Immunoinformatics approach for multi-epitope vaccine design against structural proteins and ORF1a polyprotein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)

Abstract Background The lack of effective treatment against the highly infectious SARS-CoV-2 has aggravated the already catastrophic global health issue. Here, in an attempt to design an efficient vaccine, a thorough immunoinformatics approach was followed to predict the most suitable viral proteins epitopes for building that vaccine. Methods The amino acid sequences of four structural proteins (S, M, N, E) along with one potentially antigenic accessory protein (ORF1a) of SARS-CoV-2 were inspected for the most appropriate epitopes to be used for building the vaccine construct. Several immunoinformatics tools were used to assess the antigenicity (VaxiJen server), immunogenicity (IEDB immunogenicity tool), allergenicity (AlgPred), toxigenicity (ToxinPred server), interferon-gamma inducing capacity (IFNepitope server), and the physicochemical properties of the construct (ProtParam tool). Results The final candidate vaccine construct consisted of 468 amino acids, encompassing 29 epitopes. The CTL epitopes that passed the antigenicity, allergenicity, toxigenicity and immunogenicity assessment were four epitopes from S protein, one from M protein, two from N protein, 12 from the ORF1a polyprotein and none from E protein. While the HTL epitopes that passed the antigenicity, allergenicity, toxigenicity and INF-$$\gamma$$ γ were one from S protein, three from M protein, six from the ORF1a polyprotein and none from N and E proteins. All the vaccine properties and its ability to trigger the humoral and cell-mediated immune response were validated computationally. Molecular modeling, docking to TLR3, simulation, and molecular dynamics were also carried out. Finally, a molecular clone using pET28::mAID expression plasmid vector was prepared. Conclusion The overall results of the study suggest that the final multi-epitope chimeric construct is a potential candidate for an efficient protective vaccine against SARS-CoV-2.

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Immunoinformatics approach for multi-epitope vaccine design against structural proteins and ORF1a polyproteins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2)

10.21203/rs.3.rs-108652/v1 ◽

2020 ◽

Author(s):

Khalid Mohamed Adam

Keyword(s):

Plasmid Vector ◽

Viral Proteins ◽

Amino Acid Sequences ◽

Structural Proteins ◽

Accessory Protein ◽

Potential Candidate ◽

Expression Plasmid ◽

Cell Mediated Immune Response ◽

Global Health Issue ◽

Chimeric Construct

Abstract Background The lack of effective treatment and a protective vaccine against the highly infectious SARS-CoV-2 has aggravated the already catastrophic global health issue. Here, in an attempt to design an efficient vaccine, a vigorous immunoinformatics approach was followed to predict the most suitable viral proteins epitopes for building that vaccine. Methods The amino acid sequences of four structural proteins (S, M, N, E) along with one potentially antigenic accessory protein (ORF1a) of SARS-CoV-2 were inspected for the most appropriate epitopes to be used for building the vaccine construct. Several immunoinformatics tools were used to assess the antigenicity, immunogenicity, allergenicity, toxigenicity, interferon-gamma inducing capacity, and the physicochemical properties of the product. Results The final candidate vaccine construct consisted of 468 amino acids, encompassing 30 epitopes. All the vaccine properties and its ability to trigger the humoral and cell-mediated immune response were validated computationally. Molecular modeling, docking to TLR3, simulation, and molecular dynamics were also carried out. Finally, a molecular clone using pET28: :mAID expression plasmid vector was prepared. Conclusion The overall results of the study suggest that the final multi-epitope chimeric construct is a potential candidate for an efficient protective vaccine against SARS-CoV-2.

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Structure-function investigation of a new VUI-202012/01 SARS-CoV-2 variant

10.1101/2021.01.01.425028 ◽

2021 ◽

Author(s):

Jasdeep Singh ◽

Nasreen Z. Ehtesham ◽

Syed Asad Rahman ◽

Seyed E. Hasnain

Keyword(s):

