Preliminary analysis of 11 Novel Coronavirus genomes from the Wuhan outbreak
virological.org
virological.org
"That means that the outbreak was detected almost immediately after the first case, which - given that this is flu season in China - is just amazing. Detecting an outbreak of pneumonia (similar to flu) of a novel coronavirus that fast is truly impressive."
I'm not sure I really want to wear this tin-foil hat, but it would certainly be easier to identify a novel coronavirus if it came directly from your own BSL-4 lab in Wuhan https://www.nature.com/news/inside-the-chinese-lab-poised-to...
It's a little like being astonished that a microbe could be identified so quickly in Boston or Atlanta.
Accidental releases almost always involve people with direct links to the lab in question first. That's a really obvious epidemiological link.
"A coronavirus emerged in China and got detected quickly because of solid medical infrastructure" is a way more parsimonious explanation than "Accidental release from a BSL-4 lab."
From what I've read, "solid medical infrastructure" doesn't exist in Wuhan.
For emerging infectious diseases, Wuhan is perfectly functional, and the Chinese have the necessary resources. Motorbikes with samples aren't getting stuck as roads turn into mud during the rainy season.
I'm currently an Assistant Professor of Computational Epidemiology, and my research is on healthcare-associated infections and emerging pathogens.
I dunno what are the odds, but do you know what are the odds? If you don't, then you have no base for suspicious.
Doesn't every major city the world have some lab testing some kind of virus nearby?
So which side of the argument should provide evidence? Why is the parents suspicion any less valid than your lack of suspicion? These kind of questions are particularly difficult when secretive government institutions are involved.
Both Atlanta and Boston have BSL-4 labs.
As Kristian Andersen notes, the background noise of flu season would surely drown out the weak signal of an unknown novel virus. Then to not only notice the weak signal but act on it so quickly to do primary research and characterise it as a novel virus within such a short timeframe?
Seems far less likely than simply the effect of poor operational standards.
They aren't doing infectious disease research and they definitely aren't checking for anything exotic.
Although the exact reason is unknown, it is already known that the Wuhan government has successfully implemented the maximum level of incompetence during its early response. There is no much reporting in English yet, but a now-deleted government report in Chinese [1] said the first victims of the viral infection were already been hospitalized on as early as December 8th, 2019. In other words, they were given a time of three weeks to get useful things done. Yet, the Wuhan government took no actions whatsoever other than covering up the outbreak.
It had been going on like that, until the last week in December, when the news about a new type of unknown pneumonia started to leak out. At this time, someone at a higher position probably realized a serious investigation was warranted. On December 26th, researchers from Shanghai arrived, collected samples, and brought the samples to Shanghai for analysis [4].
Meanwhile, on December 30th, the case was escalated and put under increased supervision of the national government. And On December 31th, a Wuhan government official was interviewed [2]. He was asked for whether a laboratory analysis will be started, and the reply was,
> With regarding to the pathogen determination of the unknown pneumonia, currently, the BSL-4 Lab was not activated, we are still following conventional procedures to verify the cases of infection. We are always prepared to active the Lab accordingly when it is necessary.
> So far, it is not in our considerations.
So Wuhan, still, wasn't doing any analysis at this point. Well, they have other things to do. On January 1st, Wuhan police arrested 8 citizens for spreading the "false rumor" of outbreak of a mysterious pneumonia in Wuhan to the social media online.
Later on January 7th, 2020, the first laboratory observation [3] of the virus sample under the electron microscope came out from Shanghai. And the gene sequencing was only completed in the second week of the month. [0] I guess the Shanghai labs were probably working on a 24x7 basis.
Meanwhile, Wuhan ordered a partial travel ban, only at this point - without any preparation work, Wuhan suddenly suspended the public transport for everyone, including medical workers, creating a massive chaos.
The popular belief is: The fact the analysis was performed in Shanghai is another indicator of the Beijing government's effort to bypass the provincial government to obtain real information. According to what Wuhan has done, it's possible that the Wuhan government was intentionally withholding medical samples and hampering the BSL-4 lab to do any useful work, and that Beijing didn't even receive prompt information until the last moment.
What is the lesson to learn as a citizen? Never overestimate the effectiveness of an authoritarian government, and never underestimate its incompetence. In an authoritarian government, the best interests of the ruler at a higher level is not always served by the ruler at the lower level. Sometimes, it's Nineteen Eighty-Four, other times, it's Brazil.
[0] http://engine.scichina.com/publisher/scp/journal/SCLS/doi/10...
[1] https://webcache.googleusercontent.com/search?q=cache:Cq9-K5...
