From Genetics to Epigenetics: Top 4 Aspects for Improved SARS-CoV-2 Vaccine Designs as Paradigmatic Examples

Abstract

This literature review described the genetic and biochemical factors that may have been overlooked in the formulation of vaccines and that most likely underlie possible issues with mass vaccination.

Keywords

vaccines / immunization / (epi) genetic factors

Funding

None.

Conflict of Interest

None declared.

References

[1] Halstead SB.Which dengue vaccine approach is the most promising, and should we be concerned about enhanced disease after vaccination? There is only one true winner. Cold Spring Harb Perspect Biol 2018; 10(06): a030700

[2] Boehm E, Kronig I, Neher RA, Eckerle I, Vetter P, Kaiser L.Geneva Centre for Emerging Viral Diseases. Novel SARS-CoV-2 variants: the pandemics within the pandemic. Clin Microbiol Infect 2021; 27(08): 1109-1117

[3] Kanduc D, Stufano A, Lucchese G, Kusalik A.Massive peptide sharing between viral and human proteomes. Peptides 2008; 29(10): 1755-1766

[4] Trost B, Lucchese G, Stufano A, Bickis M, Kusalik A, Kanduc D.No human protein is exempt from bacterial motifs, not even one. Self Nonself 2010; 1(04): 328-334

[5] Kanduc D.Peptide cross-reactivity: the original sin of vaccines. Front Biosci (Schol Ed) 2012; 4: 1393-1401

[6] Kanduc D.From Anti-SARS-CoV-2 Immune Responses to COVID-19 via Molecular Mimicry. Antibodies (Basel) 2020; 9(03): 33

[7] Woodruff MC, Ramonell RP, Nguyen DC.et al.Extrafollicular B cell responses correlate with neutralizing antibodies and morbidity in COVID-19. Nat Immunol 2020; 21(12): 1506-1516

[8] Huang AT, Garcia-Carreras B, Hitchings MDT.et al.A systematic review of antibody mediated immunity to coronaviruses: kinetics, correlates of protection, and association with severity. Nat Commun 2020; 11(01): 4704

[9] Legros V, Denolly S, Vogrig M.et al.A longitudinal study of SARS-CoV-2-infected patients reveals a high correlation between neutralizing antibodies and COVID-19 severity. Cell Mol Immunol 2021; 18(02): 318-327

[10] Chen Y, Zuiani A, Fischinger S.et al. Quick COVID-19 healers sustain anti-SARS-CoV-2 antibody production. Cell2020; 183 (06): 1496-1507.e16

[11] Garcia-Beltran WF, Lam EC, Astudillo MG.et al. COVID-19-neutralizing antibodies predict disease severity and survival. Cell2021; 184 (02): 476-488.e11

[12] Wang EY, Mao T, Klein J.et al; Yale IMPACT Team. Diverse functional autoantibodies in patients with COVID-19. Nature 2021; 595(7866): 283-288

[13] Cappello F.Is COVID-19 a proteiform disease inducing also molecular mimicry phenomena?. Cell Stress Chaperones 2020; 25(03): 381-382

[14] Karami A, Bookstaver B, Nolan M, Bozorgi P.Investigating diseases and chemicals in COVID-19 literature with text mining. IJIM Data Insights 2021; 1(02): 100016

[15] Kanduc D.Rare human codons and HCMV translational regulation. J Mol Microbiol Biotechnol 2017; 27(04): 213-216

[16] Kanduc D.Human codon usage: the genetic basis of pathogen latency. Glob Med Genet 2021; 8(03): 109-115

[17] Xia X.Detailed dissection and critical evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines. Vaccines (Basel) 2021; 9(07): 734

[18] Folegatti PM, Ewer KJ, Aley PK.et al; Oxford COVID Vaccine Trial Group. 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(10249): 467-478

[19] Hogan RJ. Are nonhuman primates good models for SARS?. PLoS Med2006; 3 (09): e411 , author reply e415

[20] Roberts A, Paddock C, Vogel L, Butler E, Zaki S, Subbarao K.Aged BALB/c mice as a model for increased severity of severe acute respiratory syndrome in elderly humans. J Virol 2005; 79(09): 5833-5838

[21] Nagata N, Iwata-Yoshikawa N, Taguchi F.Studies of severe acute respiratory syndrome coronavirus pathology in human cases and animal models. Vet Pathol 2010; 47(05): 881-892

[22] Kanduc D, Shoenfeld Y.Molecular mimicry between SARS-CoV-2 spike glycoprotein and mammalian proteomes: implications for the vaccine. Immunol Res 2020; 68(05): 310-313

