Characterizing SARS-CoV-2 genome diversity circulating in South American countries: Signatures of potentially emergent lineages?

Abstract

Objectives To evaluate the genomic diversity and geographic distribution of SARS-CoV-2 lineages currently circulating in South America (SA). Methods SARS-CoV-2 lineages reported from South American countries were analyzed from a public dataset of 5597 genome assemblies. Polymorphisms in the main open reading frames were identified and compared to those present in the main lineages of epidemiology concern: B.1.1.7 (from UK) and B.1.351 (from South Africa). Results A total of 169 circulating lineages across 16 South American countries were identified, revealing a predominant circulation of the major lineage B, the one with the greatest diversity and broadest geographic distribution. Sixteen lineages were selected to be comprehensively analyzed because are predominant in the region. Two lineages of concern report were remarkably identified: P.1 recognized as the Brazilian variant (with 94 genomes) and B.1.1.7 the UK variant (with 28 genomes), both displayed 33 polymorphisms compared to the reference genome, the highest number among analyzed genomes. While the most of other lineages circulating in SA displayed 24 or less polymorphisms compared to the reference strain. A high number of polymorphisms were detected in the evaluated lineages with a limited number of common variable positions amongst them, in agreement with the profiles identified in the main lineages of epidemiology concern. Conclusions The ever-increasing genetic diversity of SARS-CoV-2 continues to lead to the emergence of novel lineages. Different variants and lineages are now present across SA with the presence of major lineage B mostly. The circulation of variants as P.1 and B.1.1.7 in different countries as well as the elevated number of polymorphisms highlighted the importance of continuing with the genomic surveillance to determine introduction events, identify transmission chains, trace emergence and help to implement successful prevention, vaccination and control strategies.

SARS-CoV-2 genome sequencing with Oxford Nanopore Technology and Rapid PCR Barcoding in Bolivia

“…The variant assignment results are expected because there was a predominance of the 20A and 20B (which includes the lineages B.1.1, B.1.1.274 and B.1.1.348) SARS-COV-2 variants circulating in South America (Camacho et al 2021; Muñoz et al 2021). The five different lineages (Table 1) found in this study are correlated with the clusters observed in the phylogenomic tree (Fig.…”

Phylogenomic Evidence of Reinfection and Persistence of SARS-CoV-2: First Report from Colombia

“…COVID-19 reinfections appear to be rare with very few cases confirmed by wholegenome sequencing reported globally to date [17]. Recently, the emergence of SARS-CoV-2 variants, such as the P.1 and the B.1.351, harboring a mutational repertoire within the Spike gene has raised concerns with regard to how this genetic variability may shape and modulate tissue tropism and potentially preclude the binding of neutralizing antibodies leading to a potential risk for reinfections, as recently reported [16][17][18][19]. Additionally, in a recent report, the immune plasma of COVID-19 convalescent blood donors had 6-fold less neutralizing capacity against the P.1 than against the B-lineage.…”

“…Our patient fully recovered after the second infection (no symptoms of chronic COVID-19 illness); yet, this case underscores the vulnerabilities of the host immune response when challenged by variants even between lineages descending from the same major lineage (B as in this case). The B lineage is the most prevalent major lineage circulating in South America [16]. Understanding this variability and the evolutionary dynamics of these emerging variants is pivotal for designing prevention strategies, such as vaccination campaigns, particularly in those countries where vaccination coverage is scarce, thus potentially setting the stage for other reinfection events.…”

“…The typing and evaluation of the phylogenetic relationships of the analysed genomes, in the context of a dataset with representative genomes of SARS-CoV-2 circulating worldwide ( Figure 2; Table S1), displayed that two of the patients had the same lineage in both analysed samples. Two genomes obtained from Patient 1 classified as B.1 lineage, the most abundant and diverse lineage both worldwide and in Colombia [16]. The first genome sequenced from this patient was found to be mostly related to genomes from Colombia; however, its closest genome was one from the United States of America, the only one with a different origin within the cluster of nine genomes which it was part of, while the second genome from Patient 1 was included in a cluster of 32 genomes, which included other nine genomes from Colombia (26.5%), eight genomes from other South American countries (23.5%) and the remaining 16 from other countries ( Figure 3A).…”

Lock or Down: Effectiveness of Isolation Measures Against COVID-19

“…Existing vaccines may not be effective against some variants of severe acute respiratory syndrome coronavirus 2. However, vaccine uptake is still low in most countries, and we are not sure whether the available vaccines will be effective for the new variants or new ones that might come to eventually reach a herd immunity threshold ( 2 ).…”