128
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Identification of conserved immunogenic peptides of SARS-CoV-2 nucleocapsid protein

, , , , , , , , , & show all
Received 21 May 2023, Accepted 13 Sep 2023, Published online: 26 Sep 2023

References

  • Adhikari, U. K., Tayebi, M., & Mizanur Rahman, M. (2018). Immunoinformatics approach for epitope-based peptide vaccine design and active site prediction against polyprotein of emerging oropouche virus. Journal of Immunology Research, 2018, 6718083–6718022. https://doi.org/10.1155/2018/6718083
  • Ayaz Anwar, M., & Choi, S. (2017). Structure-activity relationship in TLR4 mutations: Atomistic molecular dynamics simulations and residue interaction network analysis. OPEN. https://doi.org/10.1038/srep43807
  • Bai, Z., Cao, Y., Liu, W., Li, J., Lundstrom, K., & Davidson, A. (2021). The SARS-CoV-2 nucleocapsid protein and its role in viral structure, biological functions, and a potential target for drug or vaccine mitigation. Viruses, 13(6), 1115. https://doi.org/10.3390/v13061115
  • Bui, H. H., Sidney, J., Dinh, K., Southwood, S., Newman, M. J., & Sette, A. (2006). Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinformatics, 7(1), 153. https://doi.org/10.1186/1471-2105-7-153
  • Bui, H. H., Sidney, J., Li, W., Fusseder, N., & Sette, A. (2007). Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics, 8(1), 361. https://doi.org/10.1186/1471-2105-8-361
  • Chavda, V. P., Balar, P., Vaghela, D., Solanki, H. K., Vaishnav, A., Hala, V., & Vora, L. (2023). Omicron variant of SARS-CoV-2: An Indian perspective of vaccination and management. Vaccines, 11(1), 160. https://doi.org/10.3390/vaccines11010160
  • Crooke, S. N., Ovsyannikova, I. G., Kennedy, R. B., & Poland, G. A. (2020). Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome. Scientific Reports, 10(1), 14179. https://doi.org/10.1038/s41598-020-70864-8
  • Dimitrov, I., Bangov, I., Flower, D. R., & Doytchinova, I. (2014). AllerTOP v.2 – A server for in silico prediction of allergens. Journal of Molecular Modeling, 20(6), 1-6. https://doi.org/10.1007/s00894-014-2278-5
  • Do, M. D., Le, L. G. H., Nguyen, V. T., Dang, T. N., Nguyen, N. H., Vu, H. A., & Mai, T. P. (2020). High-resolution HLA typing of HLA-A, -B, -C, -DRB1, and -DQB1 in Kinh Vietnamese by using next-generation sequencing. Frontiers in Genetics, 11, 383. https://doi.org/10.3389/FGENE.2020.00383/BIBTEX
  • Doytchinova, I. A., & Flower, D. R. (2007). VaxiJen: A server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics, 8(1), 1–7. https://doi.org/10.1186/1471-2105-8-4
  • EMBL-EBI. (2022). IPD-IMGT/HLA database. https://www.ebi.ac.uk/ipd/imgt/hla/about/statistics/
  • Feng, W., Xiang, Y., Wu, L., Chen, Z., Li, Q., Chen, J., Guo, Y., Xia, D., Chen, N., Zhang, L., Zhu, S., & Zhao, K. N. (2022). Nucleocapsid protein of SARS-CoV-2 is a potential target for developing new generation of vaccine. Journal of Clinical Laboratory Analysis, 36(6), e24479. https://doi.org/10.1002/jcla.24479
  • Fenoglio, D., Traverso, P., Parodi, A., Tomasello, L., Negrini, S., Kalli, F., Battaglia, F., Ferrera, F., Sciallero, S., Murdaca, G., Setti, M., Sobrero, A., Boccardo, F., Cittadini, G., Puppo, F., Criscuolo, D., Carmignani, G., Indiveri, F., & Filaci, G. (2013). A multi-peptide, dual-adjuvant telomerase vaccine (GX301) is highly immunogenic in patients with prostate and renal cancer. Cancer Immunology, Immunotherapy: CII, 62(6), 1041–1052. https://doi.org/10.1007/s00262-013-1415-9
