Portable sequencing in the field and the classroom: a retrospective examination of the circulation of DENV1 and DENV2 in Brazil

Abstract

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.

Adaptive Evolution of New Variants of Dengue Virus Serotype 1 Genotype V Circulating in the Brazilian Amazon

“…In addition, one envelope sequence (MH401997) identified from the city of Oiapoque in 2015, a municipality in the state of Amapá on the border with Guyana, grouped in the same clade as our sequences, reinforcing that the BR4 lineage was prevalent in the state in this period and disseminated locally. Later, strains of the lineage BR4 spread to other regions of Brazil, such as the Northeast, Midwest, and Southeast, being detected until the present time [ 31 ].…”

“…After its introduction, this lineage disseminated to several states in the northern region, including Amapá, in addition to other regions of Brazil, such as the Southeast, Midwest, and Northeast. Notably, the BR4 lineage remains persistent and has been identified in both southeast and northeast regions in recent years [ 31 ].…”