Just one big story today: collecting and sorting through what we know about the coronavirus’s origins, and what makes sense and what doesn’t in the theory that it originated from someone eating bats or pangolins from the Huanan Seafood Market.
What We Know and What We Don’t Know about the Source of COVID-19
Early on in this crisis, I read a November 2017 Smithsonian magazine article entitled, “Is China Ground Zero for a Future Pandemic?” (Give that reporter, editor, and headline writer a raise.)
At least two flu pandemics in the past century—in 1957 and 1968—originated in the Middle Kingdom and were triggered by avian viruses that evolved to become easily transmissible between humans. Although health authorities have increasingly tried to ban the practice, millions of live birds are still kept, sold and slaughtered in crowded markets each year. In a study published in January, researchers in China concluded that these markets were a “main source of H7N9 transmission by way of human-poultry contact and avian-related environmental exposures.”
. . . China is uniquely positioned to create a novel flu virus that kills people. On Chinese farms, people, poultry and other livestock often live in close proximity. Pigs can be infected by both bird flu and human flu viruses, becoming potent “mixing vessels” that allow genetic material from each to combine and possibly form new and deadly strains. The public’s taste for freshly killed meat, and the conditions at live markets, create ample opportunity for humans to come in contact with these new mutations.
. . . Despite such shortcomings, Western experts say Chinese officials have come a long way since their wobbly handling of the 2002 outbreak of SARS, the severe respiratory disease caused by a previously unknown coronavirus; Chinese apparatchiks initially tried to cover up the epidemic, creating a worldwide scandal.
From that point until I started doing the research for Friday’s article, “The Trail Leading Back to the Wuhan Labs,” I figured the vague but clear-enough explanation from our government’s health officials made the most sense: “Early on, many of the patients at the epicenter of the outbreak in Wuhan, Hubei Province, China had some link to a large seafood and live animal market, suggesting animal-to-person spread.” When a virus appears at the kind of insanitary markets that virologists had been warning about for years, it makes sense to apply Occam’s razor: The simplest explanation is usually the right one.
But that Smithsonian magazine article describes a lot of animals being slaughtered and sold at those markets: chickens, pigeons, quail, ducks, rabbits, pigs. You may notice one or two particular species that were not mentioned on that list.
You can find a lot of coverage of wet markets and quite a few references to the potential threat of a viral outbreak before this year — in Food Safety News, in the Singapore-based Today Online, the Japan Times, Agri-Pulse, the Daily Mail, KCRG, Culinary Backstreets, The Economist (disturbing picture of dog meat at that link), and the South China Morning Post, Foreign Policy, and CNN among others.
Those articles describe vendors selling dog meat, cats, pigs, sheep, cows, turtles, frogs, snakes, rats, foxes, and minxes.
But for what it’s worth, those articles don’t describe or mention vendors selling bats or pangolins, the anteater-like other animal species that is suspected to be a possible “transfer species” — i.e, the bat gives COVID-19 to the pangolin, some human being either eats or otherwise comes in contact with the pangolin, and contracts the virus. This doesn’t mean that those markets never sold bats or pangolins. But it does mean that they weren’t common enough to be easily witnessed and mentioned in news coverage.
(Interestingly, in 2019, a Daily Mail article reported upon the numerous unusual species openly sold at the Tomohon Extreme Market, located on the island of Sulawesi in Indonesia, including bats and dogs. I warn you, there are some seriously disturbing pictures at the link.)
There are a sufficient number of examples of human beings deliberately eating bats around the world to dismiss the “no one would ever eat a bat” argument (Although even if you didn’t find the thought inherently gross, there has to be relatively little meat on the bone compared to other species.)
Then again, vendors trading in those animals probably did their best to keep their merchandise secret. Back in 2013, the International Union for the Conservation of Nature declared the Chinese pangolin “more than likely the most traded wild mammals globally.” Back in late 2016, Quartz wrote that about 10,000 pangolins are smuggled into China from Southeast Asia each year, and described massive seizures of the animals carcasses from smugglers across Asia.
Keep in mind, there may not have been an intermediary species. One of the few fleeting references to a Chinese wet market selling bats came back in 2013 in the Wall Street Journal, in what amounted to a disturbingly prophetic report:
A decade after SARS swept through the world and killed more than 750 people, scientists have made a troubling discovery: A very close cousin of the SARS virus lives in bats and it can likely jump directly to people.
The findings create new fears about the emergence of diseases like SARS, or severe acute respiratory syndrome. The virus spread quickly from person to person in 2003 and had a mortality rate of at least 9%. Worries of a severe pandemic led the World Health Organization to issue an emergency travel advisory.
While bats have previously been fingered as a host for SARS, it was believed that the virus jumped from there to weasel-like mammals known as civets, where it went through genetic changes before infecting people. Operating on that belief, China cracked down on markets where bats, civets and other wildlife were sold for food.
The new bat-to-human discovery suggests that the control tactic may have limited effectiveness because a SARS-like virus remains loose in the wild and could potentially spark another outbreak.
SARS is caused by a germ known as a coronavirus. First discovered in 2003 in southern China, SARS went on to sicken more than 8,000 people in more than two dozen countries in North America, South America, Europe and Asia, before it was contained. No known cases have been reported anywhere since 2004.
