Characterization of SARS-CoV-2 omicron variants from Iran and evaluation of the effect of mutations on the spike, nucleocapsid, ORF8, and ORF9b proteins function

References

• Abdullaev, A., Abdurakhimov, A., Mirakbarova, Z., Ibragimova, S., Tsoy, V., Nuriddinov, S., Dalimova, D., Turdikulova, S., & Abdurakhmonov, I. (2022). Genome sequence diversity of SARS-CoV-2 obtained from clinical samples in Uzbekistan. PloS One, 17(6), e0270314. https://doi.org/10.1371/journal.pone.0270314
   PubMed Web of Science ®Google Scholar
• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1, 19–25.
   Google Scholar
• Aksamentov, I., & Roemer, C., et al. (2021). Nextclade: Clade assignment, mutation calling and
   Google Scholar
• Ali, Z., Aman, R., Mahas, A., Rao, G. S., Tehseen, M., Marsic, T., Salunke, R., Subudhi, A. K., Hala, S. M., Hamdan, S. M., Pain, A., Alofi, F. S., Alsomali, A., Hashem, A. M., Khogeer, A., Almontashiri, N. A. M., Abedalthagafi, M., Hassan, N., & Mahfouz, M. M. (2020). iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2. Virus Research, 288, 198129.
   PubMed Web of Science ®Google Scholar
• Ashton, P. M., Nair, S., Dallman, T., Rubino, S., Rabsch, W., Mwaigwisya, S., Wain, J., & O'Grady, J. (2015). MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nature Biotechnology, 33(3), 296–300. https://doi.org/10.1038/nbt.3103
   PubMed Web of Science ®Google Scholar
• Ayinde, K. S., Pinheiro, G. M., & Ramos, C. H. (2022). Binding of SARS-CoV-2 protein ORF9b to mitochondrial translocase TOM70 prevents its interaction with chaperone HSP90. Biochimie, 200, 99–106. https://doi.org/10.1016/j.biochi.2022.05.016
   PubMed Web of Science ®Google Scholar
• Banoun, H. (2021). Evolution of SARS-CoV-2: Review of mutations, role of the host immune system. Nephron, 145(4), 392–403. https://doi.org/10.1159/000515417
   PubMed Web of Science ®Google Scholar
• Chaudhari, A. M., Singh, I., Joshi, M., Patel, A., & Joshi, C. (2022). Defective ORF8 dimerization in SARS-CoV-2 delta variant leads to a better adaptive immune response due to abrogation of ORF8-MHC1 interaction. Molecular Diversity, 3, 1–13. https://doi.org/10.1007/s11030-022-10405-9
   Google Scholar
• Chen, Y., Liu, Q., & Guo, D. (2020). Emerging coronaviruses: Genome structure, replication, and pathogenesis. Journal of Medical Virology, 92(4), 418–423. https://doi.org/10.1002/jmv.25681
   PubMed Web of Science ®Google Scholar
• Cheng, X.-w., J. Li, et al. (2021). Identification of SARS-CoV-2 variants and their clinical significance in Hefei, China. Frontiers in Medicine 8, 2856.
   Web of Science ®Google Scholar
• Dai, L., & Gao, G. F. (2021). Viral targets for vaccines against COVID-19. Nature Reviews. Immunology, 21(2), 73–82. https://doi.org/10.1038/s41577-020-00480-0
   PubMed Web of Science ®Google Scholar
• DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter on Protein Crystallography, 40(1), 82–92.
   Google Scholar
• Dey, T., Chatterjee, S., Manna, S., Nandy, A., & Basak, S. C. (2021). Identification and computational analysis of mutations in SARS-CoV-2. Computers in Biology and Medicine, 129, 104166. https://doi.org/10.1016/j.compbiomed.2020.104166
   PubMed Web of Science ®Google Scholar
• Flower, T. G., Buffalo, C. Z., Hooy, R. M., Allaire, M., Ren, X., & Hurley, J. H. (2021). Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein. Proceedings of the National Academy of Sciences, 118(2), e2021785118. https://doi.org/10.1073/pnas.2021785118
   PubMed Web of Science ®Google Scholar
• Freer, G., & Lai, M., et al. (2021). Evolution of viruses and the emergence of SARS-CoV-2 variants.
