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

ABSTRACT

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, also known as lineage B.1.621, was first detected in Colombia and was responsible for a large local wave but only a few sporadic cases elsewhere. METHODS: To better understand the epidemiology of SARS-Cov-2 variants in Colombia, we used 14,049 complete SARS-CoV-2 genomes from the 32 states of Colombia. We performed Bayesian phylodynamic analyses to estimate the time of variants' introduction, their respective effective reproductive number, and effective population size, and the impact of disease control measures. RESULTS: Here, we detect a total of 188 SARS-CoV-2 Pango lineages circulating in Colombia since the pandemic's start. We show that the effective reproduction number oscillated drastically throughout the first two years of the pandemic, with Mu showing the highest transmissibility (Re and growth rate estimation). CONCLUSIONS: Our results reinforce that genomic surveillance programs are essential for countries to make evidence-driven interventions toward the emergence and circulation of novel SARS-CoV-2 variants.

Colombia reported its first COVID-19 case on 6th March 2020. By April 2022, the country had reported over 6 million infections and over 135,000 deaths. Here, we aim to understand how SARS-CoV-2, the virus that causes COVID-19, spread through Colombia over this time and how the predominant version of the virus (variant) changed over time. We found that there were multiple introductions of different variants from other countries into Colombia during the first two years of the pandemic. The Gamma variant was dominant earlier in 2021 but was replaced by the Delta variant. The Mu variant had the highest potential to be transmitted. Our findings provide valuable insights into the pandemic in Colombia and highlight the importance of continued surveillance of the virus to guide the public health response.