Last June, a sixty-year-old man in Saudi Arabia fell ill with pneumonia. His disease, it turned out, was caused by a virus no one had seen before. It was a coronavirus–in other words, it belonged to a lineage of viruses that includes ones that cause colds as well as ones that cause SARS. But this new virus was genetically distinct enough to be considered a species in its own right. Scientists now refer to it by the dreary, unpronounceable abbreviation HCoV-EMC. Eleven days after being admitted to a Jedda hospital, the man infected with this new virus died.
A single death from a new virus is hardly unheard of. But over the past few months, virus-watchers have gotten increasingly anxious about HCoV-EMC. So far, 15 people have been diagnosed with the virus, and nine have died. While some victims have turned up as far away as England, everyone with HCoV-EMC has had some connection to the Arabian Peninsula. Some victims belonged to the same family, suggesting that the virus can spread from one person to the next.
We can’t say for sure whether we’re at the beginning of a HCoV-EMC pandemic, or at the end of a minor outbreak, or experiencing something in between. But scientists are not waiting around until the virus has finished traveling down whatever path it will take. They’re working hard to figure out the biology of the virus, and they’re also trying to figure out its history. How it got into 15 people over the past 9 months might give us a hint as to what it may do in the future.
In other words, scientists have to probe the evolution of HCoV-EMC.
The closest relatives to HCoV-EMC are coronaviruses that live in European bats. That doesn’t mean HCoV-EMC came from Europe, however. Most of the diversity of coronaviruses is unmapped, especially the ones that live in animals. There could well be bats in the Near East with more closely related but undocumented cornaviruses. The fact that all the human victims were at some point in the Arabian Peninsula certainly raises the possibility that bats there spread the virus to people.
The link between bats, coronaviruses, and humans is a familiar one. SARS moved from bats to humans ten years ago, and since then scientists have found other coronaviruses that moved from bats to humans. The biology of HCoV-EMC itself offers more evidence for how this might have happened. Some viruses are very fussy about how they invade cells. They only infect one type of cell in one species. But HCoV-EMC is a lot less picky. It latches onto a receptor on cells lining the airway, and scientists have found that it can invade airway cells from not just humans, but pigs and bats. The ancestors of HCoV-EMC might have lived in bats and yet they may have already been prepared to infect humans.
Recently, a team of evolutionary biologists began to draw an evolutionary tree of HCoV-EMC based on a comparison of the viruses isolated from three victims–the first patient from June, and two later victims from England. They identified mutations that arose in each of the three lineages of viruses since they diverged from a common ancestor. Mutations accumulate at a roughly clock-like rate, which means that scientists can use them to estimate how long ago lineages split apart. In the case of the three HCoV-EMC viruses, their common ancestor dates back to 2009.
Three years is a long time for a virus to be circulating among people without anyone noticing. It’s conceivable that a lot of people passed it around and only got mildly sick. But the fact that nine out fifteen people identified so far with HCoV-EMC actually died suggests that this is a fairly deadly virus, making invisibility unlikely.
If that explanation fails, what happened? Virologists I’ve spoken to favor a phenomenon known as “viral chatter.” Viruses don’t just barge across the species barrier in one great rush. They tentatively make incursions–many of them spread across years. The SARS virus, for example, infected a few people before becoming a massive epidemic in 2003. During these incursions, animal viruses may acquire mutations that gradually prepare them to become good at spreading from person to person.
For now, thankfully, HCoV-EMC seems to be bad at that kind of transmission. Each sick person made contact with many others and almost none of the exposed people got sick as a result. Instead, people must be getting infected through contact with sick animals. They’re picking up viruses that diverged from a common ancestor a few years ago and are still circulating among animals.
It’s not likely that humans are getting sick from HCoV-EMC thanks to frequent contact with bats. When’s the last time you gave a bat a kiss? Instead, HC0V-EMC may be using a stepping-stone species to get from bats to humans.
Again, SARS offers some lessons. It appears that the SARS virus spread from Chinese horseshoe bats to civets, cat-like animals that live in East Asia, and then to humans.
A decade after the SARS epidemic, no one can say for sure how SARS got from bats to civets. But the answer must lie somewhere in their ecology. Matt Frieman, a virologist at the University of Maryland who studies bat coronaviruses, pointed me to an example of the interactions between bats and civets buried in a 2010 article about civets and coffee.
Civet cats eat wild coffee cherries and them poop them out. People collect their poop and clean off the beans they contain. The resulting coffee, the article claims, has a taste that’s “smooth, chocolaty and devoid of any bitter aftertaste.” Western appetite for this delicious coffee has led people to hunt for civet poop in forests, and to feed captive civets coffee beans on little farms.
One passage in the story should give you a jolt. A coffee supplier inspecting a batch of civet-processed beans knocks down his buying price because of some impurities: “inferior beans that the civet had spat out; beans chewed on, not by civets, but bats.”
So imagine SARS-infected bats in a rain forest chewing on the same coffee cherries as civets. It’s enough to start an epidemic, perhaps.
Ten years later, a continent away, bats with HCoV-EMC may be coming into contact with other animals as well. Goats drinking at watering holes might spend time near bats in neighboring fruit trees, for example. And the farmers of the goats might then pick up viruses from their livestock. At this point, it’s a notion–or, rather, a scientific hypothesis. The animals of the Near East will tell us whether it’s a good one or not.
(For more on the emergence of new viruses, see my book A Planet of Viruses.)