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Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein

The SARS-CoV-2 omicron variants keep accumulating a large number of mutations in the spike (S) protein, which contributes to greater transmissibility and a rapid rise to dominance within populations. The identification of mutations and their affinity to the cellular angiotensin-converting enzyme-2 (...

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Autores principales: Shikha, Sristy, Jogi, Mukesh Kumar, Jha, Ruchika, Kumar, Rana Amit, Sah, Tathagat, Singh, Pushpendra, Sagar, Ritu, Kumar, Anuj, Marwal, Robin, Ponnusamy, Kalaiarasan, Agarwal, Subhash Mohan, Kumar, R. Suresh, Arif, Nazneen, Bharadwaj, Mausumi, Singh, Shalini, Kumar, Pramod
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10577267/
https://www.ncbi.nlm.nih.gov/pubmed/37849762
http://dx.doi.org/10.3389/fimmu.2023.1209513
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author Shikha, Sristy
Jogi, Mukesh Kumar
Jha, Ruchika
Kumar, Rana Amit
Sah, Tathagat
Singh, Pushpendra
Sagar, Ritu
Kumar, Anuj
Marwal, Robin
Ponnusamy, Kalaiarasan
Agarwal, Subhash Mohan
Kumar, R. Suresh
Arif, Nazneen
Bharadwaj, Mausumi
Singh, Shalini
Kumar, Pramod
author_facet Shikha, Sristy
Jogi, Mukesh Kumar
Jha, Ruchika
Kumar, Rana Amit
Sah, Tathagat
Singh, Pushpendra
Sagar, Ritu
Kumar, Anuj
Marwal, Robin
Ponnusamy, Kalaiarasan
Agarwal, Subhash Mohan
Kumar, R. Suresh
Arif, Nazneen
Bharadwaj, Mausumi
Singh, Shalini
Kumar, Pramod
author_sort Shikha, Sristy
collection PubMed
description The SARS-CoV-2 omicron variants keep accumulating a large number of mutations in the spike (S) protein, which contributes to greater transmissibility and a rapid rise to dominance within populations. The identification of mutations and their affinity to the cellular angiotensin-converting enzyme-2 (ACE-2) receptor and immune evasion in the Delhi NCR region was under-acknowledged. The study identifies some mutations (Y505 reversion, G339H, and R346T/N) in genomes from Delhi, India, and their probable implications for altering the immune response and binding affinity for ACE-2. The spike mutations have influenced the neutralizing activity of antibodies against the omicron variant, which shows partial immune escape. However, researchers are currently exploring various mitigation strategies to tackle the potential decline in efficacy or effectiveness against existing and future variants of SARS-CoV-2. These strategies include modifying vaccines to target specific variants, such as the omicron variant, developing multivalent vaccine formulations, and exploring alternative delivery methods. To address this, it is also necessary to understand the impact of these mutations from a different perspective, especially in terms of alterations in antigenic determinants. In this study, we have done whole genome sequencing (WGS) of SARS-CoV-2 in COVID-19 samples from Delhi, NCR, and analyzed the spike’s mutation with an emphasis on antigenic alterations. The impact of mutation in terms of epitope formation, loss/gain of efficiency, and interaction of epitopes with antibodies has been studied. Some of the mutations or variant genomes seem to be the progenitors of the upcoming variants in India. Our analyses suggested that weakening interactions with antibodies may lead to immune resistance in the circulating genomes.
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spelling pubmed-105772672023-10-17 Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein Shikha, Sristy Jogi, Mukesh Kumar Jha, Ruchika Kumar, Rana Amit Sah, Tathagat Singh, Pushpendra Sagar, Ritu Kumar, Anuj Marwal, Robin Ponnusamy, Kalaiarasan Agarwal, Subhash Mohan Kumar, R. Suresh Arif, Nazneen Bharadwaj, Mausumi Singh, Shalini Kumar, Pramod Front Immunol Immunology The SARS-CoV-2 omicron variants keep accumulating a large number of mutations in the spike (S) protein, which contributes to greater transmissibility and a rapid rise to dominance within populations. The identification of mutations and their affinity to the cellular angiotensin-converting enzyme-2 (ACE-2) receptor and immune evasion in the Delhi NCR region was under-acknowledged. The study identifies some mutations (Y505 reversion, G339H, and R346T/N) in genomes from Delhi, India, and their probable implications for altering the immune response and binding affinity for ACE-2. The spike mutations have influenced the neutralizing activity of antibodies against the omicron variant, which shows partial immune escape. However, researchers are currently exploring various mitigation strategies to tackle the potential decline in efficacy or effectiveness against existing and future variants of SARS-CoV-2. These strategies include modifying vaccines to target specific variants, such as the omicron variant, developing multivalent vaccine formulations, and exploring alternative delivery methods. To address this, it is also necessary to understand the impact of these mutations from a different perspective, especially in terms of alterations in antigenic determinants. In this study, we have done whole genome sequencing (WGS) of SARS-CoV-2 in COVID-19 samples from Delhi, NCR, and analyzed the spike’s mutation with an emphasis on antigenic alterations. The impact of mutation in terms of epitope formation, loss/gain of efficiency, and interaction of epitopes with antibodies has been studied. Some of the mutations or variant genomes seem to be the progenitors of the upcoming variants in India. Our analyses suggested that weakening interactions with antibodies may lead to immune resistance in the circulating genomes. Frontiers Media S.A. 2023-10-02 /pmc/articles/PMC10577267/ /pubmed/37849762 http://dx.doi.org/10.3389/fimmu.2023.1209513 Text en Copyright © 2023 Shikha, Jogi, Jha, Kumar, Sah, Singh, Sagar, Kumar, Marwal, Ponnusamy, Agarwal, Kumar, Arif, Bharadwaj, Singh and Kumar https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Immunology
Shikha, Sristy
Jogi, Mukesh Kumar
Jha, Ruchika
Kumar, Rana Amit
Sah, Tathagat
Singh, Pushpendra
Sagar, Ritu
Kumar, Anuj
Marwal, Robin
Ponnusamy, Kalaiarasan
Agarwal, Subhash Mohan
Kumar, R. Suresh
Arif, Nazneen
Bharadwaj, Mausumi
Singh, Shalini
Kumar, Pramod
Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein
title Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein
title_full Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein
title_fullStr Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein
title_full_unstemmed Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein
title_short Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein
title_sort genome sequencing of sars-cov-2 omicron variants in delhi reveals alterations in immunogenic regions in spike glycoprotein
topic Immunology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10577267/
https://www.ncbi.nlm.nih.gov/pubmed/37849762
http://dx.doi.org/10.3389/fimmu.2023.1209513
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