The China Syndrome Part I: Outbreak
Taken on January 30, 2020 shows officials in protective suits gathered on a street after an elderly man wearing a facemask (not pictured) collapsed and died on the pavement near a hospital in Wuhan. – AFP journalists saw the body on January 30, not long before an emergency vehicle arrived carrying police and medical staff in full-body protective suits. The World Health Organization declared a global emergency over the new coronavirus, as China reported on January 31 the death toll had climbed to 213 with nearly 10,000 infections. (Photo by HECTOR RETAMAL/AFP via Getty Images)

The China Syndrome Part I: Outbreak

Philippe Lemoine
Philippe Lemoine
29 min read

Note: This is the first part of a four-part series of essays looking in detail at China’s role in the COVID-19 pandemic. This part looks at the circumstances surrounding the initial outbreak; Part Two looks at the discovery of human-to-human transmission and the immediate response; Part Three investigates allegations that the pandemic began in a “wet market” or that the virus escaped from a lab in Wuhan; Part Four examines charges that China falsified its pandemic data.


According to a poll conducted in France, Italy, Spain, the UK, and the US at the end of March, a majority of the population in each of those countries believes that China is at least somewhat to blame for the pandemic and, in both the UK and the US, a plurality believe it’s significantly to blame. Another survey taken in the US at the end of April found that a plurality of people believe that SARS-CoV-2 was probably or definitely created in a lab. At the beginning of that month, another poll had found that a majority of Americans believed that China was not reporting the impact of the epidemic over there accurately, that it was responsible for the spread of the virus and that it should be required to pay for it.

Although people disagree over what exactly China has lied or is lying about, there is widespread agreement in the media that it has engaged in some kind of cover-up. In the US, many public officials, including Donald Trump, have explicitly accused China of various manipulations. Leaks from intelligence agencies that accuse China of lying about the pandemic appear in the mainstream press regularly, so it’s not surprising that so many people have broadly accepted this claim, even when the specifics of those stories are later debunked.

For instance, back in May, the Daily Telegraph in Sydney published a story about a dossier allegedly compiled by the intelligence agencies of several Western countries (the US, Australia, New Zealand, Canada, and the UK), which it summarised like this:

[The dossier’s] major themes include the “deadly denial of human-to-human transmission,” the silencing or “disappearing” of doctors and scientists who spoke out, the destruction of evidence of the virus from genomic studies laboratories, and “bleaching of wildlife market stalls,” along with the refusal to provide live virus samples to international scientists working on a vaccine.

This dossier later turned out to have been authored by the US State Department and was based upon press reports not intelligence. It was probably leaked to the Australian press so that reports would find their way back to the US and create the impression that foreign intelligence agencies endorsed the claims being made by the Trump administration.

In this four-part series of essays, I will discuss the various accusations made against China in connection with its role in the pandemic. Needless to say, there are many reasons to dislike and distrust the Chinese regime. It runs an authoritarian one-party state, routinely engages in repression of dissidents and minorities, and enforces censorship that makes official corruption and lies more difficult—though by no means impossible—to expose. During the SARS epidemic in 2003, the Chinese authorities covered up the scale of a problem for several weeks, so we know from experience that lying about a public health crisis is not beneath them.

Nevertheless, specific accusations should be backed by sufficient evidence and it’s important to examine whether the accusations made against the Chinese for their handling of the pandemic are in fact true on the merits. If they are, then hundreds of thousands of deaths and a great deal of economic hardship might have been avoided. If they are not, then we need the clearest possible picture of what did happen and we should avoid unwarranted accusations, however unpalatable China’s actions may otherwise be. Allegations of Chinese government mendacity have already contributed to worsening relations between China and the West, which could have serious consequences in the future. There may be good reasons to adopt a more aggressive foreign policy toward China, but such a policy should not be predicated on false premises. It’s therefore crucial to examine the factual basis of the accusations against China in a rational manner.

Pneumonia of unknown aetiology

On December 31st, the Chinese authorities announced that a new virus was causing a cluster of viral pneumonia in Wuhan. According to the South China Morning Post (SCMP) which claims to have seen official Chinese documents, after the virus was identified as the cause of the outbreak, the Chinese authorities tried to find out who among the contacts of the known cases may have been infected earlier, and they found a case dating back to November 17th, 2019. This is roughly consistent with genetic evidence, which suggests that this novel coronavirus (since named SARS-CoV-2) originated in late November. The SCMP story doesn’t make it clear if they determined that this person had been infected based on interviews which revealed that he or she was exhibiting symptoms on this date, or if they performed serological tests showing this person had developed immunity to SARS-CoV-2. The language in the article suggests they are not sure.