  • Filaci, G., Fenoglio, D., Nolè, F., Zanardi, E., Tomasello, L., Aglietta, M. I. M., Del Conte, G., Carles, J., Morales-Barrera, R., Guglielmini, P., Scagliotti, G., Signori, A., Parodi, A., Kalli, F., Astone, G., Ferrera, F., Altosole, T., Lamperti, G., Criscuolo, D., Gianese, F., & Boccardo, F. (2021). Telomerase-based GX301 cancer vaccine in patients with metastatic castration-resistant prostate cancer: A randomized phase II trial. Cancer Immunology, Immunotherapy, 70(12), 3679–3692. https://doi.org/10.1007/s00262-021-03024-0
  • Forni, G., Mantovani, A., Forni, G., Mantovani, A., Moretta, L., Rappuoli, R., Rezza, G., Bagnasco, A., Barsacchi, G., Bussolati, G., Cacciari, M., Cappuccinelli, P., Cheli, E., Guarini, R., Bacci, M. L., Mancini, M., Marcuzzo, C., Morrone, M. C., Parisi, G., … Vineis, P. (2021). COVID-19 vaccines: Where we stand and challenges ahead. Cell Death and Differentiation, 28(2), 626–639. https://doi.org/10.1038/s41418-020-00720-9
  • Fourrier, A., Bégaud, B., Alpérovitch, A., Verdier-Taillefer, M. H., Touze, E., Decker, N., & Imbs, J. L. (2001). Hepatitis B vaccine and first episodes of central nervous system demyelinating disorders: A comparison between reported and expected number of cases. British Journal of Clinical Pharmacology, 51(5), 489–490. https://doi.org/10.1046/j.1365-2125.2001.01364.x
  • Freeman, B., Lester, S., Mills, L., Rasheed, M. A. U., Moye, S., Abiona, O., Hutchinson, G. B., Morales-Betoulle, M., Krapinunaya, I., Gibbons, A., Chiang, C. F., Cannon, D., Klena, J., Johnson, J. A., Owen, S. M., Graham, B. S., Corbett, K. S., & Thornburg, N. J. (2020). Validation of a SARS-CoV-2 spike protein ELISA for use in contact investigations and serosurveillance. bioRxiv : The Preprint Server for Biology, 1–12. https://doi.org/10.1101/2020.04.24.057323
  • Gupta, S., Kapoor, P., Chaudhary, K., Gautam, A., Kumar, R., & Raghava, G. P. S. (2013). In silico approach for predicting toxicity of peptides and proteins. PLoS One. 8(9), e73957. https://doi.org/10.1371/journal.pone.0073957
  • Heide, J., Schulte, S., Kohsar, M., Brehm, T. T., Herrmann, M., Karsten, H., Marget, M., Peine, S., Johansson, A. M., Sette, A., Lütgehetmann, M., Kwok, W. W., Sidney, J., & Zur Wiesch, J. S. (2021). Broadly directed SARS-CoV-2-specific CD4+ T cell response includes frequently detected peptide specificities within the membrane and nucleoprotein in patients with acute and resolved COVID-19. PLoS Pathogens, 17(9), e1009842. https://doi.org/10.1371/JOURNAL.PPAT.1009842
  • Heitmann, J. S., Bilich, T., Tandler, C., Nelde, A., Maringer, Y., Marconato, M., Reusch, J., Jäger, S., Denk, M., Richter, M., Anton, L., Weber, L. M., Roerden, M., Bauer, J., Rieth, J., Wacker, M., Hörber, S., Peter, A., Meisner, C., … Walz, J. S. (2022). A COVID-19 peptide vaccine for the induction of SARS-CoV-2 T cell immunity. Nature, 601(7894), 617–622. https://doi.org/10.1038/s41586-021-04232-5
  • Jain, S., & Baranwal, M. (2019). Computational analysis in designing T cell epitopes enriched peptides of Ebola glycoprotein exhibiting strong binding interaction with HLA molecules. Journal of Theoretical Biology, 465, 34–44. https://doi.org/10.1016/j.jtbi.2019.01.016
  • Jin, X., Ding, Y., Sun, S., Wang, X., Zhou, Z., Liu, X., Li, M., Chen, X., Shen, A., Wu, Y., Liu, B., Zhang, J., Li, J., Yang, Y., Qiu, H., Shen, C., He, Y., & Zhao, G. (2021). Screening HLA-A-restricted T cell epitopes of SARS-CoV-2 and the induction of CD8+ T cell responses in HLA-A transgenic mice. Cellular & Molecular Immunology, 18(12), 2588–2608. https://doi.org/10.1038/s41423-021-00784-8
  • Jung, H. E., & Lee, H. K. (2021). Current understanding of the innate control of toll-like receptors in response to SARS-CoV-2 infection. Viruses, 13(11), 2132. https://doi.org/10.3390/v13112132
