New strategies for treatment of COVID-19 and evolution of SARS-CoV-2 according to biodiversity and evolution theory

ABSTRACT

To treat the COVID 19, it is assumed two strategies, the first of which is design a complementary micro-RNA for 3 UTR region of virus that will be bind with it.  This might prevent the translation of virus RNA on the host ribosomes or lead to virus degradation and elimination. As for the second strategy, elevation of hydrogen ion concentration upward to alkaline pH to prevent the glycoprotein of virus envelop from binding to the host’s receptor, thereby preventing the virus from entering the cells. Also we predict further development of the virus through the transmission of genetic materials and micro RNA between viruses each other or between viruses and bacteria or viruses and its hosts when they are together and have intimate contact in a living cell. There are future fears of this development and its transformation of SARS-CoV-2 into retroviruses and transfer to cDNA by reverse transcriptase (RT) and integrates into the human genome. This will explain the presence of the virus in infected people after recovery. This article also explained how SARS-CoV-2 develops. This review might help in finding potential strategies for treatment COVID-19 and help explain the development of SARS-CoV-2.

KEYWORDS:

• COVID 19
• SARS-CoV-2
• microRNA
• alkaline and acidic pH
• virus evolution

Treatment through micro-RNA

World health organization has announced the outbreak of newly severe acute respiratory syndrome Coronavirus (SARS-CoV-2) as pandemic in December 2019 and termed the disease as Covid-19. It produced massive infection and death worldwide [1–3]. The search for treatment strategy is urgently important. In order to overcome the SARS-CoV-2 (severe acute respiratory syndrome – coronavirus – 2), it is feasible to use the same language. RNA of SARS-CoV-2 severe acute respiratory syndrome – coronavirus – 2 composed of four ribonucleotides that has the nitrogen bases adenine (A), uracil (U), guanine (G) and cytosine (C). SARS-CoV2 attacks its host through its genetic material, which is RNA. Therefore, a genetic antigen must be designed against the genetic material of the SARS-CoV-2 in order to get rid of it. This article will help researchers worldwide to overcome and treat COVID 19 through the design and synthesis of oligonucleotide or microRNA that is complementary to the 3 UTR region of the SARS-CoV-2. This might prevent virus RNA translation or lead to degradation of virus genome. These supplements can be loaded with liposome for easy access and cellular entry.

This article will add a new strategy for plants importance. Not only, the protective effects of plants through its containing antioxidants, but also considered rich source for micro-RNA, which plays a therapeutic and preventive role for many diseases and infections. Micro-RNAs (miRs) are a class of small RNAs that play essential roles in various biological processes through silencing genes. Recent evidence suggests that microRNAs in food can be absorbed into the circulatory system and organs of humans and other animals, where they regulate gene expression and biological processes in cells. These food-derived dietary microRNAs may serve as a novel functional component of food, a role that has been neglected to date [4]. The mechanism of micro RNA to exert its function was elucidated. MicroRNAs hybridize with complementary sequences in mRNA and silence genes by destabilizing mRNA or preventing translation of mRNA. Over 60% of human protein-coding genes are regulated by microRNAs, and 1881 high-confidence miRs are encoded in the human genome. Evidence suggests that micro-RNA not only are synthesized endogenously, but also might be obtained from dietary sources, and that food compounds alter the expression of endogenous micro-RNA genes. The main food matrices for studies of biological activity of dietary micro-RNA include plant foods and milk. Encapsulation of micro-RNA in exosomes and exosome-like particles confers protection against RNA degradation and creates a pathway for intestinal and vascular endothelial transport by endocytosis, as well as delivery to peripheral tissues. Evidence suggests that the amount of micro-RNA absorbed from nutritionally relevant quantities of foods is sufficient to elicit biological effects, and that endogenous synthesis of micro-RNA is insufficient to compensate for dietary miR depletion and rescue wild-type phenotypes. In addition, nutrition alters the expression of endogenous miR genes, thereby compounding the effects of nutrition micro-RNA interactions in gene regulation and disease diagnosis in liquid biopsies. For example, food components and dietary preferences may modulate serum micro-RNA profiles that may influence biological processes [5]. Another category of micro RNA called non-dietary microRNA was detected. Non-dietary of systemic xenomiRNA transfers between different organisms. Organ or stem cell transplants, blood transfusions, pregnancy, and various states of parasitism may involve direct RNA transfer from one organism to another. Inhalation of atmospheric plant material, injection of plant-based drugs, and fluid exchange (e.g. through different sexual practices) could allow RNA transfer [6].