This is why an ABC News story in April reporting that “US intelligence officials [had warned] that a contagion was sweeping through China’s Wuhan region, changing the patterns of life and business and posing a threat to the population” in late November made no sense. Unless the outbreak started much earlier—a theory supported by no evidence and contradicted by phylogenetic evidence—there is simply no way US intelligence could have known that an epidemic was underway at the time. (This leak was probably intended to make Trump look bad, since the authors of that story predictably concluded that the federal governments should have taken steps much earlier to prepare for a pandemic.) Indeed, the story was quickly denied by the director of the National Centre for Medical Intelligence and this denial was later confirmed by CNN, but not before scores of journalists working for every major news organisation enthusiastically shared it.

According to the World Health Organisation (WHO), which relayed the information it had received from the Chinese government, the first patients suffering from COVID-19 (the disease caused by SARS-CoV-2) were hospitalised in Wuhan at the beginning of December. It is unlikely that the Chinese health authorities would have understood what was going on right away. This timeline seems to be corroborated by the SCMP story, which reports that “Interviews with whistleblowers from the medical community suggest Chinese doctors only realised they were dealing with a new disease in late December.” This is also what the Wall Street Journal, which talked to several doctors in Wuhan, reported in a story in March.

On December 31st, 2019, the WHO became aware that a cluster of pneumonia of unknown aetiology had been identified in Wuhan. But Alex Azar, the US Health and Human Services Secretary, told a press conference on March 20th, 2020, (at 01:02:20 in the video) that Robert Redfield, the Director of the American CDC, was alerted by the Chinese on January 3rd. According to the China CDC Weekly, this was the same day that SARS-CoV-2 was sequenced at the National Institute of Viral Disease Control and Prevention, about a month and a half after the first known human infection. As reported by the press at the time, this discovery was made public a few days later, on January 9th, 2020. It’s unclear when the WHO was informed of that discovery exactly.

To assess the claim that the Chinese authorities knew what was going on long before they informed the rest of the world, it’s useful to compare the timeline of their response to the COVID-19 outbreak with that of the US authorities’ response to the swine influenza pandemic in 2009. The earliest known case later confirmed to have been caused by the swine influenza virus was a person in Mexico who reported onset of symptoms on March 17th, 2009. But a study published in 2012 was able to identify three unrelated clusters of influenza caused by the virus in California at the end of March, including one person who reported onset of symptoms on March 21st. As the authors of the study note, community transmission therefore probably started earlier than that, even in the US. But the CDC only identified the virus on April 14th, after they received a sample from a 10-year-old boy who lived in California. This was confirmed on April 17th, after the virus was found in another sample, taken from a nine-year-old girl with no connection to the first case, who started exhibiting symptoms on March 25th. The US reported the discovery to the WHO on April 18th and published a report about it on April 21st.

This timeline indicates that, even assuming community transmission began in California around mid-March 2009, it took about a month for US health authorities to identify the swine influenza virus. On the other hand, if we accept the official timeline provided by the Chinese health authorities, it probably took them about a month and a half to identify SARS-CoV-2 as the cause of the outbreak of pneumonia in Wuhan. Given the role that chance plays in this sort of thing, it’s not obvious to me that the American CDC would necessarily have done better had the outbreak occurred in the US. It’s also worth noting that, according to its website, the Chinese CDC employed a staff of only 2,120 for a population of almost 1.4 billion in 2016, whereas in 2012 the American CDC employed 11,223 people for a population of about 320 million. I wasn’t able to find data on the Chinese CDC’s budget, but since the American CDC had a staff more than 20 times greater per capita than its Chinese counterpart, it’s reasonable to assume it has vastly greater resources at its disposal. This undoubtably makes it much easier to monitor outbreaks of infectious diseases.

In both cases, it took about a week after the virus was first sequenced before the discovery was made public. So there is no reason to assume that, because the Chinese health authorities identified SARS-CoV-2 on January 3rd and informed the rest of the world a few days later, they were trying to cover it up. The reason for the delay between discovery of SARS-CoV-2 and the announcement of that discovery is that simply sequencing the virus was not enough to prove it was responsible for the outbreak of pneumonia in Wuhan. As the researchers who made the discovery explain in this paper, that was only the first step of a much longer process, which also involved isolating the virus, observing the cytopathogenic effects it produced after infecting susceptible cells, performing serological tests and so on. They presumably also had to test the samples for other pathogens to exclude them as the cause of the illness. That all takes time, even if everyone is working as fast as they can.