   Google Scholar
• Gao, T., Gao, Y., Liu, X., Nie, Z., Sun, H., Lin, K., Peng, H., & Wang, S. (2021). Identification and functional analysis of the SARS-COV-2 nucleocapsid protein. BMC Microbiology, 21(1), 1–10. https://doi.org/10.1186/s12866-021-02107-3
   PubMed Web of Science ®Google Scholar
• Gorkhali, R., Koirala, P., Rijal, S., Mainali, A., Baral, A., & Bhattarai, H. K. (2021). Structure and function of major SARS-CoV-2 and SARS-CoV proteins. Bioinformatics and Biology Insights, 15, 11779322211025876. https://doi.org/10.1177/11779322211025876
   Web of Science ®Google Scholar
• Grossoehme, N. E., Li, L., Keane, S. C., Liu, P., Dann, C. E., Leibowitz, J. L., & Giedroc, D. P. (2009). Coronavirus N protein N-terminal domain (NTD) specifically binds the transcriptional regulatory sequence (TRS) and melts TRS-cTRS RNA duplexes. Journal of Molecular Biology, 394(3), 544–557. https://doi.org/10.1016/j.jmb.2009.09.040
   PubMed Web of Science ®Google Scholar
• Han, L., Zheng, Y., Deng, J., Nan, M.-L., Xiao, Y., Zhuang, M.-W., Zhang, J., Wang, W., Gao, C., & Wang, P.-H. (2022). SARS‐CoV‐2 ORF10 antagonizes STING‐dependent interferon activation and autophagy. Journal of Medical Virology, 94(11), 5174–5188. https://doi.org/10.1002/jmv.27965
   PubMed Web of Science ®Google Scholar
• Han, L., Zhuang, M.-W., Deng, J., Zheng, Y., Zhang, J., Nan, M.-L., Zhang, X.-J., Gao, C., & Wang, P.-H. (2021). SARS‐CoV‐2 ORF9b antagonizes type I and III interferons by targeting multiple components of the RIG‐I/MDA‐5–MAVS, TLR3–TRIF, and cGAS–STING signaling pathways. Journal of Medical Virology, 93(9), 5376–5389. https://doi.org/10.1002/jmv.27050
   PubMed Web of Science ®Google Scholar
• Harvey, W. T., Carabelli, A. M., Jackson, B., Gupta, R. K., Thomson, E. C., Harrison, E. M., Ludden, C., Reeve, R., Rambaut, A., Peacock, S. J., & Robertson, D. L. (2021). SARS-CoV-2 variants, spike mutations and immune escape. Nature Reviews. Microbiology, 19(7), 409–424. https://doi.org/10.1038/s41579-021-00573-0
   PubMed Web of Science ®Google Scholar
• Hu, J., Peng, P., Cao, X., Wu, K., Chen, J., Wang, K., Tang, N., & Huang, A.-L. (2022). Increased immune escape of the new SARS-CoV-2 variant of concern Omicron. Cellular & Molecular Immunology, 19(2), 293–295. https://doi.org/10.1038/s41423-021-00836-z
   PubMed Web of Science ®Google Scholar
• Islam, F., Dhawan, M., Nafady, M. H., Emran, T. B., Mitra, S., Choudhary, O. P., & Akter, A. (2022). Understanding the omicron variant (B. 1.1. 529) of SARS-CoV-2: Mutational impacts, concerns, and the possible solutions. Annals of Medicine and Surgery, 78, 103737. https://doi.org/10.1016/j.amsu.2022.103737
   PubMed Web of Science ®Google Scholar
• Jiang, H.-W., Zhang, H.-N., Meng, Q.-F., Xie, J., Li, Y., Chen, H., Zheng, Y.-X., Wang, X.-N., Qi, H., Zhang, J., Wang, P.-H., Han, Z.-G., & Tao, S.-C. (2020). SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70. Cellular & Molecular Immunology, 17(9), 998–1000. https://doi.org/10.1038/s41423-020-0514-8
   PubMed Web of Science ®Google Scholar
• Korn, S. M., Lambertz, R., Fürtig, B., Hengesbach, M., Löhr, F., Richter, C., Schwalbe, H., Weigand, J. E., Wöhnert, J., & Schlundt, A. (2021). 1H, 13C, and 15N backbone chemical shift assignments of the C-terminal dimerization domain of SARS-CoV-2 nucleocapsid protein. Biomolecular NMR Assignments, 15(1), 129–135. https://doi.org/10.1007/s12104-020-09995-y
   PubMed Web of Science ®Google Scholar
• Kumar, N., Quadri, S., AlAwadhi, A. I., & AlQahtani, M. (2022). COVID-19 recovery patterns across alpha (B. 1.1. 7) and delta (B. 1.617. 2) variants of SARS-CoV-2. Frontiers in Immunology, 13, 379. https://doi.org/10.3389/fimmu.2022.812606
   Web of Science ®Google Scholar
• Kumar, S., Karuppanan, K., & Subramaniam, G. (2022). Omicron (BA. 1) and sub‐variants (BA. 1.1, BA. 2 and BA. 3) of SARS‐CoV‐2 spike infectivity and pathogenicity: A comparative sequence and structural‐based computational assessment. Journal of Medical Virology, 94(10), 4780–4791. https://doi.org/10.1002/jmv.27927
