SARS-CoV-2 genome surveillance is important for monitoring risk groups and health workers as well as data on new cases and mortality rate due to COVID-19. We characterized the circulation of SARS-CoV-2 variants from May 2021 to April 2022 in the state of Santa Catarina, southern Brazil, and evaluated the similarity between variants present in the population and healthcare workers (HCW). A total of 5291 sequenced genomes demonstrated the circulation of 55 strains and four variants of concern (Alpha, Delta, Gamma and Omicron—sublineages BA.1 and BA.2). The number of cases was relatively low in May 2021, but the number of deaths was higher with the Gamma variant. There was a significant increase in both numbers between December 2021 and February 2022, peaking in mid-January 2022, when the Omicron variant dominated. After May 2021, two distinct variant groups (Delta and Omicron) were observed, equally distributed among the five Santa Catarina mesoregions. Moreover, from November 2021 to February 2022, similar variant profiles between HCW and the general population were observed, and a quicker shift from Delta to Omicron in HCW than in the general population. This demonstrates the importance of HCW as a sentinel group for monitoring disease trends in the general population.

Morphological identification of Palaemonidae prawns often proves challenging due to the overlap in their characteristics. In this study, we evaluated the utility of 28S ribosomal DNA (rDNA) sequences as a molecular tool for accurately identifying prawns within this family. Specimens were sourced from scientific collections in the Brazilian Amazon, and sequences obtained from these samples were prioritized for constructing a reference sequence database. The efficacy of the 28S rDNA was then assessed by analyzing sequences within the reference database and applying it to identify samples from the Amazonas and Tapajós rivers. Our species delimitation analyses provided accurate molecular identification, revealing the potential of 28S rDNA sequences in addressing taxonomic inconsistencies. Notably, the results uncovered misclassifications among some specimens deposited in scientific collections, emphasizing the importance of molecular tools in refining Palaemonidae taxonomy in the Amazon.