Genomic and Proteomic Comparative Analysis of SARS-CoV-2 versus SARS-CoV-GD01

DOI: https://doi.org/10.21203/rs.3.rs-32189/v1

Abstract

Background

Since the emergence of the pandemic novel pneumonia (COVID-19) disease in Wuhan city in China in November 2019, it is becoming holistically urgent to discover and definitely determine the potential origin of causative virus of this disease, SARS-CoV2 to understand its pathogenic action an better design proper remedies.

Methods

Using bioinformatics analysis, the whole genome of SARS-CoV2 emerging in 2020 and its deduced proteome were compared with the corresponding information on SARS-CoV-GD01 having emerged in 2003 in China. The genomes squences of the two viruses were obtained from NCBI. Alignment of protein sequences for all genes of both genomes were performed and displayed using Clustal Omega data base.

Results

Bioinformatics analysis revealed 10 genes encoding 10 proteins in the SARS-CoV2 genome instead of 11 genes encoding 12 proteins in the case of SARS-CoV-GD01, where the first gene is uniquely encoding two glycoproteins. Additionally, bio-informatics analysis disclosed variations in SARS-CoV2 genome size as a result of nucleotides insertion and deletion in all genes of the virus especially orf1ab gene, spike gene, and ORF10 gene. The most conspicuous alteration is apparently noticed in the spike gene, encoding for a novel protein enabling the virus to attach to the cell membrane via the interaction with host cell receptor, initiating probably a new pathway of infection and a specific pathogenic action. This alteration is

Conclusions

The big alterations in the genome of SARS-CoV-2 from that of SARS-CoV-GD01 may be potentially responsible for the worldwide witnessed high virulence and accelerated spread. The qualified and quantified information presented in the current study on the SARS-CoV-2, detailing the specificity and the magnitude of genomic and proteomic alterations from SARS-CoV-GD01, developed probably during 16 years will not only enable designing right drugs and strategies of confronting the current viral version, but it may rather allow to extrapolate and foresee potential outbreaks of newer versions during the coming decades. At the time of epidemics, nonspecific ways and drugs should be resorted to for confronting emergent viral infections. Chemically modified positively charged proteins and peptides can offer a wealth of potential antiviral agents but need more clinical research.

Background

Severe acute respiratory syndrome coronavirus 2 also named as SARS-CoV-2, HCoV-19, SARS2, 2019-nCoV, COVID-19, COVID-19 virus, Wuhan coronavirus, Wuhan seafood market pneumonia virus, and Human coronavirus 2019 has first emerged and detected in November 2019 in Wuhan, China. Coronavirus name is derived from the latin word corona (crown), referring to the shape of proteins around the virion. SARS-CoV-2 is an ssRNA positive-strand viruses, its genome is 29903 b ss-RNA. It belongs to family of Coronaviridae Genus Betacoronavirus. The natural hosts of SARS-CoV-2 are human vertebrates, animals and bats. The primary site of infection is epithelial cells of respiratory system or enteric tracts. There are many viruses infect humans such as SARS-CoV, MERSCoV, HKU1, NL63, OC43, 229E and finally SARS-CoV-2 (Corman et al. 2018). SARS-CoV-2 interacts with ACE2 (Angiotensin-converting enzyme 2) cell receptors (Wan et al. 2020; Wrapp et al. 2020). SARS-CoV-2, was further confirmed to have a high affinity to bind human ACE2 and uses it as an entry receptor to invade target cells (Walls et al., 2020) concluding that the Cryo-EM structures of the SARS-CoV-2 spike glycoprotein as well as the inhibition of spike-mediated entry by SARS-CoV polyclonal antibodies, may provide a blueprint for the design of vaccines properly specific for this virus.

