Study Points to Evidence of Stray Dogs as Possible Source of SARS-CoV-2 Pandemic

Since the SARS-CoV-2 outbreak, scientists have been struggling to identify the species of origin to understand how the new coronavirus first jumped from its animal hosts to humans, causing the current pandemic that infects more than a million of people around the world.

Scientists have been looking for an intermediate animal host among bats, which are known to harbor many coronaviruses, and the first introduction of SARS-CoV-2 in humans.

Many animals, starting with snakes and more recently pangolins, have been presented as the likely intermediary, but the viruses isolated from them are too divergent from SARS-CoV-2, suggesting a common ancestor too far back in time. in the 1960s.

Now, University of Ottawa biology professor Xuhua Xia, who tracks coronavirus signatures in different species, has proposed that stray dogs, specifically the dog’s intestines, may have been the source of the current SARS-CoV pandemic -two.

“Our observations have allowed the formation of a new hypothesis for the origin and initial transmission of SARS-CoV-2,” said Xia. “The ancestor of SARS-CoV-2 and its closest relative, a bat coronavirus, infected the intestines of canines, likely causing the virus to evolve rapidly in canids and its release into humans. This suggests the importance to monitor SARS-like coronaviruses in wild dogs in the fight against SARS-CoV-2 “.

The findings appear in the online, advanced-access issue of the journal. Molecular Biology and Evolution.

Xia has long studied the molecular signatures of viruses on different hosts. When viruses invade a host, their genomes often bear the battle scars of fighting and evading the host’s immune system through changes and adaptations found within their genomes.

Humans and mammals have a key antiviral sentinel protein, called ZAP, that can stop a virus on its way by preventing it from multiplying in the host and degrading its genome. The viral target is a pair of chemical letters, called CpG dinucleotides, within your RNA genome. CpG dinucleotides act as a signal that a person’s immune system uses to search for and destroy a virus. ZAP patrols the human lungs and occurs in large numbers in the bone marrow and lymph nodes, where the immune system prepares its attack for the first time.

But viruses have been shown to hit back. Single-chain coronaviruses, such as SARS-CoV, can prevent ZAP by reducing these CpG signals, making ZAP impotent. A similar examination of HIV, another RNA virus, shows that this evolutionary trick has also been exploited to lose CpG in response to human antiviral defenses. One implication of this is that the remaining CpG dinucleotides in the viral genome are likely to be functionally important to the virus and could serve as a target for modification to attenuate virulence in vaccine development.

“Think of a lower amount of CpG in a viral pathogen as a greater threat to public health, while a higher amount of CpG decreases the threat of such viral pathogens,” said Xia. “A virus with a higher amount of CpG would be better targeted by the host immune system and reduce virulence, which would be similar to natural vaccines.”

To conduct the study, Xia examined all 1,252 full-length beta-coronavirus genomes deposited at GenBank to date. Xia discovered that SARS-CoV-2 and its closest related relative, a bat coronavirus (BatCoV RaTG13), have the least amount of CpG among their close relatives of coronaviruses.

“The most striking pattern is an isolated but dramatic downward shift in viral genomic CpG in the lineage leading to BatCoV RaTG13, reported to have been sampled from a bat (Rhinolophus affinis) in Yunnan province in 2013, but which the Wuhan Institute of Virology only sequenced it after the SARS-CoV-2 infection outbreak in late 2019, “Xia said. “This bat CoV genome is the closest phylogenetic relative of SARS-CoV-2, which shares a 96% sequence similarity.”

“In this context, it is regrettable that BatCoV RaTG13 was not sequenced in 2013, otherwise the downshift in CpG could have served as a warning due to two very significant implications,” Xia said. “First, the virus probably evolved into a tissue with high ZAP expression that favors viral genomes with a low CpG. Second and more important, the 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. “

Xia applied his CpG tool to reexamine the camel’s origin from MERS, and found that viruses that infect the camel’s digestive system also had lower genomic CpG than those that infect the camel’s respiratory system.

When he examined the data in dogs, he found that only the canine coronavirus (CCoV) genomes, which had caused highly contagious intestinal disease worldwide in dogs, have genomic CpG values ​​similar to those seen in SARS-CoV-2. and BatCoV RaTG13. Second, canids, like camels, also have coronaviruses that infect their digestive system with a lower CpG than those that infect 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-converting enzyme I 2). ACE2 is produced 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 a key target infected with coronavirus.

“This is consistent with the interpretation that the low CpG in SARS-CoV-2 was acquired by the ancestor of SARS-CoV-2 that evolves in mammalian digestive systems and the interpretation is further supported by a recent report by that a high proportion of COVID-19 patients also experience digestive discomfort, “Xia said. “In fact, 48.5% had digestive symptoms as their main complaint.”

Humans are the only other host species observed by Xia that produces coronavirus genomes with low genomic CpG values. In a comprehensive study of the first 12 patients with COVID-19 in the USA. In the USA, one patient reported that diarrhea was 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.

Canids 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 exchange between a gastrointestinal pathogen and a respiratory tract and a lung pathogen.

“In this context, it is significant that the bat coronavirus (BatCoV RaTG13), as documented in its genomic sequence at GenBank (MN996532), was isolated from a faecal swab. These observations are consistent with the hypothesis that SARS-CoV -2 has evolved in mammalian intestine or tissues associated with the intestine. “

Another finding from Xia’s study involves recently isolated pangolin viruses. Nine SARS-CoV-2-like genomes have recently been isolated and sequenced from pangolin and deposited in the GISAID database (gisaid.org). “The one with the highest sequence coverage (GISAID ID: EPI_ISL_410721) has an ICpG value of 0.3929, near the extreme low end of the CpG values ​​observed among the available SARS-CoV-2 genomes. Therefore, SARS -CoV-2, BatCoV RaTG13 and pangolin ones may have a common ancestor with a low CpG or evolve convergently to low CpG values. “

According to his results, Xia presents a scenario in which the coronavirus first spread from bats to stray dogs that ate bat meat. Then, the presumably strong selection against CpG in the viral RNA genome in the canine intestines resulted in a rapid evolution of the virus that led to a reduction in genomic CpG. Ultimately, reduced viral genomic CpG allowed the virus to evade the human ZAP-mediated immune response and became a severe human pathogen.

“While the specific origins of SARS-CoV-2 are of vital interest in the current global health crisis, this study more broadly suggests that important evidence of viral evolution can be revealed by considering the interaction of host defenses with viral genomes, including the selective pressure exerted by host tissues on the composition of the viral genome, “said Xia.