From the beginning of the pandemic virologists have warned COVID-19 will not be the last coronavirus to trouble humanity. Now it seems likely one was the cause of an unexplained outbreak 3 years ago. The probable source of the disease should give pause to all those who advocated killing bats to keep the next plague at bay.
In 2017-18 Sarawak, Malaysia suffered an outbreak of pneumonia, whose cause was not identified at the time. Nasal swabs were taken from children hospitalized for the condition, but they were only tested for for the usual suspects which didn't include coronaviruses known only from animals. Last year the swabs were retested by scientists at Duke University who identified the presence of an unfamiliar coronavirus.
The same team have now sequenced the virus found in one patient and published their findings in Clinical Infectious Diseases. The authors cannot definitively prove the virus in question was the reason the children got sick, and have yet to even grow it in human cells, but this is certainly a logical explanation.
Analysis of the virus shows a strong family resemblance to two viruses known to infect dogs, one found in cats, and what looks like elements from a pig-virus. It is thought the combination arose through repeated reshuffling of the genes of different viruses that infected the same animal at the same time.
Besides the fact that all the infected children recovered within a week, the most encouraging aspect of the paper's findings is that the virus may not be able to get from human to human. Instead, like many other viruses, we catch it from animals, but can't pass it on. If so, it would be the first case of a coronavirus that spreads among dogs but can replicate in humans.
We can't yet be sure what animal transmitted the virus to humans. The mostly Indigenous children who were infected live in rural areas and have exposure to far more species than the average city-dweller. Nevertheless, humanity's supposed "best friend" is a likely suspect. Not only providing two of the building blocks for this virus but also having had plenty of opportunity to infect the people they live with.
NPR reports the discovery was only made after Dr Gregory Gray became worried coronaviruses might be going unnoticed because they had yet to turn lethal. Gray asked graduate student Leshan Xiu to make a test that would find as-yet unknown coronaviruses.
The paper's first author, Dr Anastasia Vlosova of Ohio State University, succeeded in growing the virus in canine tumor cells and discovered a section of the genome had been deleted compared to the dog versions. Alarmingly, she told NPR, “It's a mutation that's very similar to one previously found in the SARS coronavirus and in [versions of] SARS-CoV-2 ... [that appeared] very soon after its introduction into the human population."
If this is more than coincidence, many animal coronaviruses may be prevented from infecting humans by this part of their genome – posing a threat when they lose it.
"These coronaviruses are likely spilling over to humans from animals much more frequently than we know,” Gray said in a statement. “We are missing them because most hospital diagnostic tests only pick up known human coronaviruses.”
SARS-CoV-2, MERS and the original SARS are all betacoronaviruses. This one (like several less harmful coronaviruses that cause common cold symptoms) belongs to the alpha class, and is therefore less likely to prove lethal, but it's a risk few want to take.
This week a therapy that stops SARS-CoV-2 replicating in mice was announced. Its developers anticipate it will work against all coronaviruses, and the need now looks more urgent.