Bat Viruses & Black Swans
A pandemic emerging from a wet market was long predicted, but it was scientists who knowingly brought viruses into Wuhan.
That SARS-CoV-2 came out of Wuhan’s Huanan Seafood Wholesale Market was, from the first, the official line of the People’s Republic of China (PRC). The explanation initially made sense. Experts had expected such an event for years. Since the SARS outbreak of 2002, their warnings have drawn immense funding for virus research in the name of preventing a global pandemic.
Viruses have the same naturally selected objective of all life, that of maximal reproductive success, but can’t copy themselves. A virus must instead break into the cells of another living thing and hijack the copying machinery inside. The process can incidentally harm or kill the life involved.
The most potentially dangerous virus to any species is one that jumps into it from another species. With no immunity, the new population is defenceless. If the virus can evolve to efficiently infect, exploit and transmit in that species, it can cause disease and death on a large scale.
“The animal origins of human disease lie behind the broadest pattern of human history,” as Jared Diamond pointed out in his 1998 classic Guns, Germs and Steel. “The major killers of humanity throughout our recent history,” he wrote, “are infectious diseases that evolved from diseases of animals.”
A virus that jumps from animal to human is “zoonotic”. The jumps are perceived to be becoming more frequent and consequential. The orthodox view, expressed in Spillover, a 2012 book by David Quammen, is that “they are not simply happening to us; they represent the unintended results of things we are doing”.
“Human-caused ecological pressures and disruptions,” Quammen summarised, “are bringing animal pathogens ever more into contact with human populations, while human technology and behavior are spreading those pathogens ever more widely and quickly.”
Ebola, HIV and avian flu are part of a recent “pattern of weird and terrible new diseases,” wrote Quammen, “emerging from unexpected sources and raising deep concern, deep foreboding, among the scientists who study them”. “The world is teetering on the edge of a pandemic,” the eminent virologist Robert Webster warned in 2003, “that could kill a large fraction of the human population.” He was specifically concerned about the H5N1 virus.
In 2005, the United Nations warned that H5N1 might kill 150 million people — if it were transmissible between humans. Some scientists argued it could become so. In 2011, they answered this “important scientific question” by making it transmissible between mammals, turning it into “one of the most dangerous viruses you can make”. Other scientists then made the virus infectious via inhalation.
This strange way of expressing deep concern and foreboding has been called “morally and ethically wrong” by other scientists. In the name of preventing a global pandemic, the number of laboratories in which such work is done has dramatically increased since 2003. For many years, some scientists have considered a laboratory accident, and not nature, the most likely origin of a future pandemic.
The received wisdom, however, is that wet markets will be their origin.
Wet markets abound throughout Asia, each “a panorama of cruelty,” in the words of the late Anthony Bourdain, the chef and culinary adventurer. Bourdain, with typically open mind, reckoned them “more honest than our [Western] system” of sealed cuts of meat in supermarket fridges. That system is however sanitised in more than one sense.
The wet markets of Asia combine the scent of cooking with “the smell of poultry excrement and fear,” in Bourdain’s evocative phrase. The smell emits from more than just chickens. During his A Cook’s Tour series he perused a menu of “roasted field mouse, lizard, chameleon, minced bat”. He opted for “palpitating cobra heart,” still beating on being cut from the snake.
Such exotic menageries are brought together and butchered together in wet markets. “Every imaginable animal,” in the brushstroke description of American infectious disease expert Michael Osterholm, “all right on top of each other.” Literally so, in many cases.
In such markets, Osterholm has seen live chickens stacked in a cage above live ferrets, something he calls “the perfect experiment” to produce new viral threats to humanity — one “no university research group would let you do”. “Ferrets are easily infected with novel flu viruses, such as those from birds,” he explained, “and being mammals might then easily breed it into a form infectious to humans.”
The H5N1 mutant unarguably represents a more perfect experiment, and one sanctioned by research bodies, but Osterholm’s point stands.
China has been the source of many past pandemics, including the Plague of Justinian in the 6th Century CE, the Black Death of the 14th Century, the Third Plague Pandemic of the mid-19th Century, the 1918 “Spanish flu”, the Asian flu and Hong Kong flu of the mid-20th Century, the 1977 “Russian flu” and SARS in 2003. It is considered the likely origin of future pandemics too.
