
Decoding evolution and transmissions of novel pneumonia coronavirus - 1_over_n
https://www.researchgate.net/publication/339351990_Decoding_evolution_and_transmissions_of_novel_pneumonia_coronavirus_SARS-CoV-2_using_the_whole_genomic_data
======
daemonk
Interesting paper. I haven't dug into the methods/data in depth. But the gist
of their interpretation is:

\- Out of the initial 41 cases, 27 were linked to the seafood market. The
first identified cases + 12 others had no link to the market.

\- Phylogenetic analysis suggests two potential ancestral haplotypes. None of
the seafood market haplotypes were the two potential ancestral.

\- The very first initial cases (family from Shenzhen) was one of the two
potential ancestral haplotype.

I am a bioinformatics phd and know enough about phylogenetic analysis to say
that it can sometimes be ambiguous and have some elements of subjectivity,
especially with low sample sizes. So I wouldn't be too fast to jump on these
results. However, I haven't gone through the data in detail to really give a
good opinion.

~~~
wpasc
Thanks for your insight! If not from the seafood market, is it possible to
speculate (in an informed way) of what the source may have been? When novel
viruses break into human populations, is some form of animal contact generally
the culprit? Is something like a bat sneezing near you (I have no idea if bats
sneeze) with an airborne virus sufficient to transfer to a human?

~~~
chrisco255
There's a level 4 virology research center in Wuhan, which means it studies
the most dangerous pathogens in the world. This facility has been collecting
SARS-like virus samples from bat populations and other animal populations for
years. Some are speculating that it may have escaped the lab.

~~~
sohkamyung
That is very speculative and currently not accepted. See this HN discussion
and the paper [1]

[1]
[https://news.ycombinator.com/item?id=22352908](https://news.ycombinator.com/item?id=22352908)

~~~
chrisco255
Not accepted by who? It is speculative, but seeing as we don't have hard
evidence of the source, it remains a very valid theory.

~~~
sohkamyung
Here's a quote from this article [1]:

> A group of 27 prominent public health scientists from outside China is
> pushing back against a steady stream of stories and even a scientific paper
> suggesting a laboratory in Wuhan, China, may be the origin of the outbreak
> of COVID-19. “The rapid, open, and transparent sharing of data on this
> outbreak is now being threatened by rumours and misinformation around its
> origins,” the scientists, from nine countries, write in a statement
> published online by The Lancet yesterday.

[1] [https://www.sciencemag.org/news/2020/02/scientists-
strongly-...](https://www.sciencemag.org/news/2020/02/scientists-strongly-
condemn-rumors-and-conspiracy-theories-about-origin-coronavirus)

~~~
chrisco255
Keyphrase: Health scientists OUTSIDE of China. They're not in China. They
don't have the independence to investigate. They have no way to say one way or
another. There has not been an independent, forensic investigation into the
origins because the CCP controls everything in China.

~~~
sohkamyung
A WHO team is just back from China and their assessment is that the outbreak
is currently declining there and the numbers provided by China are reasonably
accurate. Following are comments by WHO epidemiologist Bruce Aylward in the
following articles:

> He [Aylward] pointed to humped graphs of cases over time—they are the shape
> of an epidemic that has been hobbled, he said. Disease spread has been in
> decline since the beginning of the month, and doctors in China are honing
> their ability to treat patients. “If I had COVID-19, I’d want to be treated
> in China,” he said candidly. [1]

> There’s plenty of reason to doubt the official numbers—Chinese officials
> initially covered up the virus and arrested whistle-blowers who tried to
> expose the outbreak. Aylward acknowledged these concerns on Monday, but
> added: “The decline that we see is real.” [2]

[1] [https://arstechnica.com/science/2020/02/coronavirus-
spread-i...](https://arstechnica.com/science/2020/02/coronavirus-spread-in-us-
not-if-but-when-and-how-severe-cdc-says/)

[2] [https://www.wired.com/story/could-the-us-contain-a-
coronavir...](https://www.wired.com/story/could-the-us-contain-a-coronavirus-
outbreak/)

------
Reelin
ResearchGate wasn't linking me back to the original point of publication, and
the DOI doesn't seem to be valid (yet?). It turns out this was uploaded to the
Chinese arXiv equivalent on the 19th.

[http://www.chinaxiv.org/abs/202002.00033](http://www.chinaxiv.org/abs/202002.00033)

~~~
stallmanite
How have I never heard of chinaxiv? Thanks for bringing this to my attention.

