Genomic surveillance of severe acute respiratory syndrome coronavirus 2 variants in hospitalized patients: a cohort study from the Metropolitan Area of Valle de Aburrá, Colombia

Introduction. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been one of the most significant pandemics of the modern era. It is a coronavirus with a high mutation rate, leading to variants with changes in the spike protein, which hinders containment efforts. Genomic surveillance is crucial for adapting public health and vaccination strategies, especially in low- and middle-income countries, where the impact has been considerable. Objective. To identify viral variants and their clinical presentations in a prospective cohort of hospitalized patients with SARS-CoV-2 infection between October 2021 and February 2023. Materials and methods. We collected demographic data, medical history, vaccination status, and clinical progression. Viral genome sequencing was performed on nasopharyngeal swab samples confirmed by Real-Time Reverse Transcription Polymerase Chain Reaction (qRT-PCR) to classify strains and detect variants. Results. Among 63 SARS-CoV-2 positive samples, the predominant variant was Omicron (84%), followed by Delta (14%). A higher proportion of critical illness was observed in Delta cases (100%) compared to Omicron (30%). Mutations in the spike protein were identified and classified into four categories (A–D), along with specific mutations in the S gene. Conclusion. The mutational patterns observed in this study are consistent with global reports, with Delta cases presenting greater clinical severity. We identified spike protein mutations that may confer distinctive properties to the virus. These findings underscore the need for ongoing genomic surveillance to better understand viral dynamics and inform public health strategies.