Development of synthetic antigen vaccines for COVID-19

References

• World Health Organization (WHO). Coronavirus disease (COVID-19) dashboard. Geneva, Switzerland: World Health Organization; acessed 2021 Jul 31. https://covid19.who.int/.
   Google Scholar
• DeFrancesco L. Whither COVID-19 vaccines? Nat Biotechnol. 2020. [acessed 2021 Mar 2]. https://www.nature.com/articles/s41587-020-0697-7#citeas.
   Web of Science ®Google Scholar
• World Health Organization (WHO). Global research on coronavírus disease (COVID-19). Geneva, Switzerland: World Health Organization [acessed 2021 Feb 3]. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/global-research-on-novel-coronavirus-2019-ncov.
   Google Scholar
• Florindo HF, Kleiner R, Vaskovich-Koubi D, Acúrcio RC, Carreira B, Yeini E, Tiram G, Liubomirski Y, Satchi-Fainaro R. Immune-mediated approaches against COVID-19. Nat Nanotechnol. 2020;15(8):630–45. doi:10.1038/s41565-020-0732-3.
   PubMed Web of Science ®Google Scholar
• Bernasconi V, Kristiansen PA, Whelan M, Román RG, Bettis A, Yimer SA, Gurry C, Andersen SR, Yeskey D, Mandi H, et al. Entwicklung von Impfstoffen gegen neu auftretende Infektionskrankheiten mit epidemischem Potenzial. Bundesgesundheitsblatt - Gesundheitsforschung - Gesundheitsschutz. 2020;63(1):65–73. doi:10.1002/prot.21078.
   PubMedGoogle Scholar
• Chen W-H, Strych U, Hotez PJ, Bottazzi ME. The SARS-CoV-2 vaccine pipeline: an overview. Current Tropical Medicine Reports. 2020;7(2):61–64. doi:10.1007/s40475-020-00201-6.
   PubMedGoogle Scholar
• World Health Organization (WHO). Draft landscape and tracker of COVID-19 candidate vaccines. Geneva, Switzerland: World Health Organization [acessed 2021 Mar 21]. https://www.who.int/publications/m/item/draft-landscape-of-covid-19-candidate-vaccines.
   Google Scholar
• Palacios R, Patiño EG, de Oliveira Piorelli R, Conde MTRP, Batista AP, Zeng G, Xin Q, Kallas EG, Flores J, Ockenhouse CF, et al. Double-blind, randomized, placebo-controlled Phase III clinical trial to evaluate the efficacy and safety of treating healthcare professionals with the adsorbed COVID-19 (Inactivated) vaccine manufactured by Sinovac – PROFISCOV: a structured summary of a. Trials. 2020;21:1–3. doi:10.1186/s13063-020-04775-4.
   PubMed Web of Science ®Google Scholar
• Xia S, Duan K, Zhang Y, Zhao D, Zhang H, Xie Z, Li X, Peng C, Zhang Y, Zhang W, et al. Effect of an inactivated vaccine against SARS-CoV-2 on safety and immunogenicity outcomes. JAMA. 2020;324:951–60. doi:10.1001/jama.2020.15543.
   PubMed Web of Science ®Google Scholar
• Wang H, Zhang Y, Huang B, Deng W, Quan Y, Wang W, Xu W, Zhao Y, Li N, Zhang J, et al. Development of an inactivated vaccine candidate, BBIBP-CorV, with potent protection against SARS-CoV-2. Cell. 2020;182:713–21. doi:10.1016/j.cell.2020.06.008.
   PubMed Web of Science ®Google Scholar
• Folegatti PM, Ewer KJ, Aley PK, Angus B, Becker S, Belij-Rammerstorfer S, Bellamy D, Bibi S, Bittaye M, Clutterbuck EA, et al. Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial. Lancet. 2020;396:467–78. doi:10.1016/S0140-6736(20)31604-4.
   PubMed Web of Science ®Google Scholar
• Barrett JR, Belij-Rammerstorfer S, Dold C, Ewer KJ, Folegatti PM, Gilbride C, Halkerston R, Hill J, Jenkin D, Stockdale L, et al. Phase 1/2 trial of SARS-CoV-2 vaccine ChAdOx1 nCoV-19 with a booster dose induces multifunctional antibody responses. Nat Med. 2021;27:279–88. doi:10.1038/s41591-020-01179-4.
   PubMed Web of Science ®Google Scholar
• Voysey M, Clemens SAC, Madhi SA, Weckx LY, Folegatti PM, Aley PK, Angus B, Baillie VL, Barnabas SL, Bhorat QE, et al. Safety and efficacy of the ChAdOx1 nCoV-19 vaccine (AZD1222) against SARS-CoV-2: an interim analysis of four randomised controlled trials in Brazil, South Africa, and the UK. The Lancet. 2021;397:99–111. doi:10.1016/S0140-6736(20)32661-1.
   PubMed Web of Science ®Google Scholar
• Zhu F-C, Li Y-H, Guan X-H, Hou L-H, Wang W-J, Li J-X, Wu S-P, Wang B-S, Wang Z, Wang L, et al. Safety, tolerability, and immunogenicity of a recombinant adenovirus type-5 vectored COVID-19 vaccine: a dose-escalation, open-label, non-randomised, first-in-human trial. Lancet. 2020;395:1845–54. doi:10.1016/S0140-6736(20)31208-3.
   PubMed Web of Science ®Google Scholar
• Zhu F-C, Guan X-H, Li Y-H, Huang J-Y, Jiang T, Hou L-H, Li J-X, Yang B-F, Wang L, Wang W-J, et al. Immunogenicity and safety of a recombinant adenovirus type-5-vectored COVID-19 vaccine in healthy adults aged 18 years or older: a randomised, double-blind, placebo-controlled, phase 2 trial. Lancet. 2020;396:479–88. doi:10.1016/S0140-6736(20)31605-6.