Central China ◽

Structural Proteins ◽

Structural Function ◽

Upper Respiratory Tract ◽

E Proteins ◽

Gene Target ◽

S Protein ◽

N Protein ◽

Synonymous Mutations ◽

South East England

AbstractThe SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus) has accumulated multiple mutations during its global circulation. Recently, a new strain of SARS-CoV-2 (VUI 202012/01) had been identified leading to sudden spike in COVID-19 cases in South-East England. The strain has accumulated 23 mutations which have been linked to its immune evasion and higher transmission capabilities. Here, we have highlighted structural-function impact of crucial mutations occurring in spike (S), ORF8 and nucleocapsid (N) protein of SARS-CoV-2. Some of these mutations might confer higher fitness to SARS-CoV-2.SummarySince initial outbreak of COVID-19 in Wuhan city of central China, its causative agent; SARS-CoV-2 virus has claimed more than 1.7 million lives out of 77 million populations and still counting. As a result of global research efforts involving public-private-partnerships, more than 0.2 million complete genome sequences have been made available through Global Initiative on Sharing All Influenza Data (GISAID). Similar to previously characterized coronaviruses (CoVs), the positive-sense single-stranded RNA SARS-CoV-2 genome codes for ORF1ab non-structural proteins (nsp(s)) followed by ten or more structural/nsps [1, 2]. The structural proteins include crucial spike (S), nucleocapsid (N), membrane (M), and envelope (E) proteins. The S protein mediates initial contacts with human hosts while the E and M proteins function in viral assembly and budding. In recent reports on evolution of SARS-CoV-2, three lineage defining non-synonymous mutations; namely D614G in S protein (Clade G), G251V in ORF3a (Clade V) and L84S in ORF 8 (Clade S) were observed [2–4]. The latest pioneering works by Plante et al and Hou et al have shown that compared to ancestral strain, the ubiquitous D614G variant (clade G) of SARS-CoV-2 exhibits efficient replication in upper respiratory tract epithelial cells and transmission, thereby conferring higher fitness [5, 6]. As per latest WHO reports on COVID-19, a new strain referred as SARS-CoV-2 VUI 202012/01 (Variant Under Investigation, year 2020, month 12, variant 01) had been identified as a part of virological and epidemiological analysis, due to sudden rise in COVID-19 detected cases in South-East England [7]. Preliminary reports from UK suggested higher transmissibility (increase by 40-70%) of this strain, escalating Ro (basic reproduction number) of virus to 1.5-1.7 [7, 8]. This apparent fast spreading variant inculcates 23 mutations; 13 non-synonymous, 6 synonymous and 4 amino acid deletions [7]. In the current scenario, where immunization programs have already commenced in nations highly affected by COVID-19, advent of this new strain variant has raised concerns worldwide on its possible role in disease severity and antibody responses. The mutations also could also have significant impact on diagnostic assays owing to S gene target failures.

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Potential immune epitope map for structural proteins of SARS-CoV-2

10.21203/rs.3.rs-47663/v1 ◽

2020 ◽

Author(s):

Yengkhom Damayanti Devi ◽

Himanshu Ballav Goswami ◽

Sushmita Konwar ◽

Chandrima Doley ◽

Anutee Dolley ◽

...

Keyword(s):