SARS-CoV-2 which emerged in China and spread worldwide in a short period of time is mainly associated with COVID-19 diseases or respiratory diseases (pneumonia), with cardiac complications and transmits through respiratory droplets. There are two global hypotheses regarding the origin of SARS CoV-2. The first one is through natural selection in an animal or humans host and the second one assumes that its emergence through laboratory manipulation of a related SARS-CoV-like coronavirus.

As both of SARS CoV-2 emerging in 2019 and SARS-CoV-GD01 emerging in 2003 are endemic in China, exploring the similarities and dissimilarities between the two through the comparative bio-informatics analysis of genomic and proteomic data may cast light on the volume and identity of the evolutionary changes in the new version allowing to understand its specifications and boundaries and thus paving the way for knowledge-based remedies and drugs while also benefitting from the wealth of information on the old version. We will show the perspectives on the interconnected features of the SARS-CoV-2 and SARS Coronavirus GD01 genomes, which may promote our understanding of the new version helping us to conclude the potential pathway leading to the new version, i.e.; through natural selection or laboratory genetic .manipulations. Qualifying and quantifying the specificity and the volume of genomic and proteomic alterations between the two versions during 16 years will not only enable designing right drugs and strategies of confronting the current viral version, but it may rather allow to extrapolate and foresee potential outbreaks of newer versions during the coming decades.

Methods

Source of genomic sequences

SARS-CoV-2 and SARS CoV GD01 genome sequences were obtained from NCBI database (SARS-CoV-2 https://www.ncbi.nlm.nih.gov/nuccore/MN908947 & SARS CoV GD01 https://www.ncbi.nlm.nih.gov/nuccore/AY278489). Genomic location, gene size and protein sizes were annotated for both SARS-CoV-2 and SARS CoV GD01 genomes.

Alignment of SARS-CoV-2 and SARS CoV GD01 biological sequences

Alignment of protein sequences for all genes of both genomes were performed and displayed using Clustal Omega data base (https://www.ebi.ac.uk/Tools/msa/clustalo/) to identify the potential regions of similarity, indicating probably functional, structural and/or evolutionary relationships between two biological sequences, and showing the conserved and variable regions especially the regions of nucleotide insertion and deletion. This will ideally reflect the most evolutionally events having occurred in viruses. Comparison of number of genes and deduced proteins of both genomes were done to compare the whole proteome features which are considered as the puzzling informative base of virus strength and virulence and behavior.

Results

Genomic characteristics of SARS-CoV 2 and SARS-CoV GD01

The genomic analysis of SARS-CoV GD01 genome (29757b RNA) revealed its constitution of 11 genes encoding for 12 proteins (Table 1) arranged as shown in Fig. 1. The first gene is orf1ab (21220 b), encoding for two proteins, long and short, 7073 and amino acids, respectively. The other genes were spike (S) glycoprotein gene (3767 b) encoding for 1255 amino acids, ORF3a (824 b) gene encoding for 274 amino acids, ORF3b (500 b) gene encoding for 154 amino acids, envelope (E) gene (230 b) encoding for 76 amino acids, membrane (M) gene (665 b) encoding for 221 amino acids, ORF6 gene (191 b) encoding for 63 amino acids, ORF7a gene (368 b) encoding for 122 amino acids, ORF8 gene (368 b) encoding for 122 amino acids, Nucleocapsid (N) gene (1268 b) encoding for 422 amino acids, and ORF10 gene (296 b) encoding for 98 amino acids flanked by 248 b 5́-untranslated region (5́-UTR) and 1317 b 3́-untranslated region (3́-UTR).

