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Novel coronavirus complete genome from the Wuhan outbreak available in GenBank
- ALittleLight 7y agoWhat kind of things can be done with this? Are there tools that consume genomes and tell you something about them? Is biology advanced enough that it would be possible to create such tools? I see they have several different strains. I could imagine trying to find similarities or organize them into a tree, if that's not already done.
- asdff 7y agoIn fact that is exactly what is done. What you are describing is genome annotation and homology based phylogenetic analysis.
- a_bonobo 7y agoYes that's being done, here's a preprint using this and similar sequences and comparing them with bat coronaviruses and SARS: https://www.biorxiv.org/content/10.1101/2020.01.22.914952v1.full.pdf https://www.biorxiv.org/content/10.1101/2020.01.22.914952v1....
- OkMillennial 7y agoGoogle it kid.
- pnathan 7y agoSuper awesome. As a point of curiosity, when did this kind of complete sequencing capability get to the point where it could be turned around in under two months?
- distant_hat 7y agoIt's been a while. You can do real time sequencing now. E.g., here is a sequencing demo happening in a coffee shop in Africa. https://twitter.com/virology_chitra/status/1220065678327255040 https://twitter.com/virology_chitra/status/12200656783272550... The device connected to the laptop via USB is the sequencer.
- wiggler00m 7y agoThe company that makes that is Oxford Nanopore https://nanoporetech.com/products https://nanoporetech.com/products
- ALittleLight 7y agoThis is amazing. I'm having to restrain the part of myself that loves buying gadgets. These not only look cool, from watching their videos and reading about them, they have an awesome function. Suppose I had some of this equipment and a sick family member. Would it be possible for me to somehow isolate a virus or bacteria from the sick person's saliva or blood and then sequence the DNA/RNA and then use a catalog of genetic information to identify a likely match?
- mikhailfranco 7y agoHere is the timeline of sequencing costs: https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequencing-Costs-Data https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequen... The human genome is 3 Gbp, which is 100,000 times the size of the coronavirus at 30 kbp.
- fjfaase 7y agoThis already has been available for some time. I found it through a link on the wikipedia page. I had not see the tree before. Because it is close to coronoviruses found in bats, one could conclude that bats are the animal reservoir for this type of virus (as was the case with SARS as well). I presume that China will forbid the trade and consumption of bats.
- richajak 7y agoI also noticed the article several days ago. Just wondering if there is any basic tutorial in python to analyze this type of data.
- fjfaase 7y agoI guess there is not much to analyze. Both the RNA sequence is given and their translation into amino-acids. The capital letters give the amino-acids. https://en.wikipedia.org/wiki/Amino_acid https://en.wikipedia.org/wiki/Amino_acid The lower case letter describe the RNA sequence. Sequences of three RNA base pairs are translated to one amino-acid. A table giving the standard decoding, can be found at: https://en.wikipedia.org/wiki/Genetic_code#RNA_codon_table https://en.wikipedia.org/wiki/Genetic_code#RNA_codon_table The next step is taking the amino-acids sequence and determine the protein structure. amino-acids chains fold together in a complex structure, which determine their function. Determining how this folding happens is a very complex problem. If you want to get some more idea about it, I suggest you have a look at https://fold.it/ https://fold.it/
- zedr 7y agoDo you think research on 2019-nCoV would benefit from having available a platform for distributed computing, e.g. a dedicated Folding@Home?
- fjfaase 7y agoI am afraid not. If there would be any, I guess it would already have been organized. No, knowing the structure of the proteins that make up the virus, might give some understand about how it works. If that gives some information about prevention (developping a vaccine) or treatment (developing anti-viral drugs), I wonder. Knowing the genetic code, can be helpful with developing vaccine. I understand that one approach is to incorporate part of the DNA in a known 'disabled' virus and test if it has some protective effect in some animals, and only after positive results test it on humans.
