State of the Art in Epitope Mapping and Opportunities in COVID-19

References

• Sanchez-TrincadoJL , Gomez-PerosanzM , RechePA. Fundamentals and Methods for T- and B-Cell Epitope Prediction. Journal of Immunology Research2017, 2680160 (2017).
   PubMed Web of Science ®Google Scholar
• YangX , YuX. An introduction to epitope prediction methods and software. Reviews in Medical Virology19(2), 77–96 (2009).
   PubMed Web of Science ®Google Scholar
• Palatnik-De-SousaCB , SoaresIDS , RosaDS. Editorial: Epitope Discovery and Synthetic Vaccine Design. Frontiers in Immunology9, 1–3 (2018).
   PubMed Web of Science ®Google Scholar
• KozlovaEEG , ViartBT , DeAvila RaM , FelicoriLF , Chavez-OlorteguiC. Classification epitopes in groups based on their protein family. BMC Bioinformatics16(19), S7 (2015).
   PubMedGoogle Scholar
• GuoJ-Y , LiuIJ , LinH-Tet al.Identification of COVID-19 B-cell epitopes with phage-displayed peptide library. Journal of Biomedical Science28(1), 43 (2021).
   PubMed Web of Science ®Google Scholar
• KarT , NarsariaU , BasakSet al.A candidate multi-epitope vaccine against SARS-CoV-2. Sci Rep10(1), 10895 (2020).
   PubMed Web of Science ®Google Scholar
• CameriniD , RandallAZ , Trappl-KimmonsKet al.Mapping SARS-CoV-2 Antibody Epitopes in COVID-19 Patients with a Multi-Coronavirus Protein Microarray. Microbiol Spectr9(2), e0141621 (2021).
   PubMed Web of Science ®Google Scholar
• ZhangBZ , HuYF , ChenLLet al.Mining of epitopes on Spike protein of SARS-CoV-2 from COVID-19 patients. Cell Res30(8), 702–704 (2020).
   PubMed Web of Science ®Google Scholar
• HuangJ , HondaW. CED: a conformational epitope database. BMC Immunology7(1), 7 (2006).
   PubMedGoogle Scholar
• SunJ , XuT , WangS , LiG , WuD , CaoZ. Does difference exist between epitope and non-epitope residues? Analysis of the physicochemical and structural properties on conformational epitopes from B-cell protein antigens. Immunome research7, 1–11 (2011).
   Google Scholar
• CruseJM , LewisRE , WangH. 2 - Antigens, Immunogens, Vaccines, and Immunization. In: Immunology Guidebook.Academic Press San Diego, 17–45 (2004).
   Google Scholar
• LuštrekM , LorenzP , KreutzerMet al.Epitope Predictions Indicate the Presence of Two Distinct Types of Epitope-Antibody-Reactivities Determined by Epitope Profiling of Intravenous Immunoglobulins. PLOS ONE8(11), e78605 (2013).
   PubMed Web of Science ®Google Scholar
• DavisMM , AltmanJD , NewellEW. Interrogating the repertoire: broadening the scope of peptide-MHC multimer analysis. Nat Rev Immunol11(8), 551–558 (2011).
   PubMed Web of Science ®Google Scholar
• BakkerAH , SchumacherTNM. MHC multimer technology: current status and future prospects. Curr. Opin. Immunol.17(4), 428–433 (2005).
   PubMed Web of Science ®Google Scholar
• CecconiV , MoroM , DelMare S , DellabonaP , CasoratiG. Use of MHC class II tetramers to investigate CD4+ T cell responses: problems and solutions. Cytometry A.73A(11), 1010–1018 (2008).
   Web of Science ®Google Scholar
• MolonyRD , RiceJM , YukJSet al.Mining the Salivary Proteome with Grating-Coupled Surface Plasmon Resonance Imaging and Surface Plasmon Coupled Emission Microarrays. Curr Protoc Toxicol.53(1), 18.16.11–18.16.19 (2012).
   Google Scholar
• AhmadTA , EweidaAE , El-SayedLH. T-cell epitope mapping for the design of powerful vaccines. Vaccine Reports6, 13–22 (2016).
   Google Scholar
• WuC-H , LiuIJ , LuR-M , WuH-C. Advancement and applications of peptide phage display technology in biomedical science. Journal of Biomedical Science23(1), 8 (2016).
   PubMed Web of Science ®Google Scholar
• StoneJD , DemkowiczWE , SternLJ. HLA-restricted epitope identification and detection of functional T cell responses by using MHC–peptide and costimulatory microarrays. Proc Natl Acad Sci USA.102(10), 3744–3749 (2005).
   PubMed Web of Science ®Google Scholar
• LetschA , ScheibenbogenC. Quantification and characterization of specific T-cells by antigen-specific cytokine production using ELISPOT assay or intracellular cytokine staining. Methods31(2), 143–149 (2003).
   PubMed Web of Science ®Google Scholar
• SederRA , DarrahPA , RoedererM. T-cell quality in memory and protection: implications for vaccine design. Nature Reviews Immunology8(4), 247–258 (2008).
   PubMed Web of Science ®Google Scholar
• ClayTM , HobeikaAC , MoscaPJ , LyerlyHK , MorseMA. Assays for monitoring cellular immune responses to active immunotherapy of cancer. Clinical cancer research: an official journal of the American Association for Cancer Research7(5), 1127–1135 (2001).
   PubMed Web of Science ®Google Scholar
• MalyguineAM , StroblS , DunhamK , ShurinMR , SayersTJ. ELISPOT Assay for Monitoring Cytotoxic T Lymphocytes (CTL) Activity in Cancer Vaccine Clinical Trials. Cells1(2), 111–126 (2012).
   PubMedGoogle Scholar
• BowyerG , RamplingT , PowlsonJet al.Activation-induced Markers Detect Vaccine-Specific CD4+ T Cell Responses Not Measured by Assays Conventionally Used in Clinical Trials. Vaccines (Basel)6(3), 50 (2018).
   PubMed Web of Science ®Google Scholar
• MalherbeL. T-cell epitope mapping. Annals of Allergy, Asthma & Immunology103(1), 76–79 (2009).
