Abstract
The objective of this study was to assess the impact of variations in the surface glycoprotein of SARS-CoV-2, which is generated by the spike (S) gene, on its interaction with host receptors in seventy-six viral Iraqi samples. Out of seven SNPs in the coding regions, three missense SNPs were identified. Based on phylogenetic analysis, four distinct groups of amino acid variations were revealed. In group-1 (p.N655H), group-2 (p.H622D), and group-3 (p.L449R), one missense SNP was observed, while no missense SNP was identified in the group-4 (wild-type) samples. Due to their novel amino acid variations, both group-1 and group-2 variants occupied two distinct phylogenetic positions in the tree. Molecular docking was performed between the identified S gene variants and the host angiotensin-converting enzyme 2 (ACE2) receptor, and the effects of these variants were evaluated. Compared with the other viral variations, docking revealed that p.N655H variant exhibited the highest affinity to the ACE2 receptor. It was found that patients infected with p.N655H variants showed a higher level of severity compared to the other types of infections. In conclusion, the observed p.N655H was associated with a higher severity of SARS-CoV-2 infection, which may be associated with greater host entry capacity compared to the wild type or other identified variants. These findings provide insights into the mechanism by which these novel viral strains interact with host cell receptors. They also highlight the importance of understanding virus-host interactions for assessing the impact of the global pandemic caused by SARS-CoV-2.
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Data Availability
Data sharing of this article is available upon request to the corresponding author.
Abbreviations
- ACE2:
-
Angiotensin-converting enzyme 2
- PDB:
-
Protein Data Bank
- CTD2:
-
C-terminal domain 2
- E:
-
Envelope
- GISAID:
-
Global Initiative on Sharing All Influenza Data
- HADDOCK:
-
High Ambiguity Driven biomolecular DOCKing
- iTOL:
-
Interactive Tree of Life
- M:
-
Membrane
- N:
-
Nucleocapsid
- S:
-
Spike gene
- SNP:
-
Single nucleotide polymorphism
- WHO:
-
World Health Organization
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Acknowledgements
The authors would like to thank the medical staff of the Hilla General Teaching Hospital (Babil Province), Karbala General Teaching Hospital and Karbala Teaching Hospital for Children (Karbala Province), Hakeem Teaching Hospital (Najaf Province), and Public Health Laboratory (Baghdad) for kindly providing us with the SARS-CoV-2 infected samples.
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MRRA and KNJM; collected samples, and performed genotyping experiments. ASA; participated in the laboratory work. MBSA; designed PCR primers, analyzed data, and wrote the manuscript. All authors approved the final draft of the manuscript.
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Al-Mousawi, M.R.R., Musafer, K.N.J., Alattabi, A.S. et al. The emergence of a novel SARS-CoV-2 variant with higher efficiency of binding with the human host cell receptors in Iraqi subjects. Biologia 79, 629–641 (2024). https://doi.org/10.1007/s11756-023-01583-4
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DOI: https://doi.org/10.1007/s11756-023-01583-4