Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil
Authors: Adelino Talita Émile Ribeiro , Giovanetti Marta , Fonseca Vagner , Xavier Joilson , de Abreu Álvaro Salgado , do Nascimento Valdinete Alves , Demarchi Luiz Henrique Ferraz , Oliveira Marluce Aparecida Assunção , da Silva Vinícius Lemes , de Mello Arabela Leal e. Silva , Cunha Gabriel Muricy , Santos Roselene Hans , de Oliveira Elaine Cristina , Júnior Jorge Antônio Chamon , de Melo Iani Felipe Campos , de Filippis Ana Maria Bispo , de Abreu André Luiz , de Jesus Ronaldo , de Albuquerque Carlos Frederico Campelo , Rico Jairo Mendez , do Carmo Said Rodrigo Fabiano , Silva Joscélio Aguiar , de Moura Noely Fabiana Oliveira , Leite Priscila , Frutuoso Lívia Carla Vinhal , Haddad Simone Kashima , Martínez Alexander , Barreto Fernanda Khouri , Vazquez Cynthia Carolina , da Cunha Rivaldo Venâncio , Araújo Emerson Luiz Lima , de Oliveira Tosta Stephane Fraga , de Araújo Fabri Allison , Chalhoub Flávia Löwen Levy , da Silva Lemos Poliana , de Bruycker-Nogueira Fernanda , de Castro Lichs Gislene Garcia , Zardin Marina Castilhos Souza Umaki , Segovia Fátima María Cardozo , Gonçalves Crhistinne Cavalheiro Maymone , Grillo Zoraida Del Carmen Fernandez , Slavov Svetoslav Nanev , Pereira Luiz Augusto , Mendonça Ana Flávia , Pereira Felicidade Mota , de Magalhães Jurandy Júnior Ferraz , dos Santos Júnior Agenor de Castro Moreira , de Lima Maricélia Maia , Nogueira Rita Maria Ribeiro , Góes-Neto Aristóteles , de Carvalho Azevedo Vasco Ariston , Ramalho Dario Brock , Oliveira Wanderson Kleber , Macario Eduardo Marques , de Medeiros Arnaldo Correia , Pimentel Victor ,   Latin American Genomic Surveillance Arboviral Network, de Cerqueira Erenilde Marques , Graf Tiago , Ramalho Walter , Navegantes Wildo , Reis Renato Barbosa , Duarte Clara Guerra , Pereira Maira Alves , de Souza da Silva Paulo Eduardo , de Souza Raoni Almeida , Pauvolid-Corrêa Alex , Pereira de Paiva Anne Aline , Fritsch Hegger Machado , Mares-Guia Maria Angélica , Torres Maria Celeste , Lima Maurício Teixeira , Sequeira Patrícia , de Almeida Marques William , de Jesus Jorlan Fernandes , Naveca Felipe Gomes , Silva Alessandra Lima , Pinto Anne Cybelle , Jaiswal Arun Kumar , Lopes Élisson Nogueira , Rodrigues da Costa Francielly Morais , Quintanilha-Peixoto Gabriel , Soares Gilson Carlos , Fonseca Paula Luize Camargos , de Souza Renan Pedra , Kato Rodrigo Bentes , Santos Rodrigo Profeta Silveira , Tiwari Sandeep , Nogueira Wylerson Guimarães , da Silva Santos Beatriz Senra Álvares , Bueno Bruna Lopes , de Siqueira Isadora Cristina , Vallve Lourdes Farre , Borba Melina Mosquera Navarro , Mazzetto Alix Sandra , Aguiar Francisco de Assis Araújo , da Silva Gomes Irenio , Abrantes Jayra Juliana Paiva Alves , Watanabe Luiz Takao , da Silva Rego Marta Ferreira , Nardy Vanessa Brandão , de Aguiar Shirlei Ferreira , dos Santos Fabiana Cristina Pereira , Queiroz Alice Louize Nunes , Nunes Bruno Tardelli Diniz , Martins Lívia Carício , Nunes Márcio Roberto Teixeira , da Silva Salles Flávia Cristina , Claro Ingra Morales , de Jesus Jaqueline Goes , da Silva Cândido Darlan , Fabbri Cintia Marcela , González Claudia , Saéz Lisseth , Chen-Germán María , Barrera Jaime Lagos , Ramírez-González José Ernesto , Campos Josefina , Faller Noelia Morel , Villalobos Marta Eugenia Víquez , Kaslin Roberto , Cisneros Silvia Paola Salgado , Aburjaile Flávia Figueira , Amaral Carolina Dourado , de Sousa Freire Danielle Bandeira Costa , Cruz Laura Nogueira , Mattos Daniel , Landeira Leandro Ferreira Lopes , de Menezes Mariane Talon , Orioli Ieda Maria , Ferraz Ariane Coelho , de Oliveira Daiane Teixeira , Reis Alexandre Barbosa , de Sá Cota Renata Guerra , dos Santos Bezerra Rafael , Falcão Melissa Barreto , de Oliveira Carvalho Rodrigo Dias , Holmes Edward C. , de Oliveira Tulio , Lourenço José , Alcantara Luiz Carlos Junior 
Published: April 2021

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.