[23] Kanduc D.Lack of molecular mimicry between nonhuman primates and infectious pathogens: the possible genetic bases. Glob Med Genet 2021; 8(01): 32-37

[24] Gonçalves A, Maisonnasse P, Donati F.et al.SARS-CoV-2 viral dynamics in non-human primates. PLOS Comput Biol 2021; 17(03): e1008785

[25] van Doremalen N, Lambe T, Spencer A.et al. ChAdOx1 nCoV-19 vaccine prevents SARS-CoV-2 pneumonia in rhesus macaques. Nature 2020; 586(7830): 578-582

[26] Khehra N, Padda I, Jaferi U, Atwal H, Narain S, Parmar MS.Tozinameran (BNT162b2) vaccine: the journey from preclinical research to clinical trials and authorization. AAPS Pharm SciTech 2021; 22(05): 172

[27] Dulbecco R, Unger M, Bologna M, Battifora H, Syka P, Okada S.Cross-reactivity between Thy-1 and a component of intermediate filaments demonstrated using a monoclonal antibody. Nature 1981; 292(5825): 772-774

[28] Lafer EM, Rauch J, Andrzejewski Jr C.et al.Polyspecific monoclonal lupus autoantibodies reactive with both polynucleotides and phospholipids. J Exp Med 1981; 153(04): 897-909

[29] Muso E, Jacob L.A polyspecific monoclonal anti-DNA autoantibody also binds to cell-surface protein(s). Clin Immunol Immunopathol 1987; 42(03): 370-374

[30] Laster AJ, Pisetsky DS, Haynes BF.Polyspecific reactivity of a murine monoclonal antibody that binds to nuclear matrix-associated, chromatin-bound autoantigens. Clin Immunol Immunopathol 1987; 44(02): 187-205

[31] Garzelli C, Basolo F, Puglisi C, Pacciardi A.Multiple organ-reactivity of monoclonal autoantibodies to mouse erythrocytes. Experientia 1987; 43(08): 912-914

[32] Willers J, Lucchese A, Kanduc D, Ferrone S.Molecular mimicry of phage displayed peptides mimicking GD3 ganglioside. Peptides 1999; 20(09): 1021-1026

[33] Haynes BF, Fleming J, St Clair EW.et al.Cardiolipin polyspecific autoreactivity in two broadly neutralizing HIV-1 antibodies. Science 2005; 308(5730): 1906-1908

[34] Moreira ML, Dorneles EM, Soares RP.et al.Cross-reactivity of commercially available anti-human monoclonal antibodies with canine cytokines: establishment of a reliable panel to detect the functional profile of peripheral blood lymphocytes by intracytoplasmic staining. Acta Vet Scand 2015; 57(01): 51

[35] Cho MJ, Ellebrecht CT, Hammers CM.et al.Determinants of VH1-46 cross-reactivity to Pemphigus vulgaris autoantigen desmoglein 3 and rotavirus antigen VP6. J Immunol 2016; 197(04): 1065-1073

[36] Wang EQ, Bukowski JF, Yunis C.et al.Assessing the potential risk of cross-reactivity between anti-bococizumab antibodies and other anti-PCSK9 monoclonal antibodies. BioDrugs 2019; 33(05): 571-579

[37] Kelly RL, Zhao J, Le D, Wittrup KD.Nonspecificity in a nonimmune human scFv repertoire. MAbs 2017; 9(07): 1029-1035

[38] Li L, Wang XH, Nanfack A, Kong XP, Gorny MK.The light chain of antibodies specific to the V2 region of HIV-1 can determine their function. Hum Immunol 2021; 82(12): 923-929

[39] Jiang W, Wang J, Jiao S.et al.Characterization of MW06, a human monoclonal antibody with cross-neutralization activity against both SARS-CoV-2 and SARS-CoV. MAbs 2021; 13(01): 1953683

[40] Pinto D, Sauer MM, Czudnochowski N.et al.Broad betacoronavirus neutralization by a stem helix-specific human antibody. Science 2021; 373(6559): 1109-1116

[41] Lucchese G, Stufano A, Kanduc D.Proposing low-similarity peptide vaccines against Mycobacterium tuberculosis. J Biomed Biotechnol 2010; 2010: 832341 DOI: 10.1155/2010/832341.

