Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil.
Talita Émile Ribeiro AdelinoMarta GiovanettiVagner FonsecaJoilson XavierÁlvaro Salgado de AbreuValdinete Alves do NascimentoLuiz Henrique Ferraz DemarchiMarluce Aparecida Assunção OliveiraVinícius Lemes da SilvaArabela Leal E Silva de MelloGabriel Muricy CunhaRoselene Hans SantosElaine Cristina de OliveiraJorge Antônio Chamon JúniorFelipe Campos de Melo IaniAna Maria Bispo de FilippisAndré Luiz de AbreuRonaldo de JesusCarlos Frederico Campelo de AlbuquerqueJairo Mendez RicoRodrigo Fabiano do Carmo SaidJoscélio Aguiar SilvaNoely Fabiana Oliveira de MouraPriscila LeiteLivia Carla Vinhal FrutuosoSimone Kashima HaddadAlexander MartínezFernanda Khouri BarretoCynthia Carolina VazquezRivaldo Venâncio da CunhaEmerson Luiz Lima AraújoStephane Fraga de Oliveira TostaAllison de Araújo FabriFlávia Löwen Levy ChalhoubPoliana da Silva LemosFernanda de Bruycker-NogueiraGislene Garcia de Castro LichsMarina Castilhos Souza Umaki ZardinFátima María Cardozo SegoviaCrhistinne Cavalheiro Maymone GonçalvesZoraida Del Carmen Fernandez GrilloSvetoslav Nanev SlavovLuiz Augusto PereiraAna Flávia MendonçaFelicidade Mota PereiraJurandy Júnior Ferraz de MagalhãesAgenor de Castro Moreira Dos Santos JúniorMaricélia Maia de LimaRita Maria Ribeiro NogueiraAristóteles Góes-NetoVasco Ariston de Carvalho AzevedoDario Brock RamalhoWanderson Kleber de OliveiraEduardo Marques MacarioArnaldo Correia de MedeirosVictor Pimentelnull nullEdward C HolmesTulio de OliveiraPaul S WikramaratnaLuiz Carlos Junior AlcantaraPublished in: Nature communications (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.