Healthcare-facility-based SARS-CoV-2 genomic surveillance in Brazil: experience from the global action in healthcare network.

UNLABELLED: Genomic sequencing is essential to effectively monitor the SARS-CoV-2 evolution and spread of its lineages. Healthcare-facility-based SARS-CoV-2 genomic surveillance has been proposed as a valuable strategy, considering the characteristics of its target population. As part of the Centers for Disease Control and Prevention's Global Action in Healthcare Network program, this study aimed to describe the distribution and frequency of SARS-CoV-2 lineages in two tertiary-care hospitals in Brazil, where the genomic sequencing capacity is limited. Whole-genome sequencing of SARS-CoV-2 samples obtained from 993 healthcare workers (75.4%) and inpatients (24.6%) was analyzed between February 2023 and August 2024. In total, 113 distinct lineages were identified. Notably, we observed a temporal replacement of predominant lineages corresponding to three distinct epidemic waves: the first wave dominated by XBB.1.5 and XBB.2.3 (February 2023 to June 2023), the second by GK.1.1 and JD.1.1 (September 2023 to December 2023), and the third by JN.1 and JN.1.9 (January 2024 to April 2024). JN.1.9 was the only lineage with a significantly higher prevalence among healthcare workers compared to inpatients. Additionally, we identified cases of co-infection with genetically distinct variants, underscoring the potential for healthcare-based monitoring to capture events relevant to viral evolution. Overall, our findings were consistent with those observed across Brazil, suggesting that this strategy may be valuable for SARS-CoV-2 genomic surveillance. They also indicate a clear temporal pattern of lineage replacement, reflecting successive waves driven by emerging variants and rapid global dissemination.

IMPORTANCE: Genomic surveillance of SARS-CoV-2 remains essential for identifying emerging variants with increased transmissibility, immune escape, or pathogenicity. While most genomic surveillance efforts focus on community-based sampling, a healthcare-facility-based strategy may offer a complementary approach. In this study, we describe SARS-CoV-2 lineage dynamics over an 18-month period among healthcare workers and hospitalized patients in southern Brazil. Our findings align closely with regional and national trends, supporting the value of healthcare-facility-based SARS-CoV-2 genomic surveillance for documenting the local genomic landscape and demonstrating the feasibility and value of this approach in settings with limited genome sequencing capacity. Additionally, this approach may be applicable to other respiratory viruses in healthcare settings; however, further studies would be needed to confirm this.