   PubMed Web of Science ®Google Scholar
• IsmailN , OlanoJP , FengH-M , WalkerDH. Current status of immune mechanisms of killing of intracellular microorganims. FEMS Microbiol. Lett.207(2), 111–120 (2002).
   PubMed Web of Science ®Google Scholar
• HohdatsuT , YamatoH , OhkawaTet al.Vaccine efficacy of a cell lysate with recombinant baculovirus-expressed feline infectious peritonitis (FIP) virus nucleocapsid protein against progression of FIP. Veterinary Microbiology97(1), 31–44 (2003).
   PubMed Web of Science ®Google Scholar
• AhmadTA , EweidaAE , SheweitaSA. B-cell epitope mapping for the design of vaccines and effective diagnostics. Trials in Vaccinology5, 71–83 (2016).
   Google Scholar
• GershoniJM , Roitburd-BermanA , Siman-TovDD , TarnovitskiFreund N , WeissY. Epitope mapping: the first step in developing epitope-based vaccines. BioDrugs: clinical immunotherapeutics, biopharmaceuticals and gene therapy21(3), 145–156 (2007).
   PubMed Web of Science ®Google Scholar
• HjelmB. Epitope mapping of antibodies towards human protein targets [PhD thesis].Royal Institute of Technology School of Biotechnology,Stockholm (2011).
   Google Scholar
• LiN , LiZ , FuY , CaoS. Cryo-EM Studies of Virus-Antibody Immune Complexes. Virologica Sinica35(1), 1–13 (2020).
   PubMed Web of Science ®Google Scholar
• Baerga-OrtizA , HughesCA , MandellJG , KomivesEA. Epitope mapping of a monoclonal antibody against human thrombin by H/D-exchange mass spectrometry reveals selection of a diverse sequence in a highly conserved protein. Protein science: a publication of the Protein Society11(6), 1300–1308 (2002).
   PubMed Web of Science ®Google Scholar
• SuckauD , KöhlJ , KarwathGet al.Molecular epitope identification by limited proteolysis of an immobilized antigen-antibody complex and mass spectrometric peptide mapping. Proc Natl Acad Sci USA.87(24), 9848–9852 (1990).
   PubMed Web of Science ®Google Scholar
• ReinekeU , SchutkowskiM. Epitope mapping protocols.Springer, 1 (2009).
   Google Scholar
• KumadaY , KatohS , ImanakaH , ImamuraK , NakanishiK. Development of a one-step ELISA method using an affinity peptide tag specific to a hydrophilic polystyrene surface. Journal of Biotechnology127(2), 288–299 (2007).
   PubMed Web of Science ®Google Scholar
• NiegowskaM , PaccagniniD , MannuC , TarghettaC , SonginiM , SechiLA. Recognition of ZnT8, Proinsulin, and Homologous MAP Peptides in Sardinian Children at Risk of T1D Precedes Detection of Classical Islet Antibodies. Journal of Diabetes Research2016, 5842701 (2016).
   PubMed Web of Science ®Google Scholar
• MullettWM , LaiEPC , YeungJM. Surface Plasmon Resonance-Based Immunoassays. Methods (San Diego, Calif.)22(1), 77–91 (2000).
   PubMed Web of Science ®Google Scholar
• BrogioniB , BertiF. Surface plasmon resonance for the characterization of bacterial polysaccharide antigens: a review. MedChemComm5(8), 1058–1066 (2014).
   Web of Science ®Google Scholar
• PausD , WinterG. Mapping epitopes and antigenicity by site-directed masking. Proc Natl Acad Sci USA.103(24), 9172–9177 (2006).
   PubMed Web of Science ®Google Scholar
• LafuenteEM , RechePA. Prediction of MHC–peptide binding: a systematic and comprehensive overview. Current pharmaceutical design15(28), 3209–3220 (2009).
   PubMed Web of Science ®Google Scholar
• JensenPE. Recent advances in antigen processing and presentation. Nat Immunol8(10), 1041–1048 (2007).
   PubMed Web of Science ®Google Scholar
• PatronovA , DoytchinovaI. T-cell epitope vaccine design by immunoinformatics. Open Biol.3(1), 120139 (2013).
   PubMed Web of Science ®Google Scholar
• MartinW , SbaiH , DeGroot AS. Bioinformatics tools for identifying class I-restricted epitopes. Methods29(3), 289–298 (2003).
   PubMed Web of Science ®Google Scholar
• WangP , SidneyJ , DowC , MothéB , SetteA , PetersB. A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS computational biology4(4), e1000048–e1000048 (2008).
   PubMed Web of Science ®Google Scholar
• GalanisKA , NastouKC , PapandreouNC , PetichakisGN , PigisDG , IconomidouVA. Linear B-Cell Epitope Prediction for In Silico Vaccine Design: A Performance Review of Methods Available via Command-Line Interface. Int J Mol Sci.22(6), 3210 (2021).
   PubMed Web of Science ®Google Scholar
• DesaiDV , Kulkarni-KaleU. T-cell epitope prediction methods: an overview. Methods in molecular biology (Clifton, N.J.)1184, 333–364 (2014).
   PubMedGoogle Scholar
• ChukwudozieOS , GrayCM , FagbayiTAet al.Immuno-informatics design of a multimeric epitope peptide based vaccine targeting SARS-CoV-2 Spike glycoprotein. PLOS ONE16(3), e0248061 (2021).
   PubMed Web of Science ®Google Scholar
• PotocnakovaL , BhideM , PulzovaLB. An Introduction to B-Cell Epitope Mapping and In Silico Epitope Prediction. Journal of immunology research2016, 6760830–6760830 (2016).
   PubMed Web of Science ®Google Scholar
• KringelumJV , LundegaardC , LundO , NielsenM. Reliable B cell epitope predictions: impacts of method development and improved benchmarking. PLoS Comput Biol8(12), e1002829 (2012).
   PubMed Web of Science ®Google Scholar
• SakrMM , ElsayedNS , El-HousseinyGS. Latest updates on SARS-CoV-2 genomic characterization, drug, and vaccine development; a comprehensive bioinformatics review. Microb. Pathog.154, 104809 (2021).
