Wild Animals, Wet Markets and a World in Chaos: Exploring the Origin of Covid-19

Apparently, all it took was a global pandemic for me to return to blogging.

“All this because some twat ate a bat.” It’s a sentiment I’ve heard a lot recently, from frustrated family members in the midst of the UK’s current lockdown or in last week’s round of pandemic memes. That bats, which are known carriers of coronaviruses (the ‘family’ of viruses that includes Covid-19), are the origin of the pandemic that has thrown much of the world into turmoil has now become firmly established in pop culture. How scientists around the world investigated this is actually a pretty interesting story of missed warnings, false culprits, illegal animal trafficking and lingering unanswered questions. Let’s dive in.

First, a quick disclaimer before one of my intellectual family members yells at me for quoting misinformation (I’m like my clan’s own Billy Madison): The Covid-19 pandemic is an ongoing, rapidly evolving situation and very active research area. I’ve tried my best to use information from trusted sources for this blog post, from the confines of my living room whilst sitting in my pyjamas, but remember to interrogate any source of knowledge on this subject, look for the most up-to-date research, and fact-check everything. Also, please wash your hands.

One day at a Wet Market in Wuhan:

Coronaviruses are zoonotic diseases, which means they develop in animals and then spread to humans. The SARS (Severe Acute Respiratory Syndrome) coronavirus that emerged in China in 2002 and infected 8,098 people across 26 countries is thought to have jumped from a natural animal reservoir to another animal species and finally to humans. However, the exact species involved in the origin of the SARS pandemic remain unknown (although a jump from bats to civet cats to humans has been widely put forward).

The origin of Covid-19 is also thought to be animal-based, although again determining the animal or animals involved in the spread of the disease is not a simple task. A quick virtual trip to the place linked to the earliest Covid-19 cases will explain why.

Before its closure on 1st January 2020, the Huanan Seafood Wholesale Market in Wuhan, China harboured stalls boasting a veritable menagerie of live animals of questionable origin up for sale, alongside more common meats, poultry and fish. It’s difficult to sort through all the hearsay about what was actually on sale at the market at the time of the outbreak (unconfirmed reports of “koala” and “wolf cub” abound). By some accounts though, 30 – 75 different species of wild animal were held there, including civet cats, bamboo rats, and of course, bats.

Housed together in close proximity and unsanitary conditions, this mix of live animals, game, poultry and illegally traded wildlife would provide the perfect environment for viruses to spread between species and eventually to humans. It also makes identifying how that happened incredibly complex. In trying to determine the origin of Covid-19, scientists initially had an unenviable list of potential culprits to sort through.

Luckily, by drawing from the world’s current base coronavirus research, virologists were able to identify a few high-interest suspects.

Poor Old Pangolins:

One of the first animals to have its name tied to the Covid-19 outbreak in Wuhan was the Pangolin. This elusive, scaly creature really didn’t need any more bad press. Its widely considered to be the most trafficked non-human mammal, prized for both its meat and its keratin scales for traditional Chinese medicine. All eight species of pangolin (4 found in Asia, 4 in Africa) are threatened with extinction due to illegal trade, along with over 8700 different animal species from around the world.

The trade and consumption of pangolins is illegal under China’s Wildlife Protection Law and pangolins were not listed in the items sold at the market in Wuhan. However, as the illegal trafficking and consumption of pangolin is still thought to be widespread across China, researchers were remiss to rule out the illicit presence of the animal during the outbreak. The fact that pangolins naturally host coronaviruses in the wild only added to the intrigue.

On 7th February 2020, researchers at the South China Agricultural University suggested pangolin as the animal source of Covid-19. The research group later confirmed that they had found a pangolin coronavirus with a genome sharing 90.3% of the human coronavirus’ DNA and a receptor-binding domain (RBD – the part of the virus that allows it to enter cells) that was 99% similar. Two weeks later, other research groups from China and around the world identified 85.5% – 92.4% genomic matches between Covid-19 and coronaviruses in other illegally trafficked pangolins.

Yet, none of these were deemed similar enough for the pangolin to be labelled as the original host of Covid-19. Civet cats were only accepted as the probable incubators of SARS after a 99.8% match was found between a civet coronavirus and the one that caused the 2002 epidemic. If the pangolin was involved in the spread of Covid-19 to humans, researchers have yet to find conclusive evidence. The close match between the RBDs of pangolin and human coronaviruses doesn’t rule out its potential role as an intermediate host for Covid-19 however, which brings me right back to where this blog post (and potentially Covid-19) started.