T Cell ◽

B Cell ◽

Mhc Class I ◽

Mhc Class Ii ◽

Cell Epitope ◽

Class I ◽

Structural Proteins ◽

S Protein ◽

N Protein ◽

B Cell Epitope

Abstract Researchers around the world are developing more than 145 vaccines (DNA/mRNA/whole-virus/viral-vector/protein-based/repurposed vaccine) against the SARS-CoV-2 and 21 vaccines are in human trials. However, a limited information is available about which SARS-CoV-2 proteins are recognized by human B- and T-cell immune responses. Using a comprehensive computational prediction algorithm and stringent selection criteria, we have predicted and identified potent B- and T-cell epitopes in the structural proteins of SARS-CoV and SARS-CoV-2. The amino acid residues spanning the predicted linear B-cell epitope in the RBD of S protein (370-NSASFSTFKCYGVSPTKLNDLCFTNV-395) have recently been identified for interaction with the CR3022, a previously described neutralizing antibody known to neutralize SARS-CoV-2 through binding to the RBD of the S protein. Intriguingly, most of the amino acid residues spanning the predicted B-cell epitope (aa 331-NITNLCPFGEVFNATRFASVYAWNRK-356, 403-RGDEVRQIAPGQTGKIADYNYKLPD-427 and aa 437- NSNNLDSKVGGNYNYLYRLFRKSNL-461) of the S protein have been experimentally verified to interact with the cross-neutralizing mAbs (S309 and CB6) in an ACE2 receptor-S protein interaction independent-manner. In addition, we found that computationally predicted epitope of S protein (370-395) is likely to function as both linear B-cell and MHC class II epitope. Similarly, 403-27 and 437-461 peptides of S protein were predicted as linear B cell and MHC class I epitope while, 177-196 and 1253-1273 peptides of S protein were predicted as linear and conformational B cell epitope. We found MHC class I epitope 316-GMSRIGMEV-324 predicted as high afﬁnity epitope (HLA-A*02:03, HLA-A*02:01, HLA-A*02:06) common to N protein of both SARS-CoV-2 and SARS-CoV (N317-325) was previously shown to induce interferon-gamma (IFN-γ) in PBMCs of SARS-recovered patients. Interestingly, two MHC class I epitopes, 1041-GVVFLHVTY-1049 (HLA-A*11:01, HLA-A*68:01, HLA-A*03:01) and 1202-FIAGLIAIV-1210 (HLA-A*02:06, HLA-A*68:02) derived from SARS-CoV S protein with epitope conservancy between 85 to 100% with S protein of SARS-CoV-2 was experimentally verified using PBMCs derived from SARS-CoV patients. We observed that HLA-A*02:01, HLA-A*02:03, HLA-A*02:06, HLA-A*11:01, HLA-A*30:01, HLA-A*68:01, HLA-A*68:02, HLA-B*15:01 and HLA-B*35:01 have been predicted to bind to the maximum number of MHC class I epitope (based on the criterion of allele predicted to bind more than 30 epitopes) of S protein of SARS-CoV-2. Similarly, we observed that HLA-A*02:06, HLA-A*30:01, HLA-A*30:02, HLA-A*31:01, HLA-A*32:01, HLA-A*68:01, HLA-A*68:02, HLA-B*15:01 and HLA-B*35:01 are predicted to bind to the maximum number of MHC class I epitope of N protein of SARS-CoV-2. We found that HLA-DRB1*04:01, HLA-DRB1*04:05, HLA-DRB1*13:02, HLA-DRB1*15:01, HLA-DRB3*01:01, HLA-DRB3*02:02, HLA-DRB4*01:01, HLA-DRB5*01:01, HLA-DQA1*04:01, DQB1*04:02, HLA-DPA1*02:01, DPB1*01:01, HLA-DPA1*01:03, DPB1*02:01, HLA-DPA1*01:03, DPB1*04:01, HLA-DPA1*03:01, DPB1*04:02, HLA-DPA1*02:01, DPB1*05:01, HLA-DPA1*02:01, and DPB1*14:01 are predicted to bind to the maximum number of MHC class II epitope of S protein of SARS-CoV-2. Alleles such as HLA-DRB1*04:01, HLA-DRB1*07:01, HLA-DRB1*08:02, HLA-DRB1*09:01, HLA-DRB1*11:01, HLA-DRB1*13:02, HLA-DRB3*02:02, HLA-DRB5*01:01, HLA-DQA1*01:02, DQB1*06:02, DPB1*05:01 and HLA-DPA1*02:01 are found to interact with the maximum number of MHC class II epitope of N protein of SARS-CoV-2. Using the IEDB tool we found the occurrence of HLA alleles with population coverage of around 99% throughout the world. The findings of computational predictions of mega-pool of B- and T-cell epitopes identified in the four main structural proteins of SARS-CoV-2 provides a platform for future experimental validations and the results of present works support the use of RBD or the full-length S and N proteins in an effort towards designing of recombinant protein-based vaccine and a serological diagnostic assay for SARS-CoV-2.

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Analyses of Coronavirus Assembly Interactions with Interspecies Membrane and Nucleocapsid Protein Chimeras

Journal of Virology ◽

10.1128/jvi.03212-15 ◽

2016 ◽

Vol 90 (9) ◽

pp. 4357-4368 ◽

Cited By ~ 27

Author(s):

Lili Kuo ◽

Kelley R. Hurst-Hess ◽

Cheri A. Koetzner ◽

Paul S. Masters

Keyword(s):

