Genomic, socio-environmental, and sequencing capability patterns in the surveillance of SARS-CoV-2 in Latin America and the Caribbean up to 2023

Abstract

Latin America and the Caribbean (LAC) have been one of the most strongly impacted regions by the Coronavirus disease 2019 (COVID-19) emergency, with more than 83 million reported infections and 1.7 million deaths until December 2023, intensifying economic and social inequalities. This study aimed to provide information to the regional SARS-CoV-2 surveillance programs by determining genomic, socio-environmental, and sequencing capacity patterns associated with the circulation of the virus in Latin America up to 2023. Data from 24 countries in LAC were analyzed using public databases up to December 2023. A sampling of SARS-CoV-2 sequences from cases in the region enabled a phylogenomic study to elucidate the temporal distribution of various variants of concern (VOCs), mutations, and recombinants. Also, we identified differences in sequencing capabilities in LAC. Additionally, correlation and generalized linear model (GLM) analyses were conducted to explore potential associations between 89 socio-environmental variables and five COVID-19 indicators at the country level. The phylogenomic analyses revealed a diversity of variants with the predominance of some during specific periods, mainly VOCs and some recombinant cases, and a mutation rate of 8.39 × 10-4 substitutions per site per year, which are in line with other regions of the world. Besides, a low sequencing rate in LAC (on average 0.7% of cases) and incomplete databases in several countries were identified. In the analysis of indicators, correlations between 9 socio-environmental indicators and four COVID-19 variables associated with cases, deaths, and diagnostic tests related to the virus in the region, although not for sequencing percentages. This study provides information about the development of COVID-19 disease in LAC in terms of the viral genome, sequencing capabilities, and the region's complex socio-environmental conditions. Therefore, emphasis must be placed on implementing an integrated epidemiological surveillance approach to strengthen public health infrastructure and improve cooperation and preparedness for future infections affecting this region.

Keywords: 2 genome; 2023; COVID-19; CoV; Latin America and the Caribbean; SARS; Sequencing capability; Socio-environmental indicators.

Fig. 1

Timeline addressing the most relevant COVID-19 milestones from 2020 to 2024 for Latin America and the Caribbean.

Fig. 2

General workflow based on the use of public databases to study genomic, socio-environmental, and capability patterns regarding the circulation of the SARS-CoV-2 virus in Latin America until December 2023.

Fig. 3

Phylogenomic analysis based on maximum likelihood of SARS-CoV-2 virus sequences obtained until December 2023. The inner circle with the blue gradients indicates the years when the sequences were obtained. The outermost circle provides a visualization of SARS-CoV-2 variants.

Fig. 4

Landscape of the SARS-CoV-2 variants circulating in Latin America and the Caribbean until December 2023. (A). Distribution of SARS-CoV-2 variants. Pie charts indicate the relative abundance of distinct SARS-CoV-2 variants in each country. (B). Mutation rate of the SARS-CoV-2 genomes during the pandemic, including different variants (colors) and the model (black line).