10 ms·

Preliminary analysis of 11 Novel Coronavirus genomes from the Wuhan outbreak

161 points by partingshots 7y ago

egorfine 7y ago
I see they have published virus code. Is there build instructions? Asking for a friend
- sansnomme 7y ago
  That is literally how most gene therapies work. RTFM.
  - SketchySeaBeast 7y ago
    I'm having an issue where I'm trying to implement CAR-T but I keep melting my patients, has anyone run into this issue? Edit: Nevermind, figured it out.
- TeMPOraL 7y ago
  [closed as not constructive]
- 0x8BADF00D 7y ago
  Build servers are down, and you can’t build it locally.
  - ISL 7y ago
    Everyone can build it locally, but they'll be out sick if they do.
  - LorenPechtel 7y ago
    As a test a local build of a harmless virus has been done, it worked. You still need to be skilled, though, no terrorist is downloading the smallpox genome and cranking out a lethal agent.
ISL 7y ago
Every now and again, there is a strong reminder that we're living in the future. This is one of them. A scientific result like this was promised to us as a someday-goal of early sequencing technologies when I was a child. A lot of people have worked really hard to make this happen, and it is a human triumph, even if there is more to do.
- october_sky 7y ago
  Yes, it's completely and exceptionally awesome that we can just sign on the Internet and gain this genome sequence. But it's also important to weigh the value. As the article states: > but there is insufficient epidemiological information for it to be useful here
  - mjw1007 7y ago
    It looks to me like that quote is talking about one particular sequence that they've left out of their list (it's explaining why they did that), not about the 13 sequences that they have listed.
    - october_sky 7y ago
      Ah, ok. Thank you for pointing that out
  - Fomite 7y ago
    So the authors are using that in a particular manner that might be missed by the general HN audience. By "insufficient epidemiological information", they mean that the genome cannot, itself, be used to assemble a transmission tree, which is sort of the brass ring of sequence data. That is not to say that the genome data isn't useful for epidemiology.
wschfdkbrmcdf 7y ago
That comment on that page from Kristian G. Andersen is mildly disturbing (http://archive.is/O1vhN http://archive.is/O1vhN)... As Associate Professor, Scripps Research, Director of Infectious Disease Genomics, SRTI etc etc I assume he knows what he's talking about when he states: "That means that the outbreak was detected almost immediately after the first case, which - given that this is flu season in China - is just amazing. Detecting an outbreak of pneumonia (similar to flu) of a novel coronavirus that fast is truly impressive." I'm not sure I really want to wear this tin-foil hat, but it would certainly be easier to identify a novel coronavirus if it came directly from your own BSL-4 lab in Wuhan https://www.nature.com/news/inside-the-chinese-lab-poised-to-study-world-s-most-dangerous-pathogens-1.21487 https://www.nature.com/news/inside-the-chinese-lab-poised-to...
- platinumrad 7y ago
  Absolutely amazing that a completely unsubstantiated conspiracy theory is the top comment.
  - fsh 7y ago
    This seems to be a pattern in echo-chamber sites such as hn or reddit. If there is no reliable information, the most outrageous speculation makes it to the top.
  - perf1 7y ago
    There is also "Institute of Military Medicine Nanjing Command" that submitted an identical envelope protein 2 years ago [1]. They adapt quickly to avoid detection of the immune system [2]. People argue it would have evolved and not be the same if it didn't came fresh from a lab. [1] https://www.ncbi.nlm.nih.gov/protein/AVP78033.1 https://www.ncbi.nlm.nih.gov/protein/AVP78033.1 (Click "Identical Proteins") [2] https://en.wikipedia.org/wiki/Viral_envelope https://en.wikipedia.org/wiki/Viral_envelope
- giarc 7y ago
  It could be the result of having the lab in the same city that they could detect it so quickly. Not because the original sample (or any samples) would be tested in the BSL4, but simply because having that lab would attract talent, funding and equipment to reference labs in the same city. The index patient would likely have had a nasopharyngeal swab taken and run against the regular panel of respiratory viruses (influenza, parainfluenza, enterovirus, rhinovirus, metapneumovirus, and coronaviruses). I suspect there would have been a light signal on the coronavirus (perhaps some cross reactivity) and they would have done more investigation to determine what is was.
christkv 7y ago
I will be very interested what the guys at This week in virology say about the outbreak. They briefly talked about it on the 12th of January and it will probably be what they talk about this week with all the new developments. http://www.microbe.tv/twiv/ http://www.microbe.tv/twiv/
- stefanu 7y ago
  They have a recent blog post “A lesson from SARS-CoV for 2019-nCoV”: http://www.virology.ws/2020/01/23/a-lesson-from-sars-cov-for-2019-ncov/ http://www.virology.ws/2020/01/23/a-lesson-from-sars-cov-for...
codingslave 7y ago