   PubMed Web of Science ®Google Scholar
• Farrera-SolerL , DaguerJP , BarluengaSet al.Identification of immunodominant linear epitopes from SARS-CoV-2 patient plasma. PLOS ONE15(9), e0238089 (2020).
   PubMed Web of Science ®Google Scholar
• WanJ , XingS , DingLet al.Human-IgG-Neutralizing Monoclonal Antibodies Block the SARS-CoV-2 Infection. Cell Rep32(3), 107918 (2020).
   PubMed Web of Science ®Google Scholar
• WangD , MaiJ , ZhouWet al.Immunoinformatic Analysis of T- and B-Cell Epitopes for SARS-CoV-2 Vaccine Design. Vaccines (Basel)8(3), 355 (2020).
   PubMed Web of Science ®Google Scholar
• LiY , MaML , LeiQet al.Linear epitope landscape of the SARS-CoV-2 Spike protein constructed from 1,051 COVID-19 patients. Cell Rep34(13), 108915 (2021).
   PubMed Web of Science ®Google Scholar
• HaynesWA , KamathK , BozekowskiJet al.High-resolution epitope mapping and characterization of SARS-CoV-2 antibodies in large cohorts of subjects with COVID-19. Commun Biol4(1), 1317 (2021).
   PubMed Web of Science ®Google Scholar
• LiY , LaiDY , ZhangHNet al.Linear epitopes of SARS-CoV-2 Spike protein elicit neutralizing antibodies in COVID-19 patients. Cell Mol Immunol17(10), 1095–1097 (2020).
   PubMed Web of Science ®Google Scholar
• PohCM , CarissimoG , WangBet al.Two linear epitopes on the SARS-CoV-2 Spike protein that elicit neutralising antibodies in COVID-19 patients. Nat Commun11(1), 2806 (2020).
   PubMed Web of Science ®Google Scholar
• VitaR , MahajanS , OvertonJAet al.The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res.47(D1), D339–D343 (2019).
   PubMed Web of Science ®Google Scholar
• FarkasC , MellaA , TurgeonM , HaighJJ. A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3′ Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity. Front Microbiol12, 665041 (2021).
   PubMed Web of Science ®Google Scholar
• KoyamaT , PlattD , ParidaL. Variant analysis of SARS-CoV-2 genomes. Bull World Health Organ98(7), 495–504 (2020).
   PubMed Web of Science ®Google Scholar
• VolzE , HillV , MccroneJTet al.Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Cell184(1), 64–75e11 (2021).
   PubMed Web of Science ®Google Scholar
• ToyoshimaY , NemotoK , MatsumotoS , NakamuraY , KiyotaniK. SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. J Hum Genet65(12), 1075–1082 (2020).
   PubMed Web of Science ®Google Scholar
• PolyiamK , PhoolcharoenW , ButkhotNet al.Immunodominant linear B cell epitopes in the Spike and membrane proteins of SARS-CoV-2 identified by immunoinformatics prediction and immunoassay. Sci Rep11(1), 20383 (2021).
   PubMed Web of Science ®Google Scholar
• BahnanW , WrightonS , SundwallMet al.Spike-Dependent Opsonization Indicates Both Dose-Dependent Inhibition of Phagocytosis and That Non-Neutralizing Antibodies Can Confer Protection to SARS-CoV-2. Front Immunol12, 808932 (2021).
   PubMed Web of Science ®Google Scholar
• Beaudoin-BussieresG , ChenY , UllahIet al.A Fc-enhanced NTD-binding non-neutralizing antibody delays virus spread and synergizes with a nAb to protect mice from lethal SARS-CoV-2 infection. Cell Rep38(7), 110368 (2022).
   PubMed Web of Science ®Google Scholar
• SteffenTL , StoneET , HassertMet al.The receptor binding domain of SARS-CoV-2 Spike is the key target of neutralizing antibody in human polyclonal sera. J bioRxiv doi:10.1101/2020.08.21.261727 (2020).
   Google Scholar
• PiccoliL , ParkYJ , TortoriciMAet al.Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology. Cell183(4), 1024–1042e1021 (2020).
   PubMed Web of Science ®Google Scholar
• WangH , WuX , ZhangXet al.SARS-CoV-2 Proteome Microarray for Mapping COVID-19 Antibody Interactions at Amino Acid Resolution. ACS Cent Sci6(12), 2238–2249 (2020).
   PubMed Web of Science ®Google Scholar
• ShrockE , FujimuraE , KulaTet al.Viral epitope profiling of COVID-19 patients reveals cross-reactivity and correlates of severity. Science370(6520), eabd4250 (2020).
   PubMed Web of Science ®Google Scholar
• LuS , XieXX , ZhaoLet al.The immunodominant and neutralization linear epitopes for SARS-CoV-2. Cell Rep34(4), 108666 (2021).
   PubMed Web of Science ®Google Scholar
• JiangM , ZhangG , LiuHet al.Epitope Profiling Reveals the Critical Antigenic Determinants in SARS-CoV-2 RBD-Based Antigen. Front Immunol12, 707977 (2021).
   PubMed Web of Science ®Google Scholar
• LiangT , ChengM , TengFet al.Proteome-wide epitope mapping identifies a resource of antibodies for SARS-CoV-2 detection and neutralization. Signal Transduct Target Ther6(1), 166 (2021).
   PubMed Web of Science ®Google Scholar
• HuangY , YangC , XuXF , XuW , LiuSW. Structural and functional properties of SARS-CoV-2 Spike protein: potential antivirus drug development for COVID-19. Acta Pharmacol Sin41(9), 1141–1149 (2020).
   PubMed Web of Science ®Google Scholar
• LiuL , WangP , NairMSet al.Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 Spike. Nature584(7821), 450–456 (2020).
   PubMed Web of Science ®Google Scholar
• YamayoshiS , YasuharaA , ItoMet al.Antibody titers against SARS-CoV-2 decline, but do not disappear for several months. EClinicalMedicine32, 100734 (2021).
   PubMedGoogle Scholar
• ShahVK , FirmalP , AlamA , GangulyD , ChattopadhyayS. Overview of Immune Response During SARS-CoV-2 Infection: Lessons From the Past. Front Immunol11, 1949 (2020).
