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A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence

Vineet D Menachery, Boyd L Yount, Kari Debbink

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Sudhakar Agnihothram, Lisa E Gralinski, Jessica A Plante, Rachel L Graham, Trevor Scobey, Xing-Yi Ge, Eric F Donaldson, Scott H Randell, Antonio Lanzavecchia, Wayne A Marasco, Zhengli-Li Shi, Ralph S Baric

2015 · Nature Medicine

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16 selected excerpts · 16 total mentions

maeil
Neutral mention · rule
You're right that Daszak and the Ecohealth Alliance are culpable, but it must be noted that various USG orgs were not supportive of his actions > The report he finally did submit stated that scientists planned to create an infectious clone of Middle East Respiratory Syndrome (MERS), a novel coronavirus found in dromedaries that had emerged in Saudi Arabia in 2012 and killed 35% of the humans it infected. The report also made clear that the NIH grant had already been used to construct two chimeric coronaviruses similar to the one that caused Severe Acute Respiratory Syndrome (SARS), which emerged in 2002 and went on to cause at least 774 deaths worldwide. (A chimeric virus…
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is one that combines fragments of different viruses.) These revelations prompted the NIH’s grant specialists to ask a critical question: Should the work be subject to a federal moratorium on what was called gain-of-function research? > But the [2015 research paper he cited](https://www.nature.com/articles/nm.3985) was not particularly reassuring. In it, Shi Zhengli and a preeminent coronavirus researcher at the University of North Carolina, Ralph Baric, mixed components of SARS-like viruses from different species, and created a novel chimera that was able to directly infect human cells. (Baric did not respond to written questions seeking comment.) > If anything, the MERS study Daszak proposed was even riskier. So he pitched a compromise to the NIH: that if any of the recombined strains showed 10 times greater growth than a natural virus, “we will immediately: i) stop all experiments with the mutant, ii) inform our NIAID Program Officer and the UNC [Institutional Biosafety Committee] of these results and iii) participate in decision making trees to decide appropriate paths forward.” > This mention of UNC brought a puzzled response from an NIH program officer, who pointed out that the proposal had said the research would be performed at the WIV. “Can you clarify where the work with the chimeric viruses will actually be performed?” the officer wrote. Ten days later, with still no response from Daszak, the program officer emailed him again. On June 27, Daszak responded, buoyant as ever: > “You are correct to identify a mistake in our letter. UNC has no oversight of the chimera work, all of which will be conducted at the Wuhan Institute of Virology…. We will clarify tonight with Prof. Zhengli Shi exactly who will be notified if we see enhanced replication…my understanding is that I will be notified straight away, as [principal investigator], and that I can then notify you at NIAID. Apologies for the error!” > Allowing such risky research to go forward at the Wuhan Institute of Virology was “simply crazy, in my opinion,” says Jack Nunberg, director of the Montana Biotechnology Center. “Reasons are lack of oversight, lack of regulation, the environment in China,” where scientists who publish in prestigious journals get rewarded by the government, creating dangerous incentives. “So that is what really elevates it to the realm of, ‘No, this shouldn’t happen.’” In general, his actions make clear he's much more aligned with the Chinese government than the US, so extending Daszak to US govt purely based off of nationality seems unjust. > On January 30, Daszak went on CGTN America, the U.S. outpost for Chinese state television, and said two things that proved to be spectacularly wrong. “I’m very optimistic…that this outbreak will begin to slow down,” he said. “We’re seeing a small amount of human-to-human transmission in other countries, but it’s not uncontrollable." He went on to conclude that the Chinese government was taking all necessary steps “to be open and transparent, and work with WHO, and talk to scientists from around the world, and where necessary, bring them in to help. They’re doing that. It’s exactly what needs to happen.”
rngname22
Neutral mention · rule
> why the lab in question would be doing secret work on coronaviruses what was secret about it? the lab in Wuhan was literally doing research in 2015 on how bat coronaviruses could adapt to spread in humans vs ACE2 receptors and developed their own strain: https://www.nature.com/articles/nm.3985 from the linked study: "Using the SARS-CoV reverse genetics system, we generated and characterized a chimeric virus expressing the spike of bat coronavirus SHC014 in a mouse-adapted SARS-CoV backbone. The results indicate that group 2b viruses encoding the SHC014 spike in a wild-type backbone can efficiently use multiple orthologs of the SARS receptor human angiotensin converting…
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enzyme II (ACE2), replicate efficiently in primary human airway cells and achieve in vitro titers equivalent to epidemic strains of SARS-CoV. Additionally, in vivo experiments demonstrate replication of the chimeric virus in mouse lung with notable pathogenesis.... On the basis of these findings, we synthetically re-derived an infectious full-length SHC014 recombinant virus and demonstrate robust viral replication both in vitro and in vivo. Our work suggests a potential risk of SARS-CoV re-emergence from viruses currently circulating in bat populations."
