Method to Find the Original Source of COVID-19 by Genome Sequence and Probability of Electron Capture

The purpose of this study was to find the original source of envelope protein (spiked surface) of the Covid-19. It was assumed that the envelope protein was related to ordinary proteins like the human liver enzymes as possible original sources. A comparison was made on the genome sequences of the envelope protein and the human liver enzymes. The results of computational experiments showed that the longest sequence, common in both groups, was as follows: glutamine acid (e) - glutamine acid (e) - threonine (t) - glycine (g). Upon this finding further investigation was performed on the molecular structure of this sequence;and the probabilities of electron captures by the protons of the atoms were computed to determine which atoms could connect the amino acids using the approximation method taken from the quantum mechanics. The study was continued to identify which amino acid grew the genome sequence of the envelope protein differently from the human liver enzymes. And it was found that the electron capture by the proton of the atom could explain the process that formed the genome sequence of the Covid-19’s envelope protein out from the human liver enzymes. To our opinion this method could be used for identification of other candidate proteins so that to find the original source of the virus. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.

Cellular and extracellular levels of retrovirus-host interactions on the example of the bovine leukose virus. 2. critical stages - multiplicity and versatility (review)

The wide spread of viral infections and the ease of overcoming the species-specific barriers require the identification of critical stages in the virus interaction with multicellular organisms of mammals and the analysis of key molecular genetic systems involved. To date, a large amount of data has already been accumulated on the diversity and complexity of such systems, as well as the involvement in them the wide range of metabolic pathways. In this regard, attempts to identify some common elements that are implemented in different infectious processes are of particular relevance. This paper is such attempt made on the example of the analysis of the main events of cattle infection by bovine leukemia virus (BLV). Systems involved in the entry of BLV genetic material into the cytoplasm of host cells, the suppression of innate and adaptive immunity, as well as interactions between the genomes of the BLV provirus and the host genome are the identified critical stages. The direct participants in the reception of viral proteins are parts of some host tansmembrane systems (G.Yu. Kosovsky et al., 2017;V.I. Glazko et al., 2018;L. Bai et al., 2019;H. Sato et al., 2020). During virus reproduction in host cells, host enzymes modify virus envelope proteins by (A. De Brogniez et al., 2016;W. Assi et al., 2020). Importantly, modifications of SARS-CoV-2 spike proteins, as well as BLV envelope proteins, have a significant impact on their pathogenicity (M. Hoffmann et al., 2020). Pathogenicity and depressing effect of both BLV and SARS-CoV-2 on innate and adaptive immunity is realized in part through the activation of T regulatory cells and an increase in the expression of the growth transforming factor TGF-b (L.Y. Chang et al., 2015;G.Yu. Kosovsky et al., 2017;W. Chen et al., 2020). Intracellular mechanisms of protection against retrotranspositions, recombinations between viruses and host retrotransposons, the formation of new elements of host regulatory networks such as microRNAs, and the integration of proviral DNA into the host genome are closely related and controlled by interfering RNA (RNAi) systems with the key gene dicer1 (P.V. Maillard et al., 2019;E.Z. Poirier et al., 2021;G.Y. Kosovsky et al., 2020). These systems can provide a certain left-pointing-double-angle resistance right-pointing-double-angle of the host genome both to the integration of exogenous genetic material and to transpositions of own mobile genetic elements. Apparently, it is the polygenicity of the control of these critical stages of viral infection that leads to difficulties in predicting their development and developing methods for their prevention.

Evidence for SARS-CoV-2 Spike Protein in the Urine of COVID-19 Patients.