   PubMed Web of Science ®Google Scholar
• Logunov DY, Dolzhikova IV, Zubkova OV, Tukhvatulin AI, Shcheblyakov DV, Dzharullaeva AS, Grousova DM, Erokhova AS, Kovyrshina AV, Botikov AG, et al. Safety and immunogenicity of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine in two formulations: two open, non-randomised phase 1/2 studies from Russia. Lancet. 2020;396:887–97. doi:10.1016/S0140-6736(20)31866-3.
   PubMed Web of Science ®Google Scholar
• Logunov DY, Dolzhikova IV, Shcheblyakov DV, Tukhvatulin AI, Zubkova OV, Dzharullaeva AS, Kovyrshina AV, Lubenets NL, Grousova DM, Erokhova AS, et al. Safety and efficacy of an rAd26 and rAd5 vector-based heterologous prime-boost COVID-19 vaccine: an interim analysis of a randomised controlled phase 3 trial in Russia. Lancet. 2021;397:671–81. doi:10.1016/S0140-6736(21)00234-8.
   PubMed Web of Science ®Google Scholar
• Sadoff J, Le Gars M, Shukarev G, Heerwegh D, Truyers C, Groot AM, Stoop J, Tete S, Damme WV, Leroux-Roels I, et al. Safety and immunogenicity of the Ad26.COV2.S COVID-19 vaccine candidate: interim results of a phase 1/2a, double-blind, randomized, placebo-controlled trial. MedRxiv. 2020;1–28. doi:10.1101/2020.09.23.20199604.
   Google Scholar
• Keech C, Albert G, Cho I, Robertson A, Reed P, Neal S, Plested JS, Zhu M, Cloney-Clarck S, Zhou H, et al. Phase 1–2 Trial of a SARS-CoV-2 recombinant spike protein nanoparticle vaccine. N Engl J Med. 2020;383:2320–32. doi:10.1056/NEJMoa2026920.
   PubMed Web of Science ®Google Scholar
• Tebas P, Yang S, Boyer JD, Reuschel EL, Patel A, Christensen-Quick A, Andrade VM, Morrow MP, Kraynyak K, Agnes J, et al. Safety and immunogenicity of INO-4800 DNA vaccine against SARS-CoV-2: a preliminary report of an open-label, Phase 1 clinical trial. EClinicalMedicine. 2021;31:1–9. doi:10.1016/j.eclinm.2020.100689.
   Google Scholar
• Jackson LA, Anderson EJ, Rouphael NG, Roberts PC, Makhene M, Coler RN, McCullough MP, Chapell JD, Denison MR, Stevens LJ, et al. An mRNA vaccine against SARS-CoV-2 — preliminary report. N Engl J Med. 2020;383:1920–31. doi:10.1056/NEJMoa2022483.
   PubMed Web of Science ®Google Scholar
• Baden LR, El Sahly HM, Essink B, Kotloff K, Frey S, Novak R, Diemert D, Spector SA, Rouphael N, Creech CB, et al. Efficacy and safety of the mRNA-1273 SARS-CoV-2 vaccine. N Engl J Med. 2021;384:403–16. doi:10.1056/NEJMoa2035389.
   PubMed Web of Science ®Google Scholar
• Mulligan MJ, Lyke KE, Kitchin N, Absalon J, Gurtman A, Lockhart S, Neuzil K, Raabe V, Bailey R, Swanson KA, et al. Phase I/II study of COVID-19 RNA vaccine BNT162b1 in adults. Nature. 2020;586:589–93. doi:10.1038/s41586-020-2639-4.
   PubMed Web of Science ®Google Scholar
• Sahin U, Muik A, Derhovanessian E, Vogler I, Kranz LM, Vormehr M, Baum A, Pascal K, Quandt J, Maurus D. COVID-19 vaccine BNT162b1 elicits human antibody and TH1 T cell responses. Nature. 2020;586(7830):594–99. doi:10.1038/s41586-020-2814-7.
   PubMed Web of Science ®Google Scholar
• Walsh EE, Frenck RW, Falsey AR, Kitchin N, Absalon J, Gurtman A, Lockhart S, Neuzil K, Mulligan MJ, Bailey R, et al. Safety and Immunogenicity of Two RNA-based COVID-19 vaccine candidates. N Engl J Med. 2020;383(25):2439–50. doi:10.1056/NEJMoa2027906.
   PubMed Web of Science ®Google Scholar
• Polack FP, Thomas SJ, Kitchin N, Absalon J, Gurtman A, Lockhart S, Perez JL, Marc GP, Moreira ED, Zerbini C, et al. Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine. N Engl J Med. 2020;383(27):2603–15. doi:10.1056/NEJMoa2034577.
   PubMed Web of Science ®Google Scholar
• Maruggi G, Zhang C, Li J, Ulmer JB, Yu D. mRNA as a transformative technology for vaccine development to control infectious diseases. Mol Ther. 2019;27(4):757–72. doi:10.1016/j.ymthe.2019.01.020.
   PubMed Web of Science ®Google Scholar
• Chahal JS, Khan OF, Cooper CL, McPartlan JS, Tsosie JK, Tilley LD, Sidik SM, Lourido S, Langer R, Bavari S, et al. Dendrimer-RNA nanoparticles generate protective immunity against lethal Ebola, H1N1 influenza, and toxoplasma gondii challenges with a single dose. Proc Natl Acad Sci USA. 2016;113(29):E4133–4142. doi:10.1073/pnas.1600299113.