Nucleocapsid Protein ◽

Hepatitis Virus ◽

Virus Assembly ◽

Mouse Hepatitis Virus ◽

M Protein ◽

Growth Defect ◽

S Protein ◽

N Protein ◽

Protein Incorporation ◽

Carboxy Terminal

ABSTRACTThe coronavirus membrane (M) protein is the central actor in virion morphogenesis. M organizes the components of the viral membrane, and interactions of M with itself and with the nucleocapsid (N) protein drive virus assembly and budding. In order to further define M-M and M-N interactions, we constructed mutants of the model coronavirus mouse hepatitis virus (MHV) in which all or part of the M protein was replaced by its phylogenetically divergent counterpart from severe acute respiratory syndrome coronavirus (SARS-CoV). We were able to obtain viable chimeras containing the entire SARS-CoV M protein as well as mutants with intramolecular substitutions that partitioned M protein at the boundaries between the ectodomain, transmembrane domains, or endodomain. Our results show that the carboxy-terminal domain of N protein, N3, is necessary and sufficient for interaction with M protein. However, despite some previous genetic and biochemical evidence that mapped interactions with N to the carboxy terminus of M, it was not possible to define a short linear region of M protein sufficient for assembly with N. Thus, interactions with N protein likely involve multiple linearly discontiguous regions of the M endodomain. The SARS-CoV M chimera exhibited a conditional growth defect that was partially suppressed by mutations in the envelope (E) protein. Moreover, virions of the M chimera were markedly deficient in spike (S) protein incorporation. These findings suggest that the interactions of M protein with both E and S protein are more complex than previously thought.IMPORTANCEThe assembly of coronavirus virions entails concerted interactions among the viral structural proteins and the RNA genome. One strategy to study this process is through construction of interspecies chimeras that preserve or disrupt particular inter- or intramolecular associations. In this work, we replaced the membrane (M) protein of the model coronavirus mouse hepatitis virus with its counterpart from a heterologous coronavirus. The results clarify our understanding of the interaction between the coronavirus M protein and the nucleocapsid protein. At the same time, they reveal unanticipated complexities in the interactions of M with the viral spike and envelope proteins.

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The Coronavirus SARS-Cov-2: the Characteristics of Structural Proteins, Contagiousness, and Possible Immune Collisions

Epidemiology and Vaccinal Prevention ◽

10.31631/2073-3046-2020-19-2-13-30 ◽

2020 ◽

Vol 19 (2) ◽

pp. 13-30

Author(s):

E. Р. Kharchenko

Keyword(s):

Amino Acid ◽

Close Contact ◽

Amino Acid Content ◽

Infection Process ◽

Amino Acid Sequences ◽

Surface Proteins ◽

Structural Proteins ◽

Subunit Structure ◽

S Protein ◽

Immune Epitope

Relevance. Coronavirus SARS-Cov-2 is a novel virus demonstrating the ability to be trans¬mitted from human-to-human, via respiratory droplets or close contact, and cause the severe acute respiratory syndrome (SARS). The role of its structural proteins in the SARS pathogenesis is unknown.Aim is to characterize the features of the SARS-Cov-2 structural proteins and their changes associated with acquiring other way of transmission and analyze the possibility of heterologous immunity emergence in its infection. Materials and method. For the computer analysis and alignment, the gene sequences of SARS-Cov-2 , SARS-CoV , MERS-CoV и bat CoV HKU3 reference strains were used from the Internet. From the primary structure of their genes it were translated their structural proteins: spike (S), envelope (E),membrane (M), and nucleocapsid (N). The genetic code of structural proteins was also defined. The search of homologous sequences in the SARS-Cov-2 S-protein, surface proteins of other viruses, and human proteins was made to find immune epitope continuum of protein relationships.Results. In the SARS-Cov-2 structural proteins amino acid sequences of M, E, and N-proteins are conservative. The S1 subunit of the S-protein contains some large insertions, significant changes of the amino acid content with the predominance of arginine and lysine which is typical for the surface glycoproteins in the viruses possessing high contagiousness. The S2 subunit is rather conservative and retain negative polarity. The S-protein exhibits the immune epitope relationships with many proteins of viruses and human which may be associated with immune collisions.Conclusion: The SARSCov-2 features are determined by marked changes of the S1 subunit structure in the S-protein which may be responsible for its contagiousness and many immune collisions aggravating infection process.