- alpb 7y agoI hate saying this but I didn't expect some default-theme WordPress set up when I clicked on a link from nih.gov –with the comments section, post rating, and pingbacks enabled.
- eecc 7y agoWell, the Higgs boson was presented ok Comic Sans... they’re scientists, not webdesigner agonizing on artisanal layouts ;)
- __s 7y agoHiggs Boson slide screenshots: https://fontsinuse.com/uses/11764/higgs-boson-discovery-announcement https://fontsinuse.com/uses/11764/higgs-boson-discovery-anno...
- jansan 7y agoI bet this was done on purpose with tongue in cheek.
- konschubert 7y agoI’ve been in particle physics and I wouldn’t be so sure
- KineticLensman 7y agoThe author of the slides has stated that she likes Comic Sans and finds it cute [0]. But that doesn't explain Slide 3, which has 6 statements, each in a paragraph box with a differently garish background colour fill. [0] https://www.symmetrymagazine.org/article/april-2013/qa-with-fabiola-gianotti-higgs-hunter https://www.symmetrymagazine.org/article/april-2013/qa-with-...
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- cltsang 7y ago
- nestorD 7y agoI found out a few days ago when an, interesting, related question was posted on bioinformatics.stackexchange.com : Why does the Wuhan coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)? [0] [0]: https://bioinformatics.stackexchange.com/questions/11227/why-does-the-wuhan-coronavirus-genome-end-in-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa https://bioinformatics.stackexchange.com/questions/11227/why...
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- gexla 7y agoReminds me of the skit about the Monty Python creature of the name "The Black Beast of Aaaaaaargh."
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- flatiron 7y agoNop slide
- sumgocko 7y ago(This is baseless speculation by someone who has only taken Genetics 101) Human cell nuclei produce mRNA from DNA, which then makes it's way to the ribosome to be expressed as a chain of amino acids, or a protien. On it's way to the ribosome, it needs protection from the cell's RNA cleanup enzymes, so it leaves the nucleus with a 5' cap and a poly-A tail. Therefore, it makes sense that a virus that wishes to hijack human ribosomes would end in a poly-A tail (a bunch of As) in order to not get destroyed by human cells.
- signal_space 7y agohttps://en.m.wikipedia.org/wiki/Polyadenylation https://en.m.wikipedia.org/wiki/Polyadenylation
- zedr 7y agoPadding?
- deleted 7y ago[deleted]
- 29athrowaway 7y agoThe virus propagation was said to have started in a market that sells, among other products, snakes. 2019-nCoV can go from bats to snakes to humans. Eating snakes or bats seems like a bad idea.
- vasco 7y agoPrevious viruses came from pigs and chicken and cows. Unless you also advise to stop eating those this just seems a bit of a stretch.
- nindalf 7y agoSir, do you have a minute to talk about our lord and saviour, veganism? I’m only half kidding. It makes sense to go vegan/vegetarian during an outbreak of diseases spread by consuming meat.
- 29athrowaway 7y agoThere is an enourmous effort put into ensuring the safety and quality of the meat products you have mentioned.
- ovx99 7y agoSeems like someone's never left a first-world country before...
- M2Ys4U 7y agoHah. The US poultry industry is so bad at looking after their animals they have to wash carcasses in chlorine to even _approach_ safe levels of pathogens like salmonella and campylobacter.
- vasco 7y agoI'd assume the effort is similar between bats and snakes being sold in an open air market in a Chinese village and chicken, pigs and cows being sold in an open air market in a Chinese village.
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- nartz 7y agoAny way anyone else can 'contribute' here to reaching a cure? I'm thinking - somehow bootstrapping a node to join a distributed blockchain network of protein folding simulations ...
- drdeca 7y agoI don’t think a blockchain would really help with task specific protein folding simulation stuff?
- hanniabu 7y agoThere's projects that use blockchain and cryptocurrency as a form of incentives and payment for resources that people are putting forward for computing power.
- lawlessone 7y agoMoney that would be better spend on super computers i think
- hanniabu 7y agoI think any contributions are be welcomed.
