Should we discount the laboratory origin of COVID-19?

The dual role of toll-like receptors in COVID-19: Balancing protective immunity and immunopathogenesis

Toll-like receptors (TLRs) of human are considered as the most critical immunological mediators of inflammatory pathogenesis of COVID-19. These immunoregulatory glycoproteins are located on the surface and/or intracellular compartment act as innate immune sensors. Upon binding with distinct SARS-CoV-2 ligand(s), TLRs signal activation of different transcription factors that induce expression of the proinflammatory mediators that collectively induce 'cytokine storm'. Similarly, TLR activation is also pivotal in conferring protection to infection and invasion as well as upregulating the tissue repair pathways. This dual role of the human TLRs in deciding the fate of SARS-CoV-2 has made these receptor proteins as the critical mediators of immunoprotective and immunopathogenic consequences associated with COVID-19. Herein, pathbreaking discoveries exploring the immunobiological importance of the TLRs in COVID-19 and developing TLR-directed therapeutic intervention have been reviewed by accessing the up-to-date literatures available in the public domain/databases. In accordance with our knowledge in association with the importance of TLRs' role against viruses and identification of viral particles, they have been recognized as suitable candidates with high potential as vaccine adjuvants. In this regard, the agonists of TLR4 and TLR9 have effective potential in vaccine technology while the others need further investigations. This comprehensive review suggests that basal level expression of TLRs can act as friends to keep our body safe from strangers but act as a foe via overexpression. Therefore, selective inhibition of the overexpressed TLRs appears to be a solution to counteract the cytokine storm while TLR-agonists as vaccine adjuvants could lessen the risk of infection in the naïve population.

SARS-CoV-2 mechanisms of cell tropism in various organs considering host factors

A critical step in the drug design for SARS-CoV-2 is to discover its molecular targets. This study comprehensively reviewed the molecular mechanisms of SARS-CoV-2, exploring host cell tropism and interaction targets crucial for cell entry. The findings revealed that beyond ACE2 as the primary entry receptor, alternative receptors, co-receptors, and several proteases such as TMPRSS2, Furin, Cathepsin L, and ADAM play critical roles in virus entry and subsequent pathogenesis. Additionally, SARS-CoV-2 displays tropism in various human organs due to its diverse receptors. This review delves into the intricate details of receptors, host proteases, and the involvement of each organ. Polymorphisms in the ACE2 receptor and mutations in the spike or its RBD region contribute to the emergence of variants like Alpha, Beta, Gamma, Delta, and Omicron, impacting the pathogenicity of SARS-CoV-2. The challenge posed by mutations raises questions about the effectiveness of existing vaccines and drugs, necessitating consideration for updates in their formulations. In the urgency of these critical situations, repurposed drugs such as Camostat Mesylate and Nafamostat Mesylate emerge as viable pharmaceutical options. Numerous drugs are involved in inhibiting receptors and host factors crucial for SARS-CoV-2 entry, with most discussed in this review. In conclusion, this study may provide valuable insights to inform decisions in therapeutic approaches.

SARS-CoV-2 versus Influenza A Virus: Characteristics and Co-Treatments

For three years, the novel coronavirus disease 2019 (COVID-19) pandemic, caused by infection of the SARS-CoV-2 virus, has completely changed our lifestyles and prepared us to live with this novel pneumonia for years to come. Given that pre-existing flu is caused by the influenza A virus, we have begun unprecedently co-coping with two different respiratory diseases at the same time. Hence, we draw a comparison between SARS-CoV-2 and influenza A virus based on the general characteristics, especially the main variants’ history and the distribution of the two viruses. SARS-CoV-2 appeared to mutate more frequently and independently of locations than the influenza A virus. Furthermore, we reviewed present clinical trials on combined management against COVID-19 and influenza in order to explore better solutions against both at the same time.

The Potential of Cannabidiol for Acute Respiratory Distress Syndrome in COVID-19

COVID-19 disease manifests itself in a wide range of signs and symptoms, beginning with mild symptoms, such as fever, cough, and dyspnea, progressing to acute respiratory distress syndrome (ARDS) and death in some cases. The cytokine storm, or an excess of cytokines released locally, is assumed to be the primary cause of ARDS and mortality in COVID-19 patients. To enhance the survival rate of COVID-19 patients, early management of the cytokine storm with immunomodulators is crucial. Although the effectiveness of some immunosuppressants, such as corticosteroids and tocilizumab, has been studied in clinical trials, the administration of these drugs should be exercised cautiously. Cannabidiol (CBD) is a non-psychotropic phytocannabinoid from Cannabis sativa extracts with anti-inflammatory properties. This review is intended to discuss the possible utility of CBD for the management of COVID-19 patients, particularly those with ARDS.

