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Source: SARS-CoV-2 Research  Apr 15, 2020  3 years ago
Breaking! Research Indicates That Stray Dogs Could Be Possible Source Of SARS-CoV-2 Coronavirus
Breaking! Research Indicates That Stray Dogs Could Be Possible Source Of SARS-CoV-2 Coronavirus
Source: SARS-CoV-2 Research  Apr 15, 2020  3 years ago
SARS-CoV-2 Research: Medical and genomic researchers have been for the last few months  been trying to identify the species of origin to understand how the novel SARS-CoV-2 coronavirus first leapt from its animal hosts to humans, causing the current pandemic infecting millions globally and causing almost 200,000 deaths so far.
Researchers have been looking for an intermediate animal host between bats, which are known to harbor many coronaviruses, and the first introduction of SARS-CoV-2 into humans.
Numerous animals, beginning with snakes and most recently, pangolins, have all been put forth as the likely intermediate, but the viruses isolated from them are too divergent from SARS-CoV-2, suggesting a common ancestor too far back in time living in the 1960s.

Now a new research published in the journal Molecular Biology and Evolution by University of Ottawa Biology Professor Dr Xuhua Xia, tracing coronavirus signatures across different species, has proposed that stray dogs, specifically dog intestines may have been the origin of the current SARS-CoV-2 pandemic. https://academic.oup.com/mbe/article/doi/10.1093/molbev/msaa094/5819559
Dr Xia told Thailand Medical News, "Our observations have allowed the formation of a new hypothesis for the origin and initial transmission of SARS-CoV-2. The ancestor of SARS-CoV-2 and its nearest relative, a bat coronavirus, infected the intestine of canids, most likely resulting in a rapid evolution of the virus in canids and its jump into humans. This suggests the importance of monitoring SARS-like coronaviruses in feral dogs in the fight against SARS-CoV-2."
The new research findings appear in the advanced access online edition of the Xia has long-studied the molecular signatures of viruses in different hosts. When viruses invade a host, their genomes often bear the battle scars from fighting off and evading the host's immune system through changes and adaptations found within their genomes.
Typically, humans and mammals have a key antiviral sentinel protein, called ZAP, which can stop a virus in its tracks by preventing its multiplication in the host and degrading its genome. The viral target is a pair of chemical letters, called CpG dinucleotides, within its RNA genome. CpG dinucleotides act as a signpost that a person's immune system uses to seek and destroy a virus. ZAP patrols human lungs, and is made in large amounts in the bone marrow and lymph nodes, where the immune system first primes its attack.
However it has been shown that viruses can punch back. Single-stranded coronaviruses, like SARS-CoV, can avoid ZAP by reducing these CpG signposts, thus rendering ZAP powerless. A similar examination of HIV, another RNA virus, shows that it has also exploited this evolutionary trick to lose CpG in response to human antiviral defenses. One implication of this is that the remaining CpG dinucleotides on the viral genome are likely functionally important for the virus and could serve as target of modification to attenuate virulence in vaccine development.
Dr Xia added, "Think of a decreased amount of CpG in a viral pathogen as an increased threat to public health, while an in creased amount of CpG decreases the threat of such viral pathogens. A virus with an increased amount of CpG would be better targeted by the host immune system, and result in reduced virulence, which would be akin to natural vaccines."
In order to conduct  the study, Dr Xia examined all 1252 full-length betacoronavirus genomes deposited into GenBank to date. Xia found that SARS-CoV-2 and its most closely related known relative, a bat coronavirus (BatCoV RaTG13), have the lowest amount of CpG among its close coronavirus relatives.
She added, "The most striking pattern is an isolated but dramatic downward shift in viral genomic CpG in the lineage leading to BatCoV RaTG13 which was reported to be sampled from a bat (Rhinolophus affinis) in Yunnan Province in 2013 but only sequenced by Wuhan Institute of Virology after the outbreak of SARS-CoV-2 infection in late 2019. This bat CoV genome is the closest phylogenetic relative of SARS-CoV-2, sharing 96% sequence similarity."