   PubMed Web of Science ®Google Scholar
• SainiSK , HersbyDS , TamhaneTet al.SARS-CoV-2 genome-wide T cell epitope mapping reveals immunodominance and substantial CD8(+) T cell activation in COVID-19 patients. Sci Immunol6(58), eabf7550 (2021).
   PubMed Web of Science ®Google Scholar
• TarkeA , SidneyJ , KiddCKet al.Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases. Cell Rep Med2(2), 100204 (2021).
   PubMedGoogle Scholar
• WilsonEA , HirneiseG , SingharoyA , AndersonKS. Total predicted MHC-I epitope load is inversely associated with population mortality from SARS-CoV-2. Cell Rep Med2(3), 100221 (2021).
   PubMedGoogle Scholar
• MorsyS , MorsyA. Epitope mimicry analysis of SARS-COV-2 surface proteins and human lung proteins. J Mol Graph Model105, 107836 (2021).
   PubMed Web of Science ®Google Scholar
• KanducD. From Anti-SARS-CoV-2 Immune Response to the Cytokine Storm via Molecular Mimicry. Antibodies (Basel)10(4), 36 (2021).
   PubMedGoogle Scholar
• NgKW , FaulknerN , CornishGHet al.Preexisting and de novo humoral immunity to SARS-CoV-2 in humans. Science370(6522), 1339–1343 (2020).
   PubMed Web of Science ®Google Scholar
• Obando-PeredaG. Can molecular mimicry explain the cytokine storm of SARS-CoV-2?: an in silico approach. J. Med. Virol.93(9), 5350–5357 (2021).
   PubMed Web of Science ®Google Scholar
• PanP , ShenM , YuZet al.SARS-CoV-2 N protein promotes NLRP3 inflammasome activation to induce hyperinflammation. Nat Commun12(1), 4664 (2021).
   PubMed Web of Science ®Google Scholar
• ChengMH , ZhangS , PorrittRAet al.Superantigenic character of an insert unique to SARS-CoV-2 Spike supported by skewed TCR repertoire in patients with hyperinflammation. Proc Natl Acad Sci U S A117(41), 25254–25262 (2020).
   PubMed Web of Science ®Google Scholar
• Garcia-BeltranWF , LamEC , StDenis Ket al.Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell184(9), 2523 (2021).
   PubMed Web of Science ®Google Scholar
• WHO. Tracking SARS-CoV-2 Variants. https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/ (March 2022).
   Google Scholar
• StarrTN , GreaneyAJ , HiltonSKet al.Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. bioRxiv182(5), 1295–1310e20 doi:10.1101/2020.06.17.157982 (2020).
   Google Scholar
• Rodriguez-RivasJ , CroceG , MuscatM , WeigtM. Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes. Proc Natl Acad Sci U S A119(4), e2113118119 (2022).
   PubMed Web of Science ®Google Scholar
• WangY , LiuM , ShenYet al.Novel sarbecovirus bispecific neutralizing antibodies with exceptional breadth and potency against currently circulating SARS-CoV-2 variants and sarbecoviruses. Cell Discov8(1), 36 (2022).
   PubMed Web of Science ®Google Scholar
• GreaneyAJ , LoesAN , CrawfordKHDet al.Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies. Cell Host Microbe29(3), 463–476e466 (2021).
   PubMed Web of Science ®Google Scholar
• DeSilva TI , LiuG , LindseyBBet al.The impact of viral mutations on recognition by SARS-CoV-2 specific T cells. iScience24(11), 103353 (2021).
   PubMed Web of Science ®Google Scholar
• VianaR , MoyoS , AmoakoDGet al.Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature603(7902), 679–686 (2022).
   PubMed Web of Science ®Google Scholar
• NaranbhaiV , NathanA , KasekeCet al.T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all individuals. Cell185(6), 1041–1051e1046 (2022).
   PubMed Web of Science ®Google Scholar
• KeetonR , TinchoMB , NgomtiAet al.T cell responses to SARS-CoV-2 Spike cross-recognize Omicron. Nature603(7901), 488–492 (2022).
   PubMed Web of Science ®Google Scholar
• CameroniE , BowenJE , RosenLEet al.Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift. Nature602(7898), 664–670 (2022).
   PubMed Web of Science ®Google Scholar
• HerrscherC , EymieuxS , GaboritCet al.ELISA-Based Analysis Reveals an Anti-SARS-CoV-2 Protein Immune Response Profile Associated with Disease Severity. J Clin Med11(2), 405 (2022).
   PubMed Web of Science ®Google Scholar
• AgererB , KoblischkeM , GudipatiVet al.SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8(+) T cell responses. Sci Immunol6(57), eabg6461 (2021).
   PubMed Web of Science ®Google Scholar
• MoodyR , WilsonKL , BoerJCet al.Predicted B Cell Epitopes Highlight the Potential for COVID-19 to Drive Self-Reactive Immunity. Frontiers in Bioinformatics1, 709533 (2021).
   PubMedGoogle Scholar
• KiddM , RichterA , BestAet al.S-Variant SARS-CoV-2 Lineage B1.1.7 Is Associated With Significantly Higher Viral Load in Samples Tested by TaqPath Polymerase Chain Reaction. J. Infect. Dis.223(10), 1666–1670 (2021).
   PubMed Web of Science ®Google Scholar
• ZhaoS , LouJ , CaoLet al.Quantifying the transmission advantage associated with N501Y substitution of SARS-CoV-2 in the UK: an early data-driven analysis. J Travel Med28(2), taab011 (2021).
   PubMed Web of Science ®Google Scholar
• HamedSM , ElkhatibWF , KhairallaAS , NoreddinAM. Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiology. Sci Rep11(1), 8435 (2021).
   PubMed Web of Science ®Google Scholar
• ChenRE , ZhangX , CaseJBet al.Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Nat. Med.27(4), 717–726 (2021).
   PubMed Web of Science ®Google Scholar
• WangP , NairMS , LiuLet al.Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7. Nature593(7857), 130–135 (2021).
