Ribeiro Leite Jardim , de Freitas Andre Ricardo Ribas , Campelo de Albuquerque Carlos Frederico , Macário Eduardo Marques , dos Anjos Marlei Pickler Debiasi , Ramos Rosane Campanher , Campos Aline Alves Scarpellini , Pinter Adriano , Chame Marcia , Abdalla Livia , Riediger Irina Nastassja , Ribeiro Sérvio Pontes , Bento Ana I. , de Oliveira Tulio , Freitas Carla , Oliveira de Moura Noely Fabiana , Fabri Allison , dos Santos Rodrigues Cintia Damasceno , Dos Santos Carolina Cardoso , Barreto de Almeida Marco Antonio , dos Santos Edmilson , Cardoso Jader , Augusto Douglas Adriano , Krempser Eduardo , Mucci Luís Filipe , Gatti Renata Rispoli , Cardoso Sabrina Fernandes , Fuck João Augusto Brancher , Lopes Maria Goretti David , Belmonte Ivana Lucia , Mayoral Pedroso da Silva Gabriela , Soares Maiane Regina Ferreira , de Castilhos Marilia de Melo Santos , de Souza e Silva Joseana Cardoso , Bisetto Junior Alceu , Pouzato Emanuelle Gemin , Tanabe Laurina Setsuko , Arita Daniele Akemi , Matsuo Ricardo , dos Santos Raymundo Josiane , Silva Paula Cristina Linder , Santana Araújo Ferreira Silva Ana , Samila Sandra , Carvalho Glauco , Stabeli Rodrigo , Navegantes Wildo , Moreira Luciano Andrade , Ferreira Alvaro Gil A. , Pinheiro Guilherme Garcia , Nunes Bruno Tardelli Diniz , de Almeida Medeiros Daniele Barbosa , Cruz Ana Cecília Ribeiro , Venâncio da Cunha Rivaldo , Van Voorhis Wes , Bispo de Filippis Ana Maria , Almiron Maria , Holmes Edward C. , Ramos Daniel Garkauskas , Romano Alessandro , Lourenço José , Alcantara Luiz Carlos Junior , Duarte dos Santos Claudia Nunes 
Published: September 2023

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.