tim333
Neutral mention · rule
>the gain of function research with coronaviruses has been documented in the peer-reviewed literature The main peer reviewed gain of function research cited is https://www.nature.com/articles/nm.3985 done in 2015 in the US with one of the researchers being Shi Zhengli of the Wuhan lab. I'm not sure there are any papers on gain of function research done in Wuhan?
uvesten
Neutral mention · rule
There's so many attempts to muddy the waters it would be funny if it wasn't so serious. Even though I'm not sure you attempted to do that here, it certainly reads like it. So, basically, you're saying that (many, we know how contagious covid 19 is) people got sick and put into hospital/died with a novel respiratory disease in another (or several other) chinese cities first. However, that was covered up or unnoticed _until_ it reached wuhan, and for some reason a researcher who works with coronaviruses at the lab saw a sick patient (at the hospital?), realized "that looks like a novel coronavirus" and decided to raise the alarm? Additionally, after that only Wuhan got shut…
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down, while the other city or cities which should have had a raging epidemic by now still went unnoticed? That's what I mean, these other theories to explain away what is the most staightforward explanation makes no sense, and invokes too many unlikely scenarios or coincidences. Regarding gain-of-function, see [nature article from 2015](https://www.nature.com/news/engineered-bat-virus-stirs-debat...) questioning the safety of gain-of-function research, and the article that [triggered the reaction](https://www.nature.com/articles/nm.3985). Part of that research took place in the Wuhan lab. (Then there are the conflicts of interest of the WHO investigator Peter Daszak, who is very quick to discredit any theory that the virus might have escaped from the lab...) Again, this is a farce, and it would almost be funny if it weren't for all the dead and the generally shitty situation for most of the world at the moment.
jquaint
Neutral mention · rule
repeating my comment from the last times this was posted: https://news.ycombinator.com/item?id=27026039 https://news.ycombinator.com/item?id=27034782 This post (whether intentionally or not) is misinterpreting some of the evidence it presents. For example it gives this example research grant as evidence for chimeric viruses being made in the Wuhan lab. https://reporter.nih.gov/search/xQW6UJmWfUuOV01ntGvLwQ/proje... This is actually pretty standard virology grant. Nowhere does it say that they are making chimeric viruses. Note that "S protein sequence data, infectious clone technology, in vitro and in vivo infection experiments" is not even close to "Creating chimeric…
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viruses". This is not the same thing and it would not be rational to compare the two. The posts claim that: "What this means, in non-technical language, is that Dr. Shi set out to create novel coronaviruses with the highest possible infectivity for human cells. ". That is simply false, they are collecting and testing viruses. They were not creating new ones. This post also tries to claim that these researches had been doing genetic engineering in past work because of this paper: https://www.nature.com/articles/nm.3985 Note that Nature added an editors note here: "30 March 2020 Editors’ note, March 2020: We are aware that this article is being used as the basis for unverified theories that the novel coronavirus causing COVID-19 was engineered. There is no evidence that this is true; scientists believe that an animal is the most likely source of the coronavirus." Also note that the Wuhan lab is actually 5th author on this paper. In big publications like this order of authors is very important. 5th author usually means that they had a very minor role in the work. I.e a consulting role. This is compounded by the fact that only 2 people from the Wuhan lab worked on this paper. It is actually more likely that the "genetic engineering" took place at the University of North Carolina and not in Wuhan. The paper lists a 9 people on the project in the US. Usually the people who do the actual lab work get first author. Even further what about the 9 other virology labs that are on list? They have about the same amount of contributions to this paper? Why are they not suspect? In my opinion these are some pretty key details to leave out, especially from a science journalist who should not be hiding some of the key facts here.