Although they didn’t release many details until the discovery of the virus was announced on January 9th, the Chinese didn’t hide the fact that they were trying to identify the pathogen responsible for the outbreak in Wuhan during that period. To the contrary, on January 5th, the Wuhan Health Commission published a statement about the outbreak, which said that “respiratory pathogens such as influenza, avian influenza, adenovirus, SARS and Middle East Respiratory Syndrome (MERS) [had] been excluded” and that “pathogen identification and aetiology tracing work [were] still in progress.” From the few details that Chinese officials had released, as well as local media reports, plenty of people were already conjecturing that a new coronavirus was responsible for the outbreak at the time. As early as January 3rd, a professor of medicine at the Chinese University of Hong Kong had already explained in a radio interview that, according to a professor at Peking University he’d talked to, a new coronavirus was suspected as the cause. So, if the Chinese authorities were trying to cover this up, they were doing a terrible job.

A search of Twitter reveals that, among the few virologists and China watchers who actually cared about this at the time, there were already complaints that China was too slow to disclose what they had found. Of course, sequencing the genome of the virus should be fast with today’s technology. But as some virologists also noted, it’s understandable that, before announcing that a new coronavirus was responsible for the outbreak in Wuhan, the Chinese health authorities would want to make sure they had got it right. They likely weren’t even sure that a single pathogen was responsible for all the new cases of pneumonia they were seeing, and confirming this fact would have meant testing several samples and required a lot of work. As Florian Krammer, professor of microbiology at the Icahn School of Medicine at Mount Sinai, noted in this thread (which gives a sense of the debates virologists were having at the time), researchers would have been keen to rule out the possibility that co-infections were responsible for the illness. Eddie Holmes, a virologist at the University of Sydney, noted in reply to Krammer that something like that had actually happened with SARS, which scientists initially suspected of being caused by a metapneumovirus before they realised SARS-CoV-1 was responsible. This is complicated work, but people who don’t know that were too quick to assume a conspiracy where there was none.

Sequencing the SARS-CoV-2 genome

There is, however, compelling evidence that SARS-CoV-2 had already been sequenced by private genomics companies by January 3rd, 2020, when it was supposed to have been sequenced for the first time according to the Chinese authorities. The Chinese media outlet Caixin published a very detailed article in Chinese that sets out the evidence for this claim in February. Apparently, it’s no longer available, possibly because it was censored by the authorities, but it was archived and then translated by a Chinese dissident who now lives in the US. (Another piece on the same topic is still up on the English version of Caixin—it’s slightly less detailed overall, but it also contains a few details that are not in the Chinese-language article.) As the Caixin article explains, on December 24th, 2019, a sample was collected from a patient at Wuhan Central Hospital and sent to a private genomics company called Vision Medicals for analysis using next-generation sequencing. According to the article, after analysing the genetic material in the sample, Vision Medicals was able to sequence a genome on December 27th and found that it was 79 percent similar to SARS-CoV-1, the virus that caused the 2002–04 SARS outbreak. They didn’t send back the results, but immediately called Zhao Su, head of respiratory medicine at the hospital (who had sent them the sample), to inform him of their discovery.

This story is convincing for several reasons. First, Zhao Su confirmed it on the record, which he is unlikely to have done if the story isn’t true. (Caixin claims that Vision Medicals also confirmed the story in a social media post, but no link was provided and I haven’t been able to find it.) Moreover, a paper published in the Chinese Medical Journal on February 11th and co-authored by someone working at Vision Medicals explains how SARS-CoV-2 was identified by next-generation sequencing in samples taken from five patients, including one whose sample was collected on December 24th, 2019. (I emailed the co-author of that study requesting confirmation, but received no reply.) Of course, it’s possible that Caixin wrote the details of the story to fit this evidence. But the fact that, even according to the published study, the sample was taken on December 24th means the claim that SARS-CoV-2 had already been sequenced by December 27th is plausible. Guangzhou, where Vision Medicals is based, is only a 10-hour drive from Wuhan, so presumably they would have received the sample the day after it was collected, or perhaps even the same day. Furthermore, next-generation sequencing is very fast, so it seems not unlikely that the analysis was completed by December 27th. In any case, according to the paper, the patient had already been in ICU for two days at the time and diagnosis was therefore urgent, so it’s unlikely it wasn’t done by January 3rd, when the virus is supposed to have been sequenced for the first time. Finally, in an article it published in June, the Associated Press claims to have independently confirmed this story.

It is less clear how much the Chinese health authorities knew about all this. According to Caixin, Vision Medicals shared the data with the Chinese Academy of Medical Sciences at the time, and company executives even went to Wuhan a few days after the virus had been sequenced, where they presented their results to local hospital officials and disease control authorities. But this claim is based on a post on WeChat, a Chinese social media platform, at the end of January, the author of which claimed to be working for a private company located in the same city as Vision Medicals. This is weak evidence and deserves to be treated with scepticism. The only independently verifiable evidence that Caixin adduces is that one of the co-authors of the Chinese Medical Journal study mentioned the above works for the Chinese Academy of Medical Sciences. This is true but it doesn’t really prove anything.

