COVID-19, SARS AND BATS CORONAVIRUSES GENOMES PECULIAR HOMOLOGOUS RNA SEQUENCES
DOI:
https://doi.org/10.29121/granthaalayah.v8.i7.2020.678Keywords:
COVID-19, Bats Coronaviruses, RNA SequencesAbstract [English]
We are facing the worldwide invasion of a new coronavirus. This follows several limited outbreaks of related viruses in various locations in a recent past (SARS, MERS). Although the main current objective of researchers is to bring efficient therapeutic and preventive solutions to the global population, we need also to better understand the origin of the newly coronavirus-induced epidemic in order to avoid future outbreaks. The present molecular appraisal is to study by a bio-infomatic approach the facts relating to the virus and its
precursors. This article shows how 16 fragments (Env Pol and Integrase genes) from different strains, both diversified and very recent, of the HIV1, HIV2 and SIV retroviruses have high percentage of homology into parts of the genome of COVID_19. Moreover each of these elements is made of 18 or more nucleotides and therefore may have a function. They are called Exogenous Informative Elements (EIE).. Among these EIE, 12 are concentrated in a very small region of the COVID-19 genome, length less than 900 bases, i.e. less than 3% of the total length of this genome. In addition, these EIE are positioned in two functional genes of COVID-19: the orf1ab and S spike genes. Here are the two main facts which contribute to our hypothesis of a partially synthetic genome: A contiguous region representing 2.49% of the whole COVID-19 genome of which 40.99% is made up of 12 diverse fragments originating from various strains of HIV SIV retroviruses. Some of these 12 EIE appear concatenated. Notably, the retroviral part of these regions, which consists of 8 elements from various strains
of HIV1, HIV2 and SIV covers a length of 275 contiguous bases of COVID-19. The cumulative length of these 8 HIV/SIV elements represents 200 bases. Consequently, the HIV SIV density rate of this region of COVID-19 is 200/275 = 72.73%.
Downloads
References
WHO-SARS, https://www.google.com/url? sa=t&source=web&rct=j&url=https://www.who.int/ith/diseases/sars/en/&ved=2ahUKEwi YufHk5tDoAhXU3oUKHSTwBuYQFjAWegQIBRAB&usg=AOvVaw0bFoEUPELafXU98baC4o2k
WHO-MERS, https://www.google.com/url? sa=t&source=web&rct=j&url=https://www.who.int/emergencies/mers-cov/en/&ved=2ahUKEwjigPe059DoAhXEx4UKHU5xDDYQFjAMegQIBBAC&usg=AOvVaw1kaYVgLwAr9c7E yL7kGXQn
Perez, J.C, 2020/02/13, Wuhan nCoV-2019 SARS Coronaviruses Genomics Fractal Metastructures Evolution and Origins, DO -DOI: 10.20944/preprints202002.0025.v2, Researchgate : https://www.researchgate.net/publication/339331507_Wuhan_nCoV- 2019_SARS_Coronaviruses_Genomics_Fractal_Metastructures_Evolution_and_Origins DOI: https://doi.org/10.20944/preprints202002.0025.v2
Lyons Weiler J., 2020, 1-30-2020, On the origins of the 2019 ncov virus wuhan china, https://jameslyonsweiler.com/2020/01/30/on-the-origins-of-the-2019-ncov-virus- wuhan-china/
Perez J.C, (2020). “WUHAN COVID-19 SYNTHETIC ORIGINS AND EVOLUTION.” International Journal DOI: https://doi.org/10.29121/granthaalayah.v8.i2.2020.221
of Research - Granthaalayah, 8(2), 285-324. https://doi.org/10.5281/zenodo.3724003.
Perez J.C, Codex biogenesis - Les 13 codes de l'ADN (French Edition) [Jean-Claude ... 2009); Language: French; ISBN-10: 2874340448; ISBN-13: 978-2874340444 https://www.amazon.fr/Codex-Biogenesis-13-codes-lADN/dp/2874340448.
