Genomic epidemiology of SARS-CoV-2 variants during the first two years of the pandemic in Colombia

Background: The emergence of highly transmissible SARS-CoV-2 variants has led to surges in cases and the need for global genomic surveillance. While some variants rapidly spread worldwide, other variants only persist nationally. There is a need for more fine-scale analysis to understand transmission dynamics at a country scale. For instance, the Mu variant of interest (B.1.621) was first detected in Colombia, with substantial local impact but only sporadic cases elsewhere. Methods: Using 14,049 complete SARS-CoV-2 genomes from Colombia’s 32 states, we performed Bayesian phylogenetic analyses to estimate times of variant introductions, effective reproductive numbers, effective population sizes, and their relationships with disease control measures. Results: We detected a total of 188 SARS-CoV-2 Pango lineages in Colombia since the pandemic’s start and found that the dominant variant oscillated across the first two years, with shifts in transmissibility and growth rates. Conclusions: Periodic genomic surveillance is essential for evidence-driven interventions regarding the emergence and circulation of novel SARS-CoV-2 variants.

Cinthy Jimenez-Silva, Ricardo Rivero, Jordan Douglas, Remco Bouckaert, Ch Julian Villabona-Arenas, Katherine E Atkins, Bertha Gastelbond, Alfonso Calderón, Camilo Guzman, Daniel Echeverri-De la Hoz, Marina Muñoz, Nathalia Ballesteros, Sergio Castañeda, Luz H Patiño, Angie Ramirez, Nicolas Luna, Alberto Paniz-Mondolfi, Hector Serrano-Coll, Juan David Ramirez, Salim Mattar, Alexei J Drummond