In any event, it’s reasonably safe to conclude that, sometime after December 27th (it’s hard to say exactly when), the local health authorities were informed that a new coronavirus related to SARS-CoV-1 had been identified in a sample collected from a patient with pneumonia in Wuhan. (It’s likely that some people at the Chinese Academy of Medical Sciences were also told about it, but they probably didn’t inform the national health authorities, since as we shall see the director of the Chinese CDC apparently didn’t find out until December 30th.) After Vision Medicals sequenced the genome of SARS-CoV-2 on December 27th, 2019, Caixin adds that a sample collected from another patient was sent to a different private genomics company based in Beijing. However, this company mistakenly identified the virus in the sample as SARS-CoV-1. The test results were sent back to Wuhan Central Hospital, where they were initially received by Ai Fen, director of the emergency department at Wuhan Central Hospital, who sent them to several other doctors in Wuhan. One of those doctors was Li Wenliang, an ophthalmologist at Wuhan Central Hospital, who shared them with his medical school classmates in a private WeChat group on December 30th, 2019.

The Wuhan whistleblowers

Li Wenliang (1986–2020)

At first, Li Wenliang said that seven patients had contracted SARS at Huanan Seafood Market and were currently isolated at Wuhan Central Hospital. He later clarified that although the patients had been infected by a coronavirus, the exact virus was still being subtyped. Screenshots of what he said in that group eventually made their way to Chinese social media. (You can find a link to the screenshots, as well as a translation, on Li’s Wikipedia entry.) A few hours later, Xie Linka, a doctor at Wuhan Central Hospital, wrote a similar message in another WeChat group. (You can find a copy of that message, transcribed from a screenshot in another Caixin article, on her Wikipedia entry.) Both Li and Xie said that the virus was related to but probably different from SARS-CoV-1 (which suggests they had heard about the results of the Vision Medicals analysis, not just the erroneous identification provided by the Beijing lab), but rumours started to circulate on social media that SARS was back in Wuhan.

Li Wenliang, Xie Linka and another five doctors were all reprimanded by local police a few days later for spreading “false rumours” (Ai Fen, apparently, was not, although she was rebuked by her superiors at Wuhan Central Hospital). Li was also forced to sign a letter of admonition in which he acknowledged he’d acted inappropriately and promised not to do so again. However, contrary to popular belief, none of the doctors seems to have been detained at any point. On March 29th, the Australian TV programme 60 Minutes reported that Ai Fen was missing, a claim that was immediately repeated by other media. But there doesn’t seem to be any evidence that she was ever detained. She has since posted a video on Weibo reassuring viewers that she is fine, and on April 13th, a French journalist found her at her post in Wuhan Central Hospital:

Li has come to be known as a “whistleblower,” but that’s not really accurate. I don’t mention this to disrespect his memory or to justify the indefensible conduct of the Wuhan police department. It’s just that the term “whistleblower” suggests that Chinese officials were engaged in a conspiracy to hide the discovery of the virus at the time, which is not what was happening. On January 3rd, the same day Li was interrogated by Wuhan police, the virus was sequenced at the National Institute of Viral Disease Control and Prevention, and a public announcement would follow a few days later. Chinese health officials contacted the director of the American CDC about the outbreak in Wuhan the day the virus was sequenced, although we don’t know exactly what was said. And social media was already rife with speculation that a new coronavirus related to SARS-CoV-1 was responsible for the outbreak. Again, if the Chinese health authorities were trying to cover any of this up, they were doing a spectacularly bad job.

Nor is there any evidence that Li ever intended to alert the public to the appearance of a new coronavirus in Wuhan. In fact, in one of his messages on WeChat, Li specifically asked the members of the group not to circulate the information he was sharing. Li’s and Xie’s private warnings that SARS might have returned to Wuhan were nevertheless leaked onto social media and rumours of the disease’s reappearance started to spread. By this point, the novel coronavirus in Wuhan had not yet been definitively identified, nor had the possibility of human-to-human transmission been established. The authorities’ concern about the spread of misinformation and unverified speculation was therefore understandable and hardly unique to authoritarian countries. It’s just that, in a police state like China, instead of complaining about “fake news” and asking Twitter to take down misleading posts, the authorities issue public admonishments and compel individuals to sign Maoist apologies.

