Genome-Wide Analysis of Codon Usage Patterns of SARS-CoV-2 Virus Reveals Global Heterogeneity of COVID-19

被引：20

作者：

Khattak, Saadullah ^{[1
,2
]}

Rauf, Mohd Ahmar ^{[2
,3
]}

Zaman, Qamar ^{[4
]}

Ali, Yasir ^{[5
]}

Fatima, Shabeen ^{[6
]}

Muhammad, Pir ^{[7
]}

Li, Tao ^{[1
]}

Khan, Hamza Ali ^{[4
]}

Khan, Azhar Abbas ^{[1
,8
]}

Ngowi, Ebenezeri Erasto ^{[1
]}

Wu, Dong-Dong ^{[1
,9
]}

Ji, Xin-Ying ^{[1
,10
]}

机构：

[1] Henan Univ, Henan Int Joint Lab Nucl Prot Regulat, Sch Basic Med Sci, Kaifeng 475004, Henan, Peoples R China

[2] Henan Univ, Sch Life Sci, Kaifeng 475004, Henan, Peoples R China

[3] Wayne State Univ, Sch Pharmaceut Sci, Detroit, MI 48202 USA

[4] Hazara Univ, Dept Bioinformat, Mansehra 21120, Pakistan

[5] Quaid I Azam Univ, Natl Ctr Bioinformat, Islamabad 45320, Pakistan

[6] Capital Univ Sci & Technol, Dept Biosci & Bioinformat, Islamabad 44000, Pakistan

[7] Henan Univ, Sch Life Sci, Henan Macquarie Univ Joint Ctr Biomed Innovat, Kaifeng 475004, Henan, Peoples R China

[8] Hazara Univ, Dept Biochem, Mansehra 21110, Pakistan

[9] Henan Univ, Sch Stomatol, Kaifeng 475004, Henan, Peoples R China

[10] Henan Univ, Kaifeng Key Lab Infect & Biol Safety, Sch Basic Med Sci, Kaifeng 475004, Henan, Peoples R China

来源：

BIOMOLECULES | 2021年 / 11卷 / 06期

基金：

中国国家自然科学基金;

关键词：

Coronavirus; SARS-CoV-2; Codon usage bias; COVID-19; heterogeneity of COVID-19; mutational bias; natural selection; MULTIPLE SEQUENCE ALIGNMENT; NUCLEOTIDE COMPOSITION; MUTATION PRESSURE; MOLECULAR-BIOLOGY; BIAS; CORONAVIRUS; RNA; EVOLUTION; ADAPTATION; VACCINE;

D O I：

10.3390/biom11060912

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The ongoing outbreak of coronavirus disease COVID-19 is significantly implicated by global heterogeneity in the genome organization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The causative agents of global heterogeneity in the whole genome of SARS-CoV-2 are not well characterized due to the lack of comparative study of a large enough sample size from around the globe to reduce the standard deviation to the acceptable margin of error. To better understand the SARS-CoV-2 genome architecture, we have performed a comprehensive analysis of codon usage bias of sixty (60) strains to get a snapshot of its global heterogeneity. Our study shows a relatively low codon usage bias in the SARS-CoV-2 viral genome globally, with nearly all the over-preferred codons' A.U. ended. We concluded that the SARS-CoV-2 genome is primarily shaped by mutation pressure; however, marginal selection pressure cannot be overlooked. Within the A/U rich virus genomes of SARS-CoV-2, the standard deviation in G.C. (42.91% +/- 5.84%) and the GC3 value (30.14% +/- 6.93%) points towards global heterogeneity of the virus. Several SARS-CoV-2 viral strains were originated from different viral lineages at the exact geographic location also supports this fact. Taking all together, these findings suggest that the general root ancestry of the global genomes are different with different genome's level adaptation to host. This research may provide new insights into the codon patterns, host adaptation, and global heterogeneity of SARS-CoV-2.

引用

页数：13

共 56 条

[1] Design of a Novel Multi Epitope-Based Vaccine for Pandemic Coronavirus Disease (COVID-19) by Vaccinomics and Probable Prevention Strategy against Avenging Zoonotics [J].