Decoding evolution and transmissions of novel pneumonia coronavirus | Hacker News Reader

Decoding evolution and transmissions of novel pneumonia coronavirus

researchgate.net

99 points1_over_n55 comments

Interesting paper. I haven't dug into the methods/data in depth. But the gist of their interpretation is:

- Out of the initial 41 cases, 27 were linked to the seafood market. The first identified cases + 12 others had no link to the market.

- Phylogenetic analysis suggests two potential ancestral haplotypes. None of the seafood market haplotypes were the two potential ancestral.

- The very first initial cases (family from Shenzhen) was one of the two potential ancestral haplotype.

I am a bioinformatics phd and know enough about phylogenetic analysis to say that it can sometimes be ambiguous and have some elements of subjectivity, especially with low sample sizes. So I wouldn't be too fast to jump on these results. However, I haven't gone through the data in detail to really give a good opinion.

Thanks, it is really helpful. If the patient zero is from Shenzen, doesn't that weaken the hypothesis of an origin in a bat virus? (Population density = 6,100/km2)

I don't know enough about the cases. But initially identified cases doesn't equate to patient zero. I think it was just the first case chronologically identified.

There is a fair chance patient zero simply recovered and was never identified as carrier.

The paper cites GISAID db as their datasource. I wonder if at present the db includes sufficient number of early samples prior to the mentioned Dec 8), given the widely described massive efforts by official China to silence the early reports of the outbreak [0]?

0: https://www.businessinsider.com/china-information-crackdown-...

Thanks for your insight! If not from the seafood market, is it possible to speculate (in an informed way) of what the source may have been? When novel viruses break into human populations, is some form of animal contact generally the culprit? Is something like a bat sneezing near you (I have no idea if bats sneeze) with an airborne virus sufficient to transfer to a human?

> Is something like a bat sneezing near you (I have no idea if bats sneeze) with an airborne virus sufficient to transfer to a human?

I think the theory for SARS went something like -- lots of live animals together in a market, bat guano gets on some fruit, a civet eats guano-laced fruit, a person eats the civet later. Doesn't have to be simple transmission.

Chinese have been known to eat all kind of exotic wild animals for medicinal and recreational reasons.

The government may be trying to curb this, but a large portion of Chinese are still rural and food superstitions are rife, the regulation is not that easy I suppose.

https://youtu.be/rbHxeOQA1Mc

There's a level 4 virology research center in Wuhan, which means it studies the most dangerous pathogens in the world. This facility has been collecting SARS-like virus samples from bat populations and other animal populations for years. Some are speculating that it may have escaped the lab.

That is very speculative and currently not accepted. See this HN discussion and the paper [1]

[1] https://news.ycombinator.com/item?id=22352908

Not accepted by who? It is speculative, but seeing as we don't have hard evidence of the source, it remains a very valid theory.

Here's a quote from this article [1]:

> A group of 27 prominent public health scientists from outside China is pushing back against a steady stream of stories and even a scientific paper suggesting a laboratory in Wuhan, China, may be the origin of the outbreak of COVID-19. “The rapid, open, and transparent sharing of data on this outbreak is now being threatened by rumours and misinformation around its origins,” the scientists, from nine countries, write in a statement published online by The Lancet yesterday.

[1] https://www.sciencemag.org/news/2020/02/scientists-strongly-...

Keyphrase: Health scientists OUTSIDE of China. They're not in China. They don't have the independence to investigate. They have no way to say one way or another. There has not been an independent, forensic investigation into the origins because the CCP controls everything in China.

A WHO team is just back from China and their assessment is that the outbreak is currently declining there and the numbers provided by China are reasonably accurate. Following are comments by WHO epidemiologist Bruce Aylward in the following articles:

> He [Aylward] pointed to humped graphs of cases over time—they are the shape of an epidemic that has been hobbled, he said. Disease spread has been in decline since the beginning of the month, and doctors in China are honing their ability to treat patients. “If I had COVID-19, I’d want to be treated in China,” he said candidly. [1]

> There’s plenty of reason to doubt the official numbers—Chinese officials initially covered up the virus and arrested whistle-blowers who tried to expose the outbreak. Aylward acknowledged these concerns on Monday, but added: “The decline that we see is real.” [2]

[1] https://arstechnica.com/science/2020/02/coronavirus-spread-i...

[2] https://www.wired.com/story/could-the-us-contain-a-coronavir...