Based on the published data on SARS-CoV 2 genome sequence (8-March-2020) on the NCBI database, genomic analysis revealed the presence of 10 genes encoding for 10 proteins arranged in specific manner in SARS-CoV 2 genome (29903 b RNA) (Table 1 and Fig. 1). The first gene is orf1ab (21289 b) is encoding for 7096 amino acids followed by spike (S) glycoprotein gene (3821 b) encoding for 1273 amino acids, ORF3a (827 b) gene encoding for 275 amino acids, envelope (E) gene (227 b) encoding for 75 amino acids, membrane (M) gene (668 b) encoding for 222 amino acids, ORF6 gene (185 b) encoding for 61 amino acids, ORF7a gene (365 b) encoding for 121 amino acids, ORF8 gene (365 b) encoding for 121 amino acids, Nucleocapsid (N) gene (1259 b) encoding for 419 amino acids, and ORF10 gene (116 b) encoding for 38 amino acids flanked by 265 b 5́-untranslated region (5́-UTR) and 228 b 3́-untranslated region (3́-UTR).

Table 1

Comparison of SARS CoV 2 and SARS CoV GD01 complete genome and deduced proteins

No

SARS CoV GD01 (Wu,Qet al., 2003)

SARS CoV 2 (Wu,F. et al., 2020)

Genomic location

Gene name

Gene size

Protein

size

Genomic location

Gene name

Gene size

Protein

size

x

1..248

5'UTR

248

-

1..265

5'UTR

265

-

1

249..21469

Orf1ab

21220

7073 aa

266..21555

Orf1ab

21289

7096 aa

249..13397

4382 aa

2

21476..25243

S

3767

1255 aa

21563..25384

S

3821

1273 aa

3

25252..26076

ORF3a

824

274 aa

25393..26220

ORF3a

827

275 aa

4

25673..26137

ORF3b

500

154

-

-

-

-

5

26101..26331

E

230

76 aa

26245..26472

E

227

75 aa

6

26382..27047

M

665

221aa

26523..27191

M

668

222 aa

7

27058..27249

ORF6

191

63 aa

27202..27387

ORF6

185

61 aa

8

27257..27625

ORF7a

368

122 aa

27394..27759

ORF7a

365

121 aa

9

27763..28131

ORF8

368

122 aa

27894..28259

ORF8

365

121 aa

10

28133..29401

N

1268

422 aa

28274..29533

N

1259

419 aa

11

28143..28439

ORF10

296

98 aa

29558..29674

ORF10

116

38 aa

x

28440..29757

3'UTR

1317

-

29675..29903

3'UTR

228

-

x:Untranslated region

Molecular Evolution of Coronavirus

The current analytical comparison between SARS-CoV-2 and SARS Coronavirus GD01 genomes shows that SARS-CoV-2 genome received insertions of 72 and 6 nucleotides corresponding to alteration in amino acids at positions 993 and 1211 of the orf1ab polyprotein, respectively in the papain-like proteinase (PL-PRO) part. This change may be responsible for the cleavages incurred at the N-terminus of the replicase polyprotein and the assembly of virally induced cytoplasmic double-membrane vesicles necessary for viral replication (Wu et al. 2020). It is also observed that SARS-CoV-2 genome had undergone deletions of 9 nucleotides corresponding to the following amino acid positions, 823, 933, and 1539 (Fig. 2A). On the other hand, spike protein gene seems to have experienced deletions of 12 nucleotides leading to altered amino acid at positions 21 and 31 and insertions of 66 nucleotides corresponding to amino acid positions 69, 149, 247,483 and 679 (Fig. 2B). Big genetic variations can also be observed in ORF10 protein represented by a deletion of 180 nucleotides resulting in alteration in the amino acid positions 1, 5, and 38 on ORF10 protein (Fig. 4D) may also be impacting the viral structural and functional features.

