As the coronavirus continues to evolve, the scientific and public health focus has been on new variants in which a few mutations make the virus more infectious, or potentially more deadly.
These changes in the virus are what scientists call point mutations, the substitution of one tiny bit of genetic code for another. Coronaviruses, as a group, are not known to mutate rapidly, but the pandemic caused by the virus Sars-CoV-2 means that millions and millions of people are infected by billions and billions of viral particles, offering countless chances for change.
There is, however, another more significant way that coronaviruses change: individual viral particles exchanging larger sections of genetic material with another virus. If two different kinds of coronavirus inhabit the same cell, the result could be not a new variant, but a new species.
Three University of Liverpool researchers writing in the journal Nature Communications predicted, based on a computer analysis, that such events are far more likely than previously thought, and recommended monitoring of target animal species to watch for possible emergence of new coronavirus diseases.
The work pointed in some directions where scientists are already alert. It identified the lesser Asiatic yellow bat and the greater and intermediate horseshoe bats as animals where recombination would be more likely to occur. But the analysis also pointed to animals that scientists have been less focused on, such as the common pig, as creatures that should be monitored.
Dr Marcus Blagrove, a virus expert who wrote the report along with Dr Maya Wardeh, who specialises in computer analysis of animal disease spread, and Professor Matthew Bayliss, a veterinary public health researcher, said that coronaviruses were known for “swopping large chunks all over the place”. Emergence of new diseases through this process is not common because an animal needs to be infected with two different kinds of coronaviruses at the same time.
Professor Jeremy Luban, a virus expert at the University of Massachusetts, said such a double infection, with two kinds of viruses replicating in one cell, had yet to be documented in humans. But just such a recombination is how Sars, or severe acute respiratory syndrome, seems to have emerged, and researchers think Sars-CoV-2 may also be the result of two viruses combining. Prof Luban said that “this kind of work is extremely important” because it could come up with surprising insights that experiments and field work can follow up on.
The group of researchers at Liverpool used a kind of computer analysis called machine learning to look at a number of different data points. This includes the genetic structure of coronaviruses and mammalian species, as well as their behavioural similarity and geographic proximity, to come up with predictions of which animals were most likely to harbour the most number of coronaviruses.
They predict that 40 times as many mammalian species can be infected with four or more different kinds of coronaviruses than are now known, and that up to 126 species of mammals may be susceptible to infection by Sars-CoV-2.
As a reality check, they pointed out that their analyses correctly predicted some known associations of animals and viruses. The modelling highlighted the palm civets, the animal from which Sars seemed to have spilled over to humans, as a potential hot spot for coronavirus evolution.
Overall, they warned that the possibility of recombination resulting in the emergence of some new dangerous coronavirus is highly underestimated.