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Comment by daemonk | Hacker News Reader

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.

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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.

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.

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

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