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.