Meta-analysis to explain unknown causes of the origins of SARS-COV-2

New Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) causes the Coronavirus Disease 2019 (COVID-19), an infectious illness that has generated a pandemic crisis worldwide. One of the fundamental questions in science and society is how SARS-CoV-2 has been originated to design best practices directed to prevent and/or to cope with future hazardous pathogens. The study confronts this question here developing a meta-analysis, which endeavors to explain, whenever possible, unknown sources of the SARS-CoV-2. Findings suggest that the natural spillover of novel viral agents that generate more than 6.00 M deaths worldwide in about two years (such as, SARS-CoV-2 from February 2020 to March 2022) has a remote probability of occurrence (using an analogy with the probability of natural disasters generating a lot of fatalities), whereas science advances on hazardous viral agents and consequential lab accident have a (higher) probability of occurrence (about 13-20% like in manifold lab accidents). The findings of this meta-analysis suggest the vital role of improving the technical guidelines of biosafety at all levels in laboratories during the development of scientific research of experimental virology on hazardous pathogens to minimize risks of pandemic threats in environment and human society.

There is no "origin" to SARS-CoV-2

Since the beginning of the COVID-19 pandemic in 2020 caused by SARS-CoV-2, the question of the origin of this virus has been a highly debated issue. Debates have been, and are still, very disputed and often violent between the two main hypotheses: a natural origin through the "spillover" model or a laboratory-leak origin. Tenants of these two options are building arguments often based on the discrepancies of the other theory. The main problem is that it is the initial question of the origin itself which is biased. Charles Darwin demonstrated in 1859 that all species are appearing through a process of evolution, adaptation and selection. There is no determined origin to any animal or plant species, simply an evolutionary and selective process in which chance and environment play a key role. The very same is true for viruses. There is no determined origin to viruses, simply also an evolutionary and selective process in which chance and environment play a key role. However, in the case of viruses the process is slightly more complex because the "environment" is another living organism. Pandemic viruses already circulate in humans prior to the emergence of a disease. They are simply not capable of triggering an epidemic yet. They must evolve in-host, i.e. in-humans, for that. The evolutionary process which gave rise to SARS-CoV-2 is still ongoing with regular emergence of novel variants more adapted than the previous ones. The real relevant question is how these viruses can emerge as pandemic viruses and what the society can do to prevent the future emergence of pandemic viruses.

Thus spoke peptides: SARS-CoV-2 spike gene evolved in humans and then shortly in rats while the rest of its genome in horseshoe bats and then in treeshrews

SARS-CoV-2 is suspected to be the product of a natural or artificial recombination of two viruses – one adapted to the horseshoe bat and the other, donor of the spike protein gene, adapted to an unknown species. Here we used a new method to search for the original host of the ancestor of the SARS-CoV-2 virus and for the donor of its gene for the spike protein, the molecule responsible for binding to and entering human cells. We computed immunological T-distances (the number of different peptides that are present in the viral proteins but absent in proteins of the host) between 11 species of coronaviruses and 38 representatives of the main mammal clades. Analyses of pentapeptides, the presumed principal targets of T-cell non-self recognition, showed the smallest T-distance of the spike protein of SARS-CoV-2 to humans, while the rest of SARS-CoV-2 proteome to the horseshoe bat. This suggests that the ancestor of SARS-CoV-2 was adapted to bats, but the spike gene donor was adapted to humans. Further analyses suggest that the ancestral coronavirus adapted to bats was shortly passaged in treeshrews, while the donor of the spike gene was shortly passaged in rats before the recombination event.

Origin of COVID-19: Dismissing the Mojiang mine theory and the laboratory accident narrative

The origin of SARS-CoV-2 is still the subject of a controversial debate. The natural origin theory is confronted to the laboratory leak theory. The latter is composite and comprises contradictory theories, one being the leak of a naturally occurring virus and the other the leak of a genetically engineered virus. The laboratory leak theory is essentially based on a publication by Rahalkar and Bahulikar in 2020 linking SARS-CoV-2 to the Mojiang mine incident in 2012 during which six miners fell sick and three died. We analyzed the clinical reports. The diagnosis is not that of COVID-19 or SARS. SARS-CoV-2 was not present in the Mojiang mine. We also bring arguments against the laboratory leak narrative.

Immunological challenges of the “new” infections: corona viruses

The arrival of the most recent coronavirus in 2019, SARS-CoV-2, caught the entire world by surprise, and as a result has caused more anguish due to its rapid spread and serious health consequences for the elderly and those with underlying health conditions, and its ability to generate variants of ever increasing contagiousness. But this was not the first coronavirus to infect humans. This chapter explores the history of this virus family, the emergence of the first serious infection in 2003–04 (SARS-CoV), and the related virus MERS in 2012, and the possible origins of SARS-CoV-2. The lessons of those two outbreaks that never developed into pandemics may not all have been learnt by the world health leaders of today. Nevertheless, the rapidity of vaccine development and the conventional health measure introduced during 2020, not always in good time, has almost certainly led to lower morbidities and mortalities that would otherwise have been the case. This chapter will inevitably be out of date by time this book goes to press. Nevertheless, it is to be hoped that the origin of SARS-CoV-2 will eventually be established, but sadly not without the cooperation of the major countries having the resources to carry out such complex investigations. If such a cooperation did happen, maybe future pandemics of this will be more controllable, and even never progress beyond local outbreaks.

