
Preliminary analysis of 11 Novel Coronavirus genomes from the Wuhan outbreak - partingshots
http://virological.org/t/preliminary-phylogenetic-analysis-of-11-ncov2019-genomes-2020-01-19/329
======
wschfdkbrmcdf
That comment on that page from Kristian G. Andersen is mildly disturbing
([http://archive.is/O1vhN](http://archive.is/O1vhN))... As Associate
Professor, Scripps Research, Director of Infectious Disease Genomics, SRTI etc
etc I assume he knows what he's talking about when he states:

"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...](https://www.nature.com/news/inside-the-chinese-lab-poised-to-study-
world-s-most-dangerous-pathogens-1.21487)

~~~
giarc
It could be the result of having the lab in the same city that they could
detect it so quickly. Not because the original sample (or any samples) would
be tested in the BSL4, but simply because having that lab would attract
talent, funding and equipment to reference labs in the same city. The index
patient would likely have had a nasopharyngeal swab taken and run against the
regular panel of respiratory viruses (influenza, parainfluenza, enterovirus,
rhinovirus, metapneumovirus, and coronaviruses). I suspect there would have
been a light signal on the coronavirus (perhaps some cross reactivity) and
they would have done more investigation to determine what is was.

~~~
segfaultbuserr
No, the BSL-4 lab in Wuhan contributed _absolutely nothing_ to help during the
outbreak of the disease. The analysis on the samples and the gene sequencing
were all performed in Shanghai, by various institutions such as _Institut
Pasteur of Shanghai_ , or the _Chinese Academy of Science_ (e.g. see the list
of authors in paper [0]), not in Wuhan at all - Which was an already huge
surprise to everyone following the news in China, considering the fact that it
has one of the best labs.

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...](http://engine.scichina.com/publisher/scp/journal/SCLS/doi/10.1007/s11427-020-1637-5?slug=abstract)

[1]
[https://webcache.googleusercontent.com/search?q=cache:Cq9-K5...](https://webcache.googleusercontent.com/search?q=cache:Cq9-K5kC8GMJ:wjw.hubei.gov.cn/fbjd/dtyw/202001/t20200113_1911033.shtml)

[2]
[https://m.yicai.com/news/100452355.html](https://m.yicai.com/news/100452355.html)

[3] [https://news.sina.cn/gn/2020-01-09/detail-
iihnzhha1262297.d....](https://news.sina.cn/gn/2020-01-09/detail-
iihnzhha1262297.d.html)

[4]
[https://cfcnews.com/277356/%E8%AF%95%E5%89%82%E7%9B%92%E4%BE...](https://cfcnews.com/277356/%E8%AF%95%E5%89%82%E7%9B%92%E4%BE%9B%E4%B8%8D%E5%BA%94%E6%B1%82%EF%BC%8C%E6%AD%A6%E6%B1%89%E6%96%B0%E5%9E%8B%E5%86%A0%E7%8A%B6%E7%97%85%E6%AF%92%E8%82%BA%E7%82%8E%E7%A1%AE%E8%AF%8A%E4%B9%8B%E9%9A%BE/)

~~~
adinobro
Are you aware that the Coronavirus is also known as "The Common Cold" and is
actually fairly common?

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.

~~~
segfaultbuserr
It can explain Wuhan's early ignorance, but it cannot explain the incompetence
of the government after the case has been escalated since the end of December.

~~~
adinobro
So, you do a lab test and it comes back Coronavirus which is expected. They do
nothing (its the "cold").

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?

------
codingslave
Here is a patent from the lab in Wuhan:

[https://jvi.asm.org/content/jvi/90/6/3253.full.pdf](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.

~~~
ghostpepper
Can you link to a source for a staff member from the BSL4 lab being infected?

~~~
1_over_n
+1 if you can find this ?

------
ISL
Every now and again, there is a strong reminder that we're living in the
future. This is one of them.

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.

~~~
october_sky
Yes, it's completely and exceptionally awesome that we can just sign on the
Internet and gain this genome sequence. But it's also important to weigh the
value. As the article states:

> but there is insufficient epidemiological information for it to be useful
> here

~~~
mjw1007
It looks to me like that quote is talking about one particular sequence that
they've left out of their list (it's explaining why they did that), not about
the 13 sequences that they have listed.

~~~
october_sky
Ah, ok. Thank you for pointing that out

------
nabla9
Novel coronavirus 2019-nCoV: early estimation of epidemiological parameters
and epidemic predictions
[https://www.medrxiv.org/content/10.1101/2020.01.23.20018549v...](https://www.medrxiv.org/content/10.1101/2020.01.23.20018549v1)

>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.

~~~
greenonions
Source: "Caution: Preprints are preliminary reports of work that have not been
peer-reviewed. They should not be relied on to guide clinical practice or
health-related behavior and should not be reported in news media as
established information."

------
christkv
I will be very interested what the guys at This week in virology say about the
outbreak. They briefly talked about it on the 12th of January and it will
probably be what they talk about this week with all the new developments.
[http://www.microbe.tv/twiv/](http://www.microbe.tv/twiv/)

~~~
stefanu
They have a recent blog post “A lesson from SARS-CoV for 2019-nCoV”:
[http://www.virology.ws/2020/01/23/a-lesson-from-sars-cov-
for...](http://www.virology.ws/2020/01/23/a-lesson-from-sars-cov-
for-2019-ncov/)

------
contingencies
Today hacked together some scraped data with basic visualization at
[https://github.com/globalcitizen/2019-wuhan-coronavirus-
data...](https://github.com/globalcitizen/2019-wuhan-coronavirus-data/) ...
contributions welcome I'm about off to bed.

~~~
juiyout
Please don't include Taiwan as part of China.

------
egorfine
I see they have published virus code. Is there build instructions? Asking for
a friend

~~~
0x8BADF00D
Build servers are down, and you can’t build it locally.

~~~
LorenPechtel
As a test a local build of a harmless virus has been done, it worked. You
still need to be skilled, though, no terrorist is downloading the smallpox
genome and cranking out a lethal agent.

------
emmelaich
If you want to follow along,
[https://www.reddit.com/r/China_Flu/](https://www.reddit.com/r/China_Flu/) is
a good resource.

~~~
natalyarostova
It's a good resource for hysteria.

~~~
Zenst
Indeed - I give it a week until some real time tracking map sourced from
reddit or other like source makes the front page.

~~~
exikyut
I personally generally consider the reddit platform incompetent for surfacing
that wheat by default, and incidentally view the site as a whole somewhat
dimly as a result. I want to enjoy the internet and/or get at info I might
need. Some seem to enjoy being a pawn in what amounts to a poorly-thought-
through "crowdsourced wheat-surfacing" architecture; I find it draining.

