Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil

Abstract

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.

Dengue-2 Cosmopolitan genotype detection and emergence in South America

“…During the past epidemics, DENV outbreaks in Brazil and South America were mainly driven by the circulation of DENV-1-2 serotypes (3,4). Among them, DENV-2 contributes substantially to the dengue burden and dengue-related mortality in the region.…”

“…Each serotype is further subdivided into several phylogenetically distinct genotypes often named according to their geographic origin or other nomenclature, even though some of them have spread to other regions in the past few decades (2). During the past epidemics, DENV outbreaks in Brazil and South America were mainly driven by the circulation of DENV-1-2 serotypes (3,4). Among them, DENV-2 contributes substantially to the dengue burden and dengue-related mortality in the region.…”

“…Briefly, viral RNA was submitted to a cDNA synthesis protocol using ProtoScript II First Strand cDNA Synthesis Kit (10). Then, a multiplex tiling PCR was conducted using Q5 High Fidelity Hot-Start DNA Polymerase (New England Biolabs) and a DENV-2 sequencing primers scheme (3). Amplicons were purified using 1x AMPure XP Beads and cleaned-up PCR product concentrations were measured using Qubit dsDNA HS Assay Kit on a Qubit 3.0 fluorimeter (ThermoFisher).…”

A Retrospective Overview of Zika Virus Evolution in the Midwest of Brazil

“…Despite some work done over the large epidemic between 2015 and 2016, there is still a paucity of studies directly investigating the circulation and genetic diversity of the ZIKV in this region. In this study, using our experience with mobile laboratory ( 15 ), we used nanopore sequencing to generate ZIKV genomes from infected patients residing in Goiás and provide a retrospective reconstruction of its transmission dynamics in that state.…”

Promoting Responsible Research and Innovation (RRI) During Brazilian Activities of Genomic and Epidemiological Surveillance of Arboviruses

“…In both formats, training included all surveillance tasks, from sequencing to computational analyses and research writing. Employing genomic surveillance in the field and in the classroom, we generated and analyzed 227 novel complete genome sequences of Dengue 1–2 ( 16 ).…”