   PubMed Web of Science ®Google Scholar
• MoxonR , RechePA , RappuoliR. Editorial: Reverse Vaccinology. Front Immunol10, 2776 (2019).
   PubMed Web of Science ®Google Scholar
• ZhangG , LiJ , AiG , HeJ , WangC , FengJ. A new intrinsic aminoglycoside 6′-N-acetyltransferase subclass, AAC(6′)-III, in Burkholderia pseudomallei, Burkholderia mallei and Burkholderia oklahomensis. J. Antimicrob. Chemother.75(5), 1352–1353 (2020).
   PubMed Web of Science ®Google Scholar
• ParvizpourS , PourseifMM , RazmaraJ , RafiMA , OmidiY. Epitope-based vaccine design: a comprehensive overview of bioinformatics approaches. Drug Discov. Today25(6), 1034–1042 (2020).
   PubMed Web of Science ®Google Scholar
• NazA , ShahidF , ButtTT , AwanFM , AliA , MalikA. Designing Multi-Epitope Vaccines to Combat Emerging Coronavirus Disease 2019 (COVID-19) by Employing Immuno-Informatics Approach. Front Immunol11, 1663 (2020).
   PubMed Web of Science ®Google Scholar
• BukhariSNH , JainA , HaqE , MehbodniyaA , WebberJ. Machine Learning Techniques for the Prediction of B-Cell and T-Cell Epitopes as Potential Vaccine Targets with a Specific Focus on SARS-CoV-2 Pathogen: A Review. Pathogens11(2), 146 (2022).
   PubMed Web of Science ®Google Scholar
• SmithCC , OlsenKS , GentryKMet al.Landscape and selection of vaccine epitopes in SARS-CoV-2. Genome Med13(1), 101 (2021).
   PubMed Web of Science ®Google Scholar
• VabretN. Antibody responses to SARS-CoV-2 short-lived. Nat Rev Immunol20(9), 519 (2020).
   PubMedGoogle Scholar
• DanJM , MateusJ , KatoYet al.Immunological memory to SARS-CoV-2 assessed for up to 8 months after infection. Science371(6529), eabf4063 (2021).
   PubMed Web of Science ®Google Scholar
• FillMalfertheiner S , BrandstetterS , RothSet al.Immune response to SARS-CoV-2 in health care workers following a COVID-19 outbreak: a prospective longitudinal study. J Clin Virol130, 104575 (2020).
   PubMed Web of Science ®Google Scholar
• WajnbergA , AmanatF , FirpoAet al.Robust neutralizing antibodies to SARS-CoV-2 infection persist for months. Science370(6521), 1227–1230 (2020).
   PubMed Web of Science ®Google Scholar
• GudbjartssonDF , NorddahlGL , MelstedPet al.Humoral Immune Response to SARS-CoV-2 in Iceland. N. Engl. J. Med.383(18), 1724–1734 (2020).
   PubMed Web of Science ®Google Scholar
• CiabattiniA , PastoreG , FiorinoFet al.Evidence of SARS-CoV-2-Specific Memory B Cells Six Months After Vaccination With the BNT162b2 mRNA Vaccine. Front Immunol12, 740708 (2021).
   PubMed Web of Science ®Google Scholar
• SnyderTM , GittelmanRM , KlingerMet al.Magnitude and Dynamics of the T-Cell Response to SARS-CoV-2 Infection at Both Individual and Population Levels. medRxiv doi:10.1101/2020.07.31.20165647 (2020).
   PubMedGoogle Scholar
• PanagiotiE , KlenermanP , LeeLN , VanDer Burg SH , ArensR. Features of Effective T Cell-Inducing Vaccines against Chronic Viral Infections. Front Immunol9, 276 (2018).
   PubMed Web of Science ®Google Scholar
• KeetonR , RichardsonSI , Moyo-GweteTet al.Prior infection with SARS-CoV-2 boosts and broadens Ad26.COV2.S immunogenicity in a variant-dependent manner. Cell Host Microbe29(11), 1611–1619e1615 (2021).
   PubMed Web of Science ®Google Scholar
• RiouC , KeetonR , Moyo-GweteTet al.Escape from recognition of SARS-CoV-2 variant Spike epitopes but overall preservation of T cell immunity. Sci Transl Med14(631), eabj6824 (2022).
   PubMed Web of Science ®Google Scholar
• TarkeA , SidneyJ , MethotNet al.Impact of SARS-CoV-2 variants on the total CD4(+) and CD8(+) T cell reactivity in infected or vaccinated individuals. Cell Rep Med2(7), 100355 (2021).
   PubMedGoogle Scholar
• CunY , LiC , ShiLet al.COVID-19 coronavirus vaccine T cell epitope prediction analysis based on distributions of HLA class I loci (HLA-A, -B, -C) across global populations. Hum Vaccin Immunother17(4), 1097–1108 (2021).
   PubMed Web of Science ®Google Scholar
• MazzoccoG , NiemiecI , MyronovAet al.AI Aided Design of Epitope-Based Vaccine for the Induction of Cellular Immune Responses Against SARS-CoV-2. Front Genet12, 602196 (2021).
   PubMed Web of Science ®Google Scholar
• HeitmannJS , BilichT , TandlerCet al.A COVID-19 peptide vaccine for the induction of SARS-CoV-2 T cell immunity. Nature601(7894), 617–622 (2022).
   PubMed Web of Science ®Google Scholar
• CrookeSN , OvsyannikovaIG , KennedyRB , PolandGA. Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome. Sci Rep10(1), 14179 (2020).
   PubMed Web of Science ®Google Scholar
• FengY , JiangH , QiuMet al.Multi-Epitope Vaccine Design Using an Immunoinformatic Approach for SARS-CoV-2. Pathogens10(6), 737 (2021).
   PubMed Web of Science ®Google Scholar
• GrifoniA , SidneyJ , ZhangY , ScheuermannRH , PetersB , SetteA. A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2. Cell Host Microbe27(4), 671–680e672 (2020).