Here is a patent from the lab in Wuhan: https://jvi.asm.org/content/jvi/90/6/3253.full.pdf https://jvi.asm.org/content/jvi/90/6/3253.full.pdf "Isolation and Characterization of a Novel Bat Coronavirus Closely Related to the Direct Progenitor of Severe Acute Respiratory Syndrome Coronavirus" an excerpt: "In conclusion, we isolated and characterized a novel bat SLCoV isolate, WIV16, which is the closest ancestor to date of the SARS-CoV. Our results provide further evidence that Chinese horseshoe bats are natural reservoirs of SARS-CoVs. It should be noted that WIV16 is not the closest strain to the human SARSCoVs with regard to ORF8. Full-length ORF8 is present in several SARS-CoV genomes of early-phase patients, all civet SARS-CoVs, and bat SL-CoVs. It is split into two ORFs (ORF8a and -b) in most human SARS-CoVs from late-phase patients due to a deletion event in this part of the genome (3). Recently, two papers reported that they found a full-length ORF8 which has higher similarities to SARS-CoV GZ02 and civet SARS-CoV SZ3, suggesting that SASCoV derived from a complicated recombination and genetic evolution among different bat SL-CoVs" Reading the paper, its clear that the Wuhan lab was studying viruses almost identical to the one that emerged in Wuhan. This would make sense, as this is what they are trying to prevent. But it also raises concerns about whether the epidemic in Wuhan originated from this lab. Further evidence would be the fact that a member from the lab is reported to have contracted coranavirus.
- wschfdkbrmcdf 7y ago
  Good find
  - hobofan 7y ago
    No, that is next to meaningless. Every bigger virology lab studies coronavirus, or has studied it as some point in the past. Accordingly, you will be able to find similar publications for all of them.
- deleted 7y ago
  [deleted]
- et2o 7y ago
  This is just a standard academic publication. It’s also from 2016. I’m not really following this train of thought. They report isolating a novel coronavirus from the bat population in that province in China. It’s not clear to me that this is the same virus. In this context it seems that it just points out that the bat reservoir does have coronaviruses. Since it’s known that there was a recent animal to human crossover, which requires a bat reservoir and likely an intermediate animal reservoir, I don’t really see that this implies the virus “escaped” from the laboratory or anything.
emmelaich 7y ago
If you want to follow along, https://www.reddit.com/r/China_Flu/ https://www.reddit.com/r/China_Flu/ is a good resource.
- natalyarostova 7y ago
  It's a good resource for hysteria.
  - Zenst 7y ago
    Indeed - I give it a week until some real time tracking map sourced from reddit or other like source makes the front page.
    - exikyut 7y ago
      I personally generally consider the reddit platform incompetent for surfacing that wheat by default, and incidentally view the site as a whole somewhat dimly as a result. I want to enjoy the internet and/or get at info I might need. Some seem to enjoy being a pawn in what amounts to a poorly-thought-through "crowdsourced wheat-surfacing" architecture; I find it draining.
    - Zenst 7y ago
      Oh, seems there is one already, though I'm not going to submit it as a topic as only fuels fear, though fine in a comment for those who dug down enough :- https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6 https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.h...
  - emmelaich 7y ago
    Sure, exercise some judgement, but there's wheat amongst the chaff.
- Barrin92 7y ago
  that place appears to be full of conspiracy theories, weirdly racist comments, and the one person who is a nurse is actually being downvoted for giving an accurate statement on the state of affairs. I'd avoid that subreddit
nabla9 7y ago
Novel coronavirus 2019-nCoV: early estimation of epidemiological parameters and epidemic predictions https://www.medrxiv.org/content/10.1101/2020.01.23.20018549v1 https://www.medrxiv.org/content/10.1101/2020.01.23.20018549v... >We estimate that only 5.1% (95%CI, 4.8-5.5) of infections in Wuhan are identified, and by 21 January a total of 11,341 people (prediction interval, 9,217-14,245) had been infected in Wuhan since the start of the year. Should the epidemic continue unabated in Wuhan, we predict the epidemic in Wuhan will be substantially larger by 4 February (191,529 infections; prediction interval, 132,751-273,649) >Our model suggests that travel restrictions from and to Wuhan city are unlikely to be effective in halting transmission across China; with a 99% effective reduction in travel, the size of the epidemic outside of Wuhan may only be reduced by 24.9% on 4 February.
- greenonions 7y ago
  Source: "Caution: Preprints are preliminary reports of work that have not been peer-reviewed. They should not be relied on to guide clinical practice or health-related behavior and should not be reported in news media as established information."
contingencies 7y ago
Today hacked together some scraped data with basic visualization at https://github.com/globalcitizen/2019-wuhan-coronavirus-data/ https://github.com/globalcitizen/2019-wuhan-coronavirus-data... ... contributions welcome I'm about off to bed.
- juiyout 7y ago
  Please don't include Taiwan as part of China.

