The Omicron XBB.1 Variant and Its Descendants: Genomic Mutations, Rapid Dissemination and Notable Characteristics
The SARS-CoV-2 virus, which is a major threat to human health, has undergone many mutations during the replication process due to errors in the replication steps and modifications in the structure of viral proteins. The XBB variant was identified for the first time in Singapore in the fall of 2022....
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MDPI AG
2024-02-01
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| Series: | Biology |
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| Online Access: | https://www.mdpi.com/2079-7737/13/2/90 |
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| author | Raffaele Giancotti Ugo Lomoio Barbara Puccio Giuseppe Tradigo Patrizia Vizza Carlo Torti Pierangelo Veltri Pietro Hiram Guzzi |
| author_facet | Raffaele Giancotti Ugo Lomoio Barbara Puccio Giuseppe Tradigo Patrizia Vizza Carlo Torti Pierangelo Veltri Pietro Hiram Guzzi |
| author_sort | Raffaele Giancotti |
| collection | DOAJ |
| description | The SARS-CoV-2 virus, which is a major threat to human health, has undergone many mutations during the replication process due to errors in the replication steps and modifications in the structure of viral proteins. The XBB variant was identified for the first time in Singapore in the fall of 2022. It was then detected in other countries, including the United States, Canada, and the United Kingdom. We study the impact of sequence changes on spike protein structure on the subvariants of XBB, with particular attention to the velocity of variant diffusion and virus activity with respect to its diffusion. We examine the structural and functional distinctions of the variants in three different conformations: (i) spike glycoprotein in complex with ACE2 (1-up state), (ii) spike glycoprotein (closed-1 state), and (iii) S protein (open-1 state). We also estimate the affinity binding between the spike protein and ACE2. The market binding affinity observed in specific variants raises questions about the efficacy of current vaccines in preparing the immune system for virus variant recognition. This work may be useful in devising strategies to manage the ongoing COVID-19 pandemic. To stay ahead of the virus evolution, further research and surveillance should be carried out to adjust public health measures accordingly. |
| first_indexed | 2024-03-07T22:41:26Z |
| format | Article |
| id | doaj.art-2b3a1be5fbf94e6c834d06f18589aef1 |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-07T22:41:26Z |
| publishDate | 2024-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj.art-2b3a1be5fbf94e6c834d06f18589aef12024-02-23T15:08:09ZengMDPI AGBiology2079-77372024-02-011329010.3390/biology13020090The Omicron XBB.1 Variant and Its Descendants: Genomic Mutations, Rapid Dissemination and Notable CharacteristicsRaffaele Giancotti0Ugo Lomoio1Barbara Puccio2Giuseppe Tradigo3Patrizia Vizza4Carlo Torti5Pierangelo Veltri6Pietro Hiram Guzzi7Department of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, ItalyDepartment of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, ItalyDepartment of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, ItalySMARTEST Lab., eCampus University, 22060 Novedrate, ItalyDepartment of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, ItalyDepartment of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, ItalyDepartment of Computer Engineering, Modelling, Electronics and System, University of Calabria, 87036 Rende, ItalyDepartment of Surgical and Medical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, ItalyThe SARS-CoV-2 virus, which is a major threat to human health, has undergone many mutations during the replication process due to errors in the replication steps and modifications in the structure of viral proteins. The XBB variant was identified for the first time in Singapore in the fall of 2022. It was then detected in other countries, including the United States, Canada, and the United Kingdom. We study the impact of sequence changes on spike protein structure on the subvariants of XBB, with particular attention to the velocity of variant diffusion and virus activity with respect to its diffusion. We examine the structural and functional distinctions of the variants in three different conformations: (i) spike glycoprotein in complex with ACE2 (1-up state), (ii) spike glycoprotein (closed-1 state), and (iii) S protein (open-1 state). We also estimate the affinity binding between the spike protein and ACE2. The market binding affinity observed in specific variants raises questions about the efficacy of current vaccines in preparing the immune system for virus variant recognition. This work may be useful in devising strategies to manage the ongoing COVID-19 pandemic. To stay ahead of the virus evolution, further research and surveillance should be carried out to adjust public health measures accordingly.https://www.mdpi.com/2079-7737/13/2/90XBB variantOmicronCOVID-19genomic analysis |
| spellingShingle | Raffaele Giancotti Ugo Lomoio Barbara Puccio Giuseppe Tradigo Patrizia Vizza Carlo Torti Pierangelo Veltri Pietro Hiram Guzzi The Omicron XBB.1 Variant and Its Descendants: Genomic Mutations, Rapid Dissemination and Notable Characteristics Biology XBB variant Omicron COVID-19 genomic analysis |
| title | The Omicron XBB.1 Variant and Its Descendants: Genomic Mutations, Rapid Dissemination and Notable Characteristics |
| title_full | The Omicron XBB.1 Variant and Its Descendants: Genomic Mutations, Rapid Dissemination and Notable Characteristics |
| title_fullStr | The Omicron XBB.1 Variant and Its Descendants: Genomic Mutations, Rapid Dissemination and Notable Characteristics |
| title_full_unstemmed | The Omicron XBB.1 Variant and Its Descendants: Genomic Mutations, Rapid Dissemination and Notable Characteristics |
| title_short | The Omicron XBB.1 Variant and Its Descendants: Genomic Mutations, Rapid Dissemination and Notable Characteristics |
| title_sort | omicron xbb 1 variant and its descendants genomic mutations rapid dissemination and notable characteristics |
| topic | XBB variant Omicron COVID-19 genomic analysis |
| url | https://www.mdpi.com/2079-7737/13/2/90 |
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