   PubMed Web of Science ®Google Scholar
• FatobaAJ , MaharajL , AdelekeVT , OkpekuM , AdeniyiAA , AdelekeMA. Immunoinformatics prediction of overlapping CD8(+) T-cell, IFN-gamma and IL-4 inducer CD4(+) T-cell and linear B-cell epitopes based vaccines against COVID-19 (SARS-CoV-2). Vaccine39(7), 1111–1121 (2021).
   PubMed Web of Science ®Google Scholar
• KhanMT , IslamMJ , PariharAet al.Immunoinformatics and molecular modeling approach to design universal multi-epitope vaccine for SARS-CoV-2. Inform Med Unlocked24, 100578 (2021).
   PubMedGoogle Scholar
• GrifoniA , WeiskopfD , RamirezSIet al.Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals. Cell181(7), 1489–1501e1415 (2020).
   PubMed Web of Science ®Google Scholar
• PengY , MentzerAJ , LiuGet al.Broad and strong memory CD4 (+) and CD8 (+) T cells induced by SARS-CoV-2 in UK convalescent COVID-19 patients. bioRxiv doi:10.1101/2020.06.05.134551 (2020).
   Google Scholar
• BraunJ , LoyalL , FrentschMet al.SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19. Nature587(7833), 270–274 (2020).
   PubMed Web of Science ®Google Scholar
• Vider-ShalitT , RaffaeliS , LouzounY. Virus-epitope vaccine design: informatic matching the HLA-I polymorphism to the virus genome. Mol. Immunol.44(6), 1253–1261 (2007).
   PubMed Web of Science ®Google Scholar
• DeviYD , GoswamiHB , KonwarSet al.Immunoinformatics mapping of potential epitopes in SARS-CoV-2 structural proteins. PLOS ONE16(11), e0258645 (2021).
   PubMed Web of Science ®Google Scholar
• ConfortiA , MarraE , PalomboFet al.COVID-eVax, an electroporated DNA vaccine candidate encoding the SARS-CoV-2 RBD, elicits protective responses in animal models. Mol Ther30(1), 311–326 (2022).
   PubMed Web of Science ®Google Scholar
• HotezPJ , CorryDB , BottazziME. COVID-19 vaccine design: the Janus face of immune enhancement. Nat Rev Immunol20(6), 347–348 (2020).
   PubMed Web of Science ®Google Scholar
• HuismanW , MartinaBE , RimmelzwaanGF , GrutersRA , OsterhausAD. Vaccine-induced enhancement of viral infections. Vaccine27(4), 505–512 (2009).
   PubMed Web of Science ®Google Scholar
• GustianandaM , SulistyoBP , AgustriawanD , AndariniS. Immunoinformatics Analysis of SARS-CoV-2 ORF1ab Polyproteins to Identify Promiscuous and Highly Conserved T-Cell Epitopes to Formulate Vaccine for Indonesia and the World Population. Vaccines (Basel)9(12), 1459 (2021).
   PubMed Web of Science ®Google Scholar
• AlamA , KhanA , ImamNet al.Design of an epitope-based peptide vaccine against the SARS-CoV-2: a vaccine-informatics approach. Brief Bioinform22(2), 1309–1323 (2021).
   PubMed Web of Science ®Google Scholar
• TahirUl Qamar M , RehmanA , TusleemKet al.Designing of a next generation multiepitope based vaccine (MEV) against SARS-COV-2: immunoinformatics and in silico approaches. PLOS ONE15(12), e0244176 (2020).
   PubMed Web of Science ®Google Scholar
• JyotishaSingh S , QureshiIA. Multi-epitope vaccine against SARS-CoV-2 applying immunoinformatics and molecular dynamics simulation approaches. J Biomol Struct Dyn40(7), 2917–2933 (2022).
   PubMed Web of Science ®Google Scholar
• YangH , CaoJ , LinXet al.Developing an Effective Peptide-Based Vaccine for COVID-19: Preliminary Studies in Mice Models. Viruses.14(3), 449 (2022).
   PubMed Web of Science ®Google Scholar
• LiangQ , WangY , ZhangSet al.RBD trimer mRNA vaccine elicits broad and protective immune responses against SARS-CoV-2 variants. iScience25(4), 104043 (2022).
   PubMed Web of Science ®Google Scholar
• WeinreichDM , SivapalasingamS , NortonTet al.REGN-COV2, a Neutralizing Antibody Cocktail, in Outpatients with Covid-19. N. Engl. J. Med.384(3), 238–251 (2021).
   PubMed Web of Science ®Google Scholar
• ChapmanAP , TangX , LeeJRet al.Rapid development of neutralizing and diagnostic SARS-COV-2 mouse monoclonal antibodies. Sci Rep11(1), 9682 (2021).
   PubMed Web of Science ®Google Scholar
• LiL , ZhangW , HuYet al.Effect of Convalescent Plasma Therapy on Time to Clinical Improvement in Patients With Severe and Life-threatening COVID-19: A Randomized Clinical Trial. JAMA324(5), 460–470 (2020).
   PubMed Web of Science ®Google Scholar
• SalazarE , PerezKK , AshrafMet al.Treatment of Coronavirus Disease 2019 (COVID-19) Patients with Convalescent Plasma. Am. J. Pathol.190(8), 1680–1690 (2020).
   PubMed Web of Science ®Google Scholar
• KimC , RyuDK , LeeJet al.A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 Spike protein. Nat Commun12(1), 288 (2021).
   PubMed Web of Science ®Google Scholar
• CortiD , PurcellLA , SnellG , VeeslerD. Tackling COVID-19 with neutralizing monoclonal antibodies. Cell184(12), 3086–3108 (2021).
   PubMed Web of Science ®Google Scholar
• NelsonPN , ReynoldsGM , WaldronEE , WardE , GiannopoulosK , MurrayPG. Monoclonal antibodies. Mol Pathol53(3), 111–117 (2000).
   PubMedGoogle Scholar
• CaoY , SuB , GuoXet al.Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients' B Cells. Cell182(1), 73–84e16 (2020).
   PubMed Web of Science ®Google Scholar
• BaumA , FultonBO , WlogaEet al.Antibody cocktail to SARS-CoV-2 Spike protein prevents rapid mutational escape seen with individual antibodies. Science369(6506), 1014–1018 (2020).