   PubMed Web of Science ®Google Scholar
• Li, J., Lai, S., Gao, G. F., & Shi, W. (2021). The emergence, genomic diversity and global spread of SARS-CoV-2. Nature, 600(7889), 408–418. https://doi.org/10.1038/s41586-021-04188-6
   PubMed Web of Science ®Google Scholar
• Lowery, S. A., Sariol, A., & Perlman, S. (2021). Innate immune and inflammatory responses to SARS-CoV-2: Implications for COVID-19. Cell Host & Microbe, 29(7), 1052–1062. https://doi.org/10.1016/j.chom.2021.05.004
   PubMed Web of Science ®Google Scholar
• Mantlo, E., Bukreyeva, N., Maruyama, J., Paessler, S., & Huang, C. (2020). Antiviral activities of type I interferons to SARS-CoV-2 infection. Antiviral Research, 179, 104811. https://doi.org/10.1016/j.antiviral.2020.104811
   PubMed Web of Science ®Google Scholar
• Musa, S. S., Gyeltshen, D., Manirambona, E., Ayuba, D., & Lucero-Prisno, D. E. (2022). The new COVID-19 omicron variant: Africa must watch its spread!. Clinical Epidemiology and Global Health, 13, 100961. https://doi.org/10.1016/j.cegh.2022.100961
   PubMed Web of Science ®Google Scholar
• Nagy, Á., Pongor, S., & Győrffy, B. (2021). Different mutations in SARS-CoV-2 associate with severe and mild outcome. International Journal of Antimicrobial Agents, 57(2), 106272. https://doi.org/10.1016/j.ijantimicag.2020.106272
   PubMed Web of Science ®Google Scholar
• Oh, S. J., & Shin, O. S. (2021). SARS-CoV-2 nucleocapsid protein targets RIG-I-like receptor pathways to inhibit the induction of interferon response. Cells, 10(3), 530. https://doi.org/10.3390/cells10030530
   PubMed Web of Science ®Google Scholar
• Shapovalov, M. V., & Dunbrack, R. L. Jr(2011). A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Structure (London, England: 1993), 19(6), 844–858. https://doi.org/10.1016/j.str.2011.03.019
   PubMed Web of Science ®Google Scholar
• Shrestha, L. B., Foster, C., Rawlinson, W., Tedla, N., & Bull, R. A. (2022). Evolution of the SARS‐CoV‐2 omicron variants BA. 1 to BA. 5: Implications for immune escape and transmission. Reviews in Medical Virology, 32(5), e2381. https://doi.org/10.1002/rmv.2381
   PubMed Web of Science ®Google Scholar
• Shu, Yuelong; McCauley, John. (2017). GISAID: Global initiative on sharing all influenza data–from vision to reality. Eurosurveillance, 22(13), 30494.
   Google Scholar
• Sun, C., Xie, C., Bu, G.-L., Zhong, L.-Y., & Zeng, M.-S. (2022). Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants. Signal Transduction and Targeted Therapy, 7(1), 202–225. https://doi.org/10.1038/s41392-022-01039-2
   PubMed Web of Science ®Google Scholar
• Takatsuka, H., Fahmi, M., Hamanishi, K., Sakuratani, T., Kubota, Y., & Ito, M. (2022). In silico analysis of SARS-CoV-2 ORF8-binding proteins reveals the involvement of ORF8 in acquired-immune and innate-immune systems. Frontiers in Medicine, 9, 824622. https://doi.org/10.3389/fmed.2022.824622
   Web of Science ®Google Scholar
• Tegally, H., & Moir, M., et al. (2022). Continued emergence and evolution of Omicron in South Africa: New BA. 4 and BA. 5 lineages. medRxiv
   Google Scholar
• Thakur, S., Sasi, S., Pillai, S. G., Nag, A., Shukla, D., Singhal, R., Phalke, S., & Velu, G. S. K. (2022). SARS-CoV-2 mutations and their impact on diagnostics, therapeutics and vaccines. Frontiers in Medicine, 9, 815389. https://doi.org/10.3389/fmed.2022.815389
   PubMed Web of Science ®Google Scholar
• Walker, A. S., Vihta, K.-D., Gethings, O., Pritchard, E., Jones, J., House, T., Bell, I., Bell, J. I., Newton, J. N., Farrar, J., Diamond, I., Studley, R., Rourke, E., Hay, J., Hopkins, S., Crook, D., Peto, T., Matthews, P. C., Eyre, D. W., Stoesser, N., & Pouwels, K. B. (2021). Tracking the emergence of SARS-CoV-2 alpha variant in the United Kingdom. The New England Journal of Medicine, 385(27), 2582–2585. https://doi.org/10.1056/NEJMc2103227
