Unveiling hidden structural patterns in the SARS-CoV-2 genome: Computational insights and comparative analysis

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(4), P. e0298164 - e0298164

Published: April 4, 2024

SARS-CoV-2, the causative agent of COVID-19, is known to exhibit secondary structures in its 5’ and 3’ untranslated regions, along with frameshifting stimulatory element situated between ORF1a 1b. To identify additional regions containing conserved structures, we utilized a multiple sequence alignment related coronaviruses as starting point. We applied computational pipeline developed for identifying non-coding RNA elements. Our employed three different structural prediction approaches. identified forty genomic likely harbor ten them showing three-way consensus substructure predictions among our predictive utilities. conducted intracomparisons utilities within intercomparisons four previously published SARS-CoV-2 datasets. While there was limited agreement on precise structure, approaches seemed converge contain viral genome. By comparing combining various approaches, can predict most form well probable structure or ensemble structures. These be used guide surveillance, prophylactic measures, therapeutic efforts. Data scripts this study may found at https://doi.org/10.5281/zenodo.8298680 .

Language: Английский

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Why It Remains Statistically Probable That SARS-CoV-2 Was Isolated and Then Accidentally Lab-Leaked before the First COVID-19 Outbreak

Published: June 20, 2024

The SARS-CoV-2-induced acute COVID-19 pandemic disorder seems to have begun all of the sudden in 2020, with very little data available regarding prior times which people experienced mysterious flu-like illness symptoms characteristic disease. scientific community be divided into a few parts regards belief kind viral origins. A significant number scientists believe that virus solely has natural origins and it underwent thorough process zoonosis, independent laboratory research-based research would only catalyse zoonosis due helping gain additional function transmission virulence. Many other wide “gain-of-function” research, whilst many most genome origins, zoonotic having been artificially catalysed its latter part humans. Considerable extent evidence suggests restricted, but considerable accidentally leaked nearby environment, spillover humans was influenced by such events, given for example multidimensional pathogenetic displayed main antigen action, spike glycoprotein, causing kinds immune pathophysiology - including transient immunosuppression. Investigations novel coronavirus lasting years, seemingly no concrete end sight, molecular testing methods detect SARS-CoV-2 infection displaying less than perfect results not significantly helped process. Evidence even started pointing toward existence artificial, exposing probable accidentally-induced artificial “accelerated evolution”, could particularly dangerous because nature pathogenic agent. Likewise, is possible prevention distribution scenarios as fact constitutes censorship, rather regulation may considered based. Simultaneously, important regard hypotheses preliminary reports evidence-based, ensure diligence performed cases. integrity ultimately innovation medical solutions depends on democracy rule law, well regulating partnerships companies from world nations where autocracy rules their society.

Language: Английский

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Current Conditions and Policy Frameworks of Agri-Food Systems Transformation

Published: Jan. 1, 2023

systems approach to agri-food: Towards a crises-proof pathway 2 1.1Why do agri-food need be transformed?An overview of the ecological, health and social challenges related systems.........

Language: Английский

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Updated analysis to reject the laboratory-engineering hypothesis of SARS-CoV-2

Environmental Research, Journal Year: 2023, Volume and Issue: 224, P. 115481 - 115481

Published: Feb. 18, 2023

Language: Английский

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The concentrations of essential/toxic elements in serum of COVID-19 patients are not directly related to the severity of the disease

Journal of Trace Elements in Medicine and Biology, Journal Year: 2023, Volume and Issue: 78, P. 127160 - 127160