The genes of the other proteins have shown only minor changes, i.e. low extent of deletions and insertions. An insertion of 3 nucleotides was spotted in both ORF3a and M genes coupled with alterations in the amino acid positions 241 and 1 in ORF3a and membrane proteins, respectively (Fig. 3A, C). The ORF8 protein, which is playing probably an important role in host-virus interaction (Wu et al. 2020) has received insertion of 15 nucleotides, corresponding to the amino acid positions 15, 61 and 71, and deletion of 18 nucleotides corresponding to altered amino acids at positions 85 and 122 in the ORF8 protein (Fig. 4B). The E gene has a deletion of 3 nucleotides, leading to altered amino at position 70 of the envelope protein (Fig. 3B). The ORF6 gene has a deletion of 6 nucleotides leading to altered amino acid at position 62 on the ORF6 protein (Fig. 3D) and ORF7a gene has deletion of 3 nucleotides corresponding to an altered amino acid at position 95 on ORF7a protein (Fig. 4A) while the nucleocapsid (N) gene has two deletions of 9 nucleotides corresponding to altered amino acids at positions 8 and 420 of the nucleoprotein protein (Fig. 4C).

In fact insertion or deletion of one or more nucleotides to a genomic sequence may shift the way the sequence is read in both genomic and mRNA codons. All insertions and deletions frequencies were mentioned in Table 2. For instance, if one nucleotide is deleted from RNA genomic sequence, a disruption reading frame may occur including the mutation site and the following region. This may apparently lead to the creation of new combinations of many incorrect amino acids sequences forming the corresponding protein. In contrast, if the inserted or deleted nucleotides were three, then no change in the reading of mRNA codons will occur; however, there will be either one extra or one missing amino acid in the final protein. Therefore, insertion or deletion mutations produce different proteins with incorrect amino acids. It may be rather assumed that all above mentioned changes could normally have occurred in coronaviruses as normal evolutionary events, supporting perhaps the rejection of laboratory manipulation hypothesis. However, the big total number of insertions (168) and deletions (240) may refer to a new strain of the virus having completely new features that need to be carefully and thoroughly studied to enable competent viral management tools and curing methodologies. With such highly genetic and proteomic alterations in the new version of coronavirus it is becoming urgently demanded to find new strategies and drugs for the controlling the speedy spreading pandemics.

Table 2. Number of inserted and deleted

nucleotides of SARS CoV 2 genome

Gene

Mutation type

(No. nucleotides)

Insertion

Deletion

Orf1ab

78

9

S

66

12

ORF3a

3

-

E

-

3

M

3

-

ORF6

-

6

ORF7a

-

3

ORF8

15

18

N

-

9

ORF10

3

180

Total

168

240

Number of inserted and deleted nucleotides were

calculated based on number of deleted or inserted

amino acids multiplied by 3

Discussion

The new noticed extra amino acids, added to SARS-CoV 2 proteome especially in spike (S) glycoprotein could probably stand behind the emergent new features of this virus including its capability of binding to human cell receptors. The novel genomic characteristics of SARS-CoV-2, presented here may partly pinpoint the genomic structural changes responsible for the witnessed severe viral infectivity and the unprecedented extremely high transmissibility of this virus in humans worldwide. Although the analysis shows that SARSCoV-2 is not a manipulated virus, the available data do allow to totally discard the second hypothesis on the viral origin. Hence, more scientific research is needed on other viral isolate to discern unequivocally and unambiguously the real origin of the virus.

Corona viruses evolution started from three viral genome sequences of animal origin (Wan et al. 2005). Those viruses, originally of low-pathogenicity, were identified for 27 variation residues on the spike gene, 7 variation residues sites of which were causing 6 amino acid changes at positions 147, 228, 240, 479, 821, and 1080 of the S protein region, participating in the emergence of SARS-CoV of 2003 epidemic. Further 14 changes caused 11 amino acid residue changes, at positions 360, 462, 472, 480, 487, 609, 613, 665, 743, 765, and 1163 increase the viral pathogenicity of early-phase epidemic of SARS 2003. Finally, the six remaining variations caused four amino acid changes, at positions 227, 244, 344, and 778, shaping the virus responsible for the global epidemic (Wan et al. 2005).

