Suhana Mishra, Amir Mohammad Arsh , Varnit Chauhan
School of Biotechnology, Gautam Buddha University, Greater NOIDA, UttarPradesh, India
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With the Introduction of COVID-19 vaccine to the world, Proteomic studies of SARS-CoV-2 revealed that some regions are conserved from other human coronaviruses(CoVs) which leads to cross-recognition by the humoral immune response. Epitopes that are conserved among SARS-like coronaviruses are attractive targets for design of cross-reactive vaccines and therapeutics. The cross-reactivity of the antibodies can neutralise the SARS-CoV-2 strains on the basis of the conserved epitope regions in the structure. Considering the conservation a study found few sites of S2 subunit of Spike protein in SARS CoV 2 that have significant cross reactivity as well as cross neutralization and hence can be the potential contestant for a vaccine that will provide a broad and faster immunization. These epitopes show potential for cross-neutralization and hence can serve as the potential base for immunization and therapeutic development against SARS-CoV-2 and it’s strains.
The Coronaviridea family is a group of RNA viruses infecting a wide range of organisms including vertebrates. It consists of the largest known RNA viruses ranging from 25-32kb with virions of diameter 118-140nm . The family can be divided into two subfamilies, the Coronavirinae and the Torovirinae on the basis of their nucleocapsid. The coronavirinae subfamily can be further divided into four genera, α, β, Ɣ and δ. All family member follow the same mRNA synthesis strategy in which the complex polymerase leaps or transfers from one region of the prototype to a more distant region.The high rate of RNA recombination that occurs during genome replication may explain the need for the polymerase complex to dissociate from the template.Various member of this family infect a broad range of vertebrate, reflecting symptoms from common cold to severe fatal illnesses diseases such as MERS, SARS, the recent pandemic COVID-19. The COVID-19 pandemic originated from Wuhan, China was a result of an outbreak caused by an enveloped, single-stranded positive-sense RNA virus known as SARS-CoV-2 which belonged to the group 2 of the betacoronavirus of the Coronaviridea family(subfamily coronaviridea)[4,5]. SARS-CoV-2 is one of the members of the humans infecting CoV family, belonging to the same lineage of viruses that cause SARS. Before 2019, six human infecting virus of CoV family namely CoV 229E (HCoV-229E), HCoV-NL63, HCoV-OC43, HCoV-HKU1, SARS-CoV, and MERS-CoV were known, but being genetically mutated the novel Coronavirus SARS-CoV-2 spread as a pandemic resulting in severe to mild upper respiratory tract infections and very high death toll. Closely relating the genome of SARS-COV-2 with that of the other members of the CoV family indicates that the sequence coding for the spike protein (1273 amino acids) has 27 amino acids substitution, receptor-binding area (RBD) has six of these substitutions and six more are in the underlying subdomain (SD). Phylogenetic analysis of the SARS-CoV-2 revealed that it is 88% similar to that of SARS-like CoVs (bat-SL-CoVZC45 and bat-SL-CoVZXC21) in bats. It is also genetically similar to SARS-CoV and MERS-CoV nearly 79% and 50% respectively.
S Protein is abundant, clove shaped, type-I viral transmembrane, multifunctional proteins having three segments: a single-pass transmembrane, ectodomain and an intracellular tail. The S protein ectodomain contains S1 subunit, having a receptor-binding domain(RBD), along with a membrane fusion subunit (S2). In the initial step of viral infection the RBD on the S proteins recognise the host-cell receptor, the binding interaction between the host receptor and spike protein is the critical factor determining the cross-species transmission and host range. Coronavirus that infects humans (like HCoV-229E) recognises hAPN (human aminopeptidase N ) along with a wide variety of host receptors [15,16], and ACE2(angiotensin-converting enzyme 2) is recognized by SARS-CoV. Since S protein is common among all the corona family members, hence it is the major target for eliciting antibodies.
The structure of M Protein includes three domains – Amino terminus domain(outside the virion), Transmembrane domain, and Carboxyl terminus domain(inside the virion) . The membrane proteinM protein) gives the defined shape – by M-M interaction – to the envelope along with being the most abundant protein of the virion . Coronavirus M proteins maintain structural similarity along different genera despite the high diversity in amino acid content . Studies of genome composition and divergence of SARS CoV-2 revealed the amino acid composition of M protein is the same as that of SARS CoV .
The smallest structural protein of coronavirus – E protein – also has three domains similar to M protein. Amino terminal of E protein is hydrophilic and the transmembrane domain is hydrophobic in nature . Along with functioning as viroporin(integral membrane polypeptide ion channel) it also plays a role in pathogenesis, assembly and release of virus [21, 22]. Absence/inactivation of this protein in coronavirus cause morphological and tropism change which in turn alters the virulence . Similar to M protein the amino acid composition is the same in both SARS CoV and SARS CoV-2 .
