References
WHO. WHO Statement Regarding Cluster of Pneumonia Cases in Wuhan, China. 9 January 2020. Available online: https://www.who.int/china/news/detail/09-01-2020-who-statement-regarding-cluster-of-pneumonia-cases-in-wuhan-china (accessed on 1 October 2020).
Zhu, N.; Zhang, D.; Wang, W.; Li, X.; Yang, B.; Song, J.; Zhao, X.; Huang, B.; Shi, W.; Lu, R.; et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N. Engl. J. Med. 2020, 382, 727–733. [Google Scholar] [CrossRef] [PubMed]
Wu, J.; Yuan, X.; Wang, B.; Gu, R.; Li, W.; Xiang, X.; Tang, L.; Sun, H. Severe Acute Respiratory Syndrome Coronavirus 2: From Gene Structure to Pathogenic Mechanisms and Potential Therapy. Front. Microbiol. 2020, 11, 1576. [Google Scholar] [CrossRef]
Shah, V.K.; Firmal, P.; Alam, A.; Ganguly, D.; Chattopadhyay, S. Overview of Immune Response During SARS-CoV-2 Infection: Lessons From the Past. Front. Immunol. 2020, 11, 1–17. [Google Scholar] [CrossRef] [PubMed]
Klein, S.; Cortese, M.; Winter, S.L.; Wachsmuth-Melm, M.; Neufeldt, C.J.; Cerikan, B.; Stanifer, M.L.; Boulant, S.; Bartenschlager, R.; Chlanda, P. SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography. Nat. Commun. 2020, 11, 5885. [Google Scholar] [CrossRef] [PubMed]
Wang, Q.; Zhang, Y.; Wu, L.; Niu, S.; Song, C.; Zhang, Z.; Lu, G.; Qiao, C.; Hu, Y.; Yuen, K.-Y.; et al. Structural and functional basis of SARS-CoV-2 entry by using human ACE2. Cell 2020, 181, 894–904. [Google Scholar] [CrossRef] [PubMed]
Uddin, M.; Mustafa, F.; Rizvi, T.A.; Loney, T.; Al Suwaidi, H.; Al-Marzouqi, A.H.H.; Kamal Eldin, A.; Alsabeeha, N.; Adrian, T.E.; Stefanini, C.; et al. SARS-CoV-2/COVID-19: Viral Genomics, Epidemiology, Vaccines, and Therapeutic Interventions. Viruses 2020, 12, 526. [Google Scholar] [CrossRef] [PubMed]
Hu, Y.; Wen, J.; Tang, L.; Zhang, H.; Zhang, X.; Li, Y.; Wang, J.; Han, Y.; Li, G.; Shi, J.; et al. The M protein of SARS-CoV: Basic structural and immunological properties. Genom. Proteom. Bioinform. 2003, 1, 118–130. [Google Scholar] [CrossRef]
Neuman, B.W.; Kiss, G.; Kunding, A.H.; Bhella, D.; Baksh, M.F.; Connelly, S.; Droese, B.; Klaus, J.P.; Makino, S.; Sawicki, S.G.; et al. A structural analysis of M protein in coronavirus assembly and morphology. J. Struct. Biol. 2011, 174, 11–22. [Google Scholar] [CrossRef]
Bianchi, M.; Benvenuto, D.; Giovanetti, M.; Angeletti, S.; Ciccozzi, M.; Pascarella, S. Sars-CoV-2 Envelope and Membrane Proteins: Structural Differences Linked to Virus Characteristics? BioMed Res. Int. 2020, 2020, 4389089. [Google Scholar] [CrossRef]
Thomas, S. The structure of the membrane protein of sars-cov-2 resembles the sugar transporter semisweet. Pathog. Immun. 2020, 5, 342–363. [Google Scholar] [CrossRef]