  • Jurtz, V., Paul, S., Andreatta, M., Marcatili, P., Peters, B., & Nielsen, M. (2017). NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data. Journal of Immunology (Baltimore, Md.: 1950), 199(9), 3360–3368. https://doi.org/10.4049/jimmunol.1700893
  • Källberg, M., Margaryan, G., Wang, S., Ma, J., & Xu, J. (2014). Raptorx server: A resource for template-based protein structure modeling. Methods in Molecular Biology, 1137, 17–27. https://doi.org/10.1007/978-1-4939-0366-5_2
  • Kang, S., Yang, M., He, S., Wang, Y., Chen, X., Chen, Y. Q., Hong, Z., Liu, J., Jiang, G., Chen, Q., Zhou, Z., Zhou, Z., Huang, Z., Huang, X., He, H., Zheng, W., Liao, H. X., Xiao, F., Shan, H., & Chen, S. (2021). A SARS-CoV-2 antibody curbs viral nucleocapsid protein-induced complement hyperactivation. Nature Communications, 12(1), 2697. https://doi.org/10.1038/s41467-021-23036-9
  • Kaushal, N., Jain, S., & Baranwal, M. (2022). Computational design of immunogenic peptide constructs comprising multiple human leukocyte antigen restricted dengue virus envelope epitopes. Journal of Molecular Recognitio : JMR, 35(9), e2961. https://doi.org/10.1002/jmr.2961
  • Kayesh, M. E. H., Kohara, M., & Tsukiyama‐kohara, K. (2021). An overview of recent insights into the response of tlr to sars‐cov‐2 infection and the potential of tlr agonists as sars‐cov‐2 vaccine adjuvants. Viruses, 13(11), 2302. https://doi.org/10.3390/v13112302
  • KEGG. (2022). Nucleotide Codes, Amino Acid Codes, and Genetic Codes. https://www.genome.jp/kegg/catalog/codes1.html
  • Khan, M. T., Islam, M. J., Parihar, A., Islam, R., Jerin, T. J., Dhote, R., Ali, M. A., Laura, F. K., & Halim, M. A. (2021). Immunoinformatics and molecular modeling approach to design universal multi-epitope vaccine for SARS-CoV-2. Informatics in Medicine Unlocked, 24(April), 100578. https://doi.org/10.1016/j.imu.2021.100578
  • Ko, J., Park, H., Heo, L., & Seok, C. (2012). GalaxyWEB server for protein structure prediction and refinement. Nucleic Acids Research, 40(Web Server issue), W294–297. https://doi.org/10.1093/nar/gks493
  • Kozakov, D., Hall, D. R., Xia, B., Porter, K. A., Padhorny, D., Yueh, C., Beglov, D., & Vajda, S. (2017). The ClusPro web server for protein-protein docking. Nature Protocols, 12(2), 255–278. https://doi.org/10.1038/nprot.2016.169
  • Kumar, R., Christensen, N. D., Kaddis Maldonado, R. J., Bewley, M. C., Ostman, A., Sudol, M., Chen, E. C., Buchkovich, N. W., Gontu, A., Surendran Nair, M., Nissly, R. H., Minns, A. M., Kapur, V., Rossi, R., Kuchipudi, S. V., Lindner, S. E., Parent, L. J., Flanagan, J. M., & Buchkovich, N. J. (2021). Monoclonal antibodies to s and n sars-cov-2 proteins as probes to assess structural and antigenic properties of coronaviruses. Viruses, 13(10), 1899. https://doi.org/10.3390/V13101899/S1
  • Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/10.1107/S0021889892009944
  • Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery. Journal of Chemical Information and Modeling, 51(10), 2778–2786. https://doi.org/10.1021/ci200227u
  • Le Bert, N., Tan, A. T., Kunasegaran, K., Tham, C. Y. L., Hafezi, M., Chia, A., Chng, M. H. Y., Lin, M., Tan, N., Linster, M., Chia, W. N., Chen, M. I. C., Wang, L. F., Ooi, E. E., Kalimuddin, S., Tambyah, P. A., Low, J. G. H., Tan, Y. J., & Bertoletti, A. (2020). SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature, 584(7821), 457–462. https://doi.org/10.1038/s41586-020-2550-z
  • Liu, Y., Liang, Q. Z., Lu, W., Yang, Y.-L., Chen, R., Huang, Y. W., & Wang, B. (2021). A comparative analysis of coronavirus nucleocapsid (N) proteins reveals the SADS-CoV N protein antagonizes IFN-β production by inducing ubiquitination of RIG-I. Frontiers in Immunology, 12, 2269. https://doi.org/10.3389/FIMMU.2021.688758/BIBTEX