[2] https://m.yicai.com/news/100452355.html
[3] https://news.sina.cn/gn/2020-01-09/detail-iihnzhha1262297.d....
[4] https://cfcnews.com/277356/%E8%AF%95%E5%89%82%E7%9B%92%E4%BE...
If you take a swab of someone and it comes back as a virus that causes the common cold what response do you expect?
A person gets a cold virus ... what should happen next?
It wasn't until it was sequenced that they found it was a new variant.
Someone else wants to check it (basically luck or maybe policy since SARs) and when they do they notice it is different - 7th of January then by the 14th, they have it sampled and they have detection kits.
Because of SARs Wuhan takes a few days to figure out what to do and then decide to quarantine the entire city. It is a rush job but they don't exactly have a lot of time.
From the real discovery (7th) to massive response time is 2 weeks. In the past it has often been over a month before anything effective is done. What would you do differently?
And yes... rather worrying...
The fact that you have a state-of-the-art lab that is supposed to be the first-line of Research and Development of the most dangerous virus. And that the lab wasn't even working on it due to government mismanagement, is disturbing.
I don't think we should be concerned about the Chinese government taking this seriously. It is clearly a very serious situation, the fatality rate is lower than SARS but not hugely. It would be more concerning if they weren't taking it seriously.
Or maybe the national government is trying to find a scapegoat to blame, and the provincial government is a good target? They can massage all of this very well, because they also control the news in China.
It's definitely a possibility that cannot be ruled out.
> they also control the news in China.
Now, this point-of-view is too simplistic, First, it's certainly the truth that every single news outlet is ultimately owned and controlled by the national government, but sometimes, this model is insufficient to describe many observed complex behaviors in national politics - saying that they are all a monolithic institution is somewhat misleading. Why? Because the very same reason I stated previously,
> In an authoritarian government, the best interests of the ruler at a higher level is not always served by the ruler at the lower level.
It's usually difficult to see it in political operations, since the national politics is not transparent. On the other hand, it's relatively easy to identify this phenomenon in the media, you may even see it in a propaganda campaign with direct support from Beijing.
Before I try to explain anything, it must be understood that, in all forms of governments (perhaps with the exception of the most totalitarian governments), different interest groups or political fractions always exist. In a liberal government, the struggle over political powers, the debate on different policies, etc., are often carried out in public, via means defined by the Constitution, and governed by civil institutions - federal power vs state power, a new election, a judicial review, an impeachment, the existence of multiple political parties, or the existence of different media outlets, are all examples.
In an authoritarian government, the situation is actually not too different, except that the power struggle is not carried out by defined means in the Constitution or governed by civil institutions, instead, they are governed entirely by informal interest groups, political conspiracies and sometimes "gangs" behind the scene. Superficially, it may appear that everyone works for the government is loyal to the government, but at a closer look, it isn't the case at all. Power in a authoritarian government can be, de facto, separated, in a chaotic and pathological way.
If one studies the media outlets in China, a lot of anomalies can be identified.
1. It's different for Beijing to micro-manage every single media outlet. Some media outlets are more independent than others.
2. The national politics is too opaque, sometimes even the state media outlets have difficulties understanding the national government's real motivation, not even mention media outlets at second-tier and lower levels. As a result, everyone is forced to play an educated guess on Beijing's intention and act accordingly. Observable, sometimes significant, inconsistencies exist in the news coverage of the same topic by different media outlets.
3. Since the political system is authoritarian, even a powerful state media outlet can operate under the fear of being punished if it's not what Beijing wants, in this case, many media outlets will choose a conservative style of reporting - repeat thoughtless propaganda, withholding information, etc., ironically, sometimes it can backfire and effectively work against the interests of Beijing.
4. Media outlets are biased in their own ways. Although every media outlet is state media outlet, but they can serve the special interests of different people in power. The people who are operating these media outlets can influence the style of reporting as well, it's easy to recognize "liberal" media outlets and "nationalistic" media outlets.
5. Although state-owned, some media outlets are commercial and operate for profit. Sensationalized news is launched in exchange of more views and ads revenues. State media outlets are not immune from the impact either, bad articles can be published even at the expense of the media's reputation.
6. People themselves who are working in the media outlets, can become dissatisfied regarding to the actions of the government and secretly sabotage the propaganda in subtle ways. One example is, when the Xinhua News Agency, the mouthpiece directly represents the national government, miswrote "Obama" as "Omaba", the mistake in the original article was left unchanged and forwarded by a huge number of local media outlets. One hypothesis was that some people in media outlet identified the mistake, but left it uncorrected intentionally to ridicule the government power over media outlets.
