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

Despite the considerable morbidity and mortality of Yellow fever virus (YFV) infections in Brazil, as well as its widespread presence in non-human primate host, our understanding of disease outbreaks is hampered by limited viral genomic data. Determining the timing and spatial corridors of YFV spread, as well as the geographic hotspots that link the endemic north of the country with epidemic extra-Amazonian regions, are central to predicting and preventing future outbreak events and epidemics. Here, we tracked the recent spread of the virus by integrating genome sequences of new YFV infections sampled from infected non-human primates and humans with both epidemiological and vector data. 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 domesticatedAedes aegyptiwas able to capture the seasonality of reported human infections. Spatial modelling revealed spatial hotspots with both past reporting and low vaccination coverage, which coincided with many of the largest urban centres in the Southeast. Phylodynamic analysis unravelled the circulation of three distinct YFV lineages, and provided proof of the directionality of a known spatial corridor of viral spread that connects the endemic North with the extra-Amazonian basin. This study illustrates that genomics linked with field sampling of animals and humans within a One Health framework can provide new insights into the landscape of YFV transmission, augmenting traditional approaches to infectious disease surveillance and control.