No abstract

We performed phylogenomic analysis of severe acute respiratory syndrome coronavirus‐2 from 88 infected individuals across different regions of Colombia. Eleven different lineages were detected, suggesting multiple introduction events. Pangolin lineages B.1 and B.1.5 were the most frequent, with B.1 being associated with prior travel to high‐risk areas.

As the coronavirus disease 2019 pandemic keep tackling global public health systems worldwide. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) genome keeps mutating. In that regard, the recent emergence of the B.1.1.7 lineage in the UK has called the attention of global authorities. One point of concern is that if this lineage can be detected by traditional molecular schemes for SARS-CoV-2 detection. Herein, we showed that this lineage does not affect the Berlin-Charité protocol but can challenge the available commercial kits directed to the Spike (S) gene. All efforts should be made to continue to monitor SARS-CoV-2 genomes for potential variants that can impair diagnostic testing and lead to false negative results.

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.

The ongoing severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic has led to the design and development of multiple reverse‐transcription polymerase chain reaction kits aimed to facilitate the rapid scale‐up of molecular testing for massive screening. We evaluated the diagnostic performance of nine commercial kits, which showed optimal performance and high discriminatory power. However, we observed differences in terms of sensitivity, specificity, and E gene Ct Values and discuss these results in light of the influence of SARS‐CoV‐2 genetic variability and its potential impact in current molecular diagnostic assays.