Here's a quote from the Lancet statement:

> Scientists from multiple countries have published and analysed genomes of the causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2),1 and they overwhelmingly conclude that this coronavirus originated in wildlife

The person you're responding to above says that the lab has been collecting samples of SARS-like viruses from wildlife for study, and conjectures that maybe one of those escaped from the lab. That possibility is not contradicted by the statement in the Lancet.

Well, compared to the evidence that points to the mainstream theory, this alternative is infinitely more robust.

ResearchGate wasn't linking me back to the original point of publication, and the DOI doesn't seem to be valid (yet?). It turns out this was uploaded to the Chinese arXiv equivalent on the 19th.

http://www.chinaxiv.org/abs/202002.00033

How have I never heard of chinaxiv? Thanks for bringing this to my attention.

I worry that we may be spreading misinformation.

https://science.slashdot.org/story/20/02/21/2257228/scientis...

Your link is about "Conspiracy Theories About Origin of Coronavirus Outbreak" on social media which may cause "real consequences, including threats of violence that have occurred to our colleagues in China".

Parent's link is to a genomic analysis of COVID-19 trying to reconstruct its evolution, authored by researchers all working in China.

Unless you think that no attempt should be made to determine the origins of the virus because of what trolls might make of it, I don't see the problem. If you do think that trolls should have that power, it's pretty late to worry about it: the official narrative about it all having started in Wuhan's seafood market has been known to be incomplete at best for a while now:

https://www.sciencemag.org/news/2020/01/wuhan-seafood-market...

"Known to be"?

I really take issue with that phrase.

As maddening as it may be, we DO NOT KNOW the origins of the virus. And after reading a new paper -- we still do not know. We have to stop acting like we do.

> "Known to be"? > I really take issue with that phrase.

That's your phrase, not mine.

What I wrote is "the official narrative about it all having started in Wuhan's seafood market has been known to be incomplete at best for a while now".

> As maddening as it may be, we DO NOT KNOW the origins of the virus

Yes. That's what I said.

You are arguing against your own position, not mine.

It came across to me as stereotyping to just assume certain people engaged in something very specific without any evidence in order to look down on them.

Furthermore, it's also impossible to prove where it didn't come, also without evidence, because you can't prove a negative.

That may be so, but bush meat has been positively identified as the source of quite a few outbreaks.

As an aside, I always found it strange that eating wild land animals is looked down upon as "bushmeat" and unsustainable and unhygienic, while eating wild sea creatures is just "seafood" (with farmed aquafauna looked down upon as the inferior product).

That's a good point. There is plenty of seafood that when not dealt with properly will happily kill you or make you at a minimum severely ill. Mussels, shellfish, oysters are best avoided unless you are very sure about where they came from and how they were prepared.

Besides that, due to the liquid environment anything in the sea that is poisonous is usually so in a very potent fashion. Species jumping viruses are rare when it comes to regular fish but marine mammals are a risk.

I’m confused. SARS and COVID-19 (the current coronavirus outbreak) aren’t the same, right? Which one are we talking about here?

COVID-19 is the name of the disease

SARS-CoV-2 is the name of the new gene.

From Wikipedia [0] I think that you are right that COVID-19 is the name of the disease, but SARS-CoV-2 is the name of a coronavirus, not the name of a gene:

Citation: " During the ongoing 2019–20 coronavirus outbreak, the World Health Organization (WHO) originally recommended use of the temporary designation "2019-nCoV" (2019 novel coronavirus) to refer to the virus. However, this led to concerns that the absence of an official name might lead to the use of prejudicial informal names, and in common parlance the virus was often referred to as "the new coronavirus", "Wuhan coronavirus", or simply "coronavirus". Per 2015 WHO guidelines on the naming of viruses and diseases, the International Committee on Taxonomy of Viruses (ICTV) announced that it would introduce a suitable official name for the virus.

On 11 February 2020, the ICTV introduced the name "severe acute respiratory syndrome coronavirus 2" (SARS-CoV-2) to refer to the virus strain previously known as 2019-nCoV. Earlier the same day, the WHO officially renamed the disease caused by the virus strain from "2019-nCoV acute respiratory disease" to coronavirus disease 2019 (COVID-19). "

[0] https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndr...

"On February 11, 2020, the International Committee on Taxonomy of Viruses, charged with naming new viruses, named the novel coronavirus, first identified in Wuhan, China, severe acute respiratory syndrome coronavirus 2, shortened to SARS-CoV-2.