Published: March 27, 2023

In recent months, the current COVID-19 pandemic has generated thousands of studies directly or indirectly related with this disease and/or coronavirus SARS-CoV-2 causing infection. On August 22, 2022, database PUBMED included 287,639 publications containing term COVID-19. However, in spite importance trace elements human health, including immune system, data on levels metals/metalloids patients is very limited.The concentrations As, Cd, Cr, Cu, Hg, Fe, Mg, Mn, Pb, Se, V and Zn were determined by inductively coupled plasma-mass spectrometry (ICP-MS) 126 serum samples individuals infected SARS-CoV-2, as well 88 non-infected individuals. Participants divided into four groups: i) positive (COVID-19 +) an asymptomatic infection course; ii) suffering mild COVID-19; iii) severe COVID-19, iv) negative (COVID-19-) (control group). The occurrence analyzed was evaluated along biochemical profile, blood cell counts, lipids, proteins crucial enzymes.Serum V, Pb higher than those control group. Although no significant differences observed between different groups patients, showed a tendency to be showing symptoms being asymptomatic. Arsenic Hg rarely detected, regardless if subjects not. results did not show rest according severity (asymptomatic, severe).In here obtained, we highlight need reduce exposure minimize potential adverse health outcomes after other hand, although protective role essential found, Mg Cu

Language: Английский

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Enhancing Biosafety and Biosecurity: Quality Management in High-Containment Laboratories

Etlik Veteriner Mikrobiyoloji Dergisi, Journal Year: 2024, Volume and Issue: 35(1), P. 105 - 112

Published: May 10, 2024

Quality Management in high-containment laboratories plays a pivotal role ensuring the safe handling of biological agents and toxins, thereby mitigating potential biorisks. This paper provides comprehensive exploration key aspects Systems (QMS) tailored to unique challenges laboratories. It delves into significance QMS enhancing biosafety biosecurity measures, safeguarding laboratory personnel, community, environment. The also discusses integration international standards, risk management strategies, top fostering culture safety. Through this examination, it becomes evident that robust not only ensures compliance but promotes continual improvement innovation operations, ultimately advancing field biosecurity.

Language: Английский

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Interaction of HERVs with PAMPs in Dysregulation of Immune Response Cascade Upon SARS-CoV-2 Infections

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(24), P. 13360 - 13360

Published: Dec. 12, 2024

Human endogenous retroviruses (HERVs) are genomic fragments integrated into human DNA from germline infections by exogenous that threatened primates early in their evolution and inherited vertically the germline. So far, HERVs have been studied context of extensive immunopathogenic, neuropathogenic even oncogenic effects within host. In particular, our paper, we elaborate on aspects related to possible correlation transposable HERV elements’ activation SARS-CoV-2 spike protein’s presence cells COVID-19 patients or upon vaccination with implications for natural adaptive immunity. release cytokines TNF-α, IL-1β IL-6 occurs such cases plays a notable role sustaining chronic inflammation. Moreover, well-known interindividual variations might partially account interpersonal variability symptoms unwanted events post-vaccination. Accordingly, further studies required clarify triggering HERVs.

Language: Английский

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Molecular diagnostic approaches for SARS-CoV-2 detection and pathophysiological consequences

Molecular Biology Reports, Journal Year: 2023, Volume and Issue: 50(12), P. 10367 - 10382

Published: Oct. 10, 2023

Language: Английский

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On Classification and Taxonomy of Coronaviruses (Riboviria, Nidovirales, Coronaviridae) with Special Focus on Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV-2)

Mathematical Biology and Bioinformatics, Journal Year: 2022, Volume and Issue: 17(2), P. 289 - 311

Published: Nov. 16, 2022

Coronaviruses are highly virulent and therefore important human veterinary pathogens worldwide. This study presents the first natural hierarchical classification of Coronaviridae. We also demonstrate a “one-step” solution to incorporate principles binomial (binary) nomenclature into taxonomy strongly support complete rejection non-taxonomic category “virus” in any future taxonomic virology. will aid recognition numerous virus species, particularly currently monotypic subgenus Sarbecovirus. Commenting on nature SARS-CoV-2, authors emphasize that no member Sarbecovirus clade is an ancestor this virus, humans only known host.

Language: Английский

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Scientific evidence on the origin of SARS-CoV-2

Environmental Research, Journal Year: 2022, Volume and Issue: 216, P. 114631 - 114631

Published: Oct. 19, 2022

Language: Английский

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