Mutation accumulation of SARS-CoV-2 genome in North America, South America, and Oceania: Analysis of over 6.5 million sequences samples from Global Initiative on Sharing Avian Influenza Data

Abstract

Abstract The SARS-CoV-2 virus emerged in the world at the end of 2019, which caused a very rapid spread of COVID-19 all over the world. This respiratory illness caused the death of millions of people in different countries as the World Health Organization declared a global emergency. In this geographical evaluation, we extracted whole sequences of over 8 million reported samples from the GISAID database (until the end of January 2022). Extracted samples contain three continents including North America, South America, and Oceania, and compared the sequences to the reference SARS-CoV-2 genome. In total, 41,596, 20,195, and, 6,780 nonsynonymous substitutions were identified for North America, South America, and Oceania, respectively. NSP3 and S genes had the highest number of nonsynonymous mutations. Most of the mutations were seen in all three regions, but some were regional-specific with completely different trends. Although in majority of the cases, with a mutation in one nucleotide, which could potentially result in three different amino acids, we noticed a consistent tendency to specific amino acids in the majority of mutations. Mutations were not distributed equally across the genome, for example in the case of the S gene thirty-one mutations were found for North America, of which 5, 14, and 9 of them fell between 5-26, 139-259, and 452-684 first amino acids, respectively. In conclusion, the SARS-CoV-2 genome is changing with different patterns across the world, mutations are accumulated in specific regions of genes, and some specific amino acids are preferred by the virus, which probably is contributing to virus fitness.