Likewise other two proteins – M protein and E protein – structure of N protein also have three domains, namely, a NTD, a linker-region(LKR – binds to RNA) and the last Carboxy terminal domain . The linker-region is rochin Serine and Arginine hence also called SR domain . In terms of function N protein serves as multipurpose protein. It has a role in complex formation with the viral genome along with enhancing the transcription efficacy of viruses. It also helps M protein interaction while assembly of the virion[26,27]. In comparison with SARS CoV five amino acid mutations were found – two in IDR(intrinsically dispersed region; position 25 and 26), one in each domain(NTD-position 103, LKR-position 217 and CTD-position 334) .
PUBLIC EPITOPES BETWEEN SARS-CoV-2 AND OTHER CORONAVIRUS STRAINS
SARS-CoV and MERS-CoV have the highest predicted SARS-CoV-2 epitopes, with individuals more commonly affected with 229E, HKU1, NL63 and OC43. 112 single peptides of 794 (14%) predicted SARS-CoV-2 epitopes, shared with four common coronaviruses with high sequence similarity. Of the 112, 21 (794; 2.6%) peptides had precise matches of SARS-CoV-2 and 36 (794; 4.5%, 794: 6.9%), had one and two mismatches respectively.
ACE2 INDEPENDENT RECEPTORS IN VIRAL PATHOGENESIS
It’s already known that both SARS-CoV-2 and SARS-CoV use hACE2 receptors for the viral entry in the host cell [29,30], however lectins and vimentin are also exploited by SARS-CoV for the cell entry [31,32]. ACE-2 as well as a C-type lectin can be used by SARS-CoV to attack host cells . In contrast some research suggested that mannetic lectins interfere with viral entry, by blocking possible other interactions. SARS-CoV-2 appears to infect various cell types and it is thus fair to speculate about the possibility of an alternative route of viral invasion through separate ACE2-interactions. Because of the relevance of this subject and its huge effects on human lives, future research would need to closely assess if Non-ACE2 interactions in ACE2 are in competition to prevent viral entry or if ACE2-independent interactions have a synergistic influence with ACE2-mediated entry to intensify COVID-19 symptoms.
CROSS-REACTIVITY BETWEEN CORONAVIRUS AND INFLUENZA VIRUS
A study from Oxford found out that there is minimal potential of cross reactivity between coronavirus, specifically SARS CoV-2, and influenza virus. In this study 4,800+ epitopes from all strains of coronavirus were compared with 1,334 MHC-I influenza virus-derived epitopes .
CROSS REACTIVITY BETWEEN SARS CoV AND SARS CoV-2
According to study done, SARS CoV 2 infected patients showed antibody response towards s-protein and Receptor binding domain(RBD) of S1, on detection of Cross reactivity towards SARS CoV it was seen that cross-reactive antibodies showed response to both RBD and Non-RBD regions. On comparing sequences of SARS CoV and SARS CoV 2, S2 subunits of Spike protein have the highest conservation. Further advancement in studies resulted in the fact that even cross reactivity was significantly high, chances of cross neutralization were rare in the cohort . Considering the conservation a study found two sites, namely HR2 and FP, of S2 subunit of Spike protein in SARS CoV 2 that have significant cross reactivity as well as cross neutralization and hence can be the potential contestant for vaccine that will provide a broad and faster immunization 
The SARS-CoV-2 Spike S2 subunit consists of broadly immunogenic epitopes in conserved functional domains, including cross-reactivity with endemic HCoVs. HR2 and FP being conserved, functionally important and immunogenic sites, can elicit cross-reacting antibodies and hence can serve as potential regions for the development of broadly neutralizing responses against CoVs. Spike HR2 and FP sites vaccines may provoke a wide neutralizing spectrum of reactions, may be able more quickly to attract populations of preexisting memory B cells and may be less vulnerable to the viral escape because they have a lower tolerance for the substitution of amino acid. Future research could solve the functioning implications of such cross-reactive antibody responses and the potential impact on an individual’s history of sensitivity to endemic CoVs.
Payne S. Family Coronaviridae. Viruses. 2017:149–58. doi: 10.1016/B978-0-12-803109-4.00017-9. Epub 2017 Sep 1. PMCID: PMC7149805.
Andrew M.Q. King, Michael J. Adams, Eric B. Carstens, Elliot J. Lefkowitz, Virus Taxonomy, Elsevier, 2012, Pages 806-828, ISBN 9780123846846, https://doi.org/10.1016/B978-0-12-384684-6.00068-9.(https://www.sciencedirect.com/science/article/pii/B9780123846846000689)
Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, Niu P, Zhan F, Ma X, Wang D, Xu W, Wu G, Gao GF, Tan W, China Novel Coronavirus Investigating and Research Team. 2020. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med 382:727–733. https://doi.org/10.1056/NEJMoa2001017.
Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol. 2020 Apr;5(4):536-544. doi: 10.1038/s41564-020-0695-z. Epub 2020 Mar 2. PMID: 32123347; PMCID: PMC7095448.
Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, Si HR, Zhu Y, Li B, Huang CL, Chen HD, Chen J, Luo Y, Guo H, Jiang RD, Liu MQ, Chen Y, Shen XR, Wang X, Zheng XS, Zhao K, Chen QJ, Deng F, Liu LL, Yan B, Zhan FX, Wang YY, Xiao GF, Shi ZL. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020 Mar;579(7798):270-273. doi: 10.1038/s41586-020-2012-7. Epub 2020 Feb 3. PMID: 32015507; PMCID: PMC7095418.
Wei X, Li X, Cui J. 2020. Evolutionary perspectives on novel coronaviruses identified in pneumonia cases in China. Natl Sci Rev 7:239 –242. https://doi.org/10.1093/nsr/nwaa009.
Wu A, Peng Y, Huang B, Ding X, Wang X, Niu P, Meng J, Zhu Z, Zhang Z, Wang J, Sheng J, Quan L, Xia Z, Tan W, Cheng G, Jiang T. 2020. Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China. Cell Host Microbe 27:325–328. https://doi.org/10.1016/j.chom.2020.02.001.
Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, Wang W, Song H, Huang B, Zhu N, Bi Y, Ma X, Zhan F, Wang L, Hu T, Zhou H, Hu Z, Zhou W, Zhao L, Chen J, Meng Y, Wang J, Lin Y, Yuan J, Xie Z, Ma J, Liu WJ, Wang D, Xu W, Holmes EC, Gao GF, Wu G, Chen W, Shi W, Tan W. 2020. Genomic characterization and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet 395:565–574. https://doi.org/10.1016/S0140-6736(20)30251-8.
Lan J, Ge J, Yu J, Shan S, Zhou H, et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature. 2020;581: 215–220. 10.1038/s41586-020-2180-5
Hofmann H, Pohlmann S. Cellular entry of the SARS coronavirus. Trends Microbiol. 2004;12: 466–472. 10.1016/j.tim.2004.08.008
Vennema H, Godeke GJ, Rossen JW, Voorhout WF, Horzinek MC, et al. Nucleocapsid-independent assembly of coronavirus-like particles by co-expression of viral envelope protein genes. EMBO J. 1996;15: 2020–2028. 10.1002/j.1460-2075.1996.tb00553.x
Siu YL, Teoh KT, Lo J, Chan CM, Kien F, et al. The M, E, and N structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of virus-like particles. J Virol. 2008;82: 11318–11330. 10.1128/JVI.01052-08
Gao Y, Yan L, Huang Y, Liu F, Zhao Y, et al. Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science. 2020;368: 779–782. 10.1126/science.abb7498
Snijder EJ, Decroly E, Ziebuhr J. The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing. Adv Virus Res. 2016;96: 59–126. 10.1016/bs.aivir.2016.08.008
Mittal A, Manjunath K, Ranjan RK, Kaushik S, Kumar S, Verma V. COVID-19 pandemic: Insights into structure, function, and hACE2 receptor recognition by SARS-CoV-2. PLoS Pathog. 2020 Aug 21;16(8):e1008762. doi: 10.1371/journal.ppat.1008762. PMID: 32822426; PMCID: PMC7444525.
Wentworth DE, Holmes KV. Molecular determinants of species specificity in the coronavirus receptor aminopeptidase N (CD13): influence of N-linked glycosylation. J Virol. 2001; 75: 9741–9752. https://doi. org/10.1128/JVI.75.20.9741-9752.2001 PMID: 11559807
Arndt, A. L., Larson, B. J., & Hogue, B. G. (2010). A conserved domain in the coronavirus membrane protein tail is important for virus assembly. Journal of virology, 84(21), 11418-11428.
Nal, B., Chan, C., Kien, F., Siu, L., Tse, J., Chu, K., … & Altmeyer, R. (2005). Differential maturation and subcellular localization of severe acute respiratory syndrome coronavirus surface proteins S, M and E. Journal of general virology, 86(5), 1423-1434.
Neuman, B. W., Kiss, G., Kunding, A. H., Bhella, D., Baksh, M. F., Connelly, S., … & Buchmeier, M. J. (2011). A structural analysis of M protein in coronavirus assembly and morphology. Journal of structural biology, 174(1), 11-22.
Schoeman, D., & Fielding, B. C. (2019). Coronavirus envelope protein: current knowledge. Virology journal, 16(1), 1-22.