   PubMed Web of Science ®Google Scholar
• Carter C, Houser KV, Yamshchikov GV, Bellamy AR, May J, Enama ME, Sarwar U, Larkin B, Bailer RT, Koup R, et al. Safety and immunogenicity of investigational seasonal influenza hemagglutinin DNA vaccine followed by trivalent inactivated vaccine administered intradermally or intramuscularly in healthy adults: an open-label randomized phase 1 clinical trial. PLoS One. 2019;14(9):1–18. doi:10.1371/journal.pone.0222178.
   Web of Science ®Google Scholar
• Gupta RKW. Will SARS-CoV-2 variants of concern affect the promise of vaccines? Nature Rev Immunol. 2021;21(6):340–41. doi:10.1038/s41577-021-00556-5.
   PubMed Web of Science ®Google Scholar
• Toovey O, Harvey KN, Bird PW, Tang J. Introduction of Brazilian SARS-CoV-2 484K.V2 related variants into the UK. J Infect. 2021;82(5):e23–e24. doi:10.1016/j.jinf.2021.01.025.
   PubMed Web of Science ®Google Scholar
• Garcia V, Vig V, Peillard L, Ramdani A, Mohamed S, Halfon P. First description of two immune escape indian B. 1.1. 420 and B. 1.617. 1 SARS-CoV2 variants in France. bioRxiv. 2021:1–9. doi:10.1101/2021.05.12.443357.
   Google Scholar
• Eales O, Page A, Tang SN, Walters CE, Wang H, Haw D, Trotter AJ, Viet TL, Foster-Nyarko E, Prosolek S, et al. SARS-CoV-2 lineage dynamics in England from January to March 2021 inferred from representative community samples. medRxiv. 2021;1–33. doi:10.1101/2021.05.08.21256867.
   Google Scholar
• Hutchinson D, Williams H, Stone H. COVID-19 variants of concern in Australia, September 2020-April 2021. Global Biosecurity. 2021;3:1–22. doi:10.31646/gbio.111.
   Google Scholar
• Webb LM, Matzinger S, Grano C, Kawasaki B, Stringer G, Bankers L, Herlihy R. Identification of and Surveillance for the SARS-CoV-2 Variants B.1.427 and B.1.429 — Colorado, January–March 2021. MMWR Morb Mortal Wkly Rep. 2021;70(19):717–18. doi:10.15585/mmwr.mm7019e2.
   PubMed Web of Science ®Google Scholar
• Ozer EA, Simons LM, Adewumi OM, Fowotade AA, Omoruyi EC, Adeniji JA, Dean TJ, Taiwo BO, Hultquist JF, Lorenzo-Redondo R. High prevalence of SARS-CoV-2 B. 1.1. 7 (UK variant) and the novel B. 1.5. 2.5 lineage in Oyo State, Nigeria. medRxiv. 2021:1–22. doi:10.1101/2021.04.09.21255206.
   Google Scholar
• Khan A, Khan S, Saleem S, Nizam-Uddin N, Mohammad A, Khan T, Ahmad S, Arshad M, Ali SS, Suleman M, et al. Immunogenomics guided design of immunomodulatory multi-epitope subunit vaccine against the SARS-CoV-2 new variants, and its validation through in silico cloning and immune simulation. Comput Biol Med. 2021;133:1–11. doi:10.1016/j.compbiomed.2021.104420.
   Web of Science ®Google Scholar
• Ita K. Coronavirus disease (COVID-19): current status and prospects for drug and vaccine development. Arch Med Res. 2021;52(1):15–24. doi:10.1016/j.arcmed.2020.09.010.
   PubMed Web of Science ®Google Scholar
• Rajput VS, Sharma R, Kumari A, Vyas N, Prajapati V, Grover A. Engineering a multi epitope vaccine against SARS-CoV-2 by exploiting its non structural and structural proteins. J Biomol Struct Dyn. 2021:1–18. doi:10.1080/07391102.2021.1924265.
   Google Scholar
• Dagotto G, Yu J, Barouch DH. Approaches and challenges in SARS-CoV-2 vaccine development. Cell Host Microbe. 2020;28(3):364–70. doi:10.1016/j.chom.2020.08.002.
   PubMed Web of Science ®Google Scholar
• Song Z, Xu Y, Bao L, Zhang L, Yu P, Qu Y, Zhu H, Zhao W, Han Y, Qin C. From SARS to MERS, thrusting coronaviruses into the spotlight. Viruses. 2019;11(1):1–28. doi:10.3390/v11010059.
   Web of Science ®Google Scholar
• Kuo L, Hurst KR, Masters PS. Exceptional flexibility in the sequence requirements for coronavirus small envelope protein function. Journal of Virology. 2007;81(5):2249–62. doi:10.1128/JVI.01577-06.
   PubMed Web of Science ®Google Scholar
• Timmers L, Peixoto J, Ducati R, Bachega JF, Pereira LM, Caceres RA, Majolo F, Da Silva GL, Anton DB, Goettert MI, et al. SARS-CoV-2 mutations in Brazil: from genomics to clinical conditions. Chemrxiv. 2021;1–32. doi:10.26434/chemrxiv.14045783.v1.
   Google Scholar
• Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Marrero MC, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, et al. The global phosphorylation landscape of SARS-CoV-2. Infection Cell. 2020;8674:30811–14. doi:10.1016/j.cell.2020.06.034.
   Google Scholar
• Mu J, Xu J, Zhang L, Shu T, Wu D, Huang M, Ren Y, Li X, Geng Q, Xu Y, et al. SARS-CoV-2-encoded nucleocapsid protein acts as a viral suppressor of RNA interference in cells. Sci China Life Sci. 2020;63(9):1413–16. doi:10.1007/s11427-020-1692-1.
