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ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Virology
Volume 15 - 2024 |
doi: 10.3389/fmicb.2024.1531712
The trend of phylogenetic and epitope variations of SARS-CoV2 Omicron sub-lineages in Iran
Provisionally accepted- 1 Tehran University of Medical Sciences, Tehran, Iran
- 2 Shahid Beheshti University, Tehran, Tehran, Iran
- 3 Tarbiat Modares University, Tehran, Tehran, Iran
Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a significant public health issue worldwide in recent years. The most recently circulating variant of SARS-CoV-2, Omicron, and its rapid evolution into various sub-lineages have raised concerns regarding the effects of the immunity on the virus epitopes, in the human population. The present study evaluated and compared these important variations among different Omicron sub-lineages in Iran. Methodology: From October 2023 to August 2024, high coverage whole genome sequences of 49 SARS-CoV-2 strains were subjected to phylogenetic analysis and evaluation of B cell, CD4+, and CD8+ T cell epitopes in Iran National Influenza Centre. Results: The phylogenetic tree exhibited eight Nextstrain clades (21L, 22F, 23B, 23H, 23D, 24A, 24B, 24C) in 48 studied strains, and one recombinant strain (XDK.1). The evaluation of B cell, CD4+, and CD8+ T cell epitopes in all studied strains revealed 31%, 65% and 78%, of conservation, respectively. The low B cell epitopes conservation rate among Omicron sub-lineages underscored the escaping from neutralizing humoral immunity. T cell epitopes of the SARS-CoV-2 were considerably preserved across major Omicron sub-lineages. Conservation levels varied based on the epitope class (higher for CD8+ vs. CD4+), protein (higher for non-spike vs. spike), and clades (higher for 21L, 22F, 23B, 23H, 23D and 24B vs 24A and 24C). Conclusion: Herein, the increased conservation of CD8+ epitopes compared to CD4+ and B cell epitopes is probably attributable to the shorter length of the peptides associated with CD8+ epitopes. The high rate of T-cell epitopes conservation in non-spike proteins among different sub-lineages of the Omicron in this study highlighted the importance of cell-mediated immunity and suggested that non-spike proteins might be more attractive targets for future SARS-CoV-2 vaccines.
Keywords: SARS-CoV2, Omicron sub-lineages, phylogenetic, epitope variations, Immunity
Received: 20 Nov 2024; Accepted: 17 Dec 2024.
Copyright: © 2024 Shabani, Nejati, Yavarian, Sadeghi, Zadheidar, Ahmadi, Ghadirali, Zebardast, Abedi, Najmi, Shafiei-Jandaghi and Mokhtari-Azad. 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) or licensor 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.
* Correspondence:
Ahmad Nejati, Tehran University of Medical Sciences, Tehran, Iran
Kaveh Sadeghi, Tehran University of Medical Sciences, Tehran, Iran
Sevrin Zadheidar, Tehran University of Medical Sciences, Tehran, Iran
Akram Sadat Ahmadi, Tehran University of Medical Sciences, Tehran, Iran
Monire Ghadirali, Tehran University of Medical Sciences, Tehran, Iran
Mohammad Hossein Najmi, Tarbiat Modares University, Tehran, 14117-13116, Tehran, Iran
Nazanin-Zahra Shafiei-Jandaghi, Tehran University of Medical Sciences, Tehran, Iran
Talat Mokhtari-Azad, Tehran University of Medical Sciences, Tehran, Iran
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