Origin of the mutation profile present in SARS-CoV-2 sequences in El Salvador

Abstract

Introduction: This paper describes the mutation profile and analyzes the different mechanisms responsible for mutations in the first 6 complete sequences of the SARS-CoV-2 genome from samples of Salvadoran patients diagnosed with COVID-19. Objective: To analyze the mutation profile according to the mechanisms that give rise to the mutations present in SARS-CoV-2. Methodology: An analysis of the changes in the genome sequences of SARS-CoV-2 was performed using as reference the Wuhan sequence (NC_045512.2), once the mutations were known, we proceeded to tabulate and generate graphs of the SNPs and affected genes. The possible described mechanisms responsible for generating the mutations studied were also analyzed. Results: The analysis revealed that the mutations found have been reported worldwide, however, the sequences present greater similarity with the changes described in North America, added to this, the global analysis allowed classifying them in the GISAID GH broth, and pangolin lineage B.1.2 and B.1.370, both lineages with a high prevalence in the USA, which reinforces the hypothesis of the North American origin of the Salvadoran sequences. The pattern of changes in the SARS-CoV-2 genome in El Salvador suggests that the mutations are due to the action of APOBEC deaminase (C>T transition) and ADARs (A>G transition), to the effect of reactive oxygen species (ROS) (G>T transversion), to errors in the replication transcription complex (RTC) that escape the correction of the exonuclease activity of NSP14 and finally mutations as a result of recombination mechanisms.