As the name indicates, the virus is related to the SARS-associated coronavirus (SARS-CoV) that caused an outbreak of severe acute respiratory syndrome (SARS) in 2002-2003, however it is not the same virus." [1]

[1] https://www.cdc.gov/coronavirus/2019-ncov/faq.html

It's doubly confusing because "SARS" stands for Severe Acute Respiratory Syndrome, but SARS-CoV-19 is a virus, not the syndrome. But we aren't calling the disease SARS-19, we are calling it COVID-19...

I believe SARS-CoV-2 is the causative agent of the COVID-19 disease, maybe similar to how B. anthracis causes anthrax or HIV causes AIDS. (I'm not a virologist or epidemiologist, though.)

That's not the actual headline.

We have no way of assessing the credibility of this research.

Indeed, not the original title. Speculatively stated like a click-bait.

We've changed the title to the original now, as the site guidelines ask: "Please use the original title, unless it is misleading or linkbait; don't editorialize." (https://news.ycombinator.com/newsguidelines.html)

(Submitted title was "Genomic analysis suggests seafood market was not SARS-CoV-2 source". )

Sorry, i posted the link and the full title was too long to fit in the field. I did editorialize it as the intention was to draw attention to the claim. Noted for future posts.

Edited to include claim in journal below:

"This suggests that the source of the coronavirus in the Hua Nan market was imported from elsewhere"

Of all the possible HN users out there, stating there is no way of assessing the credibility of this research is quite a big statement.

The point of journal articles is that the methods and data can be evaluated. Hopefully, someone with experience in this technique can give their position on this research and given it's a hot topic, I'm sure it won't be long until the broader scientific community has some input.

What was it?

That's not known.

Then what is the probable possible sources?

If someone separate them by media says, twitter says, science says, conspiracy says? It will be great.

These viruses have a reservoir in bats and they jump to humans through an intermediary animal. In the case of the virus that caused SARS[1], which was another coronavirus within the same family as the current virus of interest, there is some evidence that it went bats -> palm civets -> humans. Palm civets are/were sold at wet markets in China. It's not definitive that the palm civet was the source, however, as they subsequently found the virus in other animals.

For the current virus[2], the time and place of transfer is unknown, but the current thinking seems to be that it followed the same chain as SARS (bats -> some animal -> humans).

There is absolutely zero evidence from credible scientists of any kind of "escaped from the lab" or "bioweapon" source. These are just conspiracy theories.

[1] https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndr...

[2] https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndr...

Without jumping into conspiracy bandwagon, I still can't see how "originated from bats" is better then "bioweapon" if neither has concrete evidence or proof.

One has plausibility and some evidence from DNA sequencing and mutation rates on its side, the other hasn‘t.

>the other hasn‘t

Just because some people don't believe that is likely, that does not mean it is not _plausable_

Is it plausible that there could be a biological lab in Wuhan? Yes, in fact, there is one.

Is it plausible that some countries do research on biological weapon? Yes, in fact there are multiple cases of such occasions: https://en.wikipedia.org/wiki/United_States_Army_Biological_...

Is it plausible that biological lab can leak bioweapon? Yes, in fact this happened before, e.g. https://en.wikipedia.org/wiki/Sverdlovsk_anthrax_leak

There is ample proof of a connection to bats, including a 96% similarity of SARS-CoV-2 to a sampled bat coronavirus in Hubei province. Numerous papers, with ample evidence in that direction. Just not enough to speak definitively and categorically.

There is --zero-- evidence of a bioweapon.

So it's better in the sense that it's reflective of reality, which also happens to not inflame international relations at a crucial time.

It doesn't have to be a bioweapon but there's no evidence to confirm or deny that this escaped from the Wuhan Virology Institute. It could have very easily infected a worker from the lab if safety precautions were not followed. And the CCP would never disclose it.

Interestingly enough, most information/speculation about the viruses origins are actively suppressed by google/twitter/reddit.

How do you know that? Care to share more details?

zerohedge's twitter account was blocked permanently for sharing a post on the origin of the virus. For one.

They banned them for doxing a researcher.

https://www.washingtonpost.com/technology/2020/02/01/twitter...

Is it doxing if they just republished already public information on the virology lab's website?

Debatably not, but that's not what Zero Hedge published:

The Zero Hedge post questioned the involvement of a virology institute in Wuhan, the city where the outbreak began. It listed the name, photograph and contact information for a researcher at the institute, and called on readers to “pay [him] a visit” if they want to “find out what really caused the coronavirus pandemic.”

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