   PubMed Web of Science ®Google Scholar
• Thoms M, Buschauer R, Ameismeier M, Koepke L, Denk T, Hirschenberger M, Kratzat H, Hayn M, Mackens-Kiani T, Cheng J, et al. Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science. 2020;369(6508):1249–55. doi:10.1126/science.abc8665.
   PubMed Web of Science ®Google Scholar
• Tan Y-J, Tham P-Y, Chan DZL, Chou C-F, Shen S, Fielding BC, Tan THP, Lim SG, Hong W. The severe acute respiratory syndrome coronavirus 3a protein up-regulates expression of fibrinogen in lung epithelial cells. J Virol. 2005;79:10083–87. doi:10.1128/JVI.79.15.10083-10087.2005.
   PubMed Web of Science ®Google Scholar
• Issa E, Merhi G, Panossian B, Salloum T, Tokajiana S. SARS-CoV-2 and ORF3a: nonsynonymous mutations, functional domains, and viral pathogenesis. Msystems. 2020;5(3):e00266–20. doi:10.1371/journal.pcbi.1003266.
   PubMed Web of Science ®Google Scholar
• Ren Y, Shu T, Wu D, Mu J, Wang C, Huang M, Han Y, Zhang X-Y, Zhou W, Qiu Y, et al. The ORF3a protein of SARS-CoV-2 induces apoptosis in cells. Cell Mol Immunol. 2020;17(8):881–83. doi:10.1038/s41423-020-0485-9.
   PubMed Web of Science ®Google Scholar
• Siu K-L, Yuen K-S, Castano‐Rodriguez C, Ye Z-W, Yeung M-L, Fung S-Y, Yuan S, Chan C-P, Yuen K-Y, Enjuanes L, et al. Severe acute respiratory syndrome Coronavirus ORF3a protein activates the NLRP3 inflammasome by promoting TRAF3-dependent ubiquitination of ASC. FASEB J. 2019;33(8):8865–77. doi:10.1096/fj.201802418R.
   PubMed Web of Science ®Google Scholar
• Taylor JK, Coleman CM, Postel S, Sisk JM, Bernbaum JG, Venkataraman T, Sundberg EJ, Frieman MB. Severe acute respiratory syndrome coronavirus ORF7a inhibits bone marrow stromal antigen 2 virion tethering through a novel mechanism of glycosylation interference. Journal of Virology. 2015;89(23):467–78. doi:10.1016/S0140-6736(20)31604-4.
   Web of Science ®Google Scholar
• Khailanya RA, Safdarb M, Ozaslanc M. Genomic characterization of a novel SARS-CoV- 2. Gene Rep. 2020;19:1–6. doi:10.1016/j.genrep.2020.100682.
   Web of Science ®Google Scholar
• Jin-Yan L, Ce-Heng L, Qiong W, Yong-Jun T, Rui L, Ye Q, Xing-Yi G. The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway. Virus Res. 2020;286:1–11. doi:10.1016/j.virusres.2020.198074.
   Web of Science ®Google Scholar
• Zhang Y, Zhang J, Chen Y, Luo B, Yuan Y, Huang F, Yang T, Yu F, Liu J, Liu B, et al. The ORF8 protein of SARS-CoV-2 mediates immune evasion through potently downregulating MHC-I. Nat Acad Sci. 2021;118:1–12. doi:10.1073/pnas.2024202118.
   Google Scholar
• Livingston B, Crimi C, Newman M, Higashimoto Y, Appella E, Sidney J, Sette A. A rational strategy to design multiepitope immunogens based on multiple Th lymphocyte epitopes. J Immunol. 2002;168(11):5499–506. doi:10.4049/jimmunol.168.11.5499.
   PubMed Web of Science ®Google Scholar
• Reguzova A, Antonets D, Karpenko L, Ilyichev A, Maksyutov R, Bazhan S. Design and evaluation of optimized artificial HIV-1 poly-T cell-epitope immunogens. PLoS One. 2015;10(3):1–18. doi:10.2144/00286ir01.
   Web of Science ®Google Scholar
• Bazhan SI, Karpenko LI, Ilyicheva TN, Belavin PA, Seregin SV, Danilyuk NK, Antonets DV, Ilyichev AA. Rational design based synthetic polyepitope DNA vaccine for eliciting HIV-specific CD8+ T cell responses. Mol Immunol. 2010;47(7–8):279–88. doi:10.1038/s41591-020-01179-4.
   Web of Science ®Google Scholar
• Wang Q-M, Sun S-H, Hu Z-L, Zhou F-J, Yin M, Xiao C-J, Zhang J-C. Epitope DNA vaccines against tuberculosis: spacers and ubiquitin modulates cellular immune responses elicited by epitope DNA vaccine. Scand J Immunol. 2004;60(3):W526–W531. doi:10.1093/nar/gki376.
   Web of Science ®Google Scholar
• Dong R, Chu Z, Yu F, Zha Y. Contriving multi-epitope subunit of vaccine for COVID-19: immunoinformatics approaches. Front Immunol. 2020;11:1–18. doi:10.3389/fimmu.2020.01784.
   PubMed Web of Science ®Google Scholar
• Onile OS, Ojo GJ, Oyeyemi BF, Agbowuro GO, Fadahunsi AI. Development of multiepitope subunit protein vaccines against Toxoplasma gondii using an immunoinformatics approach. NAR Genomics Bioinforma. 2020;2:48. doi:10.1093/nargab/lqaa048.
   Google Scholar
• Liu H, Shen W, Shu J, Kou Z, Jin X. A novel polyepitope vaccine elicited HIV peptide specific CD4+ T cell responses in HLA-A2/DRB1 transgenic mice. PLoS One. 2017;12:1–11. doi:10.1371/journal.pone.0184207.
