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

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. Funding Decit, SCTIE, BrMoH, CNPq, CAPES, EU Horizon 2020 through ZIKAlliance and STARBIOS2. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement Decit, SCTIE, BrMoH, CNPq, CAPES, EU Horizon 2020 through ZIKAlliance and STARBIOS2. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: This project was reviewed and approved by the Comissao Nacional de Etica em Pesquisa (CONEP) from the Brazilian Ministry of Health (BrMoH), as part of the arboviral genomic surveillance efforts within the terms of Resolution 510/2016 of CONEP, by the Pan American Health Organization Ethics Review Committee (PAHOERC) (Ref. No. PAHO-2016-08-0029), and by the Oswaldo Cruz Foundation Ethics Committee (CAAE: 90249218.6.1001.5248). The samples processed in this study were obtained anonymously from material exceeding the routine diagnosis of arboviruses in Brazilian public health laboratories that belong to the BrMoH public network. All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Newly generated DENV1 and DENV2 sequences have been deposited in GenBank and accession numbers will be provided upon final submission. All supplementary files can be found at: .