Nieto-Torres, J. L., DeDiego, M. L., Verdiá-Báguena, C., Jimenez-Guardeño, J. M., Regla-Nava, J. A., Fernandez-Delgado, R., … & Enjuanes, L. (2014). Severe acute respiratory syndrome coronavirus envelope protein ion channel activity promotes virus fitness and pathogenesis. PLoS Pathog, 10(5), e1004077.
Pervushin, K., Tan, E., Parthasarathy, K., Lin, X., Jiang, F. L., Yu, D., … & Torres, J. (2009). Structure and inhibition of the SARS coronavirus envelope protein ion channel. PLoS Pathog, 5(7), e1000511.
DeDiego, M. L., Álvarez, E., Almazán, F., Rejas, M. T., Lamirande, E., Roberts, A., … & Enjuanes, L. (2007). A severe acute respiratory syndrome coronavirus that lacks the E gene is attenuated in vitro and in vivo. Journal of virology, 81(4), 1701-1713.
McBride, R., Van Zyl, M., & Fielding, B. C. (2014). The coronavirus nucleocapsid is a multifunctional protein. Viruses, 6(8), 2991-3018.
Hurst, K. R., Koetzner, C. A., & Masters, P. S. (2009). Identification of in vivo-interacting domains of the murine coronavirus nucleocapsid protein. Journal of virology, 83(14), 7221-7234.
Chang, C. K., Sue, S. C., Yu, T. H., Hsieh, C. M., Tsai, C. K., Chiang, Y. C., … & Huang, T. H. (2006). Modular organization of SARS coronavirus nucleocapsid protein. Journal of biomedical science, 13(1), 59-72.
Sheikh, A., Al-Taher, A., Al-Nazawi, M., Al-Mubarak, A. I., & Kandeel, M. (2020). Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design. Journal of virological methods, 277, 113806.
Lee CH, Pinho MP, Buckley PR, Woodhouse IB, Ogg G, Simmons A, Napolitani G, Koohy H. Potential CD8+ T Cell Cross-Reactivity Against SARS-CoV-2 Conferred by Other Coronavirus Strains. Front Immunol. 2020 Nov 5;11:579480. Doi: 10.3389/fimmu.2020.579480. PMID: 33250893; PMCID: PMC7676914.
Li F. Structure, Function, and Evolution of Coronavirus Spike Proteins. Annu Rev Virol. 2016; 3: 237–261. https://doi.org/10.1146/annurev-virology-110615-042301 PMID: 27578435
Hoffmann M, Kleine-Weber H, Schroeder S, Kruger N, Herrler T, et al. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell. 2020; 181: 271–280 e278. https://doi.org/10.1016/j.cell.2020.02.052 PMID: 32142651
Yu YT, Chien SC, Chen IY, Lai CT, Tsay YG, et al. Surface vimentin is critical for the cell entry of SARSCoV. J Biomed Sci. 2016; 23: 14. https://doi.org/10.1186/s12929-016-0234-7 PMID: 26801988
Jeffers SA, Tusell SM, Gillim-Ross L, Hemmila EM, Achenbach JE, et al. CD209L (L-SIGN) is a receptor for severe acute respiratory syndrome coronavirus. Proc Natl Acad Sci U S A. 2004; 101: 15748–15753. https://doi.org/10.1073/pnas.0403812101 PMID: 15496474
Lee, C. H., Pinho, M. P., Buckley, P. R., Woodhouse, I. B., Ogg, G., Simmons, A., … & Koohy, H. (2020). Potential CD8+ T cell cross-reactivity against SARS-CoV-2 conferred by other coronavirus strains. Frontiers in immunology, 11, 2878.
Lv, H., Wu, N. C., Tsang, O. T. Y., Yuan, M., Perera, R. A., Leung, W. S., … & Mok, C. K. (2020). Cross-reactive antibody response between SARS-CoV-2 and SARS-CoV infections. Cell reports, 31(9), 107725.
Ladner, J. T., Henson, S. N., Boyle, A. S., Engelbrektson, A. L., Fink, Z. W., Rahee, F., … & Altin, J. A. (2021). Epitope-resolved profiling of the SARS-CoV-2 antibody response identifies cross-reactivity with endemic human coronaviruses. Cell Reports Medicine, 2(1), 100189.
Lv H, Wu NC, Tsang OT, Yuan M, Perera RAPM, Leung WS, So RTY, Chan JMC, Yip GK, Chik TSH, Wang Y, Choi CYC, Lin Y, Ng WW, Zhao J, Poon LLM, Peiris JSM, Wilson IA, Mok CKP. Cross-reactive Antibody Response between SARS-CoV-2 and SARS-CoV Infections. Cell Rep. 2020 Jun 2;31(9):107725. doi: 10.1016/j.celrep.2020.107725. Epub 2020 May 18. PMID: 33500101.
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