To enter the micro RNA to recipient cells, it needs a loading material such as high-density lipoprotein (HDL). Micro-RNAs connected with mRNA at 3UTR and exert their negative regulation through degradation or suppression of protein translation. MicroRNAs were detected in plants, food-derived plant miRNA entered mammalian circulation naturally and all murine tissue types. In addition to working inside cells, miRNAs also communicate remotely in the form of circulating miRNAs [7]. Emerging evidence has indicated that circulating miRNAs are localized in microvesicles or bind to other plasma components such as high-density lipoprotein (HDL) particles and RNA-binding proteins [8,9]. These circulating miRNAs can enter recipient cells and induce gene regulation of target genes [10].

Anti-viral activity of micro RNA is considered as one of its function. Plants, nematodes and arthropods use sRNAs to combat viral infections [11]. MicroRNAs are small regulatory noncoding RNAs that regulate various biological processes associated with neurological disorders, cardiovascular diseases, cancer and viral infection. miRNA-based therapeutics has broad applications including cancer immunotherapy, genomic engineering and protein replacement therapy. Until now, a variety of materials have been proved to be promising as non-viral nanocarriers for intracellular delivery of miRNAs, such as polymeric nanoparticles, lipid nanocapsules, and inorganic nanoparticles [12].

This article explains why plasma from COVID-19 recovering patients is used, as well as the use of some plants to treat COVID-19. The blood plasma contains antibodies and also contains antivirus microRNA as a result of infection previously. Plants and food also contain antioxidants, as well as microRNA, which play an important role as an anti-virus. Avian infectious bronchitis virus (IBV) is a coronavirus which infects chickens and causes severe economic losses to the poultry industry worldwide. MicroRNAs are important intracellular regulators and play a pivotal role in viral infections. It was found that overexpressed gga-miR-30d inhibited IBV replication [13]. In poultry, viral infections (e.g., Marek’s disease virus, avian leukosis virus, influenza A virus, and so on) can cause devastating mortality and economic losses. Because viruses are solely dependent on host cells to propagate, they alter the host intracellular microenvironment. MicroRNAs are crucial post-transcriptional regulators of gene expression in a wide spectrum of biological processes, including viral infection. Recently, microRNAs have been identified as key players in virus–host interactions [14]. RNA interference (RNAi)-based tools are used in multiple organisms to induce antiviral resistance through the sequence-specific degradation of target RNAs by complementary small RNAs. In plants, highly specific antiviral RNAi-based tools include artificial microRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs). syn-tasiRNAs have emerged as a promising antiviral tool allowing for the multi-targeting of viral RNAs through the simultaneous expression of several syn-tasiRNAs from a single precursor [15]. Multiple interplays between viral and host factors are involved in influenza virus replication and pathogenesis. Several small RNAs have recently emerged as important regulators of host response to viral infections., a critical role of Y-class small RNA and hsa-miR-1975 in host’s defense against influenza virus was demonstrated [16]. The interferon-inducible microRNA (miR) miR-128, a novel antiviral mediator that suppresses the expression of the host gene TNPO3, is known to modulate HIV-1 replication. Notably, they observed that anti-miR-128 partly neutralizes the IFN-mediated block of HIV-1. Elucidation of the mechanisms through which miR-128 impairs HIV-1 replication may provide novel candidates for the development of therapeutic interventions [17].

