An updated analysis of variations in SARS-CoV-2 genome

Turkish journal of biology

article

OSMAN MUTLUHAN UĞUREL¹  OĞUZ ATA³  DİLEK BALIK¹ 

[1] Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yıldız Technical University;Department of Basic Sciences, School of Engineering and Natural Sciences, Altınbaş University;Department of Software Engineering, School of Engineering and Natural Sciences, Altınbaş University

关键词: SARS-CoV-2;    COVID-19;    genomic diversity;    codon bias;    multiple sequence alignment;   

DOI  :  10.3906/biy-2005-111

学科分类：生物科学（综合）

来源: Scientific and Technical Research Council of Turkey - TUBITAK

【 摘 要 】

A novel pathogen, named SARS-CoV-2, has caused an unprecedented worldwide pandemic in the first half of 2020. As the SARS-CoV-2 genome sequences have become available, one of the important focus of scientists has become tracking variations in the viral genome. In this study, 30366 SARS-CoV-2 isolate genomes were aligned using the software developed by our group (ODOTool) and 11 variations in SARS-CoV-2 genome over 10% of whole isolates were discussed. Results indicated that, frequency rates of these 11 variations change between 3.56%-88.44 % and these rates differ greatly depending on the continents they have been reported. Despite some variations being in low frequency rate in some continents, C14408T and A23403G variations on Nsp12 and S protein, respectively, observed to be the most prominent variations all over the world, in general, and both cause missense mutations. It is also notable that most of isolates carry C14408T and A23403 variations simultaneously and also nearly all isolates carrying the G25563T variation on ORF3a, also carry C14408T and A23403 variations, although their location distributions are not similar. All these data should be considered towards development of vaccine and antiviral treatment strategies as well as tracing diversity of virus in all over the world.

【 授权许可】

Unknown