Fernanda de Bruycker-Nogueira

Dengue virus (DENV) transmission in Brazil is characterized by recurrent epidemics involving the introduction, persistence, and replacement of viral lineages. However, temporal gaps in genomic surveillance limit our understanding of how these processes shape successive epidemics in Rio de Janeiro. Here, in a retrospective observational molecular epidemiology study, we combined archived genomic data with publicly available sequences and epidemiological surveillance data to investigate the temporal dynamics of DENV serotypes and lineages in Rio de Janeiro. Archived DENV-positive samples were curated and subjected to whole-genome amplicon sequencing, and the resulting consensus sequences were analyzed together with publicly available sequences using time-scaled phylogenetic reconstruction and epidemiological data. We recovered 35 DENV genomes from samples collected in 2013, 2018, 2020, and 2021, including DENV-1 genotype V, DENV-2 genotypes II and III, and DENV-4 genotype II. Analysis of the combined datasets identified multiple Rio de Janeiro-associated clades with distinct temporal patterns. Publicly available sequences supported the broader clade structure and long-term temporal patterns independently of most genomes generated here. The newly generated genomes made genotype-specific contributions: the five DENV-1 genotype V genomes placed archived 2020–2021 samples within previously represented Rio de Janeiro-associated groups, while the single DENV-2 genotype II genome provided phylogenetic placement of a travel-associated 2018 case. In contrast, the 20 DENV-2 genotype III genomes identified a Rio de Janeiro-associated cluster not represented among the public sequences, and the nine DENV-4 genotype II genomes increased representation of the 2013 epidemic. Thus, the principal contribution of retrospective sequencing was to fill specific temporal and geographic gaps rather than to redefine the broader historical phylogenetic structure of all genotypes.

Dengue fever is an acute, systemic, and debilitating febrile illness that poses a significant global public health threat. Vaccination is important in combating the virus in highly prevalent countries, as it reduces the risk of symptomatic infection, hospitalizations, morbidity, and mortality. We report a unique case of atypical dengue fever in a previously healthy 42-year-old Brazilian woman. She developed dengue without the characteristic fever or elevated inflammatory markers 15 days after her initial TAK-003 (Q-denga) vaccine dose, setting her case apart from typical manifestations. ’Whether the mildness of the case was due to the vaccine’s protective effect or if it was caused by the vaccine virus itself, as genetic sequencing of DENV-2 was not possible, is unclear. In regions where the vaccine is being introduced, atypical cases, particularly those without fever, require thorough investigation, so dengue can be excluded.

Background: Malaria is endemic and represents an important public health issue in Brazil. Knowledge of risk factors for disease progression represents an important step in preventing and controlling malaria-related complications. Reports of severe forms of Plasmodium vivax malaria are now becoming a common place, but respiratory complications are described in less than 3% of global literature on severe vivax malaria. Case presentation: A severe respiratory case of imported vivax malaria in a previously healthy 40-year-old woman has been reported. The patient died after the fifth day of treatment with chloroquine and primaquine due to acute respiratory distress syndrome. Conclusions: Respiratory symptoms started 48 h after the initiation of anti-malarial drugs, raising the hypothesis that the drugs may have been involved in the genesis of the complication. The concept that vivax malaria is a benign disease that can sometimes result in the development of serious complications must be disseminated. This report highlights, once more, the crucial importance of malaria early diagnosis, a true challenge in non-endemic areas, where health personnel are not familiar with the disease and do not consider its diagnosis promptly.

In 2023, three autochthonous DENV-3 cases were detected in Roraima and one imported case in Paraná, fifteen years after the last DENV-3 outbreak in Brazil. Phylogenetic analyses confirmed all belonging to a new Asian lineage recently introduced in the Americas, raising concerns about future large dengue outbreaks in this region.

Background: Chikungunya is a viral disease that is transmitted by mosquitoes. It is characterized by an acute onset of fever and severe arthralgia. Methods: We describe six cases of acute and post-acute chikungunya in which viral RNA was detected in semen. Conclusions: The most prolonged detection period was 56 days after illness onset. We attempted to cultivate positive semen samples, but virus isolation was unsuccessful in all cases.

Background: Chikungunya is a widely distributed, re-emerging tropical disease caused by the chikungunya virus (CHIKV). Little is known about the duration for which CHIK RNA are detectable in bodily fluids, especially genital secretions, and current evidence is based on small series or case reports. An understanding of viral dynamics across different body compartments can inform diagnostic testing algorithms and public health prevention interventions. Methodology: A prospective cohort study was conducted to assess the presence and duration of detectable levels of CHIKV RNA in blood, urine, saliva, semen, and vaginal secretions. Men and women (≥ 18 years) with a positive reverse transcriptase-polymerase chain reaction (RT-PCR) test for CHIKV in the acute phase (1–14 days) of the disease were included. After enrollment, clinical data and samples were collected every 15 days over the first 2 months, and a final collection was performed 3 months after recruitment. The Kaplan–Meier interval-censoring method and the parametric Weibull model were fitted to estimate the median time of viral persistence until the lack of CHIKV RNA detection among all body fluids. Punctual estimates of the median time of CHIKV RNA persistence for each fluid were estimated using a 95% confidence interval (CI). Results: From April to December 2019, 170 participants were screened. Of these, 152 (100 women) were enrolled in the study. The median and interquartile range (IQR) ages for men and women were 39.3 (IQR: 26.9, 50.7) and 43.5 (IQR: 33.8, 53.6) years, respectively. CHIKV RNA was detected in 80.3% (122/152) of serum samples, 23.0% (35/152) of urine samples, 30.3% (46/152) of saliva samples, 14.3% (6/42) of semen samples, and 20.2% (20/99) of vaginal secretion samples. The median time until the loss of CHIKV RNA detection was 19.6 days (95% CI, 17.5–21.7) in serum, 25.3 days (95% CI, 17.8–32.8) in urine, 23.1 days (95% CI, 17.9–28.4) in saliva, and 25.8 days (95% CI, 20.6–31.1) in vaginal secretion. The number of semen samples available was too small to make statistical estimates, but a last positive sample was obtained from a participant 56 days after the onset of symptoms. Conclusions: CHIKV RNA could be detected in all bodily fluids studied, including genital secretions during the acute and convalescent phases and additional studies on viral infectivity in semen and vaginal secretions are warranted.

The Chikungunya virus infection in Brazil has raised several concerns due to the rapid dissemination of the virus and its association with several clinical complications. Nevertheless, there is limited information about the genomic epidemiology of CHIKV circulating in Brazil from surveillance studies. Thus, to better understand its dispersion dynamics in Rio de Janeiro (RJ), one of the most affected states during the 2016–2019 epidemic waves, we generated 23 near-complete genomes of CHIKV isolates from two main cities located in the metropolitan mesoregion, obtained directly from clinical samples. Our phylogenetic reconstructions suggest the 2019-CHIKV-ECSA epidemic in RJ state was characterized by the co-circulation of multiple clade (clade A and B), highlighting that two independent introduction events of CHIKV-ECSA into RJ state have occurred between 2016–2019, both mediated from the northeastern region. Interestingly, we identified that the two-clade displaying eighteen characteristic amino acids changes among structural and non-structural proteins. Our findings reinforce that genomic data can provide information about virus genetic diversity and transmission dynamics, which might assist in the arbovirus epidemics establishing of an effective surveillance framework.