6 ms·

Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete genome

43 points by kumarski 7y ago

officialjunk 7y ago
one day i expect we will have a disassembly tool for this type of compiled genetic code
- youareostriches 7y ago
  will that disassembly tool include regulator genes and all the protein-protein interactions that influence said regulator genes, ad infinitum? there's so much more complexity to life than gene sequences themselves.
- segfaultbuserr 7y ago
  For now, at least we have "grep" and "diff".
- GistNoesis 7y ago
  Virus are like 30k base pairs. It's a quite short sequence for neural networks to tackle. 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.
MuffinFlavored 7y ago
what can this data be used for?
- segfaultbuserr 7y ago
  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=2MDW41RN11N 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 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!
- 1998v2 7y ago
  There are DNA based virus detection techniques that take fragments of DNA of unknown origin and compare them to a database of known bad stuff. So I think it could allow people that have the ability to sequence DNA to identify this virus if they have, for example, a patient.
chrisco255 7y ago
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 7y ago
  Eating bats in Wuhan: 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 https://www.news.com.au/travel/travel-updates/warnings/chine...
  - chrisco255 7y ago
    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"
    - blackrock 7y ago
      This sounds like the plot of Resident Evil.
    - nikofeyn 7y ago
      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 7y ago
It’s impressive that they were able to sequence the genome of this virus so fast.

43 points by kumarski 7y ago

officialjunk 7y ago

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

youareostriches 7y ago
will that disassembly tool include regulator genes and all the protein-protein interactions that influence said regulator genes, ad infinitum? there's so much more complexity to life than gene sequences themselves.
segfaultbuserr 7y ago
For now, at least we have "grep" and "diff".
GistNoesis 7y ago
Virus are like 30k base pairs. It's a quite short sequence for neural networks to tackle. 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.

MuffinFlavored 7y ago

what can this data be used for?

segfaultbuserr 7y ago
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=2MDW41RN11N 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 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!
1998v2 7y ago
There are DNA based virus detection techniques that take fragments of DNA of unknown origin and compare them to a database of known bad stuff. So I think it could allow people that have the ability to sequence DNA to identify this virus if they have, for example, a patient.

chrisco255 7y ago

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 7y ago
Eating bats in Wuhan: 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 https://www.news.com.au/travel/travel-updates/warnings/chine...
- chrisco255 7y ago
  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"
  - blackrock 7y ago
    This sounds like the plot of Resident Evil.
  - nikofeyn 7y ago
    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 7y ago

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