A deletion in SARS-CoV-2 ORF7 identified in COVID-19 outbreak in Uruguay

The analysis of genetic diversity in SARS-CoV-2 is the focus of several studies, providing insights into how the virus emerged and evolves. Most common changes in SARS-CoV-2 are single or point nucleotide substitutions; meanwhile, insertions and deletions (indels) have been identified as a less frequent source of viral genetic variability. Here, we report the emergence of a 12-nucleotide deletion in ORF7a, resulting in a 4-amino acid in-frame deletion. The Delta 12 variant was identified in viruses from patients of a single outbreak and represents the first report of this deletion in South American isolates. Phylogenetic analysis revealed that Delta 12 strains belong to the lineage B.1.1 and clustered separated from the remaining Uruguayan strains. The increment 12 variant was detected in 14 patients of this outbreak by NGS sequencing and/or two rapid and economic methodologies: Sanger amplicon sequencing and capillary electrophoresis. The presence of strong molecular markers as the deletion described here are useful for tracking outbreaks and reveal a significant aspect of the SARS-CoV-2 evolution on the robustness of the virus to keep its functionality regardless loss of genetic material.

Automated summary

The emergence of the Delta 12 variant with a 12-nucleotide deletion in ORF7a, resulting in a loss of 4 amino acids, is reported in this study. This variant was identified in a South American outbreak and phylogenetic analysis showed significant separation from other Uruguayan strains. The presence of molecular markers like this deletion is useful for tracking outbreaks and highlights the virus's ability to maintain functionality despite genetic material loss.