But a key puzzle remained. No one ever found a live SARS virus in bats found in southern China’s wildlife markets, making it unclear that those bats were the source. So where did it come from?
Dr. Daszak and his colleagues chose to study a horseshoe bat colony in Yunnan province in southwest China—hundreds of miles from the big wildlife-for-food markets of Guangdong province, where SARS was first reported. The researchers took hundreds of samples from the horseshoe bats. A genetic analysis revealed at least seven different strains of SARS-like coronaviruses circulating in that single group of animals.
Crucially, the scientists were also able to isolate and culture a live virus that binds to a receptor on a human cell. That suggests that direct bat-to-human infection would likely occur.
This recent assessment from two microbiologists in Australia, John S. Mackenzie and David W. Smith, throws a little more cold water on the theory that COVID-19 jumped to humans through pangolins:
Evidence from the sequence analyses clearly indicates that the reservoir host of the virus was a bat, probably a Chinese or Intermediate horseshoe bat, and it is probable that, like SARS-CoV, an intermediate host was the source of the outbreak. To ensure that future cross-species transmission events of this new virus don’t occur again in the future, it is important to identify the reservoir and intermediate wildlife hosts. The closest known wildlife sequence to SARS-CoV-2 remains the sequence from the virus isolated from an Intermediate horseshoe bat, but there were significant differences in the receptor-binding domain between the two viruses. Malayan pangolins (Manis javanica) have been suggested as potential intermediate hosts, and SARS-like viruses have been identified in pangolins seized in anti-smuggling operations in southern China, but they only shared about 85–92% homology with SARS-CoV-218. No other possible intermediate wildlife host has been proposed at this time.
Those Australian microbiologists want a ban on wet markets and more enforcement of the ban on the trade of exotic species. But they also make an important point that we do not know, with absolute certainty, that the first cases were a result of someone eating bats or pangolins:
How this virus moved from animal to human populations is yet to be determined. The outbreak clearly began epidemiologically at the Wuhan market, and a number of environmental samples from around the live animal section of the market were subsequently found to be positive for SARS-CoV-212, but based on current evidence, it may not have actually emerged in the market. The earliest recognised case of infection with SARS-CoV-2 was an elderly and infirm man who developed symptoms on 1 December 2019. None of his family members became infected, and the source of his virus remains unknown13. Furthermore, 14 of the first 41 cases had no contact with the seafood market13. In another report, five of the first seven cases of COVID-19 had no link to the seafood market14. Thus, it seems very likely that the virus was amplified in the market, but the market might not have been the site of origin nor the only source of the outbreak. A recent phylo-epidemiological study has suggested that the virus was circulating but unrecognised in November, and was imported to the seafood market from elsewhere, where it subsequently was amplified15.
That study, found here, looked at the genomic data (mapping the genomes of the known samples of the virus to see how it is changing) and concluded:
H3 mutated to the H1 by two substitutions, and none of the Market samples encoded H3 in the currently available samples, suggesting that H3 might have originated and spread outside of the Market before an early stage of population expansion. The non-synonymous mutation from H3 to H1 might have enhanced the infectiousness of SARS-CoV-2, and a functional characterization should be performed to confirm this speculation. It is possible that SARS-CoV-2 in the Market had been transmitted from other places (Figure 3D), or at least, that the Market did not host the original source of SARS-CoV-2 (Cohen, 2020). As the first identified infected patients had no link to the Market (Huang et al., 2020), it is possible that infected humans transmitted the H1 haplotype of SARS-CoV-2 to workers or sellers in the market, after which it rapidly circulated there due to its special surroundings.
Could a vendor at the Huanan Seafood Market in Wuhan or elsewhere in the city have sold bats or pangolins for human consumption? Sure. But as of now, we don’t know that any of them did; that is an assumption.
We do know for certain that two laboratories in the city — the Wuhan Center for Disease Control & Prevention and the Wuhan Institute of Virology — were researching coronaviruses in bats. While it is theoretically possible that Dr. Botao Xiao is insane and/or just making it all up, his withdrawn research paper offered the surprisingly specific contention that 605 bats in total were being used in research at Wuhan Center for Disease Control & Prevention.
Yunnan province is about 850 miles from Wuhan, China. Horseshoe bats do not hibernate in cities.
The scenario where a horseshoe bat carrying COVID-19 naturally flew into the city is an extremely unlikely scenario. It is possible that someone trapped a bat 850 miles away from the city and brought it to the market to be sold for consumption. But that explanation doesn’t quite fit with the early patients who couldn’t be traced back to the market, and the genome mapping suggesting that the strain discovered at the one patient who they knew had been to the market wasn’t the original strain.
But if someone who worked at either of the two laboratories in the city researching coronaviruses in bats had been accidentally infected, and then that person traveled through the city, unwittingly infecting others, and then that person or one of the newly infected persons went to the market, becoming a “super-spreader”. . . that scenario would fit all of the available evidence that is known at this time.
Oh, wait, I’m sorry, the spread couldn’t have happened that way. Vox assures us, “The emergence of the virus in the same city as China’s only level 4 biosafety lab, it turns out, is pure coincidence.” And as that publication declared at the outset, they are “the smartest thinkers” asking “the toughest questions.”
ADDENDUM: The finest man I have ever known turns 80 today. Happy birthday, Dad. Stay safe.