Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete genome
ncbi.nlm.nih.gov
ncbi.nlm.nih.gov
Bat cave solves mystery of deadly SARS virus — and suggests new outbreak could occur (2017): https://www.nature.com/articles/d41586-017-07766-9
"...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"
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.
> 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.
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.
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.
It also theorized that the source of the SARS virus might have originated from an infected cat. And Ebola may have originated from infected bat feces, that might have landed on a girl’s toy, which she then put into her mouth. And the MERS virus in the Middle East may have come from an infected camel.
This appears to be a logical and scientific deduction.
So for this Coronavirus, it appears to follow the same pattern. Infected animal feces mutated into some virus, that made the transmission to humans.
My theory, is that perhaps an infected animal’s feces, may have mixed with other fluids, like blood, from freshly slaughtered animals, and mutated into something that infected a human with a weakened immune system (easy target), who then transmitted it to other healthy humans by contact.
On one hand, it does seem that the best way to guarantee that you’re sourcing your meat from a fresh and healthy animal, is to pick the animal that you want, and to slaughter it on the spot. This means that the meat vendor does not have to maintain a refrigeration system, and you don’t introduce other chemicals or salts to preserve your meat.
But the problem is that you have to keep the animals in captivity, and the meat vendor must handle, and clean all their urine and feces. And when animals get sick, their feces and urine gets infected, thus you increase the probability of an outbreak like this.
What’s the solution? Maybe China must begin eliminating wet markets, and eliminate the practice of keeping live animals in captivity, in order to minimize the incubation, mutation, and the transmission of such viruses. And instead, to begin using a refrigeration system, to preserve slaughtered animals.
[1] https://time.com/5770904/wuhan-coronavirus-wild-animals/
You can already use GPT-2 to generate compiled code already. You train it on known viruses and have it predict new variants.
You can also for better sample efficiency, jointly train to predict for any measurable characteristics you like, for example mortality or propagation speed, you then synthesize the various proposed DNA sequences, and inject them into hosts. Compare the results with the prediction and update your models accordingly.
Of course you will have plenty of non functioning organism, but that's probably a more efficient way of exploring this search space than what nature does with random mutations and cross-overs.
It's like giving virus the ability to virtually meet-up in the hall of fame to evolve faster.
* 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)
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...
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
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!