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.
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