Mutational Hotspot in the SARS-CoV-2 Spike Protein N-Terminal Domain Conferring Immune Escape Potential
Global efforts are being made to monitor the evolution of SARS-CoV-2, aiming for early identification of genotypes providing increased infectivity or virulence. However, viral lineage-focused tracking might fail in early detection of advantageous mutations emerging independently across phylogenies....
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-10-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/13/11/2114 |
| _version_ | 1797508228935843840 |
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| author | Slawomir Kubik Nils Arrigo Jaume Bonet Zhenyu Xu |
| author_facet | Slawomir Kubik Nils Arrigo Jaume Bonet Zhenyu Xu |
| author_sort | Slawomir Kubik |
| collection | DOAJ |
| description | Global efforts are being made to monitor the evolution of SARS-CoV-2, aiming for early identification of genotypes providing increased infectivity or virulence. However, viral lineage-focused tracking might fail in early detection of advantageous mutations emerging independently across phylogenies. Here, the emergence patterns of Spike mutations were investigated in sequences deposited in local and global databases to identify mutational hotspots across phylogenies and we evaluated their impact on SARS-CoV-2 evolution. We found a striking increase in the frequency of recruitment of diverse substitutions at a critical residue (W152), positioned in the N-terminal domain (NTD) of the Spike protein, observed repeatedly across independent phylogenetic and geographical contexts. These mutations might have an impact on the evasion of neutralizing antibodies. Finally, we found that NTD is a region exhibiting particularly high frequency of mutation recruitments, suggesting an evolutionary path in which the virus maintains optimal efficiency of ACE2 binding combined with the flexibility facilitating the immune escape. We conclude that adaptive mutations, frequently present outside of the receptor-binding domain, can emerge in virtually any SARS-CoV-2 lineage and at any geographical location. Therefore, surveillance should not be restricted to monitoring defined lineages alone. |
| first_indexed | 2024-03-10T04:59:33Z |
| format | Article |
| id | doaj.art-cc58a2f8810241f7acdaa11bf478c6e7 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T04:59:33Z |
| publishDate | 2021-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-cc58a2f8810241f7acdaa11bf478c6e72023-11-23T01:55:03ZengMDPI AGViruses1999-49152021-10-011311211410.3390/v13112114Mutational Hotspot in the SARS-CoV-2 Spike Protein N-Terminal Domain Conferring Immune Escape PotentialSlawomir Kubik0Nils Arrigo1Jaume Bonet2Zhenyu Xu3Data Science Department, SOPHiA GENETICS, La Pièce 12, 1180 Rolle, SwitzerlandData Science Department, SOPHiA GENETICS, Rue du Centre 172, 1025 Saint-Sulpice, SwitzerlandData Science Department, SOPHiA GENETICS, Rue du Centre 172, 1025 Saint-Sulpice, SwitzerlandData Science Department, SOPHiA GENETICS, Rue du Centre 172, 1025 Saint-Sulpice, SwitzerlandGlobal efforts are being made to monitor the evolution of SARS-CoV-2, aiming for early identification of genotypes providing increased infectivity or virulence. However, viral lineage-focused tracking might fail in early detection of advantageous mutations emerging independently across phylogenies. Here, the emergence patterns of Spike mutations were investigated in sequences deposited in local and global databases to identify mutational hotspots across phylogenies and we evaluated their impact on SARS-CoV-2 evolution. We found a striking increase in the frequency of recruitment of diverse substitutions at a critical residue (W152), positioned in the N-terminal domain (NTD) of the Spike protein, observed repeatedly across independent phylogenetic and geographical contexts. These mutations might have an impact on the evasion of neutralizing antibodies. Finally, we found that NTD is a region exhibiting particularly high frequency of mutation recruitments, suggesting an evolutionary path in which the virus maintains optimal efficiency of ACE2 binding combined with the flexibility facilitating the immune escape. We conclude that adaptive mutations, frequently present outside of the receptor-binding domain, can emerge in virtually any SARS-CoV-2 lineage and at any geographical location. Therefore, surveillance should not be restricted to monitoring defined lineages alone.https://www.mdpi.com/1999-4915/13/11/2114SARS-CoV-2 genomecoronavirusspike NTDW152viral evolutionneutralizing antibody |
| spellingShingle | Slawomir Kubik Nils Arrigo Jaume Bonet Zhenyu Xu Mutational Hotspot in the SARS-CoV-2 Spike Protein N-Terminal Domain Conferring Immune Escape Potential Viruses SARS-CoV-2 genome coronavirus spike NTD W152 viral evolution neutralizing antibody |
| title | Mutational Hotspot in the SARS-CoV-2 Spike Protein N-Terminal Domain Conferring Immune Escape Potential |
| title_full | Mutational Hotspot in the SARS-CoV-2 Spike Protein N-Terminal Domain Conferring Immune Escape Potential |
| title_fullStr | Mutational Hotspot in the SARS-CoV-2 Spike Protein N-Terminal Domain Conferring Immune Escape Potential |
| title_full_unstemmed | Mutational Hotspot in the SARS-CoV-2 Spike Protein N-Terminal Domain Conferring Immune Escape Potential |
| title_short | Mutational Hotspot in the SARS-CoV-2 Spike Protein N-Terminal Domain Conferring Immune Escape Potential |
| title_sort | mutational hotspot in the sars cov 2 spike protein n terminal domain conferring immune escape potential |
| topic | SARS-CoV-2 genome coronavirus spike NTD W152 viral evolution neutralizing antibody |
| url | https://www.mdpi.com/1999-4915/13/11/2114 |
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