Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil.
Adelino TÉR., Giovanetti M., Fonseca V., Xavier J., de Abreu ÁS., do Nascimento VA., Demarchi LHF., Oliveira MAA., da Silva VL., de Mello ALES., Cunha GM., Santos RH., de Oliveira EC., Júnior JAC., de Melo Iani FC., de Filippis AMB., de Abreu AL., de Jesus R., de Albuquerque CFC., Rico JM., do Carmo Said RF., Silva JA., de Moura NFO., Leite P., Frutuoso LCV., Haddad SK., Martínez A., Barreto FK., Vazquez CC., da Cunha RV., Araújo ELL., de Oliveira Tosta SF., de Araújo Fabri A., Chalhoub FLL., da Silva Lemos P., de Bruycker-Nogueira F., de Castro Lichs GG., Zardin MCSU., Segovia FMC., Gonçalves CCM., Grillo ZDCF., Slavov SN., Pereira LA., Mendonça AF., Pereira FM., de Magalhães JJF., Dos Santos Júnior ADCM., de Lima MM., Nogueira RMR., Góes-Neto A., de Carvalho Azevedo VA., Ramalho DB., Oliveira WK., Macario EM., de Medeiros AC., Pimentel V., Latin American Genomic Surveillance Arboviral Network None., Holmes EC., de Oliveira T., Lourenço J., Alcantara LCJ.
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.