Portable sequencing in the field and the classroom: a retrospective examination of the circulation of DENV1 and DENV2 in Brazil
Authors: Adelino Talita Émile Ribeiro , Giovanetti Marta , Fonseca Vagner , Xavier Joilson , de Abreu Álvaro Salgado , Nascimento Valdinete Alves do , Demarchi Luiz Henrique Ferraz , Oliveira Marluce Aparecida Assunção , Silva Vinícius Lemes da , Mello Arabela Leal e Silva de , Cunha Gabriel Muricy , Santos Roselene Hans , Oliveira Elaine Cristina de , Chamon Júnior Jorge Antônio , 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 , Said Rodrigo Fabiano do Carmo , Silva Joscélio Aguiar , Moura Noely Fabiana Oliveira de , Leite Priscila , Frutuoso Lívia Carla Vinhal , Haddad Simone Kashima , Martínez Alexander , Barreto Fernanda Khouri , Vazquez Cynthia Carolina , Cunha Rivaldo Venâncio da , Araújo Emerson Luiz Lima , de Oliveira Tosta Stephane Fraga , de Araújo Fabri Allison , Chalhoub Flávia Löwen Levy , Lemos Poliana da Silva , Bruycker-Nogueira Fernanda de , 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 , Magalhães Jurandy Júnior Ferraz de , de Castro Moreira dos Santos Agenor , Lima Maricélia Maia de , Nogueira Rita Maria Ribeiro , Neto Aristóteles Goes , de Carvalho Azevedo Vasco Ariston , Ramalho Dario Brock , Oliveira Wanderson Kleber , Medeiros Arnaldo Correia de , Pimentel Victor ,   Latin American Genomic Surveillance Arboviral Network, Holmes Edward C , Oliveira Tulio de , Lourenço José , Alcantara Luiz Carlos Junior 
Published: September 2020

Background

Brazil has experienced a large dengue virus (DENV) epidemic in 2019, highlighting a continual struggle with effective control and public health preparedness. Brazil is a world leader in real-time genomic surveillance of arboviruses, although such technology and expertise remains inaccessible for the vast majority of local researchers and public health workers. In 2019, we led field and classroom initiatives for the genomic surveillance of DENV in Brazil.

Methods

Oxford Nanopore MinION technology was used for sequencing, focusing on generating DENV1 and DENV2 complete genomes. Using phylogenetic and epidemiological approaches conducted in real-time during a training program and subsequently through online channels, we explored the recent spatio-temporal evolution and spread of these viruses in Brazil.

Findings

In the years following the Zika virus epidemic (2017-2018) reporting was at an all-time low, and significant increases in reported cases and deaths in 2019 did not reflect a higher case fatality ratio. Estimated transmission potential and reporting of other arboviruses suggests that neither arboviral reporting saturation nor climatic factors can easily explain the post-Zika period and resurgence in 2019 (respectively). Phylogenetic analysis revealed complex patterns of transmission, with lineage co-circulation and replacement, in which the North and the Southeast acted as sources of dispersion to other regions. We identified two lineages within the already reported DENV2 BR-4 clade, for which the effective reproduction number had seasonal signatures alike reported cases, with a temporal increase towards 2019 mirroring the large epidemic that year.

Interpretation

We describe the recent evolution and diffusion of DENV1 and DENV2 in Brazil. Importantly, the surveillance outputs and training initiative here described serve as proof-of-concept of the potential of portable sequencing for both research and local capacity building in the area of genomic surveillance of arboviruses.

Funding

Decit, SCTIE, BrMoH, CNPq, CAPES, EU Horizon 2020 through ZIKAlliance and STARBIOS2.