D Xia further added, "In this context, it is unfortunate that BatCoV RaTG13 was not sequenced in 2013, otherwise the downshifting in CpG might have served as a warning due to two highly significant implications. First, the virus likely evolved in a tissue with high ZAP expression which favors viral genomes with a low CpG. Second and more importantly, survival of the virus indicates that it has successfully evaded ZAP-mediated antiviral defense. In other words, the virus has become stealthy and dangerous to humans."
Dr Xia applied his CpG tool to reexamining the camel origin of MERS, and found those viruses infecting camel digestive system also had lower genomic CpG than those infecting camel respiratory system.
Upon examining the data in dogs, he found that only genomes from canine coronaviruses (CCoVs), which had caused a highly contagious intestinal disease worldwide in dogs, have genomic CpG values similar to those observed in SARS-CoV-2 and BatCoV RaTG13. Second, canids, like camels, also have coronaviruses infecting their digestive system with CpG lower than those infecting their respiratory system (canine respiratory coronavirus or CRCoV belonging to BetaCoV).
Furthermore, the known cellular receptor for SARS-CoV-2 entry into the cell is ACE2 (angiotensin I converting enzyme 2). ACE2 is made in the human digestive system, at the highest levels in the small intestine and duodenum, with relatively low expression in the lung. This suggests that mammalian digestive systems are likely to be a key target infected by coronaviruses.
Dr Xia explained, "This is consistent with the interpretation that the low CpG in SARS-CoV-2 was acquired by the ancestor of SARS-CoV-2 evolving in mammalian digestive systems and interpretation is further corroborated by a recent report that a high proportion of COVID-19 patients also suffer from digestive discomfort. In fact, 48.5% presented with digestive symptoms as their chief complaint."
According to Dr Xia, humans are the only other host species observed to produce coronavirus genomes with low genomic CpG values. In a comprehensive study of the first 12 COVID-19 patients in the U.S., one patient reported diarrhea as the initial symptom before developing fever and cough, and stool samples from 7 out of 10 patients tested positive for SARS-CoV-2, including 3 patients with diarrhea.
Dogs are often observed to lick their anal and genital regions, not only during mating but also in other circumstances. Such behavior would facilitate viral transmission from the digestive system to the respiratory system and the interchange between a gastrointestinal pathogen and a respiratory tract and lung pathogen.
Dr Xia declared, "In this context, it is significant that the bat coronavirus (BatCoV RaTG13), as documented in its genomic sequence in GenBank (MN996532), was isolated from a fecal swab. These observations are consistent with the hypothesis that SARS-CoV-2 has evolved in mammalian intestine or tissues associated with intestine."
Additional research findings in Dr Xia's study involves viruses recently isolated from pangolins. Nine SARS-CoV-2-like genomes have recently been isolated and sequenced from pangolin and deposited in GISAID database (gisaid.org).
He added, "The one with the highest sequence coverage (GISAID ID: EPI_ISL_410721) has an ICpG value of 0.3929, close to the extreme low end of the CpG values observed among available SARS-CoV-2 genomes. Thus, SARS-CoV-2, BatCoV RaTG13 and those from pangolin may either have a common ancestor with a low CpG or have convergently evolved low CpG values."
From his research findings, Dr  Xia presents a scenario in which the coronavirus first spread from bats to stray dogs eating bat meat. Next, the presumably strong selection against CpG in the viral RNA genome in canid intestines resulted in rapid evolution of the virus leading to reduced genomic CpG. Finally, the reduced viral genomic CpG allowed the virus to evade human ZAP-mediated immune response and became a severe human pathogen.
Dr Xia concluded, "While the specific origins of SARS-CoV-2 are of vital interest in the current world health crisis, this study more broadly suggests that important evidence of viral evolution can be revealed by consideration of the interaction of host defenses with viral genomes, including selective pressure exerted by host tissues on viral genome composition."

Thailand Medical News is proud to have inspired Dr Xia in his research through our calls to focus on using the BAT’s original coronaviruses as a point of study and not the SARS coronavirus of 2003. https://www.thailandmedical.news/news/editorial-are-covid-19-researchers-and-medical-experts-looking-at-the-wrong-places-for-answers
For the latest SARS-CoV-2 research, keep on logging to Thailand Medical News

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