On December 30th, the same day Li’s and Xie’s private WeChat messages were leaked, the local health authorities sent an emergency notice to every hospital in Wuhan, warning them that several patients with pneumonia and links to Huanan Seafood Market had been admitted to various hospitals. The message instructed doctors to monitor similar cases. Caixin and several other media outlets claim that this was prompted by the appearance of Li’s messages on social media. This is possible, but as far as I can tell, it is not an established fact. The Chinese version of Caixin’s report also explains that, on December 27th–29th, the local health authorities were already in receipt of several reports from various hospitals in Wuhan of people being admitted with cases of pneumonia. There is no evidence that anyone had noticed the cluster until that time, so it’s quite possible that local health authorities would have issued this warning anyway. They certainly would have done so at some point; they were not about to sit idle once they realised that a new and potentially very dangerous virus had started to circulate in their jurisdiction. Social media rumours might have accelerated the process, but absent any firm evidence, this is speculation.

What does seem clear is that it wasn’t until the end of December that medical professionals in Wuhan realised that something unusual was going on. COVID-19 patients started to be hospitalised at the beginning of December, but the numbers at the time were low and there is no evidence that anybody yet suspected that a new virus was the cause of their illness. By the end of December, however, the local health authorities had clear hints that a novel virus was circulating in the city and might be responsible for pneumonia in several patients apparently connected to Huanan Seafood Market. It’s also clear that, upon receiving this information, they tried to ensure it didn’t leak to the public, pressuring doctors to keep quiet and reprimanding those who didn’t. But this was almost certainly an attempt to control information rather than to suppress it—the latter goal was by this point a futile one, even if the authorities had wanted to pursue it, since the spread of the virus made disclosure of its existence inevitable. In fact, local health authorities didn’t order doctors not to share information with the public until after some of them had inadvertently done so.

China’s failure to notify the WHO

A number of commentators have made a big deal out of the fact that, contrary to initial statements made by the WHO, the organisation was not warned about the outbreak in Wuhan by the Chinese authorities but picked up the news on its own. This it implicitly admitted by quietly updating its “Timeline of WHO’s Response to COVID-19.” But this doesn’t have the far-reaching implications people think. The WHO now admits that it learned about the outbreak on December 31st when the Wuhan Municipal Health Commission posted a public statement about it on Weibo, after rumours that SARS had returned began to spread. Reuters even published a dispatch about the statement at the time, so it’s not surprising that people at the WHO noticed. The WHO’s Epidemic Intelligence from Open Sources also picked up a post on ProMED, which contained a translation of a news report published by SINA Finance, which had apparently obtained the December 30th warning notice issued to Wuhan hospitals. So, although the Chinese government didn’t notify the WHO about the outbreak, it was obviously not trying to keep it secret.

In fact, according to Hua Sheng, a Chinese economist who wrote a blog post defending Gao Fu, the Director of the Chinese CDC, Gao only learned about the outbreak on the evening of December 30th, because he saw the chatter that erupted on Chinese social media after Li Wenliang and Xie Linka told their friends about the test results they had seen. Gao then called the Wuhan CDC, which confirmed the story to him. Apparently, the local health authorities had not used the reporting system created following the SARS epidemic in 2003, even though the number of cases of pneumonia of unknown aetiology had already exceeded the threshold past which reporting becomes mandatory. That is why the national health authorities did not hear about the cluster until then. Gao immediately called the National Health Commission, which sent a team to Wuhan on December 31st to learn more.

It’s impossible to know for sure whether this story is true. The national health authorities might simply be trying to protect themselves from criticism by blaming the local health authorities. But it’s certainly plausible, because everybody seems to agree that no one was sent to Wuhan by the National Health Commission until December 31st. If it is true, it means that the national health authorities learned about the outbreak at the same time as the WHO, which would explain why they didn’t notify it beforehand. Had the Chinese national health authorities learned of the outbreak before the WHO, the Chinese government would surely have informed it—as it’s required to do by international law—as soon as the team sent to Wuhan by the National Health Commission had reported back, since the news was already everywhere in the media.

The destruction of samples

In addition to the test results from the two genomics companies already mentioned, Caixin reports that industry leader BGI received a sample on December 26th, 2019, and that by December 29th, it had sequenced the genome of a new coronavirus similar to SARS-CoV-1. It received a second and a third sample on December 29th and 30th, respectively, which upon analysis were also found to contain the new coronavirus. According to Caixin, on January 1st, 2020, BGI informed the Wuhan Municipal Health Commission and the Chinese CDC of this discovery. The same day, the genomics companies were instructed by Hubei’s health commission to discontinue testing immediately and destroy all their samples. On January 3rd, the National Health Commission issued a similar order, informing genomics companies that samples from patients with pneumonia in Wuhan should now be treated as highly pathogenic microorganisms and sent to authorised laboratories or destroyed. This story is now widely presented as evidence of a cover-up, including by US Secretary of State Mike Pompeo (who has also incorrectly claimed that China knew about human-to-human transmission but didn’t say anything “for a month”). But this is a misrepresentation—or, at least, a misunderstanding—of these developments.