Dramé, M.; Teguo, M.T.; Proye, E.; Hequet, F.; Hentzien, M.; Kanagaratnam, L.; Godaert, L. Should RT-PCR be considered a gold standard in the diagnosis of COVID-19? J. Med Virol. 2020, 92, 2312–2313. [Google Scholar] [CrossRef]
Amanat, F.; Stadlbauer, D.; Strohmeier, S.; Nguyen, T.H.O.; Chromikova, V.; McMahon, M.; Jiang, K.; Arunkumar, G.A.; Jurczyszak, D.; Polanco, J.; et al. A serological assay to detect SARS-CoV-2 seroconversion in humans. Nat. Med. 2020, 26, 1033–1036. [Google Scholar] [CrossRef]
Weisberg, S.P.; Connors, T.J.; Zhu, Y.; Baldwin, M.R.; Lin, W.; Wontakal, S.; Szabo, P.A.; Wells, S.B.; Dogra, P.; Gray, J.; et al. Distinct antibody responses to SARS-CoV-2 in children and adults across the COVID-19 clinical spectrum. Nat. Immunol. 2021, 22, 25–31. [Google Scholar] [CrossRef]
Borbone, N.; Piccialli, G.; Roviello, G.N.; Oliviero, G. Nucleoside Analogs and Nucleoside Precursors as Drugs in the Fight against SARS-CoV-2 and Other Coronaviruses. Molecules 2021, 26, 986. [Google Scholar] [CrossRef]
Vicidomini, C.; Roviello, V.; Roviello, G.N. Molecular Basis of the Therapeutical Potential of Clove (Syzygium aromaticium L.) and Clues to Its Anti-COVID-19 Utility. Molecules 2021, 26, 1880. [Google Scholar] [CrossRef]
Dong, Y.; Dai, T.; Wei, Y.; Zhang, L.; Zheng, M.; Zhou, F. A systematic review of SARS-CoV-2 vaccine candidates. Signal Transduct. Target. Ther. 2020, 5, 237. [Google Scholar] [CrossRef]
Galanis, K.; Nastou, K.; Papandreou, N.; Petichakis, G.; Pigis, D.; Iconomidou, V. Linear B-Cell Epitope Prediction for In Silico Vaccine Design: A Performance Review of Methods Available via Command-Line Interface. Int. J. Mol. Sci. 2021, 22, 3210. [Google Scholar] [CrossRef]
Grifoni, A.; Weiskopf, D.; Ramirez, S.I.; Mateus, J.; Dan, J.M.; Moderbacher, C.R.; Rawlings, S.A.; Sutherland, A.; Premkumar, L.; Jadi, R.S.; et al. Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals. Cell 2020, 181, 1489–1501.e15. [Google Scholar] [CrossRef]
Ainsworth, M.; Andersson, M.; Auckland, K.; Baillie, J.K.; Barnes, E.; Beer, S.; Beveridge, A.; Bibi, S.; Blackwell, L.; Borak, M.; et al. Performance characteristics of five immunoassays for SARS-CoV-2: A head-to-head benchmark comparison. Lancet Infect. Dis. 2020, 20, 1390–1400. [Google Scholar] [CrossRef]
Meyer, M.A.M.B.; Drosten, C. Serological assays for emerging coronaviruses: Challenges and pitfalls. J. Adv. Res. 2014, 24, 91–98. [Google Scholar] [CrossRef]
Corbett, K.S.; Edwards, D.K.; Leist, S.R.; Abiona, O.M.; Boyoglu-Barnum, S.; Gillespie, R.A.; Himansu, S.; Schäfer, A.; Ziwawo, C.T.; DiPiazza, A.T.; et al. SARS-CoV-2 mRNA Vaccine Design Enabled by Prototype Pathogen Preparedness. Nature 2020, 586, 567–571. [Google Scholar] [CrossRef] [PubMed]
