The First Geographic Identification by Country of Sustainable Mutations of SARS-COV-2 Sequence Samples: Worldwide Natural Selection Trends

Abstract

The high mutation rates of RNA viruses, coupled with short generation times and large population sizes, allow viruses to evolve rapidly and adapt to the host environment. The rapidity of viral mutation also causes problems in developing successful vaccines and antiviral drugs. With the spread of SARS-CoV-2 worldwide, thousands of mutations have been identified, some of which have relatively high incidences, but their potential impacts on virus characteristics remain unknown. The present study analyzed mutation patterns, SARS-CoV-2 AASs retrieved from the GISAID database containing 10,500,000 samples. Python 3.8.0 programming language was utilized to pre-process FASTA data, align to the reference sequence, and analyze the sequences. Upon completion, all mutations discovered were categorized based on geographical regions and dates. The most stable mutations were found in nsp1(8% S135R), nsp12(99.3% P323L), nsp16 (1.2% R216C), envelope (30.6% T9I), spike (97.6% D614G), and Orf8 (3.5% S24L), and were identified in the United States on April 3, 2020, and England, Gibraltar, and, New Zealand, on January 1, 2020, respectively. The study of mutations is the key to improving understanding of the function of the SARS-CoV-2, and recent information on mutations helps provide strategic planning for the prevention and treatment of this disease. Viral mutation studies could improve the development of vaccines, antiviral drugs, and diagnostic assays designed with high accuracy, specifically useful during pandemics. This knowledge helps to be one step ahead of new emergence variants. IMPORTANCEMore than two years into the global COVID-19 pandemic, the focus of attention is shifted to the emergence and spread of the SARS-CoV-2 variants that cause the evolutionary trend. Here, we analyzed and compared about 10.5 million sequences of SARS-CoV-2 to extract the stable mutations, frequencies and the substitute amino acid that changed with the wild-type one in the evolutionary trend. Also, developing and designing accurate vaccines could prepare long-term immunization against different local variants. In addition, according to the false negative results of the COVID-19 PCR test report in the diagnosis of new strains, investigating local mutation patterns could help to design local primer and vaccine.