Background: SARS-CoV-2 infection has, as of April 2021, affected >133 million people worldwide, causing >2.5 million deaths. Because the large majority of individuals infected with SARS-CoV-2 are asymptomatic, major concerns have been raised about possible long-term consequences of the infection. Methods: Wedeveloped an antigen capture assay to detect SARS-CoV-2 spike protein in urine samples from patients with COVID-19whose diagnosis was confirmed by positive PCR results from nasopharyngeal swabs (NP-PCR+) forSARS-CoV-2. We used a collection of 233 urine samples from 132 participants from Yale New Haven Hospital and the Children's Hospital of Philadelphia that were obtained during the pandemic (106 NP-PCR+ and 26 NP-PCR-), and a collection of 20 urine samples from 20 individuals collected before the pandemic. Results: Our analysis identified 23 out of 91 (25%) NP-PCR+ adult participants with SARS-CoV-2 spike S1 protein in urine (Ur-S+). Interestingly, although all NP-PCR+ children were Ur-S-, one child who was NP-PCR- was found to be positive for spike protein in their urine. Of the 23 adults who were Ur-S+, only one individual showed detectable viral RNA in urine. Our analysis further showed that 24% and 21% of adults who were NP-PCR+ had high levels of albumin and cystatin C, respectively, in their urine. Among individuals with albuminuria (>0.3 mg/mg of creatinine), statistical correlation could be found between albumin and spike protein in urine. Conclusions: Together, our data showed that one of four individuals infected with SARS-CoV-2 develop renal abnormalities, such as albuminuria. Awareness about the long-term effect of these findings is warranted.

Potential inhibitors against SARS-CoV-2 by targeting proteins responsible for envelope formation and virion assembly

Even though extreme research there is presently no efficient vaccine accessible against the new-found severe acute respiratory syndrome coronavirus-2 causing COVID-19 pandemic. The clinical administration of COVID-19 has been restricted to infection prevention along with control measures linked with supportive care. In the meantime, efforts to achieve a successful therapy to prevent virus replication, alleviate the symptoms, increase survivability as well as reduce mortality are ongoing. In this review, we found that a drug named Tipranavir (used in more than top 20 drugs in different countries against Covid-19) that can be docked against the QNH88662.1 envelope protein [Severe acute respiratory syndrome coronavirus 2] and at least cease the activity so that its action of spreading infection can be prevented. Pharmacokinetics and ADME studies show that drugs need some improvement. It is slightly heavier than Lipinski rule of five criteria. We propose improvement in future aspects.

Phylogenetic analysis of spike and envelope p roteins for a number of bat coronaviruses for understanding the hypothesis of possible origin for the novel 2019- nCoV

Coronavirus Disease 19 (COVID-19) emergence reveals globally a great health issue and due to the limited information and knowledge on the origin of this novel coronavirus 2019 (2019-nCoV). Therefore, this study aims to investigate the evolution and analysis of molecular epidemiology for both Spike and Envelope proteins of 20 available complete genome sequences of different bat coronaviruses including 2019-nCoV in order to find out which type of bat coronaviruses is more likely to be the origin of this new 2019-nCoV and also multiple amino acid sequences of Envelope protein for all bat coronaviruses were aligned for the purpose of finding the greater probability of novel 2019-nCoV original host among bat coronaviruses. Phylogenetic tree analysis for Spike protein revealed that all 2019-nCoV related coronaviruses isolated from these species of species are discovered in China and Hong Kong and the Middle East bat are less likely to contribute in spreading or to become the origin of 2019-nCoV and all coronaviruses that from Hong Kong and China are located into one clade next to the clade that contains 2019-nCoV coronaviruses which indicates that this group of coronaviruses are genetically different for 2019-nCoV;moreover, Hong Kong and USA bat coronaviruses does not contain the bat coronavirus from China and are located into one clade far from the clade that contains 2019-nCoV indicates that all coronaviruses are genetically very different from 2019-nCoV, and USA bat coronavirus may has no role in generating of 2019-nCoV. The phylogenetic trees analysis of Envelope protein showed that Envelope protein of different coronaviruses are more similar in comparison to Spike protein, USA bat coronavirus has a relatively closeness relationship to 2019-nCoV. Furthermore, Envelope protein alignment showed the closely related amino acid sequence which confirms that the outcomes of phylogenetic tree analysis in which that these bat coronaviruses have genetically close relationship together and more interestingly amino acid sequence (MG772934.1) shows 100% identity with the amino acid sequence of 2019-nCoV (NC 045512.2) and the same virus has a close relationship in both Spike and Envelope due to that in both phylogenetic tree analysis are neighbored with 2019-nCoV in the same clade.