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

• Main Authors: Saadullah Khattak, Mohd Ahmar Rauf, Qamar Zaman, Yasir Ali, Shabeen Fatima, Pir Muhammad, Tao Li, Hamza Ali Khan, Azhar Abbas Khan, Ebenezeri Erasto Ngowi, Dong-Dong Wu, Xin-Ying Ji
• Format: Article
• Language: English
• Published: MDPI AG 2021-06-01
• Series: Biomolecules
• Subjects: Coronavirus; SARS-CoV-2; Codon usage bias; COVID-19; heterogeneity of COVID-19; mutational bias
• Online Access: https://www.mdpi.com/2218-273X/11/6/912

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.