   PubMed Web of Science ®Google Scholar
• XieJ , DingC , HeJet al.Novel Monoclonal Antibodies and Recombined Antibodies Against Variant SARS-CoV-2. Front Immunol12, 715464 (2021).
   PubMed Web of Science ®Google Scholar
• ZostSJ , GilchukP , CaseJBet al.Potently neutralizing and protective human antibodies against SARS-CoV-2. Nature584(7821), 443–449 (2020).
   PubMed Web of Science ®Google Scholar
• BrouwerPJM , CanielsTG , VanDer Straten Ket al.Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability. Science369(6504), 643–650 (2020).
   PubMed Web of Science ®Google Scholar
• UenoM , Iwata-YoshikawaN , MatsunagaAet al.Isolation of human monoclonal antibodies with neutralizing activity to a broad spectrum of SARS-CoV-2 viruses including the Omicron variants. Antiviral Res.201, 105297 doi:10.1016/j.antiviral.2022.105297 (2022).
   PubMed Web of Science ®Google Scholar
• PiepenbrinkMS , ParkJG , OladunniFSet al.Therapeutic activity of an inhaled potent SARS-CoV-2 neutralizing human monoclonal antibody in hamsters. Cell Rep Med2(3), 100218 (2021).
   PubMedGoogle Scholar
• ShanS , MokCK , ZhangSet al.A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants. Front Immunol12, 766821 (2021).
   PubMed Web of Science ®Google Scholar
• YuanM , WuNC , ZhuXet al.A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV. Science368(6491), 630–633 (2020).
   PubMed Web of Science ®Google Scholar
• PintoD , ParkYJ , BeltramelloMet al.Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature583(7815), 290–295 (2020).
   PubMed Web of Science ®Google Scholar
• HansenJ , BaumA , PascalKEet al.Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail. Science369(6506), 1010–1014 (2020).
   PubMed Web of Science ®Google Scholar
• KovacechB , FialovaL , FilipcikPet al.Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. EBioMedicine76, 103818 (2022).
   PubMed Web of Science ®Google Scholar
• TaiW , ZhangX , HeY , JiangS , DuL. Identification of SARS-CoV RBD-targeting monoclonal antibodies with cross-reactive or neutralizing activity against SARS-CoV-2. Antiviral Res.179, 104820 (2020).
   PubMed Web of Science ®Google Scholar
• LaiGC , ChaoTL , LinSYet al.Neutralization or enhancement of SARS-CoV-2 infection by a monoclonal antibody targeting a specific epitope in the Spike receptor-binding domain. Antiviral Res.200, 105290 (2022).
   PubMed Web of Science ®Google Scholar
• YuanTZ , GargP , WangLet al.Rapid discovery of diverse neutralizing SARS-CoV-2 antibodies from large-scale synthetic phage libraries. MAbs14(1), 2002236 (2022).
   PubMed Web of Science ®Google Scholar
• TanTH , PattonE , MunroCA , Corzo-LeonDE , PorterAJ , PalliyilS. Monoclonal Human Antibodies That Recognise the Exposed N and C Terminal Regions of the Often-Overlooked SARS-CoV-2 ORF3a Transmembrane Protein. Viruses13(11), 2201 (2021).
   PubMed Web of Science ®Google Scholar
• ParrayHA , ChiranjiviAK , AsthanaSet al.Identification of an anti-SARS-CoV-2 receptor-binding domain-directed human monoclonal antibody from a naive semisynthetic library. J. Biol. Chem.295(36), 12814–12821 (2020).
   PubMed Web of Science ®Google Scholar
• BarnesCO , JetteCA , AbernathyMEet al.SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature588(7839), 682–687 (2020).
   PubMed Web of Science ®Google Scholar
• JuB , ZhangQ , GeJet al.Human neutralizing antibodies elicited by SARS-CoV-2 infection. Nature584(7819), 115–119 (2020).
   PubMed Web of Science ®Google Scholar
• RogersTF , ZhaoF , HuangDet al.Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model. Science369(6506), 956–963 (2020).
   PubMed Web of Science ®Google Scholar
• MccallumM , DeMarco A , LemppFAet al.N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2. Cell184(9), 2332–2347e2316 (2021).
   PubMed Web of Science ®Google Scholar
• SuryadevaraN , ShrihariS , GilchukPet al.Neutralizing and protective human monoclonal antibodies recognizing the N-terminal domain of the SARS-CoV-2 Spike protein. Cell184(9), 2316–2331e2315 (2021).
   PubMed Web of Science ®Google Scholar
• CuiZ , LiuP , WangNet al.Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron. Cell185(5), 860–871e813 (2022).
   PubMed Web of Science ®Google Scholar
• ZhangC , WangY , ZhuYet al.Development and structural basis of a two-MAb cocktail for treating SARS-CoV-2 infections. Nat Commun12(1), 264 (2021).
   PubMed Web of Science ®Google Scholar
• WangP , CasnerRG , NairMSet al.A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. Emerg Microbes Infect11(1), 147–157 (2022).
   PubMed Web of Science ®Google Scholar
• SauerMM , TortoriciMA , ParkYJet al.Structural basis for broad coronavirus neutralization. Nat Struct Mol Biol28(6), 478–486 (2021).
   PubMed Web of Science ®Google Scholar
• ZhouP , YuanM , SongGet al.A human antibody reveals a conserved site on beta-coronavirus Spike proteins and confers protection against SARS-CoV-2 infection. bioRxiv doi:10.1101/2021.03.30.437769 (2022).
   Google Scholar
• YangL , LiuW , YuX , WuM , ReichertJM , HoM. COVID-19 antibody therapeutics tracker: a global online database of antibody therapeutics for the prevention and treatment of COVID-19. Antib Ther3(3), 205–212 (2020).
   PubMedGoogle Scholar
• HoffmannM , AroraP , GrossRet al.SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies. Cell184(9), 2384–2393e2312 (2021).
   PubMed Web of Science ®Google Scholar
• TadaT , DcostaBM , ZhouH , VaillA , KazmierskiW , LandauNR. Decreased neutralization of SARS-CoV-2 global variants by therapeutic anti-Spike protein monoclonal antibodies. bioRxiv doi:10.1101/2021.02.18.431897 (2021).