   Web of Science ®Google Scholar
• Nezafat N, Ghasemi Y, Javadi G, Khoshnoud MJ, Omidinia E. A novel multi-epitope peptide vaccine against cancer: an in silico approach. J Theor Biol. 2014;349:121–34. doi:10.1016/j.jtbi.2014.01.018.
   PubMed Web of Science ®Google Scholar
• Levy A, Pitcovski J, Frankenburg S, Elias O, Altuvia Y, Margalit H, Peretz T, Golenser J, Lotem M, Zhu F-C, et al. A melanoma multiepitope polypeptide induces specific CD8+ T-cell response. Cell Immunol. 2007;250(1–2):24–30. doi:10.1016/S0140-6736(20)31605-6.
   PubMed Web of Science ®Google Scholar
• Cardinaud S, Bouziat R, Rohrlich P-S, Tourdot S, Weiss L, Langlade-Demoyen P, Burgevin A, Fiorentino S, Endert PV, Lemonnier FA. Design of a HIV-1-derived HLA-B07.02-restricted polyepitope construct. AIDS. 2009;23(15):1945–54. doi:10.1097/QAD.0b013e32832fae88.
   PubMed Web of Science ®Google Scholar
• Schneider SC, Ohmen J, Fosdick L, Gladstone B, Guo J, Ametani A, Sercarz EE, Deng H. Cutting edge: introduction of an endopeptidase cleavage motif into a determinant flanking region of hen egg lysozyme results in enhanced T cell determinant display. J Immunol. 2000;165(1):20–23. doi:10.1056/NEJMoa2026920.
   PubMed Web of Science ®Google Scholar
• Ji H, Wang T-L, Chen C-H, Pai SI, Hung C-F, Lin K-Y, Kurman RJ, Pardoll DM, Wu TC. Targeting human papillomavirus Type 16 E7 to the endosomal/lysosomal compartment enhances the antitumor immunity of DNA vaccines against murine human papillomavirus Type 16 E7-expressing tumors. Hum Gene Ther. 1999;10(17):2727–40. doi:10.1089/10430349950016474.
   PubMed Web of Science ®Google Scholar
• Verma S, Sajid A, Singh Y, Shukla P. Computational tools for modern vaccine development. Hum Vaccines Immunother. 2020;16(3):723–35. doi:10.1080/21645515.2019.1670035.
   PubMed Web of Science ®Google Scholar
• Wu F, Wang A, Liu M. Neutralizing antibody responses to SARS-CoV-2 in a COVID-19 recovered patient cohort and their implications. medRxiv. 2020;00:1–24. doi:10.2139/ssrn.3566211.
   Google Scholar
• Qamar MTU, Rehman A, Tusleem K, Ashfaq UA, Qasim M, Zhu X, Fatima I, Shahid F, Chen -L-L. Designing of a next generation multiepitope based vaccine (MEV) against SARS-COV-2: immunoinformatics and in silico approaches. PLoS One. 2020;15:1–25. doi:10.1371/journal.pone.024417.
   Web of Science ®Google Scholar
• Ahmed SF, Quadeer AA, McKay MR. Preliminary identification of potential vaccine targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV immunological studies. Viruses. 2020;12:1–15. doi:10.3390/v12030254.
   Web of Science ®Google Scholar
• Abdelmageed MI, Abdelmoneim AH, Mustafa MI, Elfadol NM, Murshed NS, Shantier SW, Makhawi AM. Design of a multiepitope-based peptide vaccine against the e protein of human COVID-19: an immunoinformatics approach. Biomed Res Int. 2020;00:1–12. doi:10.1155/2020/2683286.
   Google Scholar
• Baruah V, Bose S. Immunoinformatics-aided identification of T cell and B cell epitopes in the surface glycoprotein of 2019-nCoV. J Med Virol. 2020;92:495–500. doi:10.1002/jmv.25698.
   PubMed Web of Science ®Google Scholar
• Bhattacharya M, Sharma AR, Patra P, Ghosh P, Sharma G, Patra BC, Lee S-S CC. Development of epitope-based peptide vaccine against novel coronavirus 2019 (SARS-COV-2): immunoinformatics approach. J Med Virol. 2020;92:618–31. doi:10.1002/jmv.25736.
   PubMed Web of Science ®Google Scholar
• Enayatkhani M, Hasaniazad M, Faezi S, Gouklani H, Davoodian P, Ahmadi N, Einakian MA, Karmostaji A, Ahmadi K. Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: an in silico study. J Biomol Struct Dyn. 2020;2:1–16. doi:10.1080/07391102.2020.1756411.
   Web of Science ®Google Scholar
• Rahman MS, Hoque MN, Islam MR, Akter S, Alam ASMRU, Siddique MA, Saha O, Rahaman MM, Sultana M, Crandall KA, et al. Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approach. PeerJ. 2020;8:1–30. doi:10.7717/peerj.9572.
   Web of Science ®Google Scholar
• Moura RR, Agrelli A, Santos-Silva CA, Silva N, Assunção BR, Brandão L, Benko-Iseppon AM, Crovella S. Immunoinformatic approach to assess SARS-CoV-2 protein S epitopes recognised by the most frequent MHC-I alleles in the Brazilian population. J Clin Pathol. 2020;00:1–5. doi:10.1136/jclinpath-2020-206946.
   Google Scholar
• Khuroo MS, Khuroo M, Khuroo MS, Sofi AA, Khuroo NS. COVID-19 vaccines: a race against time in the middle of death and devastation! J Clin Exp Hepatol. 2020;10:610–21. doi:10.1016/j.jceh.2020.06.003.