Perez J.C, Deciphering Hidden DNA Meta-Codes -The Great Unification & Master Code of Biology. J Glycomics Lipidomics 5:131, 2015, doi: 10.4172/2153- 0637.1000131 https://www.longdom.org/abstract/deciphering-hidden-dna-metacodes-the-great-unification-amp-master-code-of-biology-11590.html DOI: https://doi.org/10.4172/2153-0637.1000131
Perez, J.C. Six Fractal Codes of Biological Life:perspectives in Exobiology, Cancers Basic Research and Artificial Intelligence Biomimetism Decisions Making. Preprints 2018, 2018090139 (doi: 10.20944/preprints201809.0139.v1). https://www.google.com/url?sa=t&source=web&rct=j&url=https://www.preprints.org/manuscript/201809.0139/v1&ved=2ahUKEwj9wo-A_vfqAhUrDWMBHUCEAN0QFjAAegQIBBAB&usg=AOvVaw2FjttkMu-Pz4axTeyvU459
Land A.M. Et al, Human immunodeficiency virus (HIV) type 1 proviral hypermutation correlates with CD4 count in HIV-infected women from Kenya., J Virol. 2008 Aug;82(16):8172-82. doi: 10.1128/JVI.01115- 08. Epub 2008 Jun 11., DOI: 10.1128/JVI.01115-08 https://www.ncbi.nlm.nih.gov/pubmed/18550667 DOI: https://doi.org/10.1128/JVI.01115-08
Venkatesan P, Franck Alla Plummer, The Lancet Infectious diseases, April 2020, DOI: https://doi.org/10.1016/S1473-3099(20)30188-2
DOI: https://doi.org/10.1016/S1473-3099(20)30188-2 , https://www.thelancet.com/pdfs/journals/laninf/PIIS1473- 3099(20)30188-2.pdf
Perez, J. Epigenetics Theoretical Limits of Synthetic Genomes: The Cases of Artificials Caulobacter (C. eth-2.0), Mycoplasma Mycoides (JCVI-Syn 1.0, JCVI-Syn 3.0 and JCVI_3A), E-coli and YEAST chr
XII. Preprints 2019, 2019070120 (doi:10.20944/preprints201907.0120.v1).https://www.preprints.org/manuscript/201907.0120/v1
Zhou, P et al, 2020, A pneumonia outbreak associated with a new coronavirus of probable bat origin, Nature 579 (7798), 270-273 (2020), DOI: 10.1038/s41586-020-2012-7 DOI: https://doi.org/10.1038/s41586-020-2012-7
FISABIO, 2020, http://fisabio.san.gva.es/web/fisabio/noticia/-/asset_publisher/1vZL/content/secuenciacion- coronavirus.
Andersen, K.G., Rambaut, A., Lipkin, W.I. et al. The proximal origin of SARS-CoV-2. Nat Med (2020). https://doi.org/10.1038/s41591-020-0820-9 DOI: https://doi.org/10.1038/s41591-020-0820-9
Prashant Pradhan et al, Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag,https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1 , This biorxiv preprint was withdrawn by the authors.
Yuanchen Ma et al., 2020-2-27, ACE2 shedding and furin abundance in target organs may influence the efficiency of SARS-CoV-2 , http://www.chinaxiv.org/abs/202002.00082
Xiaolu Tang, Changcheng Wu, Xiang Li, Yuhe Song, Xinmin Yao, Xinkai Wu, Yuange Duan, Hong Zhang, Yirong Wang, Zhaohui Qian, Jie Cui, Jian Lu, On the origin and continuing evolution of SARS-CoV-
, National Science Review, , nwaa036, https://doi.org/10.1093/nsr/nwaa036 DOI: https://doi.org/10.1093/nsr/nwaa036
Lu, R et al., 2020. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding The Lancet. https://www.thelancet.com/journals/lancet/article/PIIS0140-6736%2820%2930251-8/fulltext
Wei Ji, et al, Homologous recombination within the spike glycoprotein of the newly identified coronavirus 2019-nCoV may boost cross-species transmission from snake to
human, https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/jmv.2568220.
