Brazil experienced a large dengue virus (DENV) epidemic in 2019, highlighting a continuous struggle with effective control and public health preparedness. Using Oxford Nanopore sequencing, we led field and classroom initiatives for the monitoring of DENV in Brazil, generating 227 novel genome sequences of DENV1-2 from 85 municipalities (2015–2019). This equated to an over 50% increase in the number of DENV genomes from Brazil available in public databases.
Using both phylogenetic and epidemiological models we retrospectively reconstructed the recent transmission history of DENV1-2. Phylogenetic analysis revealed complex patterns of transmission, with both lineage co-circulation and replacement. We identified two lineages within the DENV2 BR-4 clade, for which we estimated the effective reproduction number and pattern of seasonality.
Overall, the surveillance outputs and training initiative described here serve as a proof-of-concept for the utility of real-time portable sequencing for research and local capacity building in the genomic surveillance of emerging viruses.
Authors: Talita Émile Ribeiro Adelino, Marta Giovanetti, Vagner Fonseca, Joilson Xavier, Álvaro Salgado de Abreu, Valdinete Alves do Nascimento, Luiz Henrique Ferraz Demarchi, Marluce Aparecida Assunção Oliveira, Vinícius Lemes da Silva, Arabela Leal e. Silva de Mello, Gabriel Muricy Cunha, Roselene Hans Santos, Elaine Cristina de Oliveira, Jorge Antônio Chamon Júnior, Felipe Campos de Melo Iani, Ana Maria Bispo de Filippis, André Luiz de Abreu, Ronaldo de Jesus, Carlos Frederico Campelo de Albuquerque, Jairo Mendez Rico, Rodrigo Fabiano do Carmo Said, Joscélio Aguiar Silva, Noely Fabiana Oliveira de Moura, Priscila Leite, Lívia Carla Vinhal Frutuoso, Simone Kashima Haddad, Alexander Martínez, Fernanda Khouri Barreto, Cynthia Carolina Vazquez, Rivaldo Venâncio da Cunha, Emerson Luiz Lima Araújo, Stephane Fraga de Oliveira Tosta, Allison de Araújo Fabri, Flávia Löwen Levy Chalhoub, Poliana da Silva Lemos, Fernanda de Bruycker-Nogueira, Gislene Garcia de Castro Lichs, Marina Castilhos Souza Umaki Zardin, Fátima María Cardozo Segovia, Crhistinne Cavalheiro Maymone Gonçalves, Zoraida Del Carmen Fernandez Grillo, Svetoslav Nanev Slavov, Luiz Augusto Pereira, Ana Flávia Mendonça, Felicidade Mota Pereira, Jurandy Júnior Ferraz de Magalhães, Agenor de Castro Moreira dos Santos Júnior, Maricélia Maia de Lima, Rita Maria Ribeiro Nogueira, Aristóteles Góes-Neto, Vasco Ariston de Carvalho Azevedo, Dario Brock Ramalho, Wanderson Kleber Oliveira, Eduardo Marques Macario, Arnaldo Correia de Medeiros, Victor Pimentel, Latin American Genomic Surveillance Arboviral Network, Edward C. Holmes, Tulio de Oliveira, José Lourenço, Luiz Carlos Junior Alcantara