[42] Kanduc D.Oligopeptides for immunotherapy approaches in ovarian cancer treatment. Curr Drug Discov Technol 2019; 16(03): 285-289

[43] Lucchese A, Mittelman A, Tessitore L, Serpico R, Sinha AA, Kanduc D.Proteomic definition of a desmoglein linear determinant common to Pemphigus vulgaris and Pemphigus foliaceous. J Transl Med 2006; 4: 37

[44] Abrams S, Kourkouni E, Sabbe M, Beutels P, Hens N.Inferring rubella outbreak risk from seroprevalence data in Belgium. Vaccine 2016; 34(50): 6187-6192

[45] Ahmed A, Sahota A, Stephenson I, Brown KE, Tang JW.Measles - A tale of two sisters, vaccine failure, and the resurgence of an old foe. J Infect 2017; 74(03): 318-320

[46] Clifford HD, Hayden CM, Khoo SK.et al.Genetic variants in the IL-4/IL-13 pathway influence measles vaccine responses and vaccine failure in children from Mozambique. Viral Immunol 2017; 30(07): 472-478

[47] Corcoran M, Mereckiene J, Cotter S.et al.Using genomics to examine the persistence of Streptococcus pneumoniae serotype 19A in Ireland and the emergence of a sub-clade associated with vaccine failures. Vaccine 2021; 39(35): 5064-5073

[48] Hahné SJ, Nic Lochlainn LM, van Burgel ND. et al. Measles outbreak among previously immunized healthcare workers, the Netherlands, 2014. J Infect Dis 2016; 214(12): 1980-1986

[49] Haralambieva IH, Ovsyannikova IG, Kennedy RB.et al.Genome-wide associations of CD46 and IFI44L genetic variants with neutralizing antibody response to measles vaccine. Hum Genet 2017; 136(04): 421-435

[50] Hong E, Terrade A, Denizon M.et al.Haemophilus influenzae type b (Hib) seroprevalence in France: impact of vaccination schedules. BMC Infect Dis 2021; 21(01): 715

[51] Iwamoto M, Hickman CJ, Colley H.et al.Measles infection in persons with secondary vaccine failure, New York City, 2018-19. Vaccine 2021; 39(38): 5346-5350

[52] King JP, McLean HQ, Meece JK. et al. Vaccine failure and serologic response to live attenuated and inactivated influenza vaccines in children during the 2013-2014 season. Vaccine 2018; 36(09): 1214-1219

[53] Leung J, Broder KR, Marin M.Severe varicella in persons vaccinated with varicella vaccine (breakthrough varicella): a systematic literature review. Expert Rev Vaccines 2017; 16(04): 391-400

[54] López López S, Del Rosal T, Jiménez Bueno S, Baquero-Artigao F.Septicemia and meningitis associated with Haemophilus influenzae type b vaccine failure. Enferm Infecc Microbiol Clin (Engl Ed) 2021; 39(08): 417-418

[55] Magez S, Li Z, Nguyen HTT.et al.The history of anti-trypanosome vaccine development shows that highly immunogenic and exposed pathogen-derived antigens are not necessarily good target candidates: enolase and ISG75 as examples. Pathogens 2021; 10(08): 1050

[56] McMickle RJ, Fryling L, Fleischman RJ. Acute demyelinating encephalomyelitis following measles infection due to vaccine failure: a case report. Clin Pract Cases Emerg Med 2021; 5(02): 171-173

[57] Miller C, Emanuelli M, Fink E.et al.FIV vaccine with receptor epitopes results in neutralizing antibodies but does not confer resistance to challenge. NPJ Vaccines 2018; 3: 16

[58] Oligbu G, Hsia Y, Folgori L, Collins S, Ladhani S.Pneumococcal conjugate vaccine failure in children: A systematic review of the literature. Vaccine 2016; 34(50): 6126-6132

[59] Ringel O, Vieillard V, Debré P, Eichler J, Büning H, Dietrich U.The hard way towards an antibody-based HIV-1 Env vaccine: lessons from other viruses. Viruses 2018; 10(04): 197

[60] Rzymski P, Pazgan-Simon M, Simon K, et al. Clinical characteristics of hospitalized COVID-19 patients who received at least one dose of COVID-19 vaccine. Vaccines (Basel) 2021; 9(07): 781

[61] Sütçü M, Aktürk H, Karagözlü F, Somer A, Gürler N, Salman N. Empyema due to Streptococcus pneumoniae serotype 9V in a child immunized with 13-valent conjugated pneumococcal vaccine. Balkan Med J 2017; 34(01): 74-77

[62] Tai CS, Wu JF, Chen HL, Ni YH, Hsu HY, Chang MH. The impact of hepatitis B vaccine failure on long-term natural course of chronic hepatitis B virus infection in hepatitis b e antigen-seropositive children. J Infect Dis 2017; 216(06): 662-669

RIGHTS & PERMISSIONS

Global Medical Genetics