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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a high transmissibility profile which favors the accumulation of mutations along its genome, providing the emergence of new variants. In this context, haplotype studies have allowed mapping specific regions and combining approaches and tracking phylogenetic changes. During the COVID-19 pandemic, it was notorious that home environments favored the circulation of SARS-CoV-2, in this study we evaluated 1,407 individuals positive for SARS-CoV-2, in which we located 53 families in the period from June 2021 to February 2023. The epidemiological data were collected in E-SUS notifica and SIVEP-gripe. Then, the genetic material was extracted using the commercial kit and the viral load was evaluated and the viral genomes were sequenced using the Illumina MiSeq methodology. In addition, the circulation of 3 variants and their respective subvariants was detected. The delta variant represented the highest number of cases with 45%, the Omicron variant 43% and the lowest number with 11% of cases the Gamma variants. There were cases of families infected by different subvariants, thus showing different sources of infection. The haplotype network showed a distribution divided into 6 large clusters that were established according to the genetic characteristics observed by the algorithm and 224 Parsimony informative sites were found. In addition, 92% of subjects were symptomatic and 8% asymptomatic. The secondary attack rate of this study was 8.32%. Therefore, we can infer that the home environment favors the spread of SARS-CoV-2, so it is of paramount importance to carry out genomic surveillance in specific groups such as intradomiciliary ones. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background: 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., Methods: Cross-sectional study conducted with a cohort of 40 chronic HDV patients, 27 with CLD and 13 without evident liver damage. Biological samples from the participants were analyzed using the polymerase chain reaction (PCR) technique, followed by sequencing by the automated Sanger method., Results: The rs8099917 T allele, from the IFNL3 gene, showed a higher frequency in both groups; however, it was not possible to establish an association with HDV infection [OR = 1.42 (0.42 - 4.75; p = 0.556 (95% CI). For IL-6, the rs1800795 G allele was superior to rs1800795 C. Analyzing both distributions in the studied groups, any association with HDV was absent (p > 0.05)., Conclusion: The results suggest that the rs8099917 T/G (IFNL3) and rs1800795 G/C (IL-6) polymorphisms are not associated with the evolution of HDV in the studied population., Competing Interests: Competing interests: The authors declare that they have no competing interests.