------
MilnerRoute
I worry that we may be spreading misinformation.

[https://science.slashdot.org/story/20/02/21/2257228/scientis...](https://science.slashdot.org/story/20/02/21/2257228/scientists-
condemn-conspiracy-theories-about-origin-of-coronavirus-outbreak)

~~~
T-A
Your link is about "Conspiracy Theories About Origin of Coronavirus Outbreak"
on social media which may cause "real consequences, including threats of
violence that have occurred to our colleagues in China".

Parent's link is to a genomic analysis of COVID-19 trying to reconstruct its
evolution, authored by researchers all working in China.

Unless you think that no attempt should be made to determine the origins of
the virus because of what trolls might make of it, I don't see the problem. If
you do think that trolls should have that power, it's pretty late to worry
about it: the official narrative about it all having started in Wuhan's
seafood market has been known to be incomplete at best for a while now:

[https://www.sciencemag.org/news/2020/01/wuhan-seafood-
market...](https://www.sciencemag.org/news/2020/01/wuhan-seafood-market-may-
not-be-source-novel-virus-spreading-globally)

~~~
MilnerRoute
"Known to be"?

I really take issue with that phrase.

As maddening as it may be, we DO NOT KNOW the origins of the virus. And after
reading a new paper -- we still do not know. We have to stop acting like we
do.

~~~
T-A
> "Known to be"? > I really take issue with that phrase.

That's your phrase, not mine.

What I wrote is "the official narrative about it all having started in Wuhan's
seafood market has been known to be incomplete at best for a while now".

> As maddening as it may be, we DO NOT KNOW the origins of the virus

Yes. That's what I said.

You are arguing against your own position, not mine.

------
anonsivalley652
It came across to me as stereotyping to just assume certain people engaged in
something very specific without any evidence in order to look down on them.

Furthermore, it's also impossible to prove where it didn't come, also without
evidence, because you can't prove a negative.

~~~
jacquesm
That may be so, but bush meat has been positively identified as the source of
quite a few outbreaks.

~~~
dTal
As an aside, I always found it strange that eating wild land animals is looked
down upon as "bushmeat" and unsustainable and unhygienic, while eating wild
sea creatures is just "seafood" (with farmed aquafauna looked down upon as the
inferior product).

~~~
jacquesm
That's a good point. There is plenty of seafood that when not dealt with
properly will happily kill you or make you at a minimum severely ill. Mussels,
shellfish, oysters are best avoided unless you are very sure about where they
came from and how they were prepared.

Besides that, due to the liquid environment anything in the sea that is
poisonous is usually so in a very potent fashion. Species jumping viruses are
rare when it comes to regular fish but marine mammals are a risk.

------
brianberns
I’m confused. SARS and COVID-19 (the current coronavirus outbreak) aren’t the
same, right? Which one are we talking about here?

~~~
sschueller
"On February 11, 2020, the International Committee on Taxonomy of Viruses,
charged with naming new viruses, named the novel coronavirus, first identified
in Wuhan, China, severe acute respiratory syndrome coronavirus 2, shortened to
SARS-CoV-2.

As the name indicates, the virus is related to the SARS-associated coronavirus
(SARS-CoV) that caused an outbreak of severe acute respiratory syndrome (SARS)
in 2002-2003, however it is not the same virus." [1]

[1]
[https://www.cdc.gov/coronavirus/2019-ncov/faq.html](https://www.cdc.gov/coronavirus/2019-ncov/faq.html)

~~~
roywiggins
It's doubly confusing because "SARS" stands for Severe Acute Respiratory
Syndrome, but SARS-CoV-19 is a virus, not the syndrome. But we aren't calling
the disease SARS-19, we are calling it COVID-19...