The SARS-CoV-2 origin dilemma: Zoonotic transfer or laboratory leak?

The COVID‐19 pandemic is responsible for millions of deaths worldwide yet its origin remains unclear. Two potential scenarios of how infection of humans initially occurred include zoonotic transfer from wild animals and a leak of the pathogen from a research laboratory. The Wuhan wet markets where wild animals are sold represent a strong scenario for zoonotic transfer. However, isolation of SARS‐CoV‐2 or its immediate predecessor from wild animals in their natural environment has yet to be documented. Due to incomplete evidence for a zoonotic origin, a laboratory origin is plausible. The Wuhan Institute of Virology is at the epicenter of the pandemic and their work has included manipulation of wild‐type coronavirus to enable infection of human cells. Although stronger evidence supports the zoonotic transfer, inconclusive reports maintain the laboratory leak hypothesis alive. It is imperative to reach a factual conclusion to prevent future pandemics.

What we know and what we need to know about the origin of SARS-CoV-2

Since the appearance of the first cases of COVID-19 in 2019, an unprecedented number of documents on that disease have been published in a short space of time. The current available information covers a large number of topics related with COVID-19 and/or the coronavirus (SARS-CoV-2) responsible of the disease. However, only a limited number of publications have been focused on a controversial issue: the origin of the SARS-CoV-2. In this paper, the scientific literature on the origin of SARS-CoV-2 has been reviewed. Documents published during 2020 and 2021 (January 1-July 19) in journals that are indexed in PubMed and/or Scopus has been considered. The revised studies were grouped according to these two potential origins: natural and unnatural. The analyses of the conclusions of the different documents here assessed show that even considering the zoonotic hypothesis as the most likely, with bats and pangolins being possibly in the origin of the coronavirus, today's date the intermediate source species of SARS-CoV-2 has not been confirmed yet. On the other hand, some researchers point to an unnatural origin of this coronavirus, but their conclusions are not strongly supported by a clear scientific evidence. Given the tremendous severity of the current pandemic, investigations to establish clearly and definitively the origin of SARS-CoV-2, are basic and essential in order to prevent potential future pandemics of similar nature.

The genetic structure of SARS-CoV-2 is consistent with both natural or laboratory origin: Response to Tyshkovskiy and Panchin (10.1002/bies.202000325)

Tyshkovskiy and Panchin have recently published a commentary on our paper in which they outline several "points of disagreement with the Segreto/Deigin hypothesis." As our paper is titled "The genetic structure of SARS-CoV-2 does not rule out a laboratory origin," points of disagreement should provide evidence that rules out a laboratory origin. However, Tyshkovskiy and Panchin provide no such evidence and instead attempt to criticize our arguments that highlight aspects of SARS-CoV-2 that could be consistent with the lab leak hypothesis. Strikingly, Tyshkovskiy and Panchin's main point of criticism is based on a false premise that we have claimed RaTG13 to be a direct progenitor of SARS-CoV-2, and their other points of criticism are either not valid, based on flawed mathematical analysis, or are unrelated to our hypotheses. Thus, the genetic structure of SARS-CoV-2 remains consistent with both natural or laboratory origin, which means that both the zoonotic and the lab leak hypothesis need to be investigated equally thoroughly.

Have artificial lighting and noise pollution caused zoonosis and the COVID-19 pandemic? A review

Where did the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) come from? Did it spread to 'patient zero' through proactive human-animal contact? Why did humans faced an increasing number of zoonotic diseases in the past few decades? In this article, we propose a new theory by which human pollution such as artificial lighting and noise accentuate pathogen shedding from bats and other wild habitants in urban environments. This theory differs from the current hypothesis that wildlife trades and bushmeat consumption largely contribute to the spillover of zoonotic pathogens to humans. As natural reservoirs, bats harbor the greatest number of zoonotic viruses among all mammalian orders, while they also have a unique immune system to maintain functioning. Some bat species roost in proximity with human settlements, including urban communities and surrounding areas that are potentially most impacted by anthropogenic activities. We review the behavioral changes of wild habitants, including bats and other species, caused by environmental pollution such as artificial lighting and noise pollution, with focus on the spillover of zoonotic pathogens to humans. We found that there is a strong positive correlation between environmental stress and the behavior and health conditions of wild species, including bats. Specifically, artificial lighting attracts insectivorous bats to congregate around streetlights, resulting in changes in their diets and improved likelihood of close contact with humans and animals. Moreover, many bat species avoid lit areas by expending more energies on commuting and foraging. Noise pollution has similar effects on bat behavior. Bats exposed to chronic noise pollution have weakened immune functions, increased viral shedding, and declined immunity during pregnancy, lactation, and vulnerable periods due to noised-induced stress. Other wild species exposed to artificial lighting and noise pollution also show stress-induced behaviors and deteriorated health. Overall, evidence supports our hypothesis that artificial lighting and noise pollution have been overlooked as long-term contributors to the spillover of zoonotic pathogens to humans in urban environments.