It is alleged that the Chinese government ordered the destruction of these samples because it wanted to hide the existence of the virus. But this accusation simply doesn’t make any sense. The same day the National Health Commission ordered private companies to destroy the samples they had, the genome of SARS-CoV-2 was sequenced at the National Institute of Viral Disease Control and Prevention, which led to the announcement on January 9th, 2020, that a new coronavirus was responsible for the outbreak of pneumonia in Wuhan. In fact, it is likely that the National Health Commission took steps to take control on January 3rd, precisely because this was the date on which it independently verified that a new coronavirus closely related to SARS-CoV-1 had appeared in Wuhan. At this point, the destruction of samples held by private genomics companies that had already been analysed could not possibly have helped to hide the existence of the virus. It’s not as if the National Health Commission ordered those companies to wipe their hard drives and we know the data didn’t disappear since, as Caixin notes, the genomes in question ended up on GISAID, a public database.

A careful reading of the Caixin story yields a far more natural interpretation of events. According to Caixin, when the National Health Commission ordered private companies to destroy their samples, it invoked the Disease Prevention and Treatment Law. It’s hard to find a lot of information on this law. However, what I gather from the Caixin story—and from an explanation offered by the director of the Chinese CDC during a 2016 forum organised by National Science Review—is that once a pathogen has been classified in a particular way, only certain laboratories are allowed to analyse samples for safety reasons. This is exactly what a Chinese official said during a press briefing in May when he was asked about it. As the Wall Street Journal reported on May 16th, many other governments, including that of the United States, “have regulations that require labs with lower biosafety ratings to destroy or transfer samples of particularly dangerous pathogens.” Even if no existing law had mandated such a move, the decision made perfect prudential sense under the circumstances. At the time, the authorities still didn’t know anything about the virus except that it had probably caused pneumonia in several people and that it was closely related to SARS-CoV-1, a virus that killed approximately 10 percent of the people it infected in 2002–04. The last thing they needed was for another outbreak to start elsewhere because someone working for a private company had accidentally been infected. In fact, according to Caixin, Vision Medicals destroyed its samples without being prompted to do so by anyone as soon it sequenced the genome of the virus on December 27th, 2019 and realized it was very similar to SARS-CoV-1. Private genomics companies that perform diagnostic tests for hospitals are not equipped to deal with new and potentially highly dangerous viruses.

Suspicions of a cover-up were also provoked by what happened to the laboratory where researchers published the first genome of SARS-CoV-2. On January 3rd, the virus was isolated and sequenced at the National Institute of Viral Disease Control and Prevention. However, a notice later published on the Wuhan Institute of Virology’s website announced that Shi Zhengli’s team had already managed to sequence the full genome the day before. According to a state media interview, another team at the Chinese Academy of Medical Sciences also sequenced the virus on January 5th.

However, as Caixin revealed in February, in addition to the samples sent to private genomic companies in December, another sample from a patient at Wuhan Central Hospital had been sent to a team led by Zhang Yong-Zhen, a virologist at the Chinese CDC who also works at Fudan University in Shanghai, where the virus was also sequenced on January 5th. Zhang uploaded the genome to GenBank, a public database managed by the National Centre for Biotechnology Information in the United States, where apparently it just sat under review for a while. The Chinese health authorities had still not published the genome of the virus after they announced its discovery on January 9th, so on January 11th, Zhang posted it on, a forum where virologists discuss recent work in their field. According to the Associated Press, which claimed to have talked to three people familiar with the matter, this move angered Chinese CDC officials. The next day, Zhang’s laboratory was ordered to close by the Chinese health authorities, who have so far refused to explain this decision.

If the closure of Zhang’s laboratory is evidence of a conspiracy or cover-up, it’s not at all clear what purpose it was supposed to serve. The Chinese health authorities had already revealed the existence of the virus, so they were obviously not going to be able to keep the sequence to themselves forever. And, by now, everyone knew that a new coronavirus related to SARS-CoV-1 was responsible for the outbreak of pneumonia in Wuhan. It looks like researchers at the Chinese CDC simply wanted to be the first to publish this data so they could take all the credit. According to Li Yize, a virologist working on coronaviruses at the University of Pennsylvania who was consulted by the Associated Press, this is probably the reason for their irritation. The Associated Press also talked to six people familiar with the system, who explained that the Chinese CDC “has long promoted staff based on how many papers they can publish in prestigious journals, making scientists reluctant to share data.”