161 points by partingshots 7y ago

egorfine 7y ago

I see they have published virus code. Is there build instructions? Asking for a friend

sansnomme 7y ago
That is literally how most gene therapies work. RTFM.
- SketchySeaBeast 7y ago
  I'm having an issue where I'm trying to implement CAR-T but I keep melting my patients, has anyone run into this issue? Edit: Nevermind, figured it out.
TeMPOraL 7y ago
[closed as not constructive]
0x8BADF00D 7y ago
Build servers are down, and you can’t build it locally.
- ISL 7y ago
  Everyone can build it locally, but they'll be out sick if they do.
- LorenPechtel 7y ago
  As a test a local build of a harmless virus has been done, it worked. You still need to be skilled, though, no terrorist is downloading the smallpox genome and cranking out a lethal agent.

ISL 7y ago

Every now and again, there is a strong reminder that we're living in the future. This is one of them. A scientific result like this was promised to us as a someday-goal of early sequencing technologies when I was a child. A lot of people have worked really hard to make this happen, and it is a human triumph, even if there is more to do.

october_sky 7y ago
Yes, it's completely and exceptionally awesome that we can just sign on the Internet and gain this genome sequence. But it's also important to weigh the value. As the article states: > but there is insufficient epidemiological information for it to be useful here
- mjw1007 7y ago
  It looks to me like that quote is talking about one particular sequence that they've left out of their list (it's explaining why they did that), not about the 13 sequences that they have listed.
  - october_sky 7y ago
    Ah, ok. Thank you for pointing that out
- Fomite 7y ago
  So the authors are using that in a particular manner that might be missed by the general HN audience. By "insufficient epidemiological information", they mean that the genome cannot, itself, be used to assemble a transmission tree, which is sort of the brass ring of sequence data. That is not to say that the genome data isn't useful for epidemiology.

wschfdkbrmcdf 7y ago

That comment on that page from Kristian G. Andersen is mildly disturbing (http://archive.is/O1vhN http://archive.is/O1vhN)... As Associate Professor, Scripps Research, Director of Infectious Disease Genomics, SRTI etc etc I assume he knows what he's talking about when he states: "That means that the outbreak was detected almost immediately after the first case, which - given that this is flu season in China - is just amazing. Detecting an outbreak of pneumonia (similar to flu) of a novel coronavirus that fast is truly impressive." I'm not sure I really want to wear this tin-foil hat, but it would certainly be easier to identify a novel coronavirus if it came directly from your own BSL-4 lab in Wuhan https://www.nature.com/news/inside-the-chinese-lab-poised-to-study-world-s-most-dangerous-pathogens-1.21487 https://www.nature.com/news/inside-the-chinese-lab-poised-to...

platinumrad 7y ago
Absolutely amazing that a completely unsubstantiated conspiracy theory is the top comment.
- fsh 7y ago
  This seems to be a pattern in echo-chamber sites such as hn or reddit. If there is no reliable information, the most outrageous speculation makes it to the top.
- perf1 7y ago
  There is also "Institute of Military Medicine Nanjing Command" that submitted an identical envelope protein 2 years ago [1]. They adapt quickly to avoid detection of the immune system [2]. People argue it would have evolved and not be the same if it didn't came fresh from a lab. [1] https://www.ncbi.nlm.nih.gov/protein/AVP78033.1 https://www.ncbi.nlm.nih.gov/protein/AVP78033.1 (Click "Identical Proteins") [2] https://en.wikipedia.org/wiki/Viral_envelope https://en.wikipedia.org/wiki/Viral_envelope
giarc 7y ago
It could be the result of having the lab in the same city that they could detect it so quickly. Not because the original sample (or any samples) would be tested in the BSL4, but simply because having that lab would attract talent, funding and equipment to reference labs in the same city. The index patient would likely have had a nasopharyngeal swab taken and run against the regular panel of respiratory viruses (influenza, parainfluenza, enterovirus, rhinovirus, metapneumovirus, and coronaviruses). I suspect there would have been a light signal on the coronavirus (perhaps some cross reactivity) and they would have done more investigation to determine what is was.

christkv 7y ago

I will be very interested what the guys at This week in virology say about the outbreak. They briefly talked about it on the 12th of January and it will probably be what they talk about this week with all the new developments. http://www.microbe.tv/twiv/ http://www.microbe.tv/twiv/

stefanu 7y ago
They have a recent blog post “A lesson from SARS-CoV for 2019-nCoV”: http://www.virology.ws/2020/01/23/a-lesson-from-sars-cov-for-2019-ncov/ http://www.virology.ws/2020/01/23/a-lesson-from-sars-cov-for...