The analytical genomic comparison showing that the orf1ab polyprotein gene of SARS-CoV-2 had undergone insertions of 72 and 6 nucleotides corresponding to alteration in amino acids at positions 993 and 1211, in the papain-like proteinase (PL-PRO) part. This change may be responsible for the cleavages incurred at the N-terminus of the replicase polyprotein and the assembly of virally induced cytoplasmic double-membrane vesicles necessary for viral replication (Wu et al. 2020). The same gene had also undergone deletions of 9 nucleotides corresponding to the three amino acid positions (823, 933, and 1539). Since spike protein is known to participate in attaching the virus to the cell membrane by interacting with the host receptor and initiating the infection (Wu et al. 2020; Grove and Marsh, 2011), this genetic modification may be responsible for some features of the current virulence, speedy spreading and high transmissibility of SARS-CoV-2. The genetic variations occurring in ORF10 protein represented by a deletion of 180 nucleotides resulting in alteration in the amino acid positions 1, 5, and 38 on ORF10 protein (Fig. 4D) may also be expected to be impacting the viral structural and functional features. The ORF8 gene, which is playing an important role in host-virus interaction (Wu et al. 2020) has also experienced significant changes represented by an insertion of 15 nucleotides, corresponding to the amino acid positions 15, 61 and 71, and deletion of 18 nucleotides corresponding to altered amino acids at positions 85 and 122. So, the structural changes in these three genes and their expressed proteins may have the most influence on the new viral version. So, the major structural changes in the new virus genes can be concluded as Spike gene, orf1ab polyprotein gene, ORF10 and ORF8 gene. Further complementary studies on structure-function relationships should be followed and intensified.

It can also concluded that the other investigated genes showed only minor structural changes, e.g. ORF3a and M genes had only alterations in the amino acid positions 241 and 1, respectively, while the envelope protein gene (E) had only a deletion of 3 nucleotides, leading to altered amino at position 70 of the envelope protein. The ORF6 and ORF7a genes has deletions of 6 and 3 nucleotides leading to altered amino acid at one position (62 and 95) at their respective expressed proteins while the nucleocapsid (N) gene has two deletions of 9 nucleotides corresponding to altered amino acids at two positions; 8 and 420 of the nucleoprotein protein. Although relatively minor changes were noticed with the other remaining genes, i.e.; ORF3a, ORF6 and ORF7a genes, membrane proteins (M), envelope protein gene (E) and nucleocapsid gene (N), have relatively minor structural alterations. However, the spread of the molecular changes in all the virus protein refer to holistic evolutionary changes that will inevitably produce major functional and reactive mechanisms in the new virus.

Currently, we are facing a critical situation where there is no specific antiviral treatment recommended for COVID-19, where a long time is required to develop specific vaccine against SARS-CoV-2 and where the most used treatments for the infected people were symptomatic based principally on oxygen therapy for patients with severe infection or dissolving blood clots. Vaccines promote the body's immune system to efficiently and specifically attack viruses in its initial complete particle stage, outside the living cells. So, it can protect healthy people from viral infection but it cannot treat infected people. Antivirals can treat infected people but they only inhibit virus development and activity and do not destroy the virus itself. The most difficult obstacle in designing vaccine or antiviral is the viral genetic variation and mutations. With such highly genetic and proteomic alterations in SARS-CoV-2, it is becoming urgently demanding to find new strategies and drugs for the controlling and the virus spreading pandemics.

Since the main concept behind designing an antiviral protein is defining the target viral protein which can be targeted by the antiviral, it may here be difficult since the new virus has nearly altered most of its proteins so the previous antivirals designed for the previous strains of corona virus have come out-of-service. New drugs should be designed prepared and tested in vitro and animal then validated in human clinical trials. This is all time and effort consuming but indispensable. One of the antiviral strategies is producing some factors which are similar to viral proteins attaching factors and thus they can bind to the host cell membrane and prevent the viral attachment or they can bind to viral protein if they were similar to the host cellular factors thus blocking its communication with the cells. This strategy of designing drugs can be very expensive and time consuming but it is necessary. Stabilizing the virus at the replication stage by developing nucleotide or nucleoside analogues that can interfere with the viral amplification and replication process. But these drugs depends also the genetic characters of the viral RNA sequences. Then these sequences have undergone major changes the old remedies will no more be of use against the new version of corona viruses.