And Now Back to Bats…

Bats have actually been the bad boys of microbiology for decades and researchers have been investigating (and warning us about) the range of coronaviruses they carry in the wild for nearly as long. Case in point – here’s an extract from a journal article written in 2007 that we really should have paid more attention to (apparently we all got tired of experts back in 2016?):

“The presence of a large reservoir of SARS-CoV-like viruses in horseshoe bats, together with the culture of eating exotic mammals in southern China, is a time bomb.”

Cheng et al. 2007, Clinical Microbiology Reviews, Vol. 20(4)

(Credit to my brother for showing me this one. Again, I’m the dumb one in the family.)

Bats have been found to harbour a huge diversity of coronaviruses, potentially as many as 5000 different strains by one estimate. It’s entirely possible that one of them is the direct progenitor of Covid-19.

(Image credit: Lesser horseshoe bats (Rhinolophus hipposideros) roosting,
Jessicajil, 2005, Flickr, CC BY-SA 2.0)

As mentioned before, a naturally-mutating coronavirus in bats is widely considered to have been the origin of the 2002 SARS epidemic, after the virus spread from bats to wild animals that were then sold at wildlife markets in Guangdong, China. In 2013, a research team led by Wuhan-based virologist Shi Zhengli sampled the blood, saliva and faecal matter of Horseshoe bats in a cave in Yunnan, China and found a coronavirus strain with a genomic sequence that was 97% identical to the SARS virus found in civets in Guangdong. Last month, the same team reported that they had tested samples from Covid-19 patients in Wuhan against the Yunnan cave coronavirus and found a 96% match. This is closest match between Covid-19 and a natural animal coronavirus that scientists have detected so far.

There are a number of differences between the Yunnan bat coronavirus and Covid-19 however, meaning that even if the virus originated from a bat, it would have to have mutated during its transmission to humans. If the mutation happened naturally, the original host species would have likely had a high population density to allow for natural selection, pointing the finger towards bats and their colony-roosting behaviour once again. However, researchers have yet to rule out the possibility that the virus spread from bats to an intermediate host, such as the poor old pangolin, before mutating to infect humans at the Huanan market. The possibility that the virus mutated within a human host following the initial zoonotic transfer is also still on the table.

As I write (30th March, 2020), no animal coronavirus has been identified that is sufficiently similar to have served as the definite progenitor of SARS-CoV-2, (the official name of Covid-19). This may be because the diversity of coronaviruses in bats and other species is massively under-sampled at present, but a rapidly growing number of studies (including one by Shi Zhengli) have put forward evidence that it’s possible that Covid-19 spread directly from bats to humans, without an intermediate host animal being involved. To stop you from permanently branding all bats as bad though, I’ll end on this point:

This is partially on us.

“The problem is not the animals, it’s that we get in contact with them.”

Sara Platto, Jianghan University, Wuhan, China

By encroaching on wildlife habitats, trafficking certain species, and clearing the forests many animals, including bats, use as roosts, humanity has put itself in closer and closer contact with wildlife, increasing the likelihood of the zoonotic spread of viruses like SARS and Covid-19. If there are no natural habitats available, bats will commonly roost together in buildings occupied by humans and livestock, (in high population densities if they can’t disperse elsewhere) adding to our vulnerability to virus exposure.

Yes, bat species can act as natural reservoirs for a variety of diseases, but they also can promote biodiversity and ecosystem health by eating pests and pollinating plants. There’s even some evidence that Daubenton’s bats practice a form of social distancing behaviour in the wild to reduce their exposure to coronaviruses. Honestly, we have a lot to learn from them.

It’s becoming increasingly difficult to ignore the link between infectious diseases like Covid-19 and SARS and the current global biodiversity crisis. Scientists have found that new pathogens tend to emerge in places undergoing substantial land uses changes, and often their origins are linked to ongoing deforestation, agricultural intensification and hunting. This means that other biologically diverse countries with high population densities besides China have the potential to become epicentres for future global public health crises. When all this is over, our relationship with the natural world might be the next thing under the microscope of the world’s virologists.