Phylogenetic analysis of SARS-CoV-2 viruses circulating in the South American region: Genetic relations and vaccine strain match

Perbolianachis, Paula; Ferla, Diego; Arce, Rodrigo; Ferreiro, Irene; Costábile, Alicia; Paz, Mercedes; Simón, Diego; Moreno, Pilar; Cristina, Juan

doi:10.1016/j.virusres.2022.198688

Cited by 2 publications

(3 citation statements)

References 66 publications

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“…Previous studies have reported similar results with sublineages of other VOCs in the region, where the circulation of these sublineages in diverse regions of the continent has favored the acquisition of different genomic characteristics which might affect the molecular diagnosis such as the emergence of new lineages [3,4]. Furthermore, genetic variation, especially in the amino acids, might generate impacts on public health [3]. Herein, we found unique and shared mutations by sublineage and country (Figure 2), most of which are found in the spike gene.…”

Section: Discussionsupporting

confidence: 65%

“…The genomic landscape of Omicron in South America provides mutational and phylogenetic information about circulating lineages. Previous studies have reported similar results with sublineages of other VOCs in the region, where the circulation of these sublineages in diverse regions of the continent has favored the acquisition of different genomic characteristics which might affect the molecular diagnosis such as the emergence of new lineages [3,4]. Furthermore, genetic variation, especially in the amino acids, might generate impacts on public health [3].…”

Section: Discussionsupporting

confidence: 64%

“…Additionally, together with public data, it allows for characterizing and dating different lineages that impact public health and/or can modulate the spread of the virus. Particularly with variants of concern (VOCs), which have higher transmissibility and virulence rates [1,2], genomic surveillance has provided insight into the genomic characteristics and global diversity of these variants [3,4].…”

Section: Introductionmentioning

confidence: 99%

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Genomic Diversity of SARS-CoV-2 Omicron Variant in South American Countries

Luna

Muñoz

Ramírez

et al. 2022

Viruses

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Genomic surveillance of SARS-CoV-2 is one of the tools that provide genomic information on circulating variants. Given the recent emergence of the Omicron (B.1.1.529) variant, this tool has provided data about this lineage’s genomic and epidemiological characteristics. However, in South America, this variant’s arrival and genomic diversity are scarcely known. Therefore, this study determined the genomic diversity and phylogenetic relationships of 21,615 Omicron genomes available in public databases. We found that in South America, BA.1 (n = 15,449, 71%) and BA.1.1 (n = 6257, 29%) are the dominant sublineages, with several mutations that favor transmission and antibody evasion. In addition, these lineages showed cryptic transmission arriving on the continent in late September 2021. This event may have contributed to the dispersal of Omicron sublineages and the acquisition of new mutations. Considering the genomic and epidemiological characteristics of these lineages, especially those with a high number of mutations in their genome, it is important to conduct studies and surveillance on the dynamics of these lineages to identify the mechanisms of mutation acquisition and their impact on public health.

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Section: Discussionsupporting

confidence: 65%

Section: Discussionsupporting

confidence: 64%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genomic Diversity of SARS-CoV-2 Omicron Variant in South American Countries

Luna

Muñoz

Ramírez

et al. 2022

Viruses

View full text Add to dashboard Cite

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

Concha-Toloza,

González,

Estrella

et al. 2024

Preprint

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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, recombinants, and patterns regarding sequencing capabilities in LAC. Additionally, correlation and generalized linear models (GLM) analyses were performed between 89 socio-environmental and five COVID-19 indicators to study possible associations between country-level factors. 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 x 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 world region.

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Phylogenetic analysis of SARS-CoV-2 viruses circulating in the South American region: Genetic relations and vaccine strain match

Cited by 2 publications

References 66 publications

Genomic Diversity of SARS-CoV-2 Omicron Variant in South American Countries

Genomic Diversity of SARS-CoV-2 Omicron Variant in South American Countries

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

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