I’m certainly not about to defend the Chinese CDC’s conduct here—the WHO and other countries needed the genome to develop tests for the virus in the event that it spread outside China (which in fact had already happened), but I don’t see in what sense this can be called a “cover-up.” It’s just the kind of petty competition that is unfortunately very common in science. By publishing the genome without informing the Chinese health authorities, Zhang deprived researchers at the Chinese CDC of the advantage they had over other scientists who didn’t have the data. It also forced the other three labs that had sequenced the virus to rush and publish their sequences, which they all did on January 12th. According to the Associated Press, however, they only did so after obtaining approval from the National Health Commission. The Chinese health authorities probably closed Zhang’s lab to punish him for not going through them before publishing the genome. This was doubtless intended to send a message to other researchers and to ensure that they would respect the chain of command before releasing any information on the virus. This kind of over-reaction and punishment by example is unfortunately how the bureaucracy in an authoritarian country keeps people in line, but it doesn’t show the Chinese authorities were engaged in a cover-up.

Decontamination of the seafood market

Something similar can be said about the decision by the local authorities to close Huanan Seafood Market and disinfect it on December 31st. This was previously believed to have happened on January 1st, but according to a very detailed account published by the Wall Street Journal in May, professional disinfection crews started spraying the market the day before. This too raised suspicions that the Chinese authorities were trying to destroy evidence, but a far more plausible explanation is that they panicked in an attempt to prevent further infections. At the time, everyone, including the “whistleblowers,” thought that the market was the source of the infection, so this is exactly the kind of response that might be expected from people who had just realised that a lethal virus was spreading there. And, in fact, although the authorities decontaminated the market almost immediately, some samples were nonetheless collected.

However, the Chinese health authorities have provided almost no details about these samples or the results of the tests they performed, even though the market was closed more than six months ago. At the end of January, state media reported that SARS-CoV-2 had been detected in 33 out of 585 environmental samples collected at the market, 31 of which were taken from the area in which stalls selling wildlife were concentrated. On February 9th, five genetic sequences found in environmental samples collected at the market were uploaded on GISAID (with accession IDs EPI_ISL_408511 to EPI_ISL_408515), three of which are partial. The Chinese health authorities refused to answer questions about this until the end of May.

No sequences found in the samples collected from animals were ever uploaded and it wasn’t until May 25th that the director the Chinese CDC announced that no virus had been detected in any of the samples taken from animals in the market. According to the Wall Street Journal, Chinese officials had already confirmed that no animal there had tested positive on January 31st during a meeting of the World Organisation for Animal Health. However, according to Ian Lipkin, a virologist at Columbia University who visited Wuhan at the end of January and spoke to the Wall Street Journal in May, the Chinese health authorities were not able to determine which animals they came from. Of course, that’s assuming the traces of the virus found in environmental samples collected at the market came from animals and not from humans, which is not obvious. If none of the samples collected from animals at the market tested positive, it’s weird that Chinese officials waited so long to confirm this finding and refused to answer questions about it for months.

Based on the investigation published by the Wall Street Journal, my impression is that in general the collection of samples at the market was rushed and poorly conducted. Indeed, it seems that samples were collected in a hurry, as disinfection crews were spraying disinfectant in the market and perhaps even after that. (According to the information on GISAID for the sequences uploaded on February 9th, the environmental samples were collected on January 1st, after the decontamination had already begun, although I wouldn’t put too much stock in that since I’m not sure how carefully researchers fill out that information.) It’s very difficult to figure out what happened, because Chinese officials have given almost no details and different researchers have heard different things. Nevertheless, I suspect that, upon realising that none of the samples collected from animals was positive, the Chinese health authorities would have liked to obtain more to double-check that no animals were infected. But by then it was too late because the market had already been decontaminated and the animals destroyed. Back in February, Caixin had already published a story, in which Lipkin was also quoted, that suggested the market had been decontaminated before enough samples could be collected.

This might explain why Chinese officials have been reluctant to share details about the samples collected in Huanan Seafood Market—they screwed up and didn’t want to admit it. However, it is also possible that, back in February, when state propaganda started peddling the absurd theory that SARS-CoV-2 may not have originated in China, Chinese officials didn’t want to talk about the origins of the pandemic in Wuhan. In any event, the Chinese government had nothing to gain by decontaminating the market before enough samples could be collected. More samples from Huanan Seafood Market would either have supported the hypothesis that SARS-CoV-2 originated there or shown that, as now seems more likely, that it came from somewhere else. Either way, I don’t see what it would have changed for the Chinese government. The decision to decontaminate the market right away was almost certainly just a combination of incompetence on the part of the local health authorities and growing fears of a public health disaster, which is exactly how such a blunder would have been reported and understood had it happened in a Western country.

