Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021

Abstract

Latin America is one of the regions in which the COVID-19 pandemic has had a stronger impact, with more than 72 million reported infections and 1.6 million deaths until June 2022. Since this region is ecologically diverse and is affected by enormous social inequalities, efforts to identify genomic patterns of the circulating SARS-CoV-2 genotypes are necessary for the suitable management of the pandemic. To contribute to the genomic surveillance of the SARS-CoV-2 in Latin America, we extended the number of SARS-CoV-2 genomes available from the region by sequencing and analyzing the viral genome from COVID-19 patients from seven countries (Argentina, Brazil, Costa Rica, Colombia, Mexico, Bolivia and Peru). Subsequently, we analyzed the genomes circulating mainly during 2021 including records from GISAID database from Latin America. A total of 1534 genome sequences were generated from seven countries, demonstrating the laboratory and bioinformatics capabilities for genomic surveillance of pathogens that have been developed locally. For Latin America, patterns regarding several variants associated with multiple re-introductions, a relatively low percentage of sequenced samples, as well as an increment in the mutation frequency since the beginning of the pandemic, are in line with worldwide data. Besides, some variants of concern (VOC) and variants of interest (VOI) such as Gamma, Mu and Lambda, and at least 83 other lineages have predominated locally with a country-specific enrichments. This work has contributed to the understanding of the dynamics of the pandemic in Latin America as part of the local and international efforts to achieve timely genomic surveillance of SARS-CoV-2.

Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants

“…Weakened selection will inhibit the evolution of new lineages and may be especially important for new VOC. Whereas other lineages may evolve through non-selective mechanisms, such as genetic drift, the existing VOC have exhibited strong signals of prior positive selection at the time of their emergence 16,[48][49][50] . The tight bottlenecks identified here will limit the development of highly mutated VOC in transmission chains of acutely infected individuals, adding to the evidence that selection over prolonged infections in immunocompromised patients may drive the evolution of SARS-CoV-2 variants of concern 6,15,51,52 .…”

Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants

“…Weakened selection will inhibit the evolution of new lineages and may be especially important for new VOC. Whereas other lineages may evolve through non-selective mechanisms, such as genetic drift, the existing VOC have exhibited strong signals of prior positive selection at the time of their emergence (16)(54–56). The tight bottlenecks identified here will limit the development of highly mutated VOC in typical transmission chains, adding to the evidence that selection over prolonged infections in immunocompromised patients may drive the evolution of SARS-CoV-2 variants of concern (6, 15, 57, 58).…”

Routes of importation and spatial dynamics of SARS-CoV-2 variants during localised interventions in Chile

“…Different SARS-CoV-2 variants emerged in South America during late 2020 and early 2021 (29). The earliest VOC described in South America was the Gamma variant, which emerged in Manaus, Brazil (5) and quickly spread to the southern half of the continent, into Argentina, Chile, Uruguay, Bolivia and Paraguay ( Fig.…”