The emergence of Omicron VOC and its rapid spread and persistence in the Western Amazon.

Genomic surveillance represents a strategy to understanding the evolutionary mechanisms, transmission, and infectivity of different SARS-CoV-2 variants. We evaluated 603 individuals positive for SARS-CoV-2 from 34 municipalities of Rondônia between December 2021 to December 2022. Nasopharyngeal samples were collected, RNA was extracted and screened using RT-qPCR for VOCs. RNA of the samples were sequenced and further analyzed for phylogeny, mutations, and lineages, totaling 96.19% of samples positive for Omicron VOC in this cohort. We observed that most individuals had at least two doses, however 18.97% were not vaccinated with any dose. 554 sequences were amenable to analysis for alignment and phylogenetic characterization; this group corresponded to the 27 subvariants of the Omicron VOC; a total of 100 mutations were identified, 48% of which were found in the S gene. In conclusion, the data demonstrated the rapid spread and persistence of Omicron VOC in Rondônia during the 12-month study period. Although high frequency of mutations was found in the analyzed samples, there were no individuals with a severe clinical profile, demonstrating that vaccination had a positive effect in those cases.

Active surveillance and early detection of community transmission of SARS-CoV-2 Mu variant (B.1.621) in the Brazilian Amazon.

Through active surveillance and contact tracing from outpatients, we aimed to identify and characterize SARS-CoV-2 variants circulating in Porto Velho-Rondônia, a city in the Brazilian Amazon. As part of a prospective cohort, we gathered information from 2,506 individuals among COVID-19 patients and household contacts. Epidemiological data, nasopharyngeal swabs, and blood samples were collected from all participants. Nasopharyngeal swabs were tested for antigen rapid diagnostic test and reverse transcription-polymerase chain reaction (RT-PCR) followed by genomic sequencing. Blood samples underwent ELISA testing for IgA, IgG, and IgM antibody levels. From 757 specimens sequenced, three were identified as Mu variant, none of the individuals carrying this variant had a travel history in the previous 15 days before diagnosis. One case was asymptomatic and two presented mild symptoms. Two infected individuals from different households caring viruses with additional amino acid substitutions ORF7a P45L and ORF1a T1055A compared to the Mu virus reference sequence. One patient presented IgG levels. Our results highlight that genomic surveillance for SARS-CoV-2 variants can assist in detecting the emergency of SARS-CoV-2 variants in the community, before its identification in other parts of the country.

Seasonal malaria transmission and variation of anopheline density in two distinct endemic areas in Brazilian Amazonia.

Studies on seasonal anopheline fauna variation were performed in two distinct settlements in the State of Rondônia, Brazil: one at the Madeira River banks (Portuchuelo) with stable native Amazonian population; the other at an inland lumber-extracting farm (Urupá) in dry land, in which adults are mostly migrants. During a 6-yr period (1994-2000), 8,638 adult anophelines were collected: 2,684 in Urupá and 5,954 in Portuchuelo. Anopheles darlingi represented >95% of total mosquitoes caught. Dissection of 4,424 A. darlingi females yielded a very low sporozoite infection index below 0.1%. Oocysts were found in both localities in approximately 0.1% of dissected mosquitoes. Determination of the hour biting rates disclosed seasonal variations in both localities. However, in Portuchuelo, mosquito density peaked at the acme of the rainy season, whereas at Urupá it peaked in the dry season. The increase in mosquito density and incidence of malaria cases were coincident. The high mosquito densities observed in the riverine settlement of Portochuelo sector B, which permits evaluation in > 10,000 mosquitoes' bites/person/year, could explain, in spite of the low mosquito's infection index, the previously described development of natural immunity in the local population that is not observed in the dry land agroindustrial settlement of Urupá.