Liu, J.; Sun, Y.; Qi, J.; Chu, F.; Wu, H.; Gao, F.; Li, T.; Yan, J.; Gao, G.F. The Membrane Protein of Severe Acute Respiratory Syndrome Coronavirus Acts as a Dominant Immunogen Revealed by a Clustering Region of Novel Functionally and Structurally Defined Cytotoxic T-Lymphocyte Epitopes. J. Infect. Dis. 2010, 202, 1171–1180. [Google Scholar] [CrossRef] [PubMed]
Liu, C.; Li, X.; Zhang, C.; Xu, S.; Shao, Y.; Zhuang, H.; Che, X.; Qiu, Y.; Yin, H.; Li, D.; et al. Establishment of a reference panel for the detection of anti-SARS-CoV antibodies. Biologicals 2007, 35, 203–210. [Google Scholar] [CrossRef] [PubMed]
Mahtarin, R.; Islam, S.; Islam, M.J.; Ullah, M.O.; Ali, M.A.; Halim, M.A. Structure and dynamics of membrane protein in SARS-CoV-2. J. Biomol. Struct. Dyn. 2020. online ahead of print. [Google Scholar] [CrossRef]
He, Y.; Zhou, Y.; Siddiqui, P.; Niu, J.; Jiang, S. Identification of Immunodominant Epitopes on the Membrane Protein of the Severe Acute Respiratory Syndrome-Associated Coronavirus. J. Clin. Microbiol. 2005, 43, 3718–3726. [Google Scholar] [CrossRef]
De Assis, R.R.; Jain, A.; Nakajima, R.; Jasinskas, A.; Felgner, J.; Obiero, J.M.; Norris, P.J.; Stone, M.; Simmons, G.; Bagri, A.; et al. Analysis of SARS-CoV-2 antibodies in COVID-19 convalescent blood using a coronavirus antigen microarray. Nat. Commun. 2021, 12, 6. [Google Scholar] [CrossRef]
Pang, H.; Liu, Y.; Han, X.; Xu, Y.; Jiang, F.; Wu, D.; Kong, X.; Bartlam, M.; Rao, Z. Protective humoral responses to severe acute respiratory syndrome-associated coronavirus: Implications for the design of an effective protein-based vaccine. J. Gen. Virol. 2004, 85, 3109–3113. [Google Scholar] [CrossRef]
Tripp, R.A.; Haynes, L.M.; Moore, D.; Anderson, B.; Tamin, A.; Harcourt, B.H.; Jones, L.P.; Yilla, M.; Babcock, G.J.; Greenough, T.; et al. Monoclonal antibodies to SARS-associated coronavirus (SARS-CoV): Identification of neutralizing and antibodies reactive to S, N, M and e viral proteins. J. Virol. Methods 2005, 128, 21–28. [Google Scholar] [CrossRef]
Howell, K.A.; Brannan, J.M.; Bryan, C.; McNeal, A.; Davidson, E.; Turner, H.L.; Vu, H.; Shulenin, S.; He, S.; Kuehne, A.; et al. Cooperativity Enables Non-neutralizing Antibodies to Neutralize Ebolavirus. Cell Rep. 2017, 19, 413–424. [Google Scholar] [CrossRef]
Qamar, M.T.U.; Rehman, A.; Tusleem, K.; Ashfaq, U.A.; 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, e0244176. [Google Scholar] [CrossRef]
Odorico, M.; Pellequer, J.-L. BEPITOPE: Predicting the location of continuous epitopes and patterns in proteins. J. Mol. Recognit. 2003, 16, 20–22. [Google Scholar] [CrossRef]
Metz, C.E. Basic principles of ROC analysis. Semin. Nucl. Med. 1978, 8, 283–298. [Google Scholar] [CrossRef]
Zweig, M.H.; Campbell, G. Receiver-operating characteristic (ROC) plots: A fundamental evaluation tool in clinical medicine. Clin. Chem. 1993, 39, 561–577. [Google Scholar] [CrossRef]
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