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. 2023 Jan 30:851:147020.
doi: 10.1016/j.gene.2022.147020. Epub 2022 Nov 4.

Geographical distribution of host's specific SARS-CoV-2 mutations in the early phase of the COVID-19 pandemic

Mohammad Khalid  1 , David Murphy  2 , Maryam Shoai  3 , Jonahunnatha Nesson George-William  4 , Yousef Al-Ebini  5
Affiliations

Geographical distribution of host's specific SARS-CoV-2 mutations in the early phase of the COVID-19 pandemic

Mohammad Khalid et al. Gene. .

Abstract

Purpose: To assess, if the SARS-CoV-2 mutate in a similar pattern globally or has a specific pattern in any given population.

Results: We report, the insertion of TTT at 11085, which adds an extra amino acid, F to the NSP6 at amino acid position 38. The highest occurrence of TTT insertion at 11,085 position was found in UK derived samples (65.97%). The second and third highest occurrence of the mutation were found in Australia (8.3%) and USA (4.16%) derived samples, respectively. Another important discovery of this study is the C27945T mutation, which translates into the termination of ORF-8 after 17 amino acids, reveals that the SARS-CoV-2 can replicate without the intact ORF-8 protein. We found that the 97% of C27945T mutation of global occurrence, occurred in Europe and the USA derived samples.

Conclusions: Two of the reported mutations (11085TTT insertion and C27945T nonsense), which seemed to reduce Type I interferon response are linked to specific geographical locations of the host and implicate region-specific mutations in the virus. The findings of this study signify that SARS-CoV-2 has the potential to adapt differently to different populations.

Keywords: Mutation; NSP6; Nucleotide sequences; ORF-8; SARS-CoV-2.

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Conflict of interest statement

Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig. 1
Fig. 1
Workflow of identification of mutations in SARS-CoV-2 genome sequences.
Fig. 2
Fig. 2
SARS-CoV-2 Mutations in different ORFs The graph shows the total mutations in the 5′-UTR and various ORFs of the SARS-CoV-2 genome.
Fig. 3
Fig. 3
SARS-CoV-2 Non-Synonymous Mutations in different ORFs The figure shows the number of non-synonymous mutations in various ORFs of the SARS-CoV-2 genome.
Fig. 4
Fig. 4
The translation of SARS-CoV-2 genomic mutation The graph shows the number of non-synonymous and synonymous mutations in each ORF. The 5′-UTR does not get translated. The figure shows one insertion mutation in ORF-1a and one non-sense mutation in ORF-8 of the SARS-CoV-2 genome.
Fig. 5
Fig. 5
The occurrence of insertion mutation in SARS-CoV-2 nsp6 The graph shows the occurrence of 11085TTT insertion mutation in SARS-CoV-2 genomes globally..
Fig. 6
Fig. 6
The occurrence of non-sense mutation in SARS-CoV-2 ORF-8 The graphs show the occurrence of C27945T (non-sense) mutation in ORF-8.
See this image and copyright information in PMC

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