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, others 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, also known as B.1621, was first detected in Colombia, yet local value but only a few sporadic cases elsewhere. Methods: To better understand the epidemiology of SARS-CoV-2 in Colombia, we used 14,049 complete SARS-CoV-2 genomes from the 32 states of Colombia. We performed Bayesian phylogenetic analyses to estimate the time of variants' introduction, their effective reproductive number, and effective population size, and the nexus of disease control measures. Results: Here, we detect a total of 188 SARS-CoV-2 Pango lineages in Colombia since the pandemic’s start. We show that the dominant variant oscillated drastically throughout the first two years of the pandemic, with shifts between high transmissibility (Re and growth rate estimation). Conclusions: Our results reinforce that periodic surveillance programs are essential for helping to make evidence-driven interventions toward 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