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

Frontiers in Immunology

Immunology

Kalaiarasan Ponnusamy¹  Robin Marwal¹  Rana Amit Kumar²  Pushpendra Singh³  Ritu Sagar³  Ruchika Jha⁴  Tathagat Sah⁵  Anuj Kumar⁶  Shalini Singh⁶  Sristy Shikha⁶  R. Suresh Kumar⁶  Nazneen Arif⁶  Pramod Kumar⁶  Mausumi Bharadwaj⁶  Subhash Mohan Agarwal⁶  Mukesh Kumar Jogi⁷ 

[1] Biotechnology Division, National Centre for Disease Control, Delhi, India;Department of Biotechnology, Anugrah Narayan College, Patna, Bihar, India;Department of Biotechnology, Central University of Haryana, Mahendergarh, Haryana, India;Department of Biotechnology, Vinoba Bhave University, Hazaribagh, Jharkhand, India;Department of Chemical Engineering and Biotechnology, Beant College of Engineering and Technology, Gurdaspur, Punjab, India;Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India;Division of Molecular Biology, Indian Council of Medical Research (ICMR)-National Institute of Cancer Prevention and Research (NICPR), Noida, India;Amity Institute of Biotechnology, Amity University, Noida, India;

关键词: SARS-CoV-2;    COVID-19;    mutation;    omicron;    epitopes;    antigenic determinant;    neutralizing antibodies;   

DOI  :  10.3389/fimmu.2023.1209513

 received in 2023-04-20, accepted in 2023-08-30,  发布年份 2023

来源: Frontiers

【 摘 要 】

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.

【 授权许可】

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Copyright © 2023 Shikha, Jogi, Jha, Kumar, Sah, Singh, Sagar, Kumar, Marwal, Ponnusamy, Agarwal, Kumar, Arif, Bharadwaj, Singh and Kumar