
Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete genome - kumarski
https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2
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chrisco255
I heard the virus originated from bats, like SARS did, not seafood.

Bat cave solves mystery of deadly SARS virus — and suggests new outbreak could
occur (2017):
[https://www.nature.com/articles/d41586-017-07766-9](https://www.nature.com/articles/d41586-017-07766-9)

~~~
mmerlin
Eating bats in Wuhan: [https://www.news.com.au/travel/travel-
updates/warnings/chine...](https://www.news.com.au/travel/travel-
updates/warnings/chinese-market-at-centre-of-coronavirus-outbreak-sells-
wolves-rats-and-bats-to-eat/news-story/40565ee222aa22612762a9f89111c0fb)

~~~
chrisco255
What's interesting is Wuhan is home to a virology research center. They were
literally testing bats inside of Wuhan for viral diseases. This makes me think
this strain broke out of the lab. From the above article:

"...to clinch the case, a team led by Shi Zheng-Li and Cui Jie of the Wuhan
Institute of Virology in China sampled thousands of horseshoe bats in
locations across the country"

~~~
nikofeyn
i am not for sure that's more likely than the situation of people eating
infected bats or other animals infected by bats. the chinese do not have great
hygiene when it comes to food sourcing, preparation, and consumption. the
chinese have all sorts of "beliefs" about food and are very stubborn to accept
change. for example, thinking hot water as a sort of elixir and cleanser
(e.g., killing parasites). oh look, it's served in hot water, so it's fine.
also, the shared eating style (i.e., using a lazy susan) is not exactly a
great way to contain illness, even if the food itself is fine.

~~~
blackrock
Well, to be fair to them, in America, we have rural hicks in the midwest
hunting rabbits, squirrels, snakes, hamsters, and other mammals for
recreational food. These are wild animals that possibly carry rabies and other
diseases. And didn’t the Hantavirus from the 90s originate from infected
rodents in the United States?

Do you want to educate these fellow Americans to not consume such possibly
infected wildlife? Because surely, they live in America, and they ought to
know better.

And if you’re on a deserted island, then you’d probably eat these animals too,
if you wanted to survive.

And sharing food on the lazy Susan is perfectly fine, just use a sterile
serving spoon, and don’t lick the handle. Don’t you eat dinner this way with
your own family meals?

Currently, the scientists don’t know yet where this vector originated from.
And they are locking down the city out of an abundance of caution.

Perhaps this episode will force them to implement strict meat sourcing
requirements. Such as, all meat sold for consumption, must come from a farm,
and pass a food handling certification process.

This is clearly a very expensive operation and administration, but they just
quarantined a city, so that is an even more expensive and politically damaging
event.

The first step in preventing such an outbreak from happening again in the
future, is in personal education, and a reinforcement of following basic
hygiene practices. Perhaps this event will finally trigger the China central
government to mandate such a national education process for everyone.

~~~
nikofeyn
the rural hicks you mentioned are an extremely small minority in the u.s.,
found in the backwoods of louisiana and kentucky and the like. the majority of
people find this practice uncouth. the one food style i mentioned is
overwhelmingly the majority in china.

> And sharing food on the lazy Susan is perfectly fine, just use a sterile
> serving spoon, and don’t lick the handle. Don’t you eat dinner this way with
> your own family meals?

i have never seen ANY chinese meal served from a lazy susan use individual
serving spoons for the individual meals. everyone uses their own chopsticks to
grab the food and put it in their plate or they simply eat directly from the
shared plate. if there is a serving spoon for a dish, sometimes provided by
restaurants, individual chopsticks are still used to help.

it is a rather major faux pas in american eating to use any utensil used by an
individual to touch or serve a shared dish. it is overwhelmingly the case that
a serving spoon is dedicated to a dish and is only used to move the food to an
individual's plate.

now, i would imagine this culture difference of eating is probably a minor one
in the grand scheme of food hygeine (preparation and sourcing being more
important i think), but i think it's pretty easy to say one is healthier than
another.

in china, it is a constant battle to ask and understand how a dish was sourced
and prepared, as most of it is taken as is by chinese. the eating habits are
unchangeable at a local level and one must deal with it.

~~~
throw445323
The vast majority of Chinese do not eat bats or other wild game either.

I don’t know a single Chinese person that has eaten bat before, and I’ve been
going to the country every year for 20 years now.

It’s only because China has such a large population that even 1% is 10 million
people.

If anyone is sick, I ALWAYS see them using a separate set of chopsticks to get
food, and they usually will put it in a separate plate.

You eat with family and friends and a sick person would take extra precautions
to not infect them.

~~~
nikofeyn
my original comment was on the likelihood of this originating in a market
versus a lab-based outbreak. of course most chinese do not eat bat. i didn't
imply they did. the comment you replied to was me dismissing the commenter's
argument. but the wuhan market and its patrons do eat bats and other animals
that could already be infected by bats. so it's not far fetched that the virus
did indeed originate there vs a lab leak.

the latter part of my comment was regarding the potential spread of disease.
your comment addresses someone who already knows they are sick. the onset
period of this virus is one to two weeks. that's a minimum of 14-21 meals
before any symptoms show up, leaving plenty of time for person to person
transmission. that plus the density of china's major cities and this
particular time of year regarding travel yields a rather fertile ground for
disease spread.

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blackrock
It’s impressive that they were able to sequence the genome of this virus so
fast.

------
officialjunk
one day i expect we will have a disassembly tool for this type of compiled
genetic code

~~~
segfaultbuserr
For now, at least we have "grep" and "diff".

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MuffinFlavored
what can this data be used for?

~~~
segfaultbuserr
Didn't you see an "analyze this sequence" menu on the right?

* Run BLAST

* Pick Primers

* Highlight Sequence Features

* Find in this Sequence

The BLAST algorithm is an interesting read.
[https://en.wikipedia.org/wiki/BLAST_(biotechnology)](https://en.wikipedia.org/wiki/BLAST_\(biotechnology\))

I can see its power even if I'm not a biologist. For example, I just submitted
(everyone can use the system) a BLAST task for a megablast search to compare
NC_045512.2 (Wuhan-Hu-1) and NC_004718.3 (SARS coronavirus) for an alignment,
and the system is able to "diff" between the two sequences (and even has an
option to visualize it in a 2D graph), and finally telling us that 82.3% of
the both genetic sequences are identical (not really close in a biological
sense). You can also search identical genetic sequences across the entire
databases by constructing a more complex query.

Here's my result:
[https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=2MDW41R...](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=2MDW41RN11N)

And apparently, the specific algorithm used to produce my result is described
in this paper.

> Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy
> algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14.

[http://pipmaker.bx.psu.edu/dist/greedy.pdf](http://pipmaker.bx.psu.edu/dist/greedy.pdf)

It looks like a simple algorithm, which can be implemented for fun as a
weekend project. One can run one's program on real DNA sequences, and compare
the outputs with NIH's implementation. Don't forget to write an article and
submit it to Hacker News when you're done. Biohacking!

