Genomic Epidemiology of Circulating SARS-CoV-2 Variants

The emergence of highly transmissible SARS-CoV-2 variants has led to surges in cases and the need for global genomic surveillance. This study explores fine-scale phylodynamic and epidemiological patterns in Colombia using over 14,000 complete viral genomes. We identify 188 lineages, analyze their introduction dates and effective reproductive numbers, and highlight the Mu variant’s high transmissibility.

Using Bayesian coalescent modeling, we estimate the time to most recent common ancestor (tMRCA), changes in effective population size (Ne), and the impact of interventions. The results reinforce the value of genomic surveillance as a critical tool for informing public health policy.

For full dataset and code used in this study, please refer to the project repository.