Listen Closely To The Bats and You Can Hear the Viral Chatter

HCoV-EMC, by Beth Fischer. Source:
HCoV-EMC, by Beth Fischer. Source: NIAID/NIH

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.)


10 thoughts on “Listen Closely To The Bats and You Can Hear the Viral Chatter

  1. Wouldn’t the roasting process kill most bacteria?

    [CZ: It’s a virus, not bacteria. And the transmission in this scenario would be from bats to civets before the coffee is collected.]

  2. I just read large spiders catch bats on every continent except Antarctica. Could a spider bite pass on the virus via saliva after eating a bat?

  3. Civet coffee is an interesting curiosity, but not necessary to explain viral transmission. If the virus can be transmitted through coffee beans (rather unlikely in my opinion), then bats gnawing on coffee cherries would be enough to infect humans. Civets just add some journalistic color to an otherwise implausible transmission pathway.

    [CZ: If you’ll notice, I explained that an expert on SARS mentioned this scenario to me. So I fail to see how you can consider this “journalistic color.” The reason Frieman mentioned the coffee cherries is that human SARS was directly transmitted to us from civets, and that the civets got it from bats. This is the pattern reflected in the viruses themselves. While this particular scenario may not necessarily be what actually happened, the two species must have had some sort of interaction.]

  4. To implicate bats without the proper evidences is wrong. Bats are necessary for a healthy ecosystem; this may prompt some more reasons for people to cull them.

    [CZ: It is possible for bats to be a source of human pathogens and to be important to ecosystems. And, in fact, that’s what all the evidence scientists have suggests. The fact that HCoV-EMC is most closely related to bat coronaviruses is compelling evidence of its sources, although the hypothesis needs to be tested by looking at more animals in the Near East. Which is what scientists are doing right now. As for culling, that would be the wrong response to this situation. Better to leave the bats undisturbed in their ecosystems, reducing contact with farm animals.]

  5. Carl, I’ve loved your work in the past on topics as varied as tattoos to parasites. I even follow you on Tumblr, but I find issue with some of your statements in this article.

    People treat bats like they are all the same when in reality there are over a thousand varieties. They are the second most diverse group of mammals after rodents and make up 20% of all mammals and with at least 50 million years of divergence among them represent a diversity that is done a disservice when they are treated as a single entity for convenience. With so many species, many of which are communal which increases disease transmission, it is not really surprising that they can be reservoirs for zoonotic diseases. I would hate for people to get the impression that bats are creatures to be feared or killed rather than respected as important parts of the ecosystem.

    Furthermore, I disagree with calling SARS a “massive pandemic” when it infected less people that influenza kills each year in the United States. Let us not forget that in 2003, the anthrax attacks and World Trade Center were still fresh in our collective consciousness and I think the media coverage of SARS played into those fears. Similarly sensational outbreaks seem to happen almost seasonally with H1N1 (swine flu) and H5N1 (bird flu) which could sweep the globe in the modern age. Of course this makes them worth studying, but I would urge against any alarmism when discussing emerging diseases.

    The high fatality rate among those diagnosed with HCoV-EMC may be an artifact of missed diagnoses (ie how many family care physicians would know of an emerging virus?) or a latent infection. Without dismissing the likelihood of a bat species as a reservoir, I would propose a different method of transition. Perhaps similarly to West Nile Virus, which manifests symptoms in less than 20% of infections but is severe in those effected, there may be a vector involved as bat species, like all animals, are not immune to parasites like mosquitoes.

    And I don’t think there are many fruit bats in Europe, though I know there are some in the Middle East.

    [CZ: I’m not picking on bats; I’m describing a consensus among scientists who study emerging viruses. Just consider the title of this new paper, “Bats and their virome: an important source of emerging viruses capable of infecting humans.” Also, see this piece in Slate by microbiologist Tara Smith on bats. As for HCoV-EMC, there’s no evidence that it’s spread by a mosquito or another vector–I know of no coronavirus that’s spread by a vector. As for SARS, I don’t consider 8090 infections and 774 deaths something to dismiss–especially given that this was an entirely new disease.]

  6. I heard the last man who died of this disease was at the camel race… can flies transmit these viruses? That would maybe explain how three people in England got the virus from their cousin who visited in Saudi Arabia.. as far as I remember he visited a farm before returning to the UK… he might have brought some fleas in his luggage and if it is possible to get infected from the flea bites that would be one explanation… as for bats- I live in Middle East and there are bats flying around and above my head frequently- this is scary.. when I walk with my dog.. the dog can easily eat something from the floor… like bat poop ( a fruit or something) .. when you think of it it is pretty scary

  7. I read with interest the posting on coronaviruses and links to bats. As a mammalogist and bat biologist, I have to somewhat agree with the comments made. But also as a person who has done quite a bit of field work, I have a problem with the way the general public approaches wildlife in general. They constantly look at wildlife as being cute and cuddely without understanding that the diseases in wildlife can be quite harsh (read deadly) to humans and have generally arisen in an evolutionarily ecological manner that may confuse the public. You cannot treat wildlife as you would the family cat or dog since we have vets to vaccinate our domestic animals and take care to keep them healthy. Wildlife is a reservoir for countless diseases that are trying to maintain “their way of life” and continue to evolve.

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