Osterholm was interviewed on The Joe Rogan Experience in early March 2020, as the world braced to be hit by SARS-CoV-2. Asked why China posed such a danger in terms of emerging viral threats, he answered, “because they have this incredibly large population. They’ve got this food supply that is largely wildlife that comes into these markets, where there’s this incredible contact between people and these animals. And the crowded nature of that society.”
His words echoed those of a paper authored a year previously by four Chinese scientists. “China is the third largest territory and is also the most populous nation in the world,” they wrote. “A vast homeland plus diverse climates bring about great biodiversity,” while “Chinese food culture maintains that live slaughtered animals are more nutritious, and this belief may enhance viral transmission.”
The paper, published in a special edition of Viruses, a leading virology journal, summarised the current knowledge of bat coronaviruses across China. The issue was entirely devoted to bats, a prime focus of zoonotic research.
Bats are highly social, make up a fifth of all mammal species, and are the only mammal capable of powered flight. The combination makes them ideal vectors for viruses. They harbour “a significantly higher proportion of zoonotic viruses” than other mammals.
The authors of the Viruses paper were China’s leading experts on bat coronaviruses. They emphasised that, in the last twenty years, such viruses have produced two serious human epidemics: Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS).
SARS originated in a colony of bats in Yunnan, China, and infected some 8,000 people worldwide from 2002 to 2003. Nearly a thousand died. SARS however had low transmissibility between people and a victim’s peak infectiousness occurred only after clinical symptoms appeared. It was contained relatively easily, but the mortality rate of 10 percent was sobering.
After the epidemic had subsided, an expert group of epidemiologists warned that “we were lucky this time”. This may not be an accurate perception. The “luck” was due primarily to low human-to-human transmissibility. That is common to most zoonotic viruses after their initial jump to people because they are adapted to another species.
It was certainly the case with MERS, a bat coronavirus which jumped to camels and then, in 2012, to humans. MERS has little if any person-to-person transmissibility. Nonetheless, some 3,000-odd victims suffered a 37 percent mortality rate. The Hendra virus, which first emerged in Australia in 1994, kills 60 percent of its human victims. Again, however, it is not transmissible between humans. In fact, it can only be caught from horses, not bats.
“It is generally believed,” wrote the authors of the 2019 paper in Viruses, “that bat-borne coronaviruses will re-emerge to cause the next disease outbreak. China is a likely hotspot. The challenge is to predict when and where, so that we can try our best to prevent such outbreaks.”
The most notable of the authors was Shi Zhengli. SARS-CoV-2 is exactly the sort of virus in which she and her research group were interested. They had literally searched the far corners of China for one like it. They had, they would eventually admit, even found one almost identical it.
The researchers had brought this virus, and a hundred others like it, back to their laboratory at the Wuhan Institute of Virology (WIV).
Wuhan has two infectious disease laboratories, the second being the Wuhan Center for Disease Control and Prevention (WHCDC). When strange cases of a viral pneumonia began appearing in the city in mid-December 2019, a national surveillance protocol brought them to its attention.
The WHCDC has done extensive research with SARS-like coronaviruses, often working with the live bats in which they originate. By 30 December, its scientists had detected such a virus, now known as SARS-CoV-2, in samples taken from the first patients. The WIV was involved immediately.
This would have been the case had the virus appeared anywhere in China. The WIV is the nation’s leading centre of research into SARS-like coronaviruses. It happened to be just 12 kilometres away, on the opposite side of the Yangtze. The lab sent patient samples over the short distance across the city in the early evening of 30 December.
Shi, China’s leading expert on SARS-like coronaviruses, was involved with equal inevitability. The institute’s director immediately ordered her to begin an investigation. “Drop whatever you are doing,” he told her over the phone that evening, “and deal with it now.”
She and several colleagues took an overnight train from Shanghai, where they were attending a conference. On the journey they “discussed ways to immediately start testing the patient samples”. At the same time, key WIV virus databases were being inexplicably scrubbed at altered.
The scientists must have arrived back in Wuhan in the early morning of 31 December. Later that same day, Wuhan’s Municipal Health Commission issued a warning notice that the Huanan Seafood Wholesale Market was the suspected origin of the virus. The wet market was consequently closed on 1 January 2020.
