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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.

Original publication

DOI

10.1038/s41467-021-22607-0

Type

Journal article

Journal

Nat Commun

Publication Date

16/04/2021

Volume

12

Keywords

Brazil, Dengue, Dengue Virus, Epidemics, Epidemiological Monitoring, Feasibility Studies, Genetic Variation, Genome, Viral, Humans, Mobile Health Units, Molecular Epidemiology, Molecular Typing, Phylogeny, Proof of Concept Study, RNA, Viral, Real-Time Polymerase Chain Reaction, Retrospective Studies, Whole Genome Sequencing