Predominance of the recombinant SARS-CoV-2 lineages XBB in Rio Grande do Sul State, Brazil: a genomic surveillance study and impact on vaccine response

Abstract Purpose The COVID-19 pandemic has been marked by novel viral variants, posing challenges to global public health. Recombination, a viral evolution tool, is implicated in SARS-CoV-2's ongoing evolution. The XBB recombinant lineage, known for evading antibody-mediated immunity, exhibits higher transmissibility without increased disease severity. We investigated the prevalence and genomic features of XBB in SARS-CoV-2-positive cases in Rio Grande do Sul (RS), Brazil. Methods We sequenced 357 samples from epidemiological weeks (EW) 47/2022 to 17/2023, and included 389 publicly available sequences. Clinical and epidemiological data were obtained from DATASUS, e-SUS, and SIVEP GRIPE (data recording systems of the Brazilian Ministry of Health) Results Of these, 143 were classified as XBB and 586 were other Omicron lineages. The BQ.1.1 lineage was most frequent. In March 2023 (EW 10), XBB became dominant, accounting for 83·3% of cases. 97·7% of XBB-infected patients successfully recovered from the infection, with a low mortality rate. Even receiving three vaccine doses and previously infected, 59·5% of the patients experienced reinfection with XBB. However, the interval between XBB infection and the last vaccine dose exceeded a year, potentially causing antibody decline. In addition, we identified 90 mutations in RS circulating XBB, spread throughout the genome, notably in the Spike protein region associated with immune resistance. Conclusion This study provides insights into the dynamics and impact of a recombinant variant becoming predominant for the first time in the state. Continued surveillance of SARS-CoV-2 genomic evolution is crucial for effective public health management.