The microRNA is not only present in all living organisms, but also, in some viruses which used it in controlling of host cells. The discovery of RNA interference and cellular microRNA has not only affected how biological research is conducted but also revealed an entirely new level of posttranscriptional gene regulation. The potential functions of the virally encoded miRNAs were identified in several pathogenic human viruses. Cellular miRNAs may have had a substantial effect on viral evolution and may continue to influence the in vivo tissue tropism of viruses [18]. Every herpesvirus that has been analyzed encodes several viral miRNAs, and the other viruses that have so far been shown to encode a single miRNA (i.e., simian virus 40 (SV40) and adenovirus) are also nuclear DNA viruses [19,20]. In contrast, the RNA viruses such as the fever virus, human immunodeficiency virus and hepatitis C virus (HCV) do not seem to encode any miRNAs 27. Viruses are obligatory intracellular parasites that rely on a wide range of cellular factors to successfully accomplish their infectious cycle. Among those, microRNAs have recently emerged as important modulators of viral infections. These small regulatory molecules act as repressors of gene expression. During infection, miRNAs can function by targeting cellular RNAs [21]. It has been observed that pathogens and some viruses that contain microRNA can induce the up-/down regulation of various host miRNAs in order to evade the host’s immune system. In contrast, some miRNAs studied could have an antiviral effect, enabling the defense mechanisms to fight the infection or, at the very least, they could induce the pathogen to enter a latent state. At the same time, some viruses encode their own miRNAs, which could further modulate the host’s signaling pathways, thus favoring the survival and replication of the virus. The clinical applications of miRNAs are extremely important, as miRNAs targeted inhibition may have substantial therapeutic impact. Inhibition effect of miRNAs can be achieved through many different methods, but chemically modified antisense oligonucleotides have shown the most prominent effects [22].

pH and COVID treatment

pH plays an important role in all biological processes, through protein receptor-binding domains. Viral glycoprotein extends from the surface of the virion and for many viruses can be observed as spikes. Most glycoprotein acts as viral attachment proteins capable of binding to structures on target cells or erythrocytes (hemagglutinins or HAs). Influenza and coronaviruses are enveloped viruses having a glycoprotein for attachments with host receptor. Interaction between the viral attachment proteins and cellular receptors firmly attach the virus to the cell. These interactions may trigger mechanisms that deliver the viral nucleocapsid into the cell. The neutral or acidic pH is optimum for fusion of an enveloped virus whether penetration occurs at the cell surface of host cell. At alkaline pH, the fusion and penetration of viruses were interrupted [23–25]. So when we try to preserve the alkaline medium of cells, then that prevents the SARS-CoV-2 from fusion to the target human cells and prevent entry to the cells, so we can protect people from COVID 19 through alkaline pH.

Evolution of COVID-19

This article also describes how SARS-CoV-2 develops. Evolution of the virus can occur through two ways. The first way is a natural evolution through the presence of different viruses with each other or with bacteria or with the host’s genome. As a result of its presence in a living medium, a transfer of the genetic material or microRNA occurs between them, which lead to the development of the coronavirus naturally. As for the second way, is through genetic engineering techniques in the laboratory, by removing or adding genetic materials to the SARS-CoV-2 that lead to develop it. COVID-19 is a viral respiratory illness caused by a new coronavirus called SARS-CoV-2. The World Health Organization declared the SARS-CoV-2 outbreak a global public health emergency. Genetic analysis of 86 complete or near-complete genomes of SARS-CoV-2 and revealed many mutations and deletions on coding and non-coding regions. These observations provided evidence of the genetic diversity and rapid evolution of this novel coronavirus [26]. A new coronavirus SARS-CoV-2 is spreading across the world [27]. Since the virus emerged at the seafood wholesale market at the end of last year [28], the number of infected cases has been rising dramatically [29]. Human-to-human transmission of SARS-CoV-2 has been confirmed [30]. The virus has been detected in bronchoalveolar-lavage [28], sputum [31], saliva [32], throat [33] and nasopharyngeal swabs [32]. Nucleotide substitution has been proposed to be one of the most important mechanisms of viral evolution in nature [34].

Forty-two missense mutations were identified in all the major non-structural and structural proteins, except the envelope protein. Twenty-nine missense mutations were in the ORF1ab polyprotein, eight in the spike surface glycoprotein, one in the matrix protein, and four in the nucleocapsid protein. Of note, three mutations (D³⁵⁴, Y³⁶⁴, and F³⁶⁷) located in the spike surface glycoprotein receptor-binding domain [26]. The spike surface glycoprotein plays an essential role in binding to receptors on the host cell and determines host tropism [35]. It is also the major target of neutralizing antibodies [36]. Mutations in the spike surface glycoprotein might induce its conformational changes, which probably led to the changing antigenicity.