  • Lu, S., Ye, Q., Singh, D., Cao, Y., Diedrich, J. K., Yates, J. R., Villa, E., Cleveland, D. W., & CoRBett, K. D. (2021). The SARS-CoV-2 nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein. Nature Communications, 12(1), 502. https://doi.org/10.1038/s41467-020-20768-y
  • Marshall, E. (1998). A shadow falls on hepatitis B vaccination effort. Science (New York, N.Y.), 281(5377), 630–631. https://doi.org/10.1126/SCIENCE.281.5377.630
  • Martynova, E., Hamza, S., Markelova, M., Garanina, E., Davidyuk, Y., Shakirova, V., Kaushal, N., Baranwal, M., Stott-Marshall, R. J., Foster, T. L., Rizvanov, A., & Khaiboullina, S. (2022). Immunogenic SARS-CoV-2 S and N protein peptide and cytokine combinations as biomarkers for early prediction of fatal COVID-19. Frontiers in Immunology, 13(March), 830715. https://doi.org/10.3389/fimmu.2022.830715
  • Matsuo, T. (2021). Viewing SARS-CoV-2 nucleocapsid protein in terms of molecular flexibility. Biology, 10(6), 454. https://doi.org/10.3390/BIOLOGY10060454
  • McBride, R., van Zyl, M., & Fielding, B. C. (2014). The coronavirus nucleocapsid is a multifunctional protein. Viruses, 6(8), 2991–3018. https://doi.org/10.3390/V6082991
  • Miotto, O., Heiny, A. T., Tan, T. W., Thomas, J. T., & Brusic, V. (2008). Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis. BMC Bioinformatics, 9 (Suppl 1), S18. https://doi.org/10.1186/1471-2105-9-S1-S18
  • NIH. (2020). Evaluate the safety, tolerability, immunogenicity and efficacy of UB-311 in mild Alzheimer’s disease (AD) patients. https://clinicaltrials.gov/ct2/show/NCT02551809
  • Noorimotlagh, Z., Karami, C., Mirzaee, S. A., Kaffashian, M., Mami, S., & Azizi, M. (2020). Immune and bioinformatics identification of T cell and B cell epitopes in the protein structure of SARS-CoV-2: A systematic review. International Immunopharmacology, 86, 106738. https://doi.org/10.1016/J.INTIMP.2020.106738
  • Park, B. S., Song, D. H., Kim, H. M., Choi, B. S., Lee, H., & Lee, J. O. (2009). The structural basis of lipopolysaccharide recognition by the TLR4-MD-2 complex. Nature, 458(7242), 1191–1195. https://doi.org/10.1038/nature07830
  • Peng, Q., Peng, R., Yuan, B., Zhao, J., Wang, M., Wang, X., Wang, Q., Sun, Y., Fan, Z., Qi, J., Gao, G. F., & Shi, Y. (2020). Structural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2. Cell Reports, 31(11), 107774. https://doi.org/10.1016/j.celrep.2020.107774
  • Pitaloka, D. A. E., Izzati, A., Amirah, S. R., & Syakuran, L. A. (2022). Multi epitope-based vaccine design for protection against Mycobacterium tuberculosis and SARS-CoV-2 coinfection. Advances and Applications in Bioinformatics and Chemistry: AABC, 15(July), 43–57. https://doi.org/10.2147/AABC.S366431
  • Planas, D., Veyer, D., Baidaliuk, A., Staropoli, I., Guivel-Benhassine, F., Rajah, M. M., Planchais, C., Porrot, F., Robillard, N., Puech, J., Prot, M., Gallais, F., Gantner, P., Velay, A., Le Guen, J., Kassis-Chikhani, N., Edriss, D., Belec, L., Seve, A., … Schwartz, O. (2021). Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature, 596(7871), 276–280. https://doi.org/10.1038/s41586-021-03777-9
  • Popi, A. F., Longo-Maugéri, I. M., & Mariano, M. (2016). An overview of B-1 cells as antigen-presenting cells. Frontiers in Immunology, 7(APR), 138. https://doi.org/10.3389/FIMMU.2016.00138/BIBTEX
  • Prawiningrum, A. F., Paramita, R. I., & Panigoro, S. S. (2022). Immunoinformatics approach for epitope-based vaccine design: Key steps for breast cancer vaccine. Diagnostics (Basel, Switzerland), 12(12), 2981. https://doi.org/10.3390/diagnostics12122981
  • Ram Benny Dessau, C. B. P. (2008). R"–project for statistical computing. Ugeskrift for Laeger, 170(5), 328–330.