frombody
Neutral mention · rule
The US government pulled funding for this, but coronavirus research was allowed to continue because they secured funding before the ban. https://www.the-scientist.com/news-opinion/lab-made-coronavi... Incidentally, most of Ralph Baric's research ended up in Wuhan with Zhengli-Li Shi and his team, where their research continued. https://www.nature.com/articles/nature12711 https://www.nature.com/articles/nm.3985
propogandist
Neutral mention · rule
One of the few bio safety level 4 labs in the world, but it's not simple as pointing a finger at a lab alone. The University of Wuhan and University of North Carolina at Chapel Hill, have worked collaboratively on research on a SARS like novel coronavirus found in Chinese Horseshoe bats back in 2015 [1]. The research, as noted on the bottom of the report, was funded by grants from National Institute of Health (under Anthony Fauci's leadership), US AID Emerging Pandemic Threats program and other funding sources, including many US based researchers. [1]- https://nature.com/articles/nm.3985
burntoutfire
Neutral mention · rule
The origin of the virus. The mainstream media assumes the virus was created in a natural process of mutation and jumping species, while there's this little paper [1] in Nature Medicine from 2015 where authors (virologists) confirm that they created a novel, human-transmisible coronavirus, based on a new virus they discovered among bats. Some of the authors of the paper are from Key Laboratory of Special Pathogens and Biosafety at the Wuhan Institute of Virology... [1] https://www.nature.com/articles/nm.3985
eric_bullington
Neutral mention · rule
With modern genomic science, we can pinpoint almost the exact time and place Covid-19 jumped from an animal host (likely pangolins intermediate host from bat reservoir) to humans. It almost certainly jumped hosts to humans in November of 2019[1]. It has not been circulating in humans for long. Indeed, several scientific publications have come out in the past decade that more or less predicted that a similar strain of SARS would jump hosts and become a pandemic disease[2]. Also, technically the Spanish Flu was just a bad flu season, right? Now, few believe now that Covid-19 will be nearly as bad as the 1918 pandemic (at least in its current mutation), but it will almost…
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certainly worse than the 1957 flu pandemic, which was bad enough and which resulted in many governmental edicts similar to today, with many school and library closings. I agree we need to keep cool and not overreact or panic, but we also need to take this thing very seriously. Even the experts are trying to figure this thing out. Disease modeling has come a long way since 1918, but modelers are not seers. 1. https://www.statnews.com/2020/01/24/dna-sleuths-read-coronav... 2. https://www.nature.com/articles/nm.3985 3. https://www.encyclopedia.com/media/educational-magazines/inf...
c789a123
Neutral mention · rule
The doctors were not jailed, because luckily CCP need them to work to fight the virus. Some of them died for it already, mostly due to the hard work, insufficient protection CCP provided to the doctors, and in one case at least, intentionally punish the doc by delay his treatment. Talking about the origin of this virus, this paper of 2015 is quite interesting: https://www.nature.com/articles/nm.3985 . In this paper, the wuhan P4 institute people basically described how they produced a prototype of the 2019 wuhan virus.
kjaftaedi
Neutral mention · rule
You don't need to believe this is a bio-weapon .. although that certainly is now the end results. I'm not implying causation, but what you are saying about them not developing viruses is not true. In fact, they were working on specifically this. Here is an article from January talking about the virus orgins: https://www.sciencemag.org/news/2020/01/mining-coronavirus-g... How does Shi Zheng-Li of the Wuhan Institute of Virology know so much about this topic? Because he's been working on exactly this for almost a decade. Here's an early paper. https://www.nature.com/articles/nature12711 Years later he ends up working with a team from the US on a man-made coronavirus paper…
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here: https://www.nature.com/articles/nm.3985 The US government pulled funding for all programs like this, but this one was allowed to continue because they had secured funding before the ban. Discussion here: https://www.the-scientist.com/news-opinion/lab-made-coronavi... Whether they accurately predicted the future, or made a huge lab error is up for debate in my book, and is something that should at least be investigated. Lab mistakes happen all of the time, and we're talking about something that has a subsantial ability to spread itself. Here is an expert's unbiased analysis of whether this could be man made: https://threadreaderapp.com/thread/1221990534643929089.html Given all of this, I don't think it's wholly unreasonable to consider whether or not human error played a role in all of this.
jquaint
Neutral mention · rule
repeating my comment from the last times this was posted: https://news.ycombinator.com/item?id=27026039 https://news.ycombinator.com/item?id=27034782 This post (whether intentionally or not) is misinterpreting some of the evidence it presents. For example it gives this example research grant as evidence for chimeric viruses being made in the Wuhan lab. https://reporter.nih.gov/search/xQW6UJmWfUuOV01ntGvLwQ/proje... This is actually pretty standard virology grant. Nowhere does it say that they are making chimeric viruses. Note that "S protein sequence data, infectious clone technology, in vitro and in vivo infection experiments" is not even close to "Creating chimeric…
Read the full comment
viruses". This is not the same thing and it would not be rational to compare the two. The posts claim that: "What this means, in non-technical language, is that Dr. Shi set out to create novel coronaviruses with the highest possible infectivity for human cells. ". That is simply false, they are collecting and testing viruses. They were not creating new ones. This post also tries to claim that these researches had been doing genetic engineering in past work because of this paper: https://www.nature.com/articles/nm.3985 Note that Nature added an editors note here: "30 March 2020 Editors’ note, March 2020: We are aware that this article is being used as the basis for unverified theories that the novel coronavirus causing COVID-19 was engineered. There is no evidence that this is true; scientists believe that an animal is the most likely source of the coronavirus." Also note that the Wuhan lab is actually 5th author on this paper. In big publications like this order of authors is very important. 5th author usually means that they had a very minor role in the work. I.e a consulting role. This is compounded by the fact that only 2 people from the Wuhan lab worked on this paper. It is actually more likely that the "genetic engineering" took place at the University of North Carolina and not in Wuhan. The paper lists a 9 people on the project in the US. Usually the people who do the actual lab work get first author. Even further what about the 9 other virology labs that are on list? They have about the same amount of contributions to this paper? Why are they not suspect? In my opinion these are some pretty key details to leave out, especially from a science journalist who should not be hiding some of the key facts here.
