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

被引：0

作者：

Macarena Concha-Toloza ^{[1
]}

Luis Collado González ^{[1
]}

Alfredo Herrera Estrella ^{[2
]}

Darío Fernández Do Porto ^{[3
]}

Rebeca Campos Sánchez ^{[4
]}

Jose Arturo Molina-Mora ^{[5
]}

机构：

[1] Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia

[2] Advanced Genomics Unit, Center for Research and Advanced Studies. Irapuato, Guanajuato

[3] Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires CONICET, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires

[4] Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San José

[5] Facultad de Microbiología, Centro de Investigación en Enfermedades Tropicales (CIET) and Centro de investigación en Hematología y Trastornos Afines (CIHATA), Universidad de Costa Rica, San José

来源：

Scientific Reports | / 15卷 / 1期

关键词：

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

D O I：

10.1038/s41598-025-98829-9

中图分类号：

学科分类号：

摘要：

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. © The Author(s) 2025.

引用

共 59 条

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