- ryanlol 7y agoYou don’t need either of those for incentives and payment for resources that people put forward.
- camdenlock 7y ago29,903 base pairs (4 bit values), so that’s 119,612 bits, or about 15 KB of information total. A devious little self-replicator in 15 KB which runs on our bio substrate!
- kijin 7y agoI wonder how many of those base pairs are devoted to evading the host's immune system, as opposed to the primary function of being a fork bomb.
- majewsky 7y ago> opposed to the primary function of being a fork bomb /me realizes that every organism is a fork bomb
- zaarn 7y agoProbably not that many, it should be sufficient that the immune system doesn't have anything to specifically deal with it, so it only has to evade the complement system (which for a virus isn't terribly hard). It also helps that the strategy is simply "replicate and just swarm the defense".
- GistNoesis 7y agoThere are 4 base types (A,T,C,G) so it's only 2-bit values. There is also some redundancy coding in the amino acid sequence that follow the DNA. So if you compute the information of the codons sequence it's even lower. It's quite compact. What would be interesting to know, is the percentage of programs still running when a few bits are modified, to know how sharp is the search space. Exploring living programs space, you probably can use some advance neural network techniques, like GPT-2 to explore it more efficiently, directly in its compressed representation to provide an high level interface with slider controlling the high-level properties.
- Avamander 7y agoGene overlap is also possible and exists in viruses, so the true amount of data is actually usually a bit larger than the the sequence's length because of this "compression".
- peter303 7y agoKudos to the scientists who developed this so fast. I rember it took four YEARS to identify the HIV virus and another two years for a test.
- throwawaynpc123 7y agoyes, they have the source code
- vikramkr 7y agoIt's really amazing how much more powerful biological tools have become since then!
- Smerity 7y agoDoes anyone know of an easy way to download the nucleotide sequences for the entire set of pneumonia / coronavirus viruses? I've looked at the FTP mirror but can't connect it with the nucleotide locus I find on the site itself. I work in language modeling and want to see about using those unsupervised / self-supervised methods for genome annotation / phylogenetic tree construction. Even if it's more of a curiousity than a useful tool I have experience with small datasets, most recently focused on character level language modeling on ~90MB of training data, so if I can get (90MB / (29 kilobases * 2 bits per base) =) approximately 12,000 related samples I should be able to at least make a dataset out of it.
- jerven 7y agohttps://viralzone.expasy.org/8676 https://viralzone.expasy.org/8676 Is a good start.
- BioGeek 7y agoUsing Biopython. Note that the search query that I am using currently returns 70605 results, so you might want to tweak it fit your needs. from Bio import Entrez import time from urllib.error import HTTPError DB = 'nucleotide' QUERY = '("pneumoviridae"[Organism] OR "Coronaviridae"[Organism])' Entrez.email = 'your.email@provider.com' handle = Entrez.esearch(db=DB, term=QUERY, rettype='fasta') record = Entrez.read(handle) handle = Entrez.esearch(db=DB, term=QUERY, retmax=count, rettype='fasta') record = Entrez.read(handle) id_list = record['IdList'] count = len(id_list) post_xml = Entrez.epost(DB, id=",".join(id_list)) search_results = Entrez.read(post_xml) webenv = search_results['WebEnv'] query_key = search_results['QueryKey'] batch_size = 200 with open('viruses.fasta', 'w') as out_handle: for start in range(0, count, batch_size): end = min(count, start+batch_size) print(f"Going to download record {start+1} to {end}") attempt = 0 success = False while attempt < 3 and not success: attempt += 1 try: fetch_handle = Entrez.efetch(db=DB, rettype='fasta', retstart=start, retmax=batch_size, webenv=webenv, query_key=query_key) success = True except HTTPError as err: if 500 <= err.code <= 599: print(f"Received error from server {err}") print("Attempt {attempt} of 3") time.sleep(15) else: raise data = fetch_handle.read() fetch_handle.close() out_handle.write(data)
- dharma1 7y agoI wonder how realistic it is to expect a vaccine in 3 months, given that we don't have a vaccine for MERS 8 years later (and not really one for SARS either)? Is it just a question of allocating resources and shifting priorities?