jquaint
Neutral mention · rule
repeating my comment from the last time this was posted: https://news.ycombinator.com/item?id=27026039 This post (whether intentionally or not) is misinterpreting some of the evidence it presents. For example it gives this example research grant as evidence for chimeric viruses being made in the Wuhan lab. https://reporter.nih.gov/search/xQW6UJmWfUuOV01ntGvLwQ/proje... This is actually pretty standard virology grant. Nowhere does it say that they are making chimeric viruses. Note that "S protein sequence data, infectious clone technology, in vitro and in vivo infection experiments" is not even close to "Creating chimeric viruses". This is not the same thing and it would…
Read the full comment
not be rational to compare the two. The posts claim that: "What this means, in non-technical language, is that Dr. Shi set out to create novel coronaviruses with the highest possible infectivity for human cells. ". That is simply false, they are collecting and testing viruses. They were not creating new ones. This post also tries to claim that these researches had been doing genetic engineering in past work because of this paper: https://www.nature.com/articles/nm.3985 Note that Nature added an editors note here: "30 March 2020 Editors’ note, March 2020: We are aware that this article is being used as the basis for unverified theories that the novel coronavirus causing COVID-19 was engineered. There is no evidence that this is true; scientists believe that an animal is the most likely source of the coronavirus." Also note that the Wuhan lab is actually 5th author on this paper. In big publications like this order of authors is very important. 5th author usually means that they had a very minor role in the work. I.e a consulting role. This is compounded by the fact that only 2 people from the Wuhan lab worked on this paper. It is actually more likely that the "genetic engineering" took place at the University of North Carolina and not in Wuhan. The paper lists a 9 people on the project in the US. Usually the people who do the actual lab work get first author. Even further what about the 9 other virology labs that are on list? They have about the same amount of contributions to this paper? Why are they not suspect? In my opinion these are some pretty key details to leave out, especially from a science journalist who should not be hiding some of the key facts here.
jquaint
Neutral mention · rule
This post (whether intentionally or not) is misinterpreting some of the evidence it presents. For example it gives this example research grant as evidence for chimeric viruses being made in the Wuhan lab. https://reporter.nih.gov/search/xQW6UJmWfUuOV01ntGvLwQ/proje... This is actually pretty standard virology grant. Nowhere does it say that they are making chimeric viruses. Note that "S protein sequence data, infectious clone technology, in vitro and in vivo infection experiments" is not even close to "Creating chimeric viruses". This is not the same thing and it would not be rational to compare the two. The posts claim that: "What this means, in non-technical language,…
Read the full comment
is that Dr. Shi set out to create novel coronaviruses with the highest possible infectivity for human cells. ". That is simply false, they are collecting and testing viruses. They were not creating new ones. This post also tries to claim that these researches had been doing genetic engineering in past work because of this paper: https://www.nature.com/articles/nm.3985 Note that Nature added an editors note here: "30 March 2020 Editors’ note, March 2020: We are aware that this article is being used as the basis for unverified theories that the novel coronavirus causing COVID-19 was engineered. There is no evidence that this is true; scientists believe that an animal is the most likely source of the coronavirus." Also note that the Wuhan lab is actually 5th author on this paper. In big publications like this order of authors is very important. 5th author usually means that they had a very minor role in the work. I.e a consulting role. This is compounded by the fact that only 2 people from the Wuhan lab worked on this paper. It is actually more likely that the "genetic engineering" took place at the University of North Carolina and not in Wuhan. The paper lists a 9 people on the project in the US. Usually the people who do the actual lab work get first author. Even further what about the 9 other virology labs that are on list? They have about the same amount of contributions to this paper? Why are they not suspect? In my opinion these are some pretty key details to leave out, especially from a science journalist who should not be hiding some of the key facts here.
kjaftaedi
Neutral mention · rule
I have no doubt Zhengli-Li Shi likely knows more about this than anyone else in the world https://www.nature.com/articles/nature12711 https://www.nature.com/articles/nm.3985 But given the fact that he and the Wuhan Institute of Virology are at the direct center of the outbreak, I wouldn't trust them not to be covering their own asses if they happened to be at fault.

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