The Spike Protein of SARS-coV2 19B (S) Clade Mirrors Critical Features of Viral Adaptation and Coevolution
Pathogens including viruses evolve in tandem with diversity in their animal and human hosts. For <i>SARS-coV2</i>, the focus is generally for understanding such coevolution on the virus spike protein, since it demonstrates high mutation rates compared to other genome regions, particularl...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-10-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/10/10/2017 |
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| author | Bidour K. Hussein Omnia M. Ibrahium Marwa F. Alamin Lamees A. M. Ahmed Safa A. E. Abuswar Mohammed H. Abdelraheem Muntaser E. Ibrahim |
| author_facet | Bidour K. Hussein Omnia M. Ibrahium Marwa F. Alamin Lamees A. M. Ahmed Safa A. E. Abuswar Mohammed H. Abdelraheem Muntaser E. Ibrahim |
| author_sort | Bidour K. Hussein |
| collection | DOAJ |
| description | Pathogens including viruses evolve in tandem with diversity in their animal and human hosts. For <i>SARS-coV2</i>, the focus is generally for understanding such coevolution on the virus spike protein, since it demonstrates high mutation rates compared to other genome regions, particularly in the receptor-binding domain (RBD). Viral sequences of the <i>SARS-coV2</i> 19B (S) clade and variants of concern from different continents were investigated, with a focus on the A.29 lineage, which presented with different mutational patterns within the 19B (S) lineages in order to learn more about how <i>SARS-coV2</i> may have evolved and adapted to widely diverse populations globally. Results indicated that <i>SARS-coV2</i> went through evolutionary constrains and intense selective pressure, particularly in Africa. This was manifested in a departure from neutrality with excess nonsynonymous mutations and a negative Tajima D consistent with rapid expansion and directional selection as well as deletion and deletion–frameshifts in the N-terminal domain (NTD region) of the spike protein. In conclusion, we hypothesize that viral transmission during epidemics through populations of diverse genomic structures and marked complexity may be a significant factor for the virus to acquire distinct patterns of mutations within these populations in order to ensure its survival and fitness, explaining the emergence of novel variants and strains. |
| first_indexed | 2024-03-09T19:44:19Z |
| format | Article |
| id | doaj.art-55c3bc7179234bd7999ffd0920ccba38 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T19:44:19Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-55c3bc7179234bd7999ffd0920ccba382023-11-24T01:27:03ZengMDPI AGMicroorganisms2076-26072022-10-011010201710.3390/microorganisms10102017The Spike Protein of SARS-coV2 19B (S) Clade Mirrors Critical Features of Viral Adaptation and CoevolutionBidour K. Hussein0Omnia M. Ibrahium1Marwa F. Alamin2Lamees A. M. Ahmed3Safa A. E. Abuswar4Mohammed H. Abdelraheem5Muntaser E. Ibrahim6Unit of Disease and Diversity, Department of Molecular Biology, Institute of Endemic Diseases, Khartoum University, Khartoum P.O Box 102, SudanUnit of Disease and Diversity, Department of Molecular Biology, Institute of Endemic Diseases, Khartoum University, Khartoum P.O Box 102, SudanUnit of Disease and Diversity, Department of Molecular Biology, Institute of Endemic Diseases, Khartoum University, Khartoum P.O Box 102, SudanUnit of Disease and Diversity, Department of Molecular Biology, Institute of Endemic Diseases, Khartoum University, Khartoum P.O Box 102, SudanUnit of Disease and Diversity, Department of Molecular Biology, Institute of Endemic Diseases, Khartoum University, Khartoum P.O Box 102, SudanUnit of Disease and Diversity, Department of Molecular Biology, Institute of Endemic Diseases, Khartoum University, Khartoum P.O Box 102, SudanUnit of Disease and Diversity, Department of Molecular Biology, Institute of Endemic Diseases, Khartoum University, Khartoum P.O Box 102, SudanPathogens including viruses evolve in tandem with diversity in their animal and human hosts. For <i>SARS-coV2</i>, the focus is generally for understanding such coevolution on the virus spike protein, since it demonstrates high mutation rates compared to other genome regions, particularly in the receptor-binding domain (RBD). Viral sequences of the <i>SARS-coV2</i> 19B (S) clade and variants of concern from different continents were investigated, with a focus on the A.29 lineage, which presented with different mutational patterns within the 19B (S) lineages in order to learn more about how <i>SARS-coV2</i> may have evolved and adapted to widely diverse populations globally. Results indicated that <i>SARS-coV2</i> went through evolutionary constrains and intense selective pressure, particularly in Africa. This was manifested in a departure from neutrality with excess nonsynonymous mutations and a negative Tajima D consistent with rapid expansion and directional selection as well as deletion and deletion–frameshifts in the N-terminal domain (NTD region) of the spike protein. In conclusion, we hypothesize that viral transmission during epidemics through populations of diverse genomic structures and marked complexity may be a significant factor for the virus to acquire distinct patterns of mutations within these populations in order to ensure its survival and fitness, explaining the emergence of novel variants and strains.https://www.mdpi.com/2076-2607/10/10/2017<i>SARS-coV2</i>Spike protein19B (S) cladeN-terminal domain (NTD region)synonymous and nonsynonymous mutationsdeletion |
| spellingShingle | Bidour K. Hussein Omnia M. Ibrahium Marwa F. Alamin Lamees A. M. Ahmed Safa A. E. Abuswar Mohammed H. Abdelraheem Muntaser E. Ibrahim The Spike Protein of SARS-coV2 19B (S) Clade Mirrors Critical Features of Viral Adaptation and Coevolution Microorganisms <i>SARS-coV2</i> Spike protein 19B (S) clade N-terminal domain (NTD region) synonymous and nonsynonymous mutations deletion |
| title | The Spike Protein of SARS-coV2 19B (S) Clade Mirrors Critical Features of Viral Adaptation and Coevolution |
| title_full | The Spike Protein of SARS-coV2 19B (S) Clade Mirrors Critical Features of Viral Adaptation and Coevolution |
| title_fullStr | The Spike Protein of SARS-coV2 19B (S) Clade Mirrors Critical Features of Viral Adaptation and Coevolution |
| title_full_unstemmed | The Spike Protein of SARS-coV2 19B (S) Clade Mirrors Critical Features of Viral Adaptation and Coevolution |
| title_short | The Spike Protein of SARS-coV2 19B (S) Clade Mirrors Critical Features of Viral Adaptation and Coevolution |
| title_sort | spike protein of sars cov2 19b s clade mirrors critical features of viral adaptation and coevolution |
| topic | <i>SARS-coV2</i> Spike protein 19B (S) clade N-terminal domain (NTD region) synonymous and nonsynonymous mutations deletion |
| url | https://www.mdpi.com/2076-2607/10/10/2017 |
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