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Hundreds of mammalian species could serve as incubators for coronaviruses to mix with each other, potentially forming new viruses and fueling the future pandemics, predicts a new study. These species include wild animals, such as bats and monkeys, as well as domestic animals, such as pigs and cats.
The study, published on February 16 in the journal Nature communications, highlights the potential of coronavirus infect a wide range of hosts. In fact, the work identifies hundreds of animal species that could be infected with known coronaviruses, although many of these infections have yet to be seen in the wild.
Coronaviruses are a large family of viruses that can infect both birds and mammals; SARS-CoV-2, the virus that causes COVID-19, is just one member of the coronavirus family. For the research, the team pulled the genetic sequences of 411 coronaviruses from GenBank, a National Institutes of Health database, and screened these sequences using a computer algorithm. The sequences represented 92 different species of coronavirus, with some species being represented by more than one strain of the virus.
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The algorithm predicted that, on average, each virus has more than 12 mammalian hosts. Each animal species examined, in turn, was expected to be a potential host for more than five coronaviruses, on average.
Animals that can serve as hosts for many coronaviruses pose the greatest threat; when several strains of coronavirus invade the same cell, their genes can be mixed and matched during their replication, thus generating a new patchwork virus.
This genetic the card shuffling, known as “recombination,” could be particularly dangerous if SARS-CoV-2 swaps genes with another coronavirus, the authors wrote. This is because the resulting virus could potentially be as infectious to humans as SARS-CoV-2, but could possibly invade additional tissue or cause more serious illness. The model identified 126 non-human species that may harbor SARS-CoV-2 and at least one other coronavirus, which could allow this troubling scenario to unfold.
“More surprising than any individual animal was the wide array of animals that are expected to be hosts for large numbers of coronaviruses,” wrote study authors Maya Wardeh, a data scientist, and Marcus Blagrove , a virologist from the University of Liverpool in England a joint statement to Live Science. “Everybody knows that bats are important, but we have found many high-risk hosts throughout mammals, including rodents, primates [and] hoofed animals. “
That said, just because two coronaviruses can invade the same animal doesn’t mean they can and will recombine, said Arinjay Banerjee, a virologist at McMaster University in Ontario who was not involved in the study. Recombination requires viruses to enter the same cell type and infections to peak at the same time, among other logistics, he said. But the new study provides a practical list of mammalian species that should be monitored for coronavirus infections and recombination events in the future, he said.
A network of potential infections
To predict which mammals are likely coronavirus hosts, the authors created a computer algorithm who mapped the connections between potential hosts and known coronaviruses. The algorithm analyzed known coronaviruses and looked at the animals they are known to infect. He then looked at other animals that were closely related, lived in similar habitats, or ate the same types of diets, as they would likely be suspected of harboring similar coronavirus populations as well. The algorithm also compared the genome sequences of different coronaviruses, with the idea that closely related coronaviruses would likely be able to infect similar hosts.
After finding these connections, the algorithm identified mammals that could potentially host many coronaviruses and, therefore, be foci of coronavirus recombination.
The team examined 876 mammalian species using this algorithm, including 185 known coronavirus hosts. The remaining 691 species belonged to the same genus as a known host. The algorithm tested for potential links between these animals and the 411 coronaviruses for which the RNA the sequence is already known.
“These 411 viruses contain the seven coronaviruses known to infect humans, as well as the full range of other coronaviruses whose genomes have been sequenced,” the authors said.
Although all of the sequenced SARS-CoV-2 strains were included in the analysis, they were treated as a single entity in the analysis. “The SARS-CoV-2 variants are all very similar, with only relatively minor mutations; we would not expect our results for host specificity to be very different from each other,” the authors told Live Science.
Of the 126 species identified as potential SARS-CoV-2 hosts, several animals stood out as presenting the highest risk of recombination. Some of these animals have already been reported as potential recombinant hosts for SARS-CoV-2, as well as for the related virus SARS-CoV, which caused outbreaks of severe acute respiratory syndrome in the early 2000s.
