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

Abstract

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. To provide a better understanding of the epidemiology of SARS-Cov-2 variants in Colombia, we used 14,049 complete SARS-CoV-2 genomes from the 32 states of Colombia, and 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. We detected a total of 188 SARS-CoV-2 Pango lineages circulating in Colombia since the start of the pandemic. We showed 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). Our results reinforce that genomic surveillance programs are essential for countries to make evidence-driven interventions towards the emergence and circulation of novel SARS-CoV-2 variants.

Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages

“…Similar to our study, B.1 was detected in Spain through waves 2 to 4 [ 28 ]. B.1 was detected in less than 1% of SARS-CoV-2 genomes from Peru in 2021, whereas it was detected at a high frequency of 46.3% in Colombia [ 29 , 30 ].…”

“…The number of mutations present in Beta increased from ~20 to 37 from November 2020 to June 2021, respectively. Several Delta sub-lineages were observed from June to November 2021, with Delta 21A having the lowest number of mutations (21)(22)(23)(24)(25)(26)(27)(28)(29) and Delta 21J with up to 51 mutations. Omicron B.1.1.529 had ~52-62 mutations; its sub-lineages BA.1 and BA.2 had up to 72 mutations, while BA.4 and BA.…”