   PubMed Web of Science ®Google Scholar
• Saade F, Petrovsky N. Technologies for enhanced efficacy of DNA vaccines. Expert Rev Vaccines. 2012;11:189–209. doi:10.1586/erv.11.188.
   PubMed Web of Science ®Google Scholar
• Desai DV, Kulkarni-Kale U. T-cell epitope prediction methods: an overview. In: De R, Tomar N, editors. Immunoinformatics. methods in molecular biology (Methods and Protocols). New York (NY): Humana Press; 2014. p. 333–64.
   Google Scholar
• Jurtz V, Paul S, Andreatta M, Marcatili P, Peters B, Nielsen M. NetMHCpan-4.0: improved peptide–MHC Class I interaction predictions integrating eluted ligand and peptide binding affinity data. J Immunol. 2017;199:3360–68. doi:10.4049/jimmunol.1700893.
   PubMed Web of Science ®Google Scholar
• Peters B, Sette A. Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinform. 2005;6:1–9. doi:10.1186/1471-2105-6-132.
   PubMed Web of Science ®Google Scholar
• Peters B, Bulik S, Tampe R, Van Endert PM, Holzhutter HG. Identifying MHC Class I epitopes by predicting the TAP transport efficiency of epitope precursors. J Immunol. 2003;171:1741–49. doi:10.4049/jimmunol.171.4.1741.
   PubMed Web of Science ®Google Scholar
• Peters B, Tong W, Sidney J, Sette A, Weng Z. Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules. Bioinformatics. 2003;19:1765–72. doi:10.1093/bioinformatics/btg247.
   PubMed Web of Science ®Google Scholar
• Tenzer S, Peters B, Bulik S, Schoor O, Lemmel C, Schatz MM, Kloetzel PM, Rammensee HG, Schild H, Holzhutter HG. Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding. Cell Mol Life Sci. 2005;62:1025–37. doi:10.1007/s00018-005-4528-2.
   PubMed Web of Science ®Google Scholar
• Wang S-C. Artificial neural network (ANNs). In: interdisciplinary computing in Java programming. Springer,Boston. 2003;743:81–100. doi:10.1007/978-1-4615-0377-4_5.
   Google Scholar
• Peters B, Sette A. Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinform. 2005;6:1–9. doi:10.1186/1471-2105-6-132.
   PubMed Web of Science ®Google Scholar
• Keşmir C, Nussbaum AK, Schild H, Detours V, Brunak S. Prediction of proteasome cleavage motifs by neural networks. Protein Eng. 2002;15:287–96. doi:10.1093/protein/15.4.287.
   PubMedGoogle Scholar
• Larsen MV, Lundegaard C, Lamberth K, Buus S, Brunak S, Lund O, Nielsen M. An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions. Eur J Immunol. 2005;35:2295–303. doi:10.1002/eji.200425811.
   PubMed Web of Science ®Google Scholar
• Nielsen M, Lundegaard C, Lund O, Keşmir C. The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics. 2005;57:33–41. doi:10.1007/s00251-005-0781-7.
   PubMed Web of Science ®Google Scholar
• Stranzl T, Larsen MV, Lundegaard C, Nielsen M. NetCTLpan: pan-specific MHC class I pathway epitope predictions. Immunogenetics. 2010;62:357–68. doi:10.1007/s00251-010-0441-4.
   PubMed Web of Science ®Google Scholar
• Wang P, Sidney J, Dow C, Mothé B, Sette A, Peters B. A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comput Biol. 2008;4:1–10. doi:10.1371/journal.pcbi.1000048.
   Web of Science ®Google Scholar
• Jørgensen KW, Rasmussen M, Buus S, Nielsen M. NetMHCstab - Predicting stability of peptide-MHC-I complexes; impacts for cytotoxic T lymphocyte epitope discovery. Immunology. 2014;141:18–26. doi:10.1111/imm.12160.
   PubMed Web of Science ®Google Scholar
• Rasmussen M, Fenoy E, Harndahl M, Kristensen AB, Nielsen IK, Nielsen M, Buss S. Pan-specific prediction of peptide–MHC Class I complex stability, a correlate of T cell immunogenicity. J Immunol. 2016;197:1517–24. doi:10.4049/jimmunol.1600582.
   PubMed Web of Science ®Google Scholar
• Larsen MV, Lundegaard C, Lamberth K, Buus S, Lund O, Nielsen M. Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinform. 2007;8:1–12. doi:10.1186/1471-2105-8-424.
   PubMed Web of Science ®Google Scholar
• Singh H, Raghava GPS. ProPred: prediction of HLA-DR binding sites. Bioinformatics. 2001;17:1236–37. doi:10.1093/bioinformatics/17.12.1236.
   PubMed Web of Science ®Google Scholar
• Singh H, Raghava GPS. ProPred1: prediction of promiscuous MHC class-I binding sites. Bioinformatics. 2003;19:1009–14. doi:10.1093/bioinformatics/btg108.
   PubMed Web of Science ®Google Scholar
• Reche PA, Reinherz EL. Prediction of peptide-MHC binding using profiles. Methods Mol Biol. 2007;409:185–200. doi:10.1007/978-1-60327-118-9_13.
   PubMedGoogle Scholar
• Grifoni A, Weiskopf D, Ramirez SI, Mateus J, Dan JM, Moderbacher CR, Rawlings SA, Sutherland A, Premkumar L, Jadi RS, et al. Targets of T cell responses to SARS-CoV-2 Coronavirus in humans with COVID-19 disease and unexposed individuals. Cell. 2020;181:1489–501. doi:10.1016/j.cell.2020.05.015.