   Google Scholar
• YueS , LiZ , LinYet al.Sensitivity of SARS-CoV-2 Variants to Neutralization by Convalescent Sera and a VH3-30 Monoclonal Antibody. Front Immunol12, 751584 (2021).
   PubMed Web of Science ®Google Scholar
• LiQ , WuJ , NieJet al.The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. Cell182(5), 1284–1294e1289 (2020).
   PubMed Web of Science ®Google Scholar
• LiW , ChenY , PrevostJet al.Structural basis and mode of action for two broadly neutralizing antibodies against SARS-CoV-2 emerging variants of concern. Cell Rep38(2), 110210 (2022).
   PubMed Web of Science ®Google Scholar
• HuangKA , ZhouD , TanTKet al.Structures and therapeutic potential of anti-RBD human monoclonal antibodies against SARS-CoV-2. Theranostics12(1), 1–17 (2022).
   PubMed Web of Science ®Google Scholar
• TzouPL , TaoK , PondSLK , ShaferRW. Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons. PLOS One17(3), e0261045 (2022).
   PubMed Web of Science ®Google Scholar
• HansenJ , BaumA , PascalKEet al.Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail. Science369(6506), 1010–1014 (2020).
   PubMed Web of Science ®Google Scholar
• AbdicheYN , MalashockDS , PinkertonA , PonsJ. Exploring blocking assays using Octet, ProteOn, and Biacore biosensors. Anal. Biochem.386(2), 172–180 (2009).
   PubMed Web of Science ®Google Scholar
• BrooksBD , ClosmoreA , YangJet al.Characterizing Epitope Binding Regions of Entire Antibody Panels by Combining Experimental and Computational Analysis of Antibody: Antigen Binding Competition. Molecules25(16), 3659 (2020).
   PubMed Web of Science ®Google Scholar
• WangY-T , AllenRD , KimKet al.SARS-CoV-2 monoclonal antibodies with therapeutic potential: broad neutralizing activity and No evidence of antibody-dependent enhancement. Antiviral Res.195, 105185 (2021).
   PubMed Web of Science ®Google Scholar
• RosenthalPJ. The Importance of Diagnostic Testing during a Viral Pandemic: Early Lessons from Novel Coronavirus Disease (COVID-19). Am. J. Trop. Med. Hyg.102(5), 915–916 (2020).
   PubMed Web of Science ®Google Scholar
• VandenbergO , MartinyD , RochasO , Van BelkumA , KozlakidisZ. Considerations for diagnostic COVID-19 tests. Nat Rev Microbiol19(3), 171–183 (2021).
   PubMed Web of Science ®Google Scholar
• YamaokaY , MiyakawaK , JeremiahSSet al.Highly specific monoclonal antibodies and epitope identification against SARS-CoV-2 nucleocapsid protein for antigen detection tests. Cell Rep Med2(6), 100311 (2021).
   PubMedGoogle Scholar
• PandaPK , ArulMN , PatelPet al.Structure-based drug designing and immunoinformatics approach for SARS-CoV-2. Sci Adv6(28), eabb8097 (2020).
   PubMed Web of Science ®Google Scholar
• XiangF , WangX , HeXet al.Antibody Detection and Dynamic Characteristics in Patients With Coronavirus Disease 2019. Clin. Infect. Dis.71(8), 1930–1934 (2020).
   PubMed Web of Science ®Google Scholar
• BurbeloPD , RiedoFX , MorishimaCet al.Sensitivity in Detection of Antibodies to Nucleocapsid and Spike Proteins of Severe Acute Respiratory Syndrome Coronavirus 2 in Patients With Coronavirus Disease 2019. J. Infect. Dis.222(2), 206–213 (2020).
   PubMed Web of Science ®Google Scholar
• TianX , MoC , ZhouLet al.Epitope mapping of severe acute respiratory syndrome-related coronavirus nucleocapsid protein with a rabbit monoclonal antibody. Virus Res.300, 198445 (2021).
   PubMed Web of Science ®Google Scholar
• TianY , ZhangG , LiuHet al.Screening and identification of B cell epitope of the nucleocapsid protein in SARS-CoV-2 using the monoclonal antibodies. Appl. Microbiol. Biotechnol.106(3), 1151–1164 (2022).
   PubMed Web of Science ®Google Scholar
• LeeJ-H , JungY , LeeS-Ket al.Rapid Biosensor of SARS-CoV-2 Using Specific Monoclonal Antibodies Recognizing Conserved Nucleocapsid Protein Epitopes. Viruses14(2), 255 (2022).
   PubMed Web of Science ®Google Scholar
• NielsenM , LundegaardC , WorningPet al.Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics. 20(9), 1388–1397 (2004).
   PubMed Web of Science ®Google Scholar
• Sanchez-TrincadoJL , Gomez-PerosanzM , RechePA. Fundamentals and Methods for T- and B-Cell Epitope Prediction. J Immunol. Res. 2017, 2680160 (2017).
   PubMed Web of Science ®Google Scholar
• BianH , HammerJ. Discovery of promiscuous HLA-II-restricted T cell epitopes with TEPITOPE. Methods (San Diego, Calif.). 34(4), 468–475 (2004).
   PubMed Web of Science ®Google Scholar
• GuanP , DoytchinovaIA , ZygouriC , FlowerDR. MHCPred: a server for quantitative prediction of peptide–MHC binding. Nucleic Acids Res. 31(13), 3621–3624 (2003).
   PubMed Web of Science ®Google Scholar
• PetersB , TongW , SidneyJ , SetteA , WengZ. Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules. Bioinformatics. 19(14), 1765–1772 (2003).
   PubMed Web of Science ®Google Scholar
• LemanJK , MuellerR , KarakasM , WoetzelN , MeilerJ. Simultaneous prediction of protein secondary structure and transmembrane spans. Proteins. 81(7), 1127–1140 (2013).
   PubMed Web of Science ®Google Scholar
• SchmitzAJ , TurnerJS , LiuZet al.Avaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. Immunity. 54(9), 2159–2166; e2156 (2021).
   PubMed Web of Science ®Google Scholar