Fortunately, mutations in the genome region of the virus’s spikes may weaken the virus’s attachment to its receptors in the host cell. This may explain the extent of the variation in the severity of the response between people each other and between different countries of this disease (COVID-19). Interactions between the SARS-CoV spike protein receptor-binding domain (RBD) and its host receptor angiotensin-converting enzyme 2 (ACE2) regulate both the cross-species and human-to-human transmissions of SARS-CoV. The sequence of 2019-nCoV RBD, including its receptor-binding motif (RBM) that directly contacts ACE2, is similar to that of SARS-CoV, strongly suggesting that 2019-nCoV uses ACE2 as its receptor [37]. The crystal structure of the C-terminal domain of SARS-CoV-2 (SARS-CoV-2-CTD) spike (S) protein was demonstrated, in complex with human ACE2 (hACE2), which reveals a hACE2-binding mode similar overall to that observed for SARS-CoV. These findings shed light on the viral pathogenesis and provide important structural information regarding development of therapeutic countermeasures against the emerging virus [38].

Viruses evolute like all organisms. We assumed a theory of biodiversity and gen evolution, thisclarifies the mechanisms of biological diversity and the genetic development of all living organisms and viruses on a molecular level and launched the term micro-evolution in relation to the evolution process, so that the evolution of any organism can be measured at any time at the level of adding or deleting a nitrogenous base in its genome. The theory was announced at the International Conference held at Aswan University (2020). The statement of theory: {Evolution of organisms and biodiversity depends mainly on gene evolution through the appearance of novel genes. Biodiversity results from the DNA modifications that induced by visible and non-visible environmental effects, variation of gene expression, stresses, mutation and invasion of genetic materials. Each individual belongs to the same species of living organisms has its own identity of DNA fingerprint} [38]. Through the application of theory, we will be able to explain the evolution of SARS-CoV-2. It has evolved from the SARS virus, and this development resulted from the transmission of genes or micro-RNA between the virus and its host through horizontal gene transfer. The degree of development of the virus is calculated by comparing the genome of the SARS-CoV-2 with the SARS virus and we calculate the number of nucleotides that have changed between them and this number represents the degree of SARS-CoV-2 evolution. So the virus developed itself from genetic materials from its host. Environmental stressors (visible and non-visible things) including, pollutions, chemicals, and biomaterials such as viruses, bacteria fungi and environmental DNA or invader DNA lead to DNA modifications that results in biodiversity and ± microevolution. This theory is used and applied to explain the emergence of new types of organisms through generating new genes, gene duplication, horizontal gene transfer (HGT), transposable elements, ± mutation and DNA polymorphisms to resist various environmental stressors [39]. In addition, it illustrates the relationship between host and parasite that depends on the transfer of DNA and RNA in between them [40]. The central dogma of biodiversity and evolution was designed by Hassab El-Nabi according to theory of biodiversity and evolution and listened to ”environmental effects on the genetic material (DNA) of living organisms lead to modifications of DNA and these modifications lead to biological diversity and ± micro-evolution” based on the current theory. The theory clarifies the relationship between evolution and adaptation, as any adaptation or modification is considered ± micro-evolution [39]. The definition of evolution unit, which is the permanent change or modification in one base pair in the entire individual genome compared to its previous ancestor, was identified. The evolution can be measured quantitatively according to this formula: Degree of evolution = numbers of + micro-evolution unit. Hassab Elnabi (2020). So according to theory of biodiversity and evolution, SARS-CoV-2 gets 93 mutations over its entire genome [26], hence it has 93evolution unit. The transfer of genetic materials between SARS-CoV 2 and its host, also mutations play an important role in its evolution. The intimate contact which frequently occurs in parasitism, symbiosis, pathogen, epiphyte, entophyte, and grafting interactions could promote HGTs between two species. Besides these direct transfer methods, gene can be exchanged with a vector as a bridge, possible vectors include pollen, fungi, bacteria, viruses, viroids, plasmids, transposons, and insects. HGT, especially when involving horizontal transfer of transposable elements, is recognized as a significant force propelling genomic variation and biological innovation, playing an important functional and evolutionary role in both eukaryotic and prokaryotic genomes (Gao et al., 2014) [41]. A central role of HGT in fueling evolution as a powerful mechanism promotes rapid often dramatic genotypic and phenotypic changes. The profound reshaping of the preexisting geno/phenotype allows the recipient bacteria to explore new ways of functioning, far beyond the mere acquisition of a novel function [42].

Disclosure statement

No potential conflict of interest was reported by the author.