The Chinese Centre for Disease Control and Prevention (CCDC) began investigations at the market the same day. China allowed no international participation in the investigation. An ongoing process of disinfecting the market had begun the day previously, at about the same time Shi and her colleagues were arriving back in Wuhan.
The immediate Chinese state response to the outbreak also concerned itself with shutting down anyone who spoke out about it. On 30 December, Li Wenliang, an ophthalmologist at Wuhan Central Hospital, received an internal report on a suspected SARS case. Naturally concerned, he shared it with other doctors to warn them. “He was told by police to ‘stop making false comments’ and was investigated for ‘spreading rumours’.”
Li died from covid-19 on 7 February, a month after unknowingly being infected by the new SARS virus while treating a patient.
On 1 January, the Wuhan Public Security Bureau also “summoned eight people for posting and spreading ‘rumors’ about Wuhan hospitals receiving SARS-like cases”. They were doctors. Their detentions “were reported on ‘Xinwen Lianbo,’ a newscast watched by tens of millions”. It was clearly meant as a warning to other citizens considering speaking out.
Wuhan’s health authority immediately locked the world’s focus onto the market as the origin of the virus. Its notices were the “main official source of public information” about the initial outbreak. These “repeatedly noted that there was no evidence of human-to-human transmission and that most cases linked to the market”.
The former claim can never have been true. Shi nonetheless maintained the same line when she publicly confirmed transmission between people was happening. “Most of the early cases had contact history with the original seafood market,” she wrote in a paper submitted to Nature on 20 January. “However, the disease has now progressed to be transmitted by human-to-human contact.”
In fact, it was soon known that the virus was both very stable and well-adapted to human-to-human transmission from the beginning — just two of its strange features. By 2 January, the virus had infected 41 laboratory-confirmed cases. All were transferred to Wuhan’s Jin Yin-tan Hospital and isolated, starting from 31 December.
By 7 January, Shi claims her team at the WIV had “determined that the new virus had indeed caused the disease those patients suffered”. Professor John Mackenzie, an advisor on the Emergency Committee of the World Health Organization (WHO), questioned this timeline in April.
Mackenzie claimed that, “by the time the [Chinese] government alerted the WHO on 31 December, scientists in China had already determined via genome sequencing that the outbreak was caused by coronavirus.” Shi admits this is true.
The virus sequence had in fact been determined by 2 January. “Yet the government didn’t confirm that until 7 January,” Mackenzie observed, “and the full genome sequence was not officially shared until 12 January.” The WHO consequently lost “at least two weeks” in effective response to the outbreak.
Regardless, at Jin Yin-tan Hospital in January, the first 41 victims of the disease that would become known as covid-19 were assessed by an “expert team of physicians, epidemiologists, virologists and government officials”. They reported their findings in The Lancet on 15 February. A third of the patients, they revealed, had no direct exposure to the wet market.
This was true of three of the first four infected. And these four included the first known patient, who contracted the virus on 1 December 2019 after no contact with the market whatsoever. Also, “No epidemiological link was found between the first patient and later cases”.
Meanwhile, the first known patient outside of China, a Chinese tourist in Thailand who had travelled from Wuhan, had been reported on 13 January. That person too, according to the International Journal of Infectious Disease the following day, showed “no epidemiological linkage to the Huanan Seafood Wholesale Market”.
On 12 January, the day before the first case of covid-19 appeared outside of China, the CCDC finished collecting samples from the wet market. A fortnight later, Xinhua, the state-run media of the PRC, reported that only 33 of the 585 samples tested positive for the virus. The headline spun this into “China detects large quantity of novel coronavirus at Wuhan seafood market”.
All but two of the positive samples were reported to have been collected from “where booths of wildlife trading concentrated”. Xinhua, referring to unnamed “experts,” claimed this indicated “that the virus stems from wild animals on sale at the market”.
From just which species the samples had been taken, which was the critical information, was not mentioned. The positive samples anyway appear to never have existed. “In the period since,” it was reported in May, “tissue samples from the market’s animals have revealed no trace of the virus.”
The genetic sequence of the virus had however indicated its original host species by mid-January. Akin to the software program of the virus, this nucleotide sequence was released to the WHO on 12 January by Shi’s team at the WIV.