codingslave 7y ago

Here is a patent from the lab in Wuhan: https://jvi.asm.org/content/jvi/90/6/3253.full.pdf https://jvi.asm.org/content/jvi/90/6/3253.full.pdf "Isolation and Characterization of a Novel Bat Coronavirus Closely Related to the Direct Progenitor of Severe Acute Respiratory Syndrome Coronavirus" an excerpt: "In conclusion, we isolated and characterized a novel bat SLCoV isolate, WIV16, which is the closest ancestor to date of the SARS-CoV. Our results provide further evidence that Chinese horseshoe bats are natural reservoirs of SARS-CoVs. It should be noted that WIV16 is not the closest strain to the human SARSCoVs with regard to ORF8. Full-length ORF8 is present in several SARS-CoV genomes of early-phase patients, all civet SARS-CoVs, and bat SL-CoVs. It is split into two ORFs (ORF8a and -b) in most human SARS-CoVs from late-phase patients due to a deletion event in this part of the genome (3). Recently, two papers reported that they found a full-length ORF8 which has higher similarities to SARS-CoV GZ02 and civet SARS-CoV SZ3, suggesting that SASCoV derived from a complicated recombination and genetic evolution among different bat SL-CoVs" Reading the paper, its clear that the Wuhan lab was studying viruses almost identical to the one that emerged in Wuhan. This would make sense, as this is what they are trying to prevent. But it also raises concerns about whether the epidemic in Wuhan originated from this lab. Further evidence would be the fact that a member from the lab is reported to have contracted coranavirus.

wschfdkbrmcdf 7y ago
Good find
- hobofan 7y ago
  No, that is next to meaningless. Every bigger virology lab studies coronavirus, or has studied it as some point in the past. Accordingly, you will be able to find similar publications for all of them.
deleted 7y ago
[deleted]
et2o 7y ago
This is just a standard academic publication. It’s also from 2016. I’m not really following this train of thought. They report isolating a novel coronavirus from the bat population in that province in China. It’s not clear to me that this is the same virus. In this context it seems that it just points out that the bat reservoir does have coronaviruses. Since it’s known that there was a recent animal to human crossover, which requires a bat reservoir and likely an intermediate animal reservoir, I don’t really see that this implies the virus “escaped” from the laboratory or anything.

emmelaich 7y ago

If you want to follow along, https://www.reddit.com/r/China_Flu/ https://www.reddit.com/r/China_Flu/ is a good resource.

natalyarostova 7y ago
It's a good resource for hysteria.
- Zenst 7y ago
  Indeed - I give it a week until some real time tracking map sourced from reddit or other like source makes the front page.
  - exikyut 7y ago
    I personally generally consider the reddit platform incompetent for surfacing that wheat by default, and incidentally view the site as a whole somewhat dimly as a result. I want to enjoy the internet and/or get at info I might need. Some seem to enjoy being a pawn in what amounts to a poorly-thought-through "crowdsourced wheat-surfacing" architecture; I find it draining.
  - Zenst 7y ago
    Oh, seems there is one already, though I'm not going to submit it as a topic as only fuels fear, though fine in a comment for those who dug down enough :- https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6 https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.h...
- emmelaich 7y ago
  Sure, exercise some judgement, but there's wheat amongst the chaff.
Barrin92 7y ago
that place appears to be full of conspiracy theories, weirdly racist comments, and the one person who is a nurse is actually being downvoted for giving an accurate statement on the state of affairs. I'd avoid that subreddit

nabla9 7y ago

Novel coronavirus 2019-nCoV: early estimation of epidemiological parameters and epidemic predictions https://www.medrxiv.org/content/10.1101/2020.01.23.20018549v1 https://www.medrxiv.org/content/10.1101/2020.01.23.20018549v... >We estimate that only 5.1% (95%CI, 4.8-5.5) of infections in Wuhan are identified, and by 21 January a total of 11,341 people (prediction interval, 9,217-14,245) had been infected in Wuhan since the start of the year. Should the epidemic continue unabated in Wuhan, we predict the epidemic in Wuhan will be substantially larger by 4 February (191,529 infections; prediction interval, 132,751-273,649) >Our model suggests that travel restrictions from and to Wuhan city are unlikely to be effective in halting transmission across China; with a 99% effective reduction in travel, the size of the epidemic outside of Wuhan may only be reduced by 24.9% on 4 February.

greenonions 7y ago
Source: "Caution: Preprints are preliminary reports of work that have not been peer-reviewed. They should not be relied on to guide clinical practice or health-related behavior and should not be reported in news media as established information."

contingencies 7y ago

Today hacked together some scraped data with basic visualization at https://github.com/globalcitizen/2019-wuhan-coronavirus-data/ https://github.com/globalcitizen/2019-wuhan-coronavirus-data... ... contributions welcome I'm about off to bed.

juiyout 7y ago
Please don't include Taiwan as part of China.