SARS-CoV-2 sublineages recovered from southern Brazilian cases during Omicron wave in 2023, early introduction of JN.1

Since the emergence of the novel coronavirus SARS-CoV-2, public health measures have adapted as the virus evolve and acquired greater transmissibility and escape from the previous immune response. Genomic surveillance is a reliable and decisive tool for monitoring the evolutionary dynamics of the virus and its nucleotide diversity. Rio Grande do Sul is a southern Brazilian state that borders Argentina and Uruguay, and genomic and epidemiological surveillance led to early detection of COVID-19 variants, as seen in P.1 lineage. The study aimed to investigate the genetic characterization of SARS-CoV-2 Omicron sublineages in Rio Grande do Sul, Brazil, during 2023. By obtaining viral RNA from nasopharyngeal swabs positive for SARS-CoV-2, we performed high-throughput sequencing and data were analyzed using bioinformatic approaches. Our results revealed a dynamic change in Omicron sublineages during 2023, with the occurrence of JN.1+JN.1* reads during December 2023, parallel to the first JN.1 official record in Brazil, occurred in Ceará state, which is in the northeast region of Brazil. These data revealed a distinct nucleotide diversity in S gene of JN.1 reads, highlighting the importance of genomic surveillance in Rio Grande do Sul for the early detection of the entry of future SARS-CoV-2 variants into Brazil.