   PubMed Web of Science ®Google Scholar
• Barquera R, Collen E, Di D, Buhler S, Teixeira J, Llamas B, Nunes JM, Sanchez‐Mazas A. Binding affinities of 438 HLA proteins to complete proteomes of seven pandemic viruses and distributions of strongest and weakest HLA peptide binders in populations worldwide. HLA. 2020;96:277–98. doi:10.1111/tan.13956.
   PubMed Web of Science ®Google Scholar
• Gonzalez-Galarza FF, McCabe A, Santos EJM, Jones J, Takeshita L, Ortega-Rivera ND, Cid-Pavon GMD, Ramsbottom K, Ghattaoraya G, Alfirevic A, et al. Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools. Nucleic Acids Res. 2020;48:783–88. doi:10.1093/nar/gkz1029.
   PubMed Web of Science ®Google Scholar
• Feltkamp MCW, Vierboom MPM, Kast WM, Melief CJM. Efficient MHC class I-peptide binding is required but does not ensure MHC class I-restricted immunogenicity. Mol Immunol. 1994;31:1391–401. doi:10.1016/0161-5890(94)90155-4.
   PubMed Web of Science ®Google Scholar
• Calis JJA, Maybeno M, Greenbaum JA, Weiskopf D, De Silva AD, Sette A, Kesmir C, Peters B. Properties of MHC Class I presented peptides that enhance immunogenicity. PLoS Comput Biol. 2013;9:1–13. doi:10.1371/journal.pcbi.1003266.
   Web of Science ®Google Scholar
• Kardani K, Bolhassani A, Namvar A. An overview of in silico vaccine design against different pathogens and cancer. Expert Rev Vaccines. 2020;19:699–726. doi:10.1080/14760584.2020.1794832.
   PubMed Web of Science ®Google Scholar
• Rapin N, Lund O, Bernaschi M, Castiglione F. Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system. PLoS One. 2010;5:1–14. doi:10.1371/journal.pone.0009862.
   Web of Science ®Google Scholar
• Saha S, Raghava GPS. Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins Struct Funct Genet. 2006;65:40–48. doi:10.1002/prot.21078.
   PubMed Web of Science ®Google Scholar
• Jespersen MC, Peters B, Nielsen M, Marcatili P. BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res. 2017;45:W24–W29. doi:10.1093/nar/gkx346.
   PubMed Web of Science ®Google Scholar
• Doytchinova IA, Flower DR. VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinform. 2007;8:1–7. doi:10.1186/1471-2105-8-4.
   PubMed Web of Science ®Google Scholar
• Dhanda SK, Vaughan K, Schulten V, Grifoni A, Weiskopf D, Sidney J, Peters B, Sette A. Development of a novel clustering tool for linear peptide sequences. Immunology. 2018;155:331–45. doi:10.1111/imm.12984.
   PubMed Web of Science ®Google Scholar
• Scholzen A, Richard G, Moise L, Moise L, Baeten LA, Reeves PM, Martin WD, Brauns TA, Boyle CM, Paul SR, et al. Promiscuous Coxiella burnetii CD4 epitope clusters associated with human recall responses are candidates for a novel T-Cell targeted multi-epitope Q fever vaccine. Front Immunol. 2019;10:1–22. doi:10.3389/fimmu.2019.00207.
   PubMed Web of Science ®Google Scholar
• Bui HH, Sidney J, Li W, Fusseder N, Sette A. Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinform. 2007;8:1–6. doi:10.1186/1471-2105-8-361.
   PubMed Web of Science ®Google Scholar
• Bui HH, Sidney J, Dinh K, Southwood S, Newman MJ, Sette A. Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinform. 2006;7:1–5. doi:10.1186/1471-2105-7-153.
   PubMed Web of Science ®Google Scholar
• Kibria KMK, Islam MSB, Ullah H, Miah M. The multi-epitope vaccine prediction to combat Pandemic SARS-CoV-2, an immunoinformatic approach. Research Square Preprint. 2020;00:1–20. doi:10.21203/rs.3.rs-21853/v1.
   Google Scholar
• Vajda S, Yueh C, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Kozakov D. New additions to the ClusPro server motivated by CAPRI. Proteins Struct Funct Bioinforma. 2017;85:435–44. doi:10.1002/prot.25219.
   PubMed Web of Science ®Google Scholar
• Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res. 2005;33:363–67. doi:10.1093/nar/gki481.
   PubMed Web of Science ®Google Scholar
• De Vries SJ, Van Dijk M, Bonvin AMJJ. The HADDOCK web server for data-driven biomolecular docking. Nat Protoc. 2010;5:883–97. doi:10.1038/nprot.2010.32.
   PubMed Web of Science ®Google Scholar
• Kurcinski M, Jamroz M, Blaszczyk M, Kolinski A, Kmiecik S. CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site. Nucleic Acids Res. 2015;43:419–24. doi:10.1093/nar/gkv456.
   PubMed Web of Science ®Google Scholar
• Pierce BG, Wiehe K, Hwang H, Kim BH, Vreven T, Weng Z. ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics. 2014;30:1771–73. doi:10.1093/bioinformatics/btu097.
   PubMed Web of Science ®Google Scholar
• Kalergis AM, Boucheron N, Doucey MA, Palmieri E, Goyarts EC, Vegh Z, Luescher IF, Nathenson SG. Efficient T cell activation requires an optimal dwell-time of interaction between the TCR and the pMHC complex. Nat Immunol. 2001;2:229–34. doi:10.1038/85286.
   PubMed Web of Science ®Google Scholar
• Stothard P. The sequence manipulation suite: javaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques. 2000;28:1102–04. doi:10.2144/00286ir01.