The other mechanism of counteracting virus is through stimulating the body's immune system to attack a range of pathogens, .e.g. interferons, inhibiting viral synthesis in infected cells (Samuel, 2001). However, viruses can become resistant through spontaneous mutations. A deletion at amino acid position 245–248 in the neuraminidase gene of influenza A virus subtype H3N2 occurred after initiation of treatment with oseltamivir highly reduced its inhibition against oseltamivir (Trebbien et al. 2018). The most commonly used method for treating resistant viruses is combination therapy, which uses multiple antivirals in one treatment regimen. This is thought to decrease the likelihood that one mutation could cause antiviral resistance, as the antivirals in the cocktail target different stages of the viral life cycle (Moscona, 2009).

At the start of the COVID-19 epidemic control most treatments were mainly symptomatic. Due to the lack of efficient and specific treatments and the need to contain the epidemic, some of the old antiviral or general drugs have been resorted to; e.g. chloroquine, remdesivir, lopinavir, ribavirin or ritonavir and teicoplanin (Baron et al. 2020). Remdesivir was reported as a successful antiviral treatment against SARS-CoV2 either in vitro or in human infection (Holshue et al. 2020; Wang et al. 2020b). Likewise chloroquine was proved effective against SARS-CoV2 either in vitro or in human infection (Cortegiani et al. 2020; Devaux et al. 2020; Gao et al. 2020; Wang et al. 2020b). Other drugs have been suggested and tried with less success. Remdesivir is a nucleotide analog, was confirmed to inhibit SARS-CoV-2 replication in vitro (Choy et al. 2020) by getting into viral RNA chains, causing their premature termination. Chloroquine has multiple mechanisms of action. Chloroquine can inhibit a pre-entry step of the viral cycle by interfering with viral particles binding to their cellular cell surface receptor and it can inhibit quinone reductase 2 (Devaux et al. 2020). Virus may also develop new resistance of these new substances.

To totally avoid the viral genomic and proteomic alterations which enable viruses to escape the natural and development immunity, another pathway may be potentially effective after receiving the due research. This approach represents the basic proteins and peptides which have been confirmed antibacterial active then few studies proved their effectiveness against viruses. These proteins can be found natively available e.g. lactoferrin or can be chemically prepared by esterification which neutralizes the negatively charged carboxyl groups of the aspartyl and glutamyl residues on protein molecules, transforming the protein net charge into positive (Sitohy et al. 2000). Cationic esterified proteins can interact with many microorganisms by virtue of their positive charge as well as their hydrophobic domains. Different reports have confirmed this action with bacteria and fungi (Osman et al. 2014a, 2016a, 2018; Abdel-Shafi et al. 2016; Mahgoub et al. 2011, 2013, 2016; Sitohy and Osman 2010; Sitohy et al. 2011a and b, 2013). Esterified proteins were proven to in vitro interact with and complex DNA (Sitohy et al. 2002, 2001a, 2001b) and were subsequently found to inhibit DNA amplification in vitro (Sitohy et al. 2001c) and the replication of M13 bacteriophage and lactococcal bacteriophages (Sitohy at al. 2006, 2005). Human viruses were also found susceptible to esterified proteins (Chobert et al. 2007, Sitohy et al. 2001, 2008) and even plant viruses (Abdelbacki et al. 20104). More relevantly, human Influenza virus A subtype H1N1 and human influenza virus A subtype H3N2 infected into MDCK cell lines were observed to be inhibited by methylated β-lactoglobulin. (Sitohy et al. 2010a and b). A lethal Egyptian avian influenza A (H5N1) virus infected to MDCK cell lines was reported to be significantly inhibited by esterified whey proteins fractions (Taha et al. 2010). Globally, these results suggest the wide-spectrum specificity of these chemically modified proteins against different virus and pathogenic bacteria nominating them as potential effective candidate in treating Covid-19 and other epidemic viral outbreaks. They can be prepared from many available native proteins, their properties can be controlled and well designed and they have been primarily proven non-toxic (Sitohy et al. 2013). Nevertheless, further pharmacological and pharmaceutical studies are required to define the best treating approach with due insight into the potential mechanism and the due requirements to get the best antiviral action of these substance against SARS-CoV2.