All of these above occur from time to time, and remember, they are only a few selected examples of anomalies on the management and reporting of the media. Now imagine the situation of national politics in China behind the scene, or the internal politics within the CPC. Often, it's not something that the Western press like the New York Times is willing to report - not all journalists are familiar with the situation, and the internal politics inside the authoritarian government of China is simply too complex to even make sense of.
What is the moral of this story? Remember, nobody knows anything about China, including the Chinese government.
* https://foreignpolicy.com/2018/03/21/nobody-knows-anything-a...
Zhou, et al., "Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin."
https://www.biorxiv.org/content/10.1101/2020.01.22.914952v2....
This[1] is what I'd expect a bioweapon accident to look like or maybe a multiply drug resistant outbreak of plague.
And then China worrying about their international reputation attributing it to a seafood market.
The reemergence of H1N1 in 1977 is believed to have been the result of a lab accident or vaccine trial gone awry, for example: http://www.virology.ws/2009/03/02/origin-of-current-influenz...
You are totally right about how insane it would be to use a coronavirus as a bioweapon
Well, guess what -- SARS is also a type of corona virus, and perhaps the hospitals in China had ready corona virus tests and used them on everybody that came in with pneumonia symptoms. So perhaps they were just doing their jobs?
There is another option though, which has nearly been proven by people that have talked to physicians in Wuhan. That is the theory that this virus has been around much longer than initially reported by China. I find this a bit more likely given China's history of censoring things like this.
Now, I don't think it would have been a weapon. China isn't so stupid as to try to weaponize a coronavirus. However, it does make sense that this might be a leak from studying it. The genetic study really only shows when the population was one, not where it came from.
[1] https://www.ncbi.nlm.nih.gov/protein/AVP78033.1 (Click "Identical Proteins")
The models to which they were replying put the date range of the most common recent ancestor potentially as far back as October.
Please don’t compound the error bars.
https://jvi.asm.org/content/jvi/90/6/3253.full.pdf
"Isolation and Characterization of a Novel Bat Coronavirus Closely Related to the Direct Progenitor of Severe Acute Respiratory Syndrome Coronavirus"
an excerpt:
"In conclusion, we isolated and characterized a novel bat SLCoV isolate, WIV16, which is the closest ancestor to date of the SARS-CoV. Our results provide further evidence that Chinese horseshoe bats are natural reservoirs of SARS-CoVs. It should be noted that WIV16 is not the closest strain to the human SARSCoVs with regard to ORF8. Full-length ORF8 is present in several SARS-CoV genomes of early-phase patients, all civet SARS-CoVs, and bat SL-CoVs. It is split into two ORFs (ORF8a and -b) in most human SARS-CoVs from late-phase patients due to a deletion event in this part of the genome (3). Recently, two papers reported that they found a full-length ORF8 which has higher similarities to SARS-CoV GZ02 and civet SARS-CoV SZ3, suggesting that SASCoV derived from a complicated recombination and genetic evolution among different bat SL-CoVs"
Reading the paper, its clear that the Wuhan lab was studying viruses almost identical to the one that emerged in Wuhan. This would make sense, as this is what they are trying to prevent. But it also raises concerns about whether the epidemic in Wuhan originated from this lab.
Further evidence would be the fact that a member from the lab is reported to have contracted coranavirus.
They report isolating a novel coronavirus from the bat population in that province in China. It’s not clear to me that this is the same virus. In this context it seems that it just points out that the bat reservoir does have coronaviruses. Since it’s known that there was a recent animal to human crossover, which requires a bat reservoir and likely an intermediate animal reservoir, I don’t really see that this implies the virus “escaped” from the laboratory or anything.
A scientific result like this was promised to us as a someday-goal of early sequencing technologies when I was a child.
A lot of people have worked really hard to make this happen, and it is a human triumph, even if there is more to do.
> but there is insufficient epidemiological information for it to be useful here
By "insufficient epidemiological information", they mean that the genome cannot, itself, be used to assemble a transmission tree, which is sort of the brass ring of sequence data.
That is not to say that the genome data isn't useful for epidemiology.
>We estimate that only 5.1% (95%CI, 4.8-5.5) of infections in Wuhan are identified, and by 21 January a total of 11,341 people (prediction interval, 9,217-14,245) had been infected in Wuhan since the start of the year. Should the epidemic continue unabated in Wuhan, we predict the epidemic in Wuhan will be substantially larger by 4 February (191,529 infections; prediction interval, 132,751-273,649)
>Our model suggests that travel restrictions from and to Wuhan city are unlikely to be effective in halting transmission across China; with a 99% effective reduction in travel, the size of the epidemic outside of Wuhan may only be reduced by 24.9% on 4 February.
Edit: Nevermind, figured it out.
I'd avoid that subreddit