   PubMed Web of Science ®Google Scholar
• Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, 8(2), 127–134. https://doi.org/10.1093/protein/8.2.127
   PubMedGoogle Scholar
• Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C.-L., Abiona, O., Graham, B. S., & McLellan, J. S. (2020). Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science (New York, N.Y.), 367(6483), 1260–1263. https://doi.org/10.1126/science.abb2507
   PubMed Web of Science ®Google Scholar
• Xia, X. (2021). Domains and functions of spike protein in Sars-Cov-2 in the context of vaccine design. Viruses, 13(1), 109. https://doi.org/10.3390/v13010109
   PubMed Web of Science ®Google Scholar
• Xue, L. C., Rodrigues, J. P., Kastritis, P. L., Bonvin, A. M., & Vangone, A. (2016). PRODIGY: A web server for predicting the binding affinity of protein–protein complexes. Bioinformatics (Oxford, England), 32(23), 3676–3678. https://doi.org/10.1093/bioinformatics/btw514
   PubMed Web of Science ®Google Scholar
• Yang, Z., Lasker, K., Schneidman-Duhovny, D., Webb, B., Huang, C. C., Pettersen, E. F., Goddard, T. D., Meng, E. C., Sali, A., & Ferrin, T. E. (2012). UCSF Chimera, MODELLER, and IMP: An integrated modeling system. Journal of Structural Biology, 179(3), 269–278. https://doi.org/10.1016/j.jsb.2011.09.006
   PubMed Web of Science ®Google Scholar
• Yavarian, J., Nejati, A., Salimi, V., Shafiei Jandaghi, N. Z., Sadeghi, K., Abedi, A., Sharifi Zarchi, A., Gouya, M. M., & Mokhtari-Azad, T. (2022). Whole genome sequencing of SARS-CoV2 strains circulating in Iran during five waves of pandemic. PloS One, 17(5), e0267847. https://doi.org/10.1371/journal.pone.0267847
   PubMed Web of Science ®Google Scholar
• Yu, T., Ling, Q., Xu, M., Wang, N., Wang, L., Lin, H., Cao, M., Ma, Y., Wang, Y., Li, K., Du, L., Jin, Y., Li, Y., Guo, D., Peng, X., Chen, Y.-Q., Zhao, B., & Pan, J.-A. (2022). ORF8 protein of SARS‐CoV‐2 reduces male fertility in mice. Journal of Medical Virology, 94(9), 4193–4205. https://doi.org/10.1002/jmv.27855
   PubMed Web of Science ®Google Scholar
• Zandi, M., Shafaati, M., Kalantar-Neyestanaki, D., Pourghadamyari, H., Fani, M., Soltani, S., Kaleji, H., & Abbasi, S. (2022). The role of SARS-CoV-2 accessory proteins in immune evasion. Biomedicine & Pharmacotherapy, 156, 113889. https://doi.org/10.1016/j.biopha.2022.113889
   PubMed Web of Science ®Google Scholar
• Zhang, Q., Chen, Z., Huang, C., Sun, J., Xue, M., Feng, T., Pan, W., Wang, K., & Dai, J. (2021). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Membrane (M) and Spike (S) proteins antagonize host type I Interferon Response. Frontiers in Cellular and Infection Microbiology, 11, 766922. https://doi.org/10.3389/fcimb.2021.766922
   Web of Science ®Google Scholar
• Zhang, Q., Xiang, R., Huo, S., Zhou, Y., Jiang, S., Wang, Q., & Yu, F. (2021). Molecular mechanism of interaction between SARS-CoV-2 and host cells and interventional therapy. Signal Transduction and Targeted Therapy, 6(1), 1–19. https://doi.org/10.1038/s41392-021-00653-w
   PubMed Web of Science ®Google Scholar
• Zhang, Y., Chen, Y., Li, Y., Huang, F., Luo, B., Yuan, Y., Xia, B., Ma, X., Yang, T., Yu, F., Liu, J., Liu, B., Song, Z., Chen, J., Yan, S., Wu, L., Pan, T., Zhang, X., Li, R., … Zhang, H. (2021). The ORF8 protein of SARS-CoV-2 mediates immune evasion through down-regulating MHC-Ι. Proceedings of the National Academy of Sciences, 118(23), e2024202118. https://doi.org/10.1073/pnas.2024202118
   PubMed Web of Science ®Google Scholar
• Zhao, X., Chen, D., Li, X., Griffith, L., Chang, J., An, P., & Guo, J.-T. (2022). Interferon control of human coronavirus infection and viral evasion: Mechanistic insights and implications for antiviral drug and vaccine development. Journal of Molecular Biology, 434(6), 167438. https://doi.org/10.1016/j.jmb.2021.167438
   PubMed Web of Science ®Google Scholar