  • Rehman, Z., Fahim, A., & Bhatti, M. F. (2021). Scouting the receptor-binding domain of SARS coronavirus 2: A comprehensive immunoinformatics inquisition. Future Virology, 16(2), 117–132. https://doi.org/10.2217/fvl-2020-0269
  • Reynisson, B., Barra, C., Kaabinejadian, S., Hildebrand, W. H., Peters, B., Peters, B., Nielsen, M., & Nielsen, M. (2020). Improved prediction of MHC II antigen presentation through integration and motif deconvolution of mass spectrometry MHC eluted ligand data. Journal of Proteome Research, 19(6), 2304–2315. https://doi.org/10.1021/acs.jproteome.9b00874
  • Rodríguez, Y., M., Rojas, S., Beltran, F., Polo, L., Camacho-Domínguez, S. D., Morales, M., Eric, Gershwin., & J.-M., Anaya. (2022). Autoimmune and autoinflammatory conditions after COVID-19 vaccination. New case reports and updated literature review. Journal of Autoimmunity, 132, 102898. https://doi.org/10.1016/j.jaut.2022.102898
  • Snyder, T. M., Gittelman, R. M., Klinger, M., May, D. H., Osborne, E. J., Taniguchi, R., Zahid, H. J., Kaplan, I. M., Dines, J. N., Noakes, M. T., Pandya, R., Chen, X., Elasady, S., Svejnoha, E., Ebert, P., Pesesky, M. W., De ALMeida, P., O’Donnell, H., DeGottardi, Q., … Field, R. H. (2020). Magnitude and dynamics of the T-Cell response to SARS-CoV-2 infection at both individual and population levels.  The Preprint Server for Health Sciences.
  • Srinivasan, S., Selvaraj, G., Gopalan, V., Padmanabhan, P., Ramesh, K., Govindan, K., Chandran, A., Dhandapani, P., Krishnasamy, K., & Kitambi, S. (2022). Epitope identification and designing a potent multi-epitope vaccine construct against SARS-CoV-2 including the emerging variants. Journal of Global Infectious Diseases, 14(1), 24–30. https://doi.org/10.4103/jgid.jgid_96_21
  • Tao, K., Tzou, P. L., Nouhin, J., Gupta, R. K., de Oliveira, T., Kosakovsky Pond, S. L., Fera, D., & Shafer, R. W. (2021). The biological and clinical significance of emerging SARS-CoV-2 variants. Nature Reviews. Genetics, 22(12), 757–773. https://doi.org/10.1038/s41576-021-00408-x
  • Tarke, A., Sidney, J., Kidd, C. K., Dan, J. M., Ramirez, S. I., Yu, E. D., Mateus, J., da Silva Antunes, R., Moore, E., Rubiro, P., Methot, N., Phillips, E., Mallal, S., Frazier, A., Rawlings, S. A., Greenbaum, J. A., Peters, B., Smith, D. M., Crotty, S., … Sette, A. (2021). Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases. Cell Reports. Medicine, 2(2), 100204. https://doi.org/10.1016/j.xcrm.2021.100204
  • Team, V. G. C. V. T. (2023). Vaccines candidates in clinical trials. https://covid19.trackvaccines.org/vaccines/#approved
  • 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(February), 815389. https://doi.org/10.3389/fmed.2022.815389
  • Tilocca, B., Soggiu, A., Sanguinetti, M., Musella, V., Britti, D., Bonizzi, L., Urbani, A., & Roncada, P. (2020). Comparative computational analysis of SARS-CoV-2 nucleocapsid protein epitopes in taxonomically related coronaviruses. Microbes and Infection, 22(4-5), 188–194. https://doi.org/10.1016/j.micinf.2020.04.002
  • Trollfors, B. (2020). Itching nodules and aluminium allergy following vaccination with aluminium-adsorbed vaccines—Not a negligible problem. Acta Paediatrica (Oslo, Norway: 1992), 109(12), 2444–2445. https://doi.org/10.1111/apa.15487
  • Vadalà, M., Poddighe, D., Laurino, C., & Palmieri, B. (2017). Vaccination and autoimmune diseases: Is prevention of adverse health effects on the horizon? The EPMA Journal, 8(3), 295–311. https://doi.org/10.1007/s13167-017-0101-y