------
MilnerRoute
That's not the actual headline.

We have no way of assessing the credibility of this research.

~~~
dang
We've changed the title to the original now, as the site guidelines ask: "
_Please use the original title, unless it is misleading or linkbait; don 't
editorialize._"
([https://news.ycombinator.com/newsguidelines.html](https://news.ycombinator.com/newsguidelines.html))

(Submitted title was "Genomic analysis suggests seafood market was not SARS-
CoV-2 source". )

~~~
1_over_n
Sorry, i posted the link and the full title was too long to fit in the field.
I did editorialize it as the intention was to draw attention to the claim.
Noted for future posts.

Edited to include claim in journal below:

"This suggests that the source of the coronavirus in the Hua Nan market was
imported from elsewhere"

------
sahin-boydas
What was it?

~~~
dangrossman
That's not known.

~~~
sahin-boydas
Then what is the probable possible sources?

If someone separate them by media says, twitter says, science says, conspiracy
says? It will be great.

~~~
pbourke
These viruses have a reservoir in bats and they jump to humans through an
intermediary animal. In the case of the virus that caused SARS[1], which was
another coronavirus within the same family as the current virus of interest,
there is some evidence that it went bats -> palm civets -> humans. Palm civets
are/were sold at wet markets in China. It's not definitive that the palm civet
was the source, however, as they subsequently found the virus in other
animals.

For the current virus[2], the time and place of transfer is unknown, but the
current thinking seems to be that it followed the same chain as SARS (bats ->
some animal -> humans).

There is absolutely zero evidence from credible scientists of any kind of
"escaped from the lab" or "bioweapon" source. These are just conspiracy
theories.

[1]
[https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndr...](https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus)

[2]
[https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndr...](https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2)

~~~
wetpaws
Without jumping into conspiracy bandwagon, I still can't see how "originated
from bats" is better then "bioweapon" if neither has concrete evidence or
proof.

~~~
fhars
One has plausibility and some evidence from DNA sequencing and mutation rates
on its side, the other hasn‘t.

~~~
wetpaws
>the other hasn‘t

Just because some people don't believe that is likely, that does not mean it
is not _plausable_

Is it plausible that there could be a biological lab in Wuhan? Yes, in fact,
there is one.

Is it plausible that some countries do research on biological weapon? Yes, in
fact there are multiple cases of such occasions:
[https://en.wikipedia.org/wiki/United_States_Army_Biological_...](https://en.wikipedia.org/wiki/United_States_Army_Biological_Warfare_Laboratories)

Is it plausible that biological lab can leak bioweapon? Yes, in fact this
happened before, e.g.
[https://en.wikipedia.org/wiki/Sverdlovsk_anthrax_leak](https://en.wikipedia.org/wiki/Sverdlovsk_anthrax_leak)

------
corporateslave5
Interestingly enough, most information/speculation about the viruses origins
are actively suppressed by google/twitter/reddit.

~~~
vincnetas
How do you know that? Care to share more details?

~~~
z92
zerohedge's twitter account was blocked permanently for sharing a post on the
origin of the virus. For one.

~~~
MilnerRoute
They banned them for doxing a researcher.

[https://www.washingtonpost.com/technology/2020/02/01/twitter...](https://www.washingtonpost.com/technology/2020/02/01/twitter-
zero-hedge-coronavirus/)

~~~
kolanos
Is it doxing if they just republished already public information on the
virology lab's website?

~~~
oasisbob
Debatably not, but that's not what Zero Hedge published:

 _The Zero Hedge post questioned the involvement of a virology institute in
Wuhan, the city where the outbreak began. It listed the name, photograph and
contact information for a researcher at the institute, and called on readers
to “pay [him] a visit” if they want to “find out what really caused the
coronavirus pandemic.”_