Conclusion

Evolution changes in viruses by insertion and deletion of nucleotides occurred normally in Coronaviruses as normal evolution events producing different viral proteins with multiple incorrect or altered amino acids. Our analyses clearly show that SARS-CoV-2 has been molecularly developed from SARS Coronavirus GD01 after major alterations in the viral genes and their translated proteins. We strongly concluded that variable regions in SARS-CoV-2 genome especially in orf1ab, spike and ORF10 genes must be used in molecular diagnosis of this virus and may be the target of designing specific antiviral drugs. The genomic and proteomic alterations in the virus necessitate the search for new remedies and vaccines.

The Qualified and quantified specific genomic and proteomic alterations between the two versions of the coronaviruses during 16 years will not only enable designing right drugs and strategies for confronting the current viral version, but it may rather allow to extrapolate and foresee potential outbreaks of newer versions during the coming decades and thus be prepared beforehand.

Since developing specific vaccines or other specific antivirals requires long time, new antiviral drugs of non-specific character should be developed to be used in the time of epidemics and pandemics. Positively charged proteins and their peptides, can be isolated from natural sources or chemically prepared, can be a good choice to confront globally spreading SARS-CoV2 and other epidemic viral outbreaks, based on their wide-spectrum specificity against virus and pathogenic bacteria, and their health safety. Yet, extensive pharmacological and pharmaceutical studies are critically and urgently needed for best medical practices against SARS-CoV2 the causative virus of Covid-19 disease.

Abbreviations

SARS-CoV: Severe acute respiratory syndrome coronaviruses; COVID-19: Coronavirus disease 2019; MERS-CoV: Middle East respiratory syndrome Coronavirus; ACE2: angiotensin I converting enzyme 2; NCBI: National Center for Biotechnology Information;  HCoV-19: Human Coronavirus-19; 2019-nCoV: 2019 Novel Coronavirus; ss-RNA: Single- stranded RNA; aa: Amino acid; nt: Nucleotide; S: Spike glycoprotein; M: Membrane protein; E: Envelope protein; N: Nucleoprotein; PL-PRO: papain-like proteinase; MDCK cell: Madin-Darby Canine Kidney Cell

Declarations

Ethics approval and consent to participate

Not applicable

Consent for publication

All authors agree on the publication of this article

Availability of data and material

All the data are included in the manuscript. Any other supporting data will be provided when requested.

Competing interests

The authors declare the absence of any conflict of interest regarding this article.

Funding

No specific funding was allocated for this work.

Authors' contributions

All authors have worked and collaborated equally in producing this work. A.H. has conducted the initial genomic and proteomic bio-informatics analysis which was revised, discussed and interpreted by all authors. A.H. wrote the draft manuscript which was revised by E.M and B.S. The final manuscript was written by M.S. and revised by all authors.

Acknowledgements

The authors would like to thank both Zagazig University and Umea University for supporting the publication of this work.

Author details

1Genetics Department, Faculty of Agriculture, Zagazig University, Egypt. 2Department of Clinical Microbiology, Immunology, 3 Department of Radiation Sciences, Oncology, Umeå University, SE-90185 Umeå, Sweden. 4Biochemistry Department, Faculty of Agriculture, Zagazig University, Egypt

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