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Virtual Screening for the Identification of Potential Candidate Molecules Against Envelope (E) and Membrane (M) Proteins of SARS-CoV-2

Journal of Computational Biophysics and Chemistry ◽

10.1142/s2737416521500083 ◽

2020 ◽

pp. 2150008

Author(s):

Abbas Alibakhshi ◽

Mohammad Mehdi Ranjbar ◽

Shaghayegh Haghjooy Javanmard ◽

Fatemeh Yarian ◽

Shahrzad Ahangarzadeh

Keyword(s):

Md Simulation ◽

Structural Proteins ◽

Potential Candidate ◽

Therapeutic Approaches ◽

E Proteins ◽

Virus Life Cycle ◽

M Proteins ◽

The World ◽

Collective Motions ◽

The Stability

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) causes COVID-19, a disease currently spreading around the world. Some drugs are underway or being used to combat this disease. Several proteins of the virus can be targeted in therapeutic approaches. Two structural proteins, membrane (M), envelope (E) have critical roles in virus life cycle, such as assembly, budding, envelope formation and pathogenesis. Here, we employed the in silico strategies to identify and evaluate the selected potential compounds against M and E proteins. For this, the structures of proteins were modeled and then several groups of compounds as FDA approved, natural products or under clinical trials were screened from DrugBank and ZINC databases. The selected dockings were analyzed and the ligands with best binding affinity scores were subjected to evaluate drug-likeness and medicinal chemistry friendliness through prediction of ADMET properties. Normal mode analyses were also performed for six selected complexes to explore the collective motions of proteins. Molecular dynamic (MD) simulation was also performed to calculate the stability of two docked protein–ligand complexes. The results revealed that several compounds had high affinity to the proteins along with some acceptable profiles of mobility and deformability, especially, for M protein.

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In Silico Validation of Middle East Respiratory Syndrome (MERS) Virus Proteins for Better Drug Development

International Journal of Applied Sciences and Biotechnology ◽

10.3126/ijasbt.v1i4.9184 ◽

2013 ◽

Vol 1 (4) ◽

pp. 272-278

Author(s):

D. S. Mundaganore ◽

Y. D. Mundagnore ◽

K. V. Ashokan

Keyword(s):

Amino Acid ◽

Practical Implication ◽

3D Structure ◽

Chemical Study ◽

Test Tube ◽

M Protein ◽

Virus Protein ◽

S Protein ◽

N Protein ◽

Thermo Stability

MERS Co-virus protein sequence of N, M, E and S-protein was validated by bioinformatics servers and tools. The study revealed that S-protein shows highest percentage of amino acid and the least in M and E-protein. The bit score also shows the same trend but the E-value is maximum in E and M protein. The amino acid composition revealed that N-protein is rich in glycine and M-protein rich in leucin. Pyrrolysine, Selenocysteine and cystein (N-Protein) are absent in all the protein studied an indication of low thermo stability. The physico-chemical study showed that M, N, and E proteins are positively charged due to specific amino acids (Arginin and lysine) and S-protein is negatively charged due to aspartic acid and glutamic acid. EC is maximum in S-protein. Instability Index (II) shows that E and S-proteins are more stable in test tube than other proteins. Further all proteins are hydrophobic with GRAVY below ‘0’. To get clearer picture of the physical and chemical attribute of the protein we generated 3D model and the model was validated and observed that the 3D structure falls in the accepted limits. The practical implication of the study is that the result will assists the pharmacologist and other drug developers and Government bodies to better knowledge on these proteins and develop possible new vaccine against MERS Co-virus.DOI: http://dx.doi.org/10.3126/ijasbt.v1i4.9184 Int J Appl Sci Biotechnol, Vol. 1(4): 272-278

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Characterization of the Coronavirus M Protein and Nucleocapsid Interaction in Infected Cells

Journal of Virology ◽

10.1128/jvi.74.17.8127-8134.2000 ◽

2000 ◽

Vol 74 (17) ◽

pp. 8127-8134 ◽

Cited By ~ 141

Author(s):

Krishna Narayanan ◽

Akihiko Maeda ◽

Junko Maeda ◽

Shinji Makino

Keyword(s):

