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.

We report on the first isolation of dengue virus serotype 4 (DENV-4) in the State of Mato Grosso do Sul, Brazil, in February, 2012. The cases were isolated in the city of Campo Grande, the state capital, and presented the classic signs and symptoms of dengue fever. DENV-4 was primarily identified through viral isolation in C6/36 clone lineage of Aedes albopictus cells; followed by indirect immunofluorescence, using type-specific monoclonal antibodies. The results were subsequently confirmed by Nested RT-PCR tests. The first description of the introduction of DENV-4 in a state whose population is susceptible to this serotype and the circulation of three other serotypes in the area is cause for concern due to the increased possibility of severe and lethal cases of the disease, and of huge epidemics.

The emergence and reemergence of mosquito-borne diseases in Brazil such as yellow fever, zika, chikungunya, and dengue have had serious impacts on public health. Concerns have been raised due to the rapid dissemination of the chikungunya virus across the country since its first detection in 2014 in Northeast Brazil. In this work, we carried out on-site training activities in genomic surveillance in partnership with the National Network of Public Health Laboratories that have led to the generation of 422 chikungunya virus genomes from 12 Brazilian states over the past two years (2021–2022), a period that has seen more than 312 thousand chikungunya fever cases reported in the country. These genomes increased the amount of available data and allowed a more comprehensive characterization of the dispersal dynamics of the chikungunya virus East-Central-South-African lineage in Brazil. Tree branching patterns revealed the emergence and expansion of two distinct subclades. Phylogeographic analysis indicated that the northeast region has been the leading hub of virus spread towards other regions. Increased frequency of C > T transitions among the new genomes suggested that host restriction factors from the immune system such as ADAR and AID/APOBEC deaminases might be driving the genetic diversity of the chikungunya virus in Brazil.

Rationale: A sudden onset of anosmia has been recently recognized as a symptom of coronavirus disease (COVID-19). Patient concerns: Here, we describe a case of complete anosmia in a young male with COVID-19. Although he had fever and odynophagia, no abnormalities were observed in his nasopharyngeal mucosa, suggesting that his anosmia resulted from olfactory neuropathy. Diagnoses: COVID-19 was confirmed by RNA detection in nasopharyngeal swab specimen. Interventions: The patient received olfactory training and B complex vitamins. Outcomes: On day 30, the patient reported complete recovery of his sense of smell. Lessons: As early diagnosis is fundamental to control the spread of COVID-19 infection, we emphasize that anosmia identified in febrile cases during the COVID-19 epidemic may be a symptom indicative of the disease. Moreover, COVID-19-related anosmia can be completely reversible.