Within ten days, other Chinese scientists had identified 2019-nCoV (as it had then been named) as “a recombinant virus between the bat coronavirus and an origin‐unknown coronavirus”. A snake was suspected to be the source of the unknown genetic makeup of the virus. Within a month it would be identified as a pangolin. This has now been proven a cipher. No intermediate host is known.
Regardless, the unknown genetic component of the virus was only a fraction of its structure. Before the end of the month, another group of Chinese scientists reported that “2019-nCoV was closely related (with 88% identity) to two bat-derived SARS-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected in 2018 in Zhoushan, eastern China”.
The two scientific papers containing these findings still accepted and advocated the wet market origin of the virus. They claimed that “poultry, bats, snakes; and other wildlife animals were also sold” there, and “birds and rabbits were also on sale before the outbreak”.
There was building concern about the virus in the West at the time, and this information combined to produce a reactionary Western view, particularly online. It amounted to a judgement that neither wet markets nor the cultural practice of eating bats should exist.
Such opinion was deemed racist by mainstream media in the West. Journalists quickly acted to inform the public that bats were never sold at the Huanan wet market. Further, bats are not even part of the local cuisine of Hubei province, of which Wuhan is the capital. “Don’t blame bat soup for the virus,” one headline admonished readers.
Two scientists affiliated with the Wuhan University of Science and Technology, in a report posted to the internet in mid-February, confirmed eating bats could not have been the cause. Botao Xiao and Lei Xiao claimed that, “According to municipal reports and the testimonies of 31 residents and 28 visitors, the bat was never a food source in the city, and no bat was traded in the market” (no citation of this report was however provided).
Shi was personally astonished that SARS-CoV-2 appeared “in central China” at all, let alone central Wuhan. Her own work has definitively established that SARS-related bat coronaviruses viruses are scarcely present in Hubei province, of which Wuhan is the capital. Hubei also lacks the dense populations of bats and viruses that she, to considerable acclaim, has found are necessary to produce a virus like SARS (and, by inference, SARS-CoV-2).
SARS-CoV-2 anyway originates in a bat species, Rhinolophus affinis, that is not even present in Hubei according to official Chinese surveys. Shi claims to have trapped a handful in the mountains in 2004, but the bat doesn’t roost in cities (Wuhan is the size of Greater London). It also lives at elevations above 600 metres (Wuhan is at sea level) and enters hibernation around September as autumn begins (SARS-CoV-2 appeared in Wuhan around November).
They were unlikely to be flying a month or two later, least of all over the dense city centre of Wuhan.
By the end of January 2020, some Western media outlets had begun to express doubt that the virus emerged from the wet market. By April, a few opinion pieces were admitting the “initial origin story is shaky”. It took until the last week of May for the Chinese Communist Party (CCP) to officially admit it was wrong. “Gao Fu, the director of the Chinese CDC, told Chinese state media: ‘It now turns out that the market is one of the victims’.”
Yet the CCP and the mainstream media in the West were equally adamant the virus had not escaped from a lab. This was despite the fact that the WIV and the WHCDC were the only known reservoirs of coronaviruses in Wuhan, and that the surrounding province was not a natural reservoir.
Intriguingly, the same week the PRC officially conceded the wet market was not the origin of SARS-CoV-2, Shi appeared on China Global Television Network (CGTN), a branch of China’s state-run media. Shi had only talked to the media twice since the outbreak, and her previous interview in February was also well-timed. In May, she was asked how she would assess the work of her team since the outbreak. “I think we have done a good job,” Shi replied.
Early in January, Xinhua reported that Chinese experts reckoned “the geographical distribution of the cases indicated a close relationship between the epidemic and the seafood market”. In May, the PRC retreated to the position that, as a nodal point of community interaction, it may instead have simply been a “super-spreader” of the virus.
Another possibility is that the geographical relationship of the virus outbreak was not only with the market, but also with the WHCDC. As the report by Botao Xiao and Lei Xiao pointed out, this facility “hosted animals in laboratories for research purpose[s], one of which was specialized in pathogens collection and identification”.
These included hundreds of bats, Rhinolophus affinis among them. This was not baseless allegation, but readily available information from scientific journals and media publications published over the last several years.
The PRC apparently attempted to suppress the report, which included a useful Google street map of Wuhan. It showed the WHCDC was less than 300 metres away from the Huanan Seafood Wholesale Market.