Protein Interaction ◽

Hepatitis Virus ◽

Viral Envelope ◽

M Protein ◽

E Proteins ◽

N Protein ◽

Golgi Compartment ◽

Infected Cells ◽

Rnase Treatment ◽

In Cells

ABSTRACT Coronavirus contains three envelope proteins, M, E and S, and a nucleocapsid, which consists of genomic RNA and N protein, within the viral envelope. We studied the macromolecular interactions involved in coronavirus assembly in cells infected with a murine coronavirus, mouse hepatitis virus (MHV). Coimmunoprecipitation analyses demonstrated an interaction between N protein and M protein in infected cells. Pulse-labeling experiments showed that newly synthesized, unglycosylated M protein interacted with N protein in a pre-Golgi compartment, which is part of the MHV budding site. Coimmunoprecipitation analyses further revealed that M protein interacted with only genomic-length MHV mRNA, mRNA 1, while N protein interacted with all MHV mRNAs. These data indicated that M protein interacted with the nucleocapsid, consisting of N protein and mRNA 1, in infected cells. The M protein-nucleocapsid interaction occurred in the absence of S and E proteins. Intracellular M protein-N protein interaction was maintained after removal of viral RNAs by RNase treatment. However, the M protein-N protein interaction did not occur in cells coexpressing M protein and N protein alone. These data indicated that while the M protein-N protein interaction, which is independent of viral RNA, occurred in the M protein-nucleocapsid complex, some MHV function(s) was necessary for the initiation of M protein-nucleocapsid interaction. The M protein-nucleocapsid interaction, which occurred near or at the MHV budding site, most probably represented the process of specific packaging of the MHV genome into MHV particles.

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The Coronavirus SARS-Cov-2: the Characteristics of Structural Proteins, Contagiousness, and Possible Immune Collisions

Epidemiology and Vaccinal Prevention ◽

10.31631/2073-3046-2020-20-2-13-30 ◽

2020 ◽

Vol 19 (2) ◽

pp. 13-30

Author(s):

E. Р. Kharchenko

Keyword(s):

Amino Acid ◽

Close Contact ◽

Amino Acid Content ◽

Infection Process ◽

Amino Acid Sequences ◽

Surface Proteins ◽

Structural Proteins ◽

Subunit Structure ◽

S Protein ◽

Immune Epitope

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Structure and Function of Major SARS-CoV-2 and SARS-CoV Proteins

Bioinformatics and Biology Insights ◽

10.1177/11779322211025876 ◽

2021 ◽

Vol 15 ◽

pp. 117793222110258

Author(s):

Ritesh Gorkhali ◽

Prashanna Koirala ◽

Sadikshya Rijal ◽

Ashmita Mainali ◽

Adesh Baral ◽

...

Keyword(s):

Genomic Organization ◽

Membrane Vesicles ◽

Structural Proteins ◽

Host Immune System ◽

Accessory Proteins ◽

Nonstructural Proteins ◽

N Protein ◽

Small Proteins ◽

Methylation Mark ◽

And Function

SARS-CoV-2 virus, the causative agent of COVID-19 pandemic, has a genomic organization consisting of 16 nonstructural proteins (nsps), 4 structural proteins, and 9 accessory proteins. Relative of SARS-CoV-2, SARS-CoV, has genomic organization, which is very similar. In this article, the function and structure of the proteins of SARS-CoV-2 and SARS-CoV are described in great detail. The nsps are expressed as a single or two polyproteins, which are then cleaved into individual proteins using two proteases of the virus, a chymotrypsin-like protease and a papain-like protease. The released proteins serve as centers of virus replication and transcription. Some of these nsps modulate the host’s translation and immune systems, while others help the virus evade the host immune system. Some of the nsps help form replication-transcription complex at double-membrane vesicles. Others, including one RNA-dependent RNA polymerase and one exonuclease, help in the polymerization of newly synthesized RNA of the virus and help minimize the mutation rate by proofreading. After synthesis of the viral RNA, it gets capped. The capping consists of adding GMP and a methylation mark, called cap 0 and additionally adding a methyl group to the terminal ribose called cap1. Capping is accomplished with the help of a helicase, which also helps remove a phosphate, two methyltransferases, and a scaffolding factor. Among the structural proteins, S protein forms the receptor of the virus, which latches on the angiotensin-converting enzyme 2 receptor of the host and N protein binds and protects the genomic RNA of the virus. The accessory proteins found in these viruses are small proteins with immune modulatory roles. Besides functions of these proteins, solved X-ray and cryogenic electron microscopy structures related to the function of the proteins along with comparisons to other coronavirus homologs have been described in the article. Finally, the rate of mutation of SARS-CoV-2 residues of the proteome during the 2020 pandemic has been described. Some proteins are mutated more often than other proteins, but the significance of these mutation rates is not fully understood.

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