- hanniabu 7y agoI read they have a few SARS vaccines, but non that have gone through human trials yet. Side not: I'm always concerned when we're put in a situation like this where we're pressured to put out a vaccine quickly because it opens the door for a less than optimal solution to become a mainstay. For example since it's an emergency you may put forward a solution, have it go through human trials, find some side effect, but given the current circumstance say that it's "good enough" and give it the green light of approval. Now I understand that in such an urgent circumstance that this may be justified, but after the urgency is over it's my understanding that this solution that may or may not be approved under regular circumstances will remain approved.
- mrfusion 7y agoWhy should a given vaccine have more side effects than existing vaccines? It’s just broken up pieces of the virus. If produced properly and rendered inert Why should it trigger major side effects?
- vikramkr 7y agoBecause biology is complicated and it's never that simple. You could trigger too strong an immune response, no response at all, or you could end up with a situation like on dengue where the vaccine makes the disease worse (https://www.statnews.com/2019/05/01/fda-dengue-vaccine-restrictions/ https://www.statnews.com/2019/05/01/fda-dengue-vaccine-restr...)
- _npmx 7y agoThis is an interesting question, and I can confidently say the technology exists to have some quantity of human vaccine within 3 months. Will it be enough to have an impact? Probably not. We're talking about needing millions of doses. But if the companies in the space can succeed at at least showing the turn-around-time for some quantity of working vaccine is possible, then it becomes an engineering problem and not a scientific problem. Then you just need to marshal resources and you could be at a place where bulk vaccine could be produced in that short window of time. This 2019-nCoV marks an inflection point for humanity IMHO where sequencing costs, data transmissions, and vaccine technology are all good enough to actually accomplish a real-time vaccine. The science is here, now it's just turning a bigger crank.
- gexla 7y agoMore interesting to me is the process the medical industry has to go through to deal with the testing kits. Apparently they are in short supply. Lots of good nuggets in this thread. Yes, it's Twitter, but this can be cross-checked. https://twitter.com/luchenhist/status/1220497118755987456 https://twitter.com/luchenhist/status/1220497118755987456 * Testing is a long process * Kit distribution is supply chain constrained due to holiday * Only severe cases are being tested * Hospitals are overwhelmed * People not getting tested are being turned back * Government offering compensation for testing but only if it's actually Coronavirus The author has other interesting Tweets as well. Might be worth a follow if this is of interest.
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- tgvaughan 7y agoThere are already 27 genomes on GISAID. Very little diversity at this stage though, so phylodynamic analyses are more noise than signal. https://www.gisaid.org/epiflu-applications/next-betacov-app/ https://www.gisaid.org/epiflu-applications/next-betacov-app/
- throwawaynpc123 7y agoIt was patented years ago so of course it is.
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- mikhailfranco 7y agoLooks like the Chinese military had the same Bat SARS-like Coronavirus in their possession 2 years ago. Here is the NIH page showing Identical Protein Matches of the envelope protein from Wuhan 2019-nCoV: https://www.ncbi.nlm.nih.gov/ipg/QHO62113.1 https://www.ncbi.nlm.nih.gov/ipg/QHO62113.1 Notice there are two entries not from the recent Wuhan seafood market outbreak: https://www.ncbi.nlm.nih.gov/protein/AVP78033.1 https://www.ncbi.nlm.nih.gov/protein/AVP78033.1 https://www.ncbi.nlm.nih.gov/protein/AVP78044.1 https://www.ncbi.nlm.nih.gov/protein/AVP78044.1 Both sequences were provided on 05-JAN-2018 by: Institute of Military Medicine Nanjing Command, NO. 293 East Zhongshan Road, Nanjing, JangSu 210002, China