Genomic epidemiology of SARS-CoV-2 in Bolivia, 2020-2024

The COVID-19 pandemic has severely impacted Bolivia due to its high social vulnerability and limited healthcare resources. In response to the limited local capacity for genomic surveillance during the pandemic, we characterized the genetic diversity and geographic distribution of SARS-CoV-2 variants across Bolivia from 2020 to 2024. A total of 714 SARS-CoV-2 genomic sequences were analyzed, including 313 newly sequenced samples and 401 retrieved from GISAID, allowing us to track viral evolution across six epidemic waves. The first wave, dominated by the Wuhan B.1 lineage, resulted in 8,943 deaths, while the fourth wave, characterized by the Omicron BA variant, had the highest infection rates, with approximately 80,000 confirmed cases. While mortality decreased in later waves, case numbers remained high due to the emergence of variants with increased transmissibility and immune escape. Our findings underscore the dynamic evolution of SARS-CoV-2 in Bolivia and highlight the critical need for sustained genomic surveillance to monitor emerging variants and inform public health strategies, particularly in resource-limited settings. Strengthening genomic surveillance, especially in cross-border regions, will mitigate future epidemic waves and improve pandemic preparedness.IMPORTANCEBolivia's response to the COVID-19 pandemic was challenged by a fragile healthcare system and high social vulnerability. Despite early containment measures, including strict quarantine, the virus spread widely, leading to multiple epidemiological waves that strained the healthcare system and caused significant economic disruption. In this context, genomic surveillance is essential for understanding the evolution of SARS-CoV-2, identifying emerging variants, tracking transmission patterns, and evaluating mitigation strategies. Our study comprehensively analyzes viral dynamics in Bolivia, identifying key transmission hubs and variant replacements across six epidemic waves. These findings underscore the importance of sustained genomic surveillance in resource-limited settings, where real-time monitoring is crucial to anticipate epidemiological trends and enhance pandemic preparedness. Strengthening genomic surveillance capabilities will enhance Bolivia's ability to respond to future health crises and contribute to regional and global pandemic surveillance efforts.