Red tape and incompetence

To the extent that Chinese officials mishandled this crisis at the outset, their missteps are better explained by administrative red tape and bureaucratic incompetence than a conspiracy to hide the discovery of SARS-CoV-2. Those who claim the Chinese government knew exactly what was going on and tried to cover it up seem to assume that officials knew then what we know now about the virus. But everything indicates that even the local health authorities didn’t realise there was an outbreak of viral pneumonia in Wuhan, let alone that it had been caused by a new virus, until sometime between December 28th and December 30th. At least one bureaucrat working for the Wuhan Municipal Health Commission probably heard that Vision Medicals had found a new coronavirus in a sample collected from a patient with pneumonia at Wuhan Central Hospital on December 27th. But that doesn’t mean they immediately understood the significance of that discovery. Of course, now that we know what happened next, it seems obvious that it should have alarmed them, but at the time it was not obvious. According to Caixin, even the technicians at BGI didn’t realise the implications when they first sequenced the SARS-CoV-2 genome. As one of their employees remarked, they routinely see a large number of viruses, including new viruses, as part of their work. So when they discovered a new coronavirus in the sample from Wuhan, they “did not know whether it was ‘good’ or ‘bad.’”

Admittedly, BGI’s employees probably didn’t know that several people had already been infected by this virus in Wuhan and were suffering from pneumonia. But it’s not obvious that anyone notified of Vision Medicals’ findings at the Wuhan Municipal Health Commission would have known that either. By the time BGI and the Beijing-based company had sequenced the virus and returned the results (a few days after Vision Medicals called Zhao Su), the local health authorities had realized there was a cluster of pneumonia cases in Wuhan, which is precisely when they started taking steps to deal with the problem and to initiate the process that eventually led to the identification of SARS-CoV-2 at the National Institute of Viral Disease Control and Prevention. They should certainly have investigated this sooner and looked into it as soon as Zhao Su heard from Vision Medicals, but this is just ordinary bureaucratic incompetence, not conclusive evidence of a cover-up.

The truth is that, all things considered, and despite a few mistakes at the end of December, the identification of SARS-CoV-2 as the cause of the outbreak was remarkably fast. It could probably have been identified even faster had the cluster of pneumonia been noticed sooner. According to the New York Times, which relied on Chinese media reports and interviews with former officials, the system created after the SARS epidemic in 2002–04 to detect outbreaks of infectious diseases didn’t work properly. Every suspicious case was supposed to be immediately reported to the national health authorities in Beijing, who employ people trained to detect contagious outbreaks and take steps to suppress them before they spread. This system was created to prevent precisely the kind of political interference that had kept Beijing in the dark and delayed the response at the beginning of the first SARS outbreak in 2002. According to the Times, it didn’t work because the local health authorities insisted on controlling what was reported to Beijing instead of allowing doctors to report the information, as intended. That is why the national health authorities only realized there was a cluster of unusual pneumonia in Wuhan on December 30th, when rumours of SARS began to appear on social media.

It is also possible that the national health authorities received at least some of the information before December 30th, but didn’t act on it and are now trying to shift the blame onto local health officials. Bureaucratic inertia and incompetence are plentiful in China, and not just among local officials, even though apparatchiks in Beijing frequently use them as scapegoats for their own corruption. I suspect that some Wuhan doctors may also have tried to pass the blame for their mistakes to local health officials, because they should have reported some of their cases earlier but didn’t follow protocol. The New York Times suggests they didn’t report the pneumonia cases in the system because they didn’t know how to classify them, but as the article also notes “pneumonia of unknown aetiology” would have sufficed. Just as there is no reason to assume that only the local health authorities can be incompetent and not the national health authorities, there is also no reason that doctors in Wuhan are infallible. That’s not true of doctors anywhere else, so I don’t see why it would be true of doctors in Wuhan.

Needless to say, bureaucratic ineptitude is hardly unique to authoritarian countries in general, or to China in particular. It is a consequence of human frailty, and the conduct of many countries during this pandemic—including, and perhaps especially, some of the West’s democracies—offers countless examples of bureaucratic incompetence. We’ll probably never know exactly what went wrong in those very early days of the pandemic and who bears personal responsibility for China’s mistakes, because police states do not conduct public inquiries that risk undermining their own legitimacy and authority. We can speculate that, had everything worked exactly as it was supposed to, SARS-CoV-2 might have been identified as the cause of the pneumonia outbreak a few days, or perhaps a week, sooner. But we don’t live in a world without human error, we live in this one.

Part Two of this series can be read here.

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Philippe Lemoine

Philippe Lemoine is a PhD candidate in philosophy at Cornell University. He maintains a blog where he writes about politics, philosophy, and social science.