For example, the Asian palm civet (Paradoxurus hermaphroditus) was a predicted host for 32 coronaviruses, in addition to SARS-CoV-2. The big horseshoe bat (Rhinolophus ferrumequinum) and the intermediate horseshoe bat (Rhinolophus affinis) were intended hosts for 67 and 44 additional coronaviruses, respectively, and the pangolin (Manis javanica) for 14.
In addition to these suspicious hosts, the model revealed wild animals that had not previously been linked to the SARS-CoV-2 recombination. These included the Lesser Asiatic Yellow Bat (Scotophilus kuhlii), chimpanzee (Pan troglodytes) and African green monkey (Chlorocebus Aethiops). The common hedgehog (Erinaceus europaeus), European rabbit (Oryctolagus cuniculus) and domestic cat (Cat) are also likely hosts for co-infection and recombination, depending on the model.
But the “most important result for a SARS-CoV-2 recombinant host is the pig (known), “is expected to harbor 121 coronaviruses in addition to SARS-CoV-2, the authors wrote.
“Given the large number of coronaviruses our framework predicts pigs can be infected with, we suggest monitoring ‘high risk’ pigs [living conditions]For example, pigs raised near other high-risk farm animals would be considered high risk, while pigs isolated from other animals would be relatively low risk, they said.
High risk scenarios
The study also identified 102 potential species that could be co-infected with SARS-CoV-2 and MERS-CoV, the coronavirus responsible for Middle East respiratory syndrome (MERS). MERS has a much higher case fatality rate than COVID-19, estimated at about 35%, so the recombination of these two viruses could be extremely dangerous, making the resulting virus both highly transmissible and likely to cause serious disease, the authors said.
The model also predicted possible interactions that did not include SARS-CoV-2 at all. The team found that many genetically diverse coronaviruses might be able to mix and exchange their RNA; for example, 291 mammalian species were predicted coronavirus hosts from four or more different subgenera, a taxonomic subcategory less than genus and greater than species.
However, coronaviruses from the same subgenus are more likely to recombine than viruses from different subgenres, Banerjee said. “We don’t know if different subgenres would recombine; it’s unlikely, but it hasn’t been shown experimentally,” he said.
Domestic pig, Asian little yellow bat, and large and medium horseshoe bats all appeared as likely hosts for these recombination events, but other species also appeared on the high risk list. Notably, this included the dromedary camel (Camelus dromedarius), a known coronavirus host and the primary transmitter of MERS-CoV to humans.
Going forward, the study authors plan to develop a similar model for avian species, to see which birds could be a source of coronavirus recombination; Known hosts of avian coronavirus include turkey (Meleagris gallopavo) and guinea fowl (Numlda Meleagrls), among others, according to a report published in 2005 Avian pathology. After collecting data on birds, the team wants to model how often potential coronavirus hosts across the animal kingdom come in contact with each other.
“This will allow estimating where in the geographic range a host species is most threatened, and thus targeting monitoring more specifically both on ‘what and where’,” the authors said. Additionally, they plan to incorporate clinically relevant data into their predictions, identifying viruses known to cause disease in humans and the type of symptoms they trigger.
For now, the likelihood of recombination in different species is uncertain, as is the risk that these theoretical mixes could make people sick, Banerjee said. But “what I take away from this manuscript is [to] expanding surveillance to under-researched and underestimated potential reservoirs of coronavirus, “Banerjee said. A reservoir species would carry coronaviruses without getting sick on its own but then pass the viruses on to other animals that do get sick; mice are a major reservoir for coronaviruses, for example.
Such early identification of potential hosts for coronaviruses could help scientists develop targeted surveillance programs to catch recombination “as and before a major outbreak,” the authors wrote. And in the event of an outbreak, scientists could easily reference the record of coronaviruses found in high-risk animals to identify the new pathogen, Banerjee said.
Originally posted on Live Science.
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