Peng Zhou et al, Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin, BioRxiv, January 2020, https://doi.org/10.1101/2020.01.22.914952 DOI: https://doi.org/10.1101/2020.01.22.914952
Leoz M, Feyertag F, Kfutwah A, Mauclère P, Lachenal G, et al. (2015) The Two-Phase Emergence of Non Pandemic HIV-1 Group O in Cameroon. PLOS Pathogens 11(8):
e1005029. https://doi.org/10.1371/journal.ppat.1005029 DOI: https://doi.org/10.1371/journal.ppat.1005029
Hangping Yao, et al., Patient-derived mutations impact pathogenicity of SARS-CoV-2
medRxiv 2020.04.14.20060160; doi: . https://doi.org/10.1101/2020.04.14.20060160 DOI: https://doi.org/10.1101/2020.04.14.20060160
D. B. T. Cox et al., RNA editing with CRISPR-Cas13 , Science 24 Nov 2017: Vol. 358, Issue 6366, pp. 1019-1027, DOI: 10.1126/science.aaq0180 DOI: https://doi.org/10.1126/science.aaq0180
LaRinda A. Holland et al, An 81 nucleotide deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020), Journal of Virology (2020). DOI: 10.1128/JVI.00711-20 DOI: https://doi.org/10.1128/JVI.00711-20
ue Wu Zhang et al, Structural similarity between HIV1 gp41 and SARS-CoV S2 proteins suggests an analogous membrane fusion mechanism May 2004Journal of Molecular Structure THEOCHEM 677(1):73- 76, DOI: 10.1016/j.theochem.2004.02.018 DOI: https://doi.org/10.1016/j.theochem.2004.02.018
Pilani et al, In silico comparison of spike protein-ACE2 binding affinities across species;significance for the possible origin of the SARS-CoV-2 virus, https://arxiv.org/abs/2005.06199
Perez, j., & Montagnier, L. (2020, April 25). COVID-19, SARS and Bats Coronaviruses Genomes unexpected Exogeneous RNA Sequences. https://doi.org/10.31219/osf.io/d9e5g DOI: https://doi.org/10.31219/osf.io/d9e5g
Seong-Tshool Hong et al., The emergence of SARS-CoV-2 by an unusual genome
reconstitution, DOI 10.21203/rs.3.rs-33201/v1 https://www.researchsquare.com/article/rs-33201/v1
Zhang, M., Kaneko, I., Tsao, T. et al. A highly infectious Plasmodium yoelii parasite, bearing Plasmodium falciparum circumsporozoite protein. Malar J 15, 201 (2016). DOI: https://doi.org/10.1186/s12936-016-1248-z
F. Castro-Chavez, (June 2020), Anticovidian v.2: COVID-19: Hypothesis of the Lab Origin versus a Zoonotic
Event Which Can Also be of a Lab Origin, GJSFR (Submitted; to appear in: [https://pubmed.ncbi.nlm.nih.gov/? term=%22Castro-Chavez%20F%22])
Perez JC (2018) The Optimal Multi-Isotopic Atomic Code of Life: Perspectives in Astrobiology. Astrobiol Outreach 6: 165. doi: 10.4172/2332-2519.1000165 , https://www.longdom.org/open-access/the-optimal- multiisotopic-atomic-code-of-life-perspectives-in-astrobiology-2332-2519-1000166.pdf
Zhang et Al. The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity,
doi: https://doi.org/10.1101/2020.06.12.148726 DOI: https://doi.org/10.1101/2020.06.12.148726
A Bauer & R. Sachez, Vivre au temps du Coronavirus, Cerf 2020, (ISBN : 978-2-204-14203-8),
https://www.amazon.fr/Comment-vivre-temps-coronavirus-comprendre-
Sorensen, B. et Al, Biovacc-19: A Candidate Vaccine for Covid-19 (SARS-CoV-2) Developed from Analysis of its General Method of Action for Infectivity, DOI:https://doi.org/10.1017/qrd.2020.8 , Published online by Cambridge University Press: 02 June 2020.
Published
How to Cite
Issue
Section
License
With the licence CC-BY, authors retain the copyright, allowing anyone to download, reuse, re-print, modify, distribute, and/or copy their contribution. The work must be properly attributed to its author.
It is not necessary to ask for further permission from the author or journal board.
This journal provides immediate open access to its content on the principle that making research freely available to the public supports a greater global exchange of knowledge.
