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.