   PubMed Web of Science ®Google Scholar
• Grote A, Hiller K, Scheer M, Münch R, Nörtemann B, Hempel DC, Jahn D. JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res. 2005;33:526–31. doi:10.1093/nar/gki376.
   PubMed Web of Science ®Google Scholar
• Slathia PS, Vaccine DNA. Design for Chikungunya virus based on the conserved epitopes derived from structural protein. Assoc Comput Mach. 2013:849–50. doi:10.1145/2506583.2516950.
   Google Scholar
• Kutzler MA, Weiner DB. DNA vaccines: ready for prime time? Nat. Rev Genet. 2008;9:776–88. doi:10.1038/nrg2432.
   Google Scholar
• Wang S, Zhang C, Zhang L, Li J, Huang Z, Lu S. The relative immunogenicity of DNA vaccines delivered by the intramuscular needle injection, electroporation and gene gun methods. Vaccine. 2008;26:2100–10. doi:10.1016/j.vaccine.2008.02.033.
   PubMed Web of Science ®Google Scholar
• Kudela J. Immunization with analog peptide in combination with CpG and montanide expands tumor antigen-specific CD8+ T cells in melanoma patients. J Immunother. 2008;31:781–91. doi:10.1097/CJI.0b013e318183af0b.
   PubMed Web of Science ®Google Scholar
• Longhi MP, Trumpfheller C, Idoyaga J, Caskey M, Matos I, Kluger C, Salazar AM, Colonna M, Steinman RM. Dendritic cells require a systemic type I interferon response to mature and induce CD4+ Th1 immunity with poly IC as adjuvant. J Exp Med. 2009;206:1589–602. doi:10.1084/jem.20090247.
   PubMed Web of Science ®Google Scholar
• Ma J, Wang H, Zheng X, Xue X, Wang B, Wu H, Zhang K, Fan S, Wang T, Li N, et al. CpG/Poly (I:C) mixed adjuvant priming enhances the immunogenicity of a DNA vaccine against eastern equine encephalitis virus in mice. Int Immunopharmacol. 2014;19:74–80. doi:10.1016/j.intimp.2014.01.002.
   PubMed Web of Science ®Google Scholar
• Suschak JJ, Williams JA, Schmaljohn CS. Advancements in DNA vaccine vectors, non-mechanical delivery methods, and molecular adjuvants to increase immunogenicity. Hum Vaccines Immunother. 2017;13:2837–48. doi:10.1080/21645515.2017.1330236.
   PubMed Web of Science ®Google Scholar
• Henke A, Rohland N, Zell R, Wutzler P. Co-expression of interleukin-2 by a bicistronic plasmid increases the efficacy of DNA immunization to prevent influenza virus infections. Intervirology. 2006;49:249–52. doi:10.1159/000092487.
   PubMedGoogle Scholar
• Hu H, Tao L, Wang Y, Chen L, Yang J, Wang H. Enhancing immune responses against SARS-cov nucleocapsid DNA vaccine by co-inoculating interleukin-2 expressing vector in mice. Biotechnol Lett. 2009;31:1685–93. doi:10.1007/s10529-009-0061-y.
   PubMed Web of Science ®Google Scholar
• Barouch DH, Santra S, Schmitz JE, Kuroda MJ, Fu TM, Wagner W, Bilska M, Craiu A, Zheng XX, Krivulka GR, et al. Control of viremia prevention of clinical AIDS in rhesus monkeys by cytokine-augmented DNA vaccination. Science. 2000;290:486–92. doi:10.1126/science.290.5491.486.
   PubMed Web of Science ®Google Scholar
• Kalams SA, Parker SD, Elizaga M, Metch B, Edupuganti S, Hural J, Rosa SD, Carter DK, Rybczyk K, Frank I, et al. Safety and comparative immunogenicity of an HIV-1 DNA vaccine in combination with plasmid interleukin 12 and impact of intramuscular electroporation for delivery. J Infect Dis. 2013;208:818–29. doi:10.1093/infdis/jit236.
   PubMed Web of Science ®Google Scholar
• Jalah R, Patel V, Kulkarni V, Rosati M, Alicea C, Ganneru B, Gegerfelt AV, Huang W, Guan Y, Broderick KE, et al. IL-12 DNA as molecular vaccine adjuvant increases the cytotoxic T cell responses and breadth of humoral immune responses in SIV DNA vaccinated macaques. Hum Vaccines Immunother. 2012;8:1620–29. doi:10.4161/hv.21407.
   PubMed Web of Science ®Google Scholar
• Zhang C, Maruggi G, Shan H, Li J. Advances in mRNA vaccines for infectious diseases. Front Immunol. 2019;10:1–13. doi:10.3389/fimmu.2019.00594.
   PubMed Web of Science ®Google Scholar
• Diken M, Kreiter S, Selmi A, Britten CM, Huber C, Ö T, Sahin U. Selective uptake of naked vaccine RNA by dendritic cells is driven by macropinocytosis and abrogated upon DC maturation. Gene Ther. 2011;18:702–08. doi:10.1038/gt.2011.17.
   PubMed Web of Science ®Google Scholar
• Miao L, Li L, Huang Y, Delcassian D, Chahal J, Han J, Shi Y, Sadtler K, Gao W, Lin J, et al. Delivery of mRNA vaccines with heterocyclic lipids increases anti-tumor efficacy by STING-mediated immune cell activation. Nat Biotechnol. 2019;37:1174–85. doi:10.1038/s41587-019-0247-3.
   PubMed Web of Science ®Google Scholar
• Graham RL, Donaldson EF, Baric RS. A decade after SARS: strategies for controlling emerging coronaviruses. Nat Rev Microbiol. 2013;11:836–48. doi:10.1038/nrmicro3143.
   PubMed Web of Science ®Google Scholar