Background: Dengue virus (DENV) causes an important disease and directly affects public health, being the arbovirus that presents the highest number of infections and deaths in the Western Brazilian Amazon. This virus is divided into 4 serotypes that have already circulated in the region. Methodology: Molecular characterization of a cohort containing 841 samples collected from febrile patients between 2021 and 2023 was analyzed using a commercial kit to detect the main arboviruses circulating in Brazil: Zika, DENV-1, DENV-2, DENV-3, DENV-4 and, Chikungunya. Subsequently, Sanger sequencing was performed for positive samples. Results: The cohort detected 162 positive samples, 12 for DENV-1 and 150 identified as DENV-2, indicating co-circulation of serotypes. The samples were subjected to sequencing and the analysis of the sequences that obtained good quality revealed that 5 samples belonged to the V genotype of DENV-1 and 46 were characterized as DENV-2 Cosmopolitan genotype—lineage 5. Conclusion: The results allowed us to identify for the first time the Cosmopolitan genotype in Rondônia, Brazilian Western Amazon, and its fast spread dispersion.

: The Mayaro virus (MAYV) is a significant reemerging arbovirus of public health concern, responsible for outbreaks in several countries including Brazil. In this study, 857 samples of patients with acute fever in the state of Rondônia, Brazil, were analyzed by reverse transcriptase qualitative polymerase chain reaction (RT-qPCR) to detect Zika, dengue, and chikungunya viruses. The mean age of the population was 38 years (SD = 17.46). Negative samples were subjected to duplex RT-qPCR to detect MAYV and Oropouche virus. One MAYV-positive sample with a negative result for all other viruses tested was identified and subsequently sequenced using the automated Sanger method and, through phylogenetic analysis, was characterized as belonging to genotype D, making it the first case of Mayaro in humans isolated in Rondônia. The symptoms reported by the positive patient were fever, vomiting, back pain, nausea, severe arthralgia, and retro-orbital pain. The study reinforces the need for differential diagnosis for Mayaro in the laboratory routine and the importance of genomic surveillance of this virus, mainly due to the similarity of symptoms with other arboviruses, which makes this screening difficult.

The Brazilian Amazon region is a highly endemic area for hepatitis Delta and has areas that are difficult to access. Understanding the dynamics of HDV transmission in these remote locations is important for elucidating the routes of infection. To investigate this, a molecular analysis of HDV was conducted to assess the spatio-temporal dynamics of HDV cases. Between 2010 and 2023, 35 patients were recruited from the Viral Hepatitis Outpatient Clinic in Rondônia, Brazil. Conventional PCR was used to amplify the complete HDV genome followed by nucleotide sequencing via the Sanger method. The HDV genotype was determined using maximum likelihood phylogenetic reconstruction. A Skygrid coalescent approach with a Relaxed Random Walk phylogeographic model was used for the spatio-temporal analysis. Most individuals were males (21/35), with a median age of 39 years. HDV-3 was identified in all samples (35/35; 100%). The tMRCA was estimated to be 1824, with a substitution rate of 8.2 × 10⁻⁴ substitutions/site/year. The results suggest that HDV likely entered Brazil around 1820, in the state of Amazonas, subsequently spreading to Acre and Rondônia. Notable migration events were observed starting from 2010. This study suggests that HDV-3 has a complex evolutionary history spanning over two centuries, with intricate transmission routes in different locations in Brazil.

The relationship between viral infections and host factors holds high hopes for identifying the role of Interferon Lambda 3 (IFNL3) and Interleukin 6 (IL-6) polymorphisms in the development of Chronic Liver Disease (CLD) in patients infected with hepatitis Delta virus (HDV) in the Western Brazilian Amazon.

Genomic surveillance represents an important strategy for understanding evolutionary mechanisms, transmission profile, and infectivity of different SARS-CoV-2 variants. We assessed the epidemiological profile of 366 individuals who tested positive for SARS-CoV-2 from 29 municipalities in Rondônia between December 2021 to March 2022. Samples were collected, RNA was ex-tracted and screened using RT-qPCR for Alpha, Beta, Gamma, Delta and Omicron VOCs and viral quantification was performed. Sequences were analyzed for phylogeny, mutations and lineages. Of the samples analyzed, 93.71% were positive for the Omicron variant and 6.28% were positive for the Delta variant. The symptoms observed were cough, sore throat, and fever, with a mean duration of 5 days; no hospitalizations or deaths were reported. We noted that among the positive individuals, 51% had been immunized with two doses, 22% received three doses, 13% received one dose, and 13% were not immunized. Just 242 samples were amenable to analysis for alignment and phylogenetic characterization; corresponding to variants BA.1 and BA.1.1; a total of 120 mutations were identified, 36% of which were found in the S gene. In conclusion, there was a high frequency of mutations in the SARS-CoV-2 genome, but no record of clinical severity, demonstrating the positive effect of vaccination.

In Brazil, the Amazon region has the highest rate of infection by the hepatitis Delta virus, and owing to regional difficulties in transporting and storing samples, especially in remote regions and isolated populations, the expansion of molecular diagnosis has become a significant public health problem. This study aims to analyze the stability of HDV under different temperature and storage conditions, providing essential information for the expansion of the molecular diagnosis of Hepatitis Delta. Whole blood, serum, and plasma samples were collected from chronic HDV patients. The samples were subjected to different temperatures and storage conditions, and HDV-RNA detection was performed via RT-qPCR. HDV was stable under various temperature conditions, including high temperatures, with minimal variations in Ct values. Compared with cryopreserved samples, DBS samples presented greater variation. The results suggest that HDV can remain detectable for up to 96 h when stored at room temperature, 4 °C, -30 °C, and − 80 °C and for up to 72 h at temperatures ranging from 4 °C to 42 °C, in addition to the possibility of detection via filter paper, although with reduced sensitivity. HDV is stable under different conditions, which is crucial for molecular diagnostics in regions with adverse storage conditions.