  • Verhagen, J., van der Meijden, E. D., Lang, V., Kremer, A. E., Völkl, S., Mackensen, A., Aigner, M., & Kremer, A. N. (2021). Human CD4+ T cells specific for dominant epitopes of SARS-CoV-2 Spike and Nucleocapsid proteins with therapeutic potential. Clinical and Experimental Immunology, 205(3), 363–378. https://doi.org/10.1111/cei.13627
  • Wang, Q., McLoughlin, R. M., Cobb, B. A., Charrel-Dennis, M., Zaleski, K. J., Golenbock, D., TzIAnabos, A. O., & Kasper, D. L. (2006). A bacterial carbohydrate links innate and adaptive responses through Toll-like receptor 2. The Journal of Experimental Medicine, 203(13), 2853–2863. https://doi.org/10.1084/JEM.20062008
  • Waqas, M., Haider, A., Rehman, A., Qasim, M., Umar, A., Sufyan, M., Akram, H. N., Mir, A., RaZZaq, R., Rasool, D., Tahir, R. A., & Sehgal, S. A. (2021). Immunoinformatics and molecular docking studies predicted potential multiepitope-based peptide vaccine and novel compounds against novel SARS-CoV-2 through virtual screening. BioMed Research International, 2021, 1596834–1596820. https://doi.org/10.1155/2021/1596834
  • Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M., & Barton, G. J. (2009). Jalview Version 2-A multiple sequence alignment editor and analysis workbench. Bioinformatics (Oxford, England), 25(9), 1189–1191. https://doi.org/10.1093/bioinformatics/btp033
  • WHO. (2023). WHO Coronavirus (COVID-19) Dashboard. World Health Organization. https://covid19.who.int/
  • Wieczorek, M., Abualrous, E. T., Sticht, J., Álvaro-Benito, M., Stolzenberg, S., Noé, F., & Freund, C. (2017). Major histocompatibility complex (MHC) class I and MHC class II proteins: Conformational plasticity in antigen presentation. Frontiers in Immunology, 8(MAR), 292. https://doi.org/10.3389/fimmu.2017.00292
  • World health organization (WHO). (2022a). COVID-19 advice for the public: Getting vaccinated. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/covid-19-vaccines/advice
  • World health organization (WHO). (2022b). Statement on Omicron sublineage BA.2. WHO. https://www.who.int/news/item/22-02-2022-statement-on-omicron-sublineage-ba.2
  • Yadav, P. D., Sahay, R. R., Sapkal, G., Nyayanit, D., Shete, A. M., Deshpande, G., Patil, D. Y., Gupta, N., Kumar, S., Abraham, P., Panda, S., & Bhargava, B. (2021). Comparable neutralization of SARS-CoV-2 Delta AY.1 AND Delta with individuals sera vaccinated with BBV152. Journal of Travel Medicine, 28(8), 1–4. https://doi.org/10.1093/jtm/taab154
  • Ye, Q., Lu, S., & Corbett, K. D. (2021). Structural basis for SARS-CoV-2 nucleocapsid protein recognition by single-domain antibodies. Frontiers in Immunology, 12(858), 719037. https://doi.org/10.3389/fimmu.2021.719037
  • Zaheer, T., Waseem, M., Waqar, W., Dar, H. A., Shehroz, M., Naz, K., Ishaq, Z., Ahmad, T., Ullah, N., Bakhtiar, S. M., Muhammad, S. A., & Ali, A. (2020). Anti-COVID-19 multi-epitope vaccine designs employing global viral genome sequences. PeerJ. 8, e9541. https://doi.org/10.7717/peerj.9541
  • Zhao, J., Wang, L., Schank, M., Dang, X., Lu, Z., Cao, D., Khanal, S. u. shant., Nguyen, L. N., Nguyen, L. N. T., Zhang, J., Zhang, Y., Adkins, J. L., Baird, E. M., Wu, X. Y., Ning, S., Gazzar, M. E., Moorman, J. P., & Yao, Z. Q. (2021). Z. Q. (2021). SARS-CoV-2 specific memory T cell epitopes identified in COVID-19-recovered subjects. Virus Research, 304, 198508. https://doi.org/10.1016/J.VIRUSRES.2021.198508
  • Zhou, P., Jin, B., Li, H., & Huang, S. Y. (2018). HPEPDOCK: A web server for blind peptide-protein docking based on a hierarchical algorithm. Nucleic Acids Research, 46(W1), W443–W450. https://doi.org/10.1093/nar/gky357

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.