Comment by pmayrgundter | Hacker News Reader

Comment by pmayrgundter | Hacker News Reader

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Good summary, thanks!

Related to the origin hypotheses, the hypothesis of zoonotic outbreak from a wet market in mid-Dec no longer seems as relevant. It was first laid out in a widely disseminated paper in The Lancet [1, see Figure 1B], but since then retrospective wastewater analyses from Italy[2], Spain[3], Brazil and others[4] have found it was circulating much earlier.

"The Italian National Institute of Health looked at 40 sewage samples collected from wastewater treatment plants in northern Italy between October 2019 and February 2020. An analysis released on Thursday said samples taken in Milan and Turin on Dec. 18 showed the presence of the SARS-Cov-2 virus." [2]

and

"Most COVID-19 cases show mild influenza-like symptoms (14) and it has been suggested that some uncharacterized influenza cases may have masked COVID-19 cases in the 2019-2020 season (11). This possibility prompted us to analyze some archival WWTP samples from January 2018 to December 2019 (Figure 2). All samples came out to be negative for the presence of SARS-CoV-2 genomes with the exception of March 12, 2019, in which both IP2 and IP4 target assays were positive. This striking finding indicates circulation of the virus in Barcelona long before the report of any COVID-19 case worldwide." [3]

[1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159299/ [2] https://www.reuters.com/article/us-health-coronavirus-italy-... [3] https://www.medrxiv.org/content/10.1101/2020.06.13.20129627v... [4] https://twitter.com/LMeigre/status/1282819131390210050

I think the “hypothesis of zoonotic outbreak from a wet market in mid-Dec” is still very relevant, and the few papers claiming to have evidence of SARS-CoV-2 prior to Dec 2019 outside China are still very questionable. It’s not like they tested old samples in a few places and the virus promptly showed up. Rather, lots of old samples were tested all over the place, and the virus almost never showed up, except in a very few instances that night more parsimoniously be explained with false positives.

Why not both?

There could have been a baseline level of the virus or a close brother of it in circulation early in 2019, but the conditions of the wet market ecosystem in late 2019 let it suddenly spiral out of control, or make a final evolution to its current high-transmissiveness form.

Sort of like how we can find, retrospectively, intermittent cases of HIV back to the early part of the 20th century, but it suddenly exploded in the 1980s.

It's actually been hypothesised from the beginning that ancestors of Covid-19 passed back and forth between humans and animals several times before taking its current form. The idea being that an ancestor of the virus was first transferred to humans where it 'learned' how to adapt to the human body before transmitting back to an animal host and mutated to become more deadly to humans and then transferred back to humans. This is partly based on the idea that a successful virus wouldn't adapt to be more lethal to its host and that close cousins of Covid-19 have been found in several species of bats and other animals.

This actually makes China a much better candidate than Europe for the place where the most important step in its evolution occurred. China has much more vibrant trade in wild animals for clothing, consumption, and traditional medicine. China also happens to be the place where the first reports of widespread hospitalisations occurred.

I don't think it's possible that Covid-19 in its current form could have floated around with its current high level of transmissivity or even the lower level of transmissibility of the Chinese strain without being detected for more than a month.

As we've seen from America's second wave (bumpy first wave?) the virus replicates exponentially (even with some social distancing), so tens of thousands of people can be infected within two weeks. So we ought to see pretty strong signal in ICU admissions within about 5 weeks of an outbreak (allowing ramp up time, incubation period, and time for symptoms to progress). We'd also expect to see all-cause mortality rates of people over 65 to increase significantly within about 7 to 8 weeks of the outbreak occurring as the average time to mortality is about 18 days.

I fail to see how it'd be possible for the health system of any developed nation to miss all that, but a developing country that has a culture of secrecy and suppressing information from both its own people and central authorities? Yeah I could believe that.

> Sort of like how we can find, retrospectively, intermittent cases of HIV back to the early part of the 20th century, but it suddenly exploded in the 1980s.

That's in large part because HIV collided with African urbanisation, significant international air travel deflation, an explosion of homosexual activity (unprotected sex), an industrialised blood transfer system, and a drug epidemic with administration using shared syringes. I can't think of a similar set of factors changing in our current society that could have allowed for the explosion of a coronavirus.

I would consider the final evolutionary jump to not have been at the wet market, but the virology lab where someone who works with the bat virus caught the one in circulation worldwide - this more deadly virus broke out in Wuhan because that was where the last jump occurred.

Some viruses lie dormant in our bodies for years, was someone at the lab infected with a bat SARs virus at some point, and all it needed was this other virus to come along for it to share some of its virulence?

It isn’t relevant, and hasn’t been since almost the beginning of the pandemic. We’ve known since March that the earliest retroactively identified case of the disease in China was from October and had no connection with the Wuhan wet market. The wet market may be the the earliest identified widespread outbreak, but it is clear that the crossover event happened earlier and the virus had been circulating at low levels prior to that.

> but it is clear that the crossover event happened earlier and the virus had been circulating at low levels prior to that.

Source? Definitely some experts think it is not impossible that it was brought to the wet market very early in the outbreak, that's not implausible at all. But the idea that it was circulating globally or widely at all before that is not backed by the evidence.

There are some Brazilian researchers in the process of mapping the whole genome of some samples collected and frozen back in November 2019 that they believe to be SARS-CoV-2.

It will be interesting to see how that compares to a Wuhan sample and see if it had most of the novel features of COVID-19, but is maybe missing one thing like how it binds to ACE2 which is probably implicated in all the cardiovascular issues it causes.

> Related to the origin hypotheses, the hypothesis of zoonotic outbreak from a wet market in mid-Dec no longer seems as relevant

Perhaps in your mind, but this is not at all a fair representation of the general scientific consensus - most still hold the weight of the evidence leans towards a November '19 origin in Wuhan

How did you determine the general scientific consensus?

Reading peer-reviewed papers & following field leaders on Twitter.

I have experience in academia, so it might be easier to parse because of that, but news articles are certainly not sufficient.

He cited papers, you referenced a "general scientific consensus". This is a gun fight, sir, so you'd best put that knife away.

I see you’ve played knifey spoony before!

He cited two scientific papers, one which is peer-reviewed and indicates that the virus originated in Wuhan and one which is an un-peer reviewed pre-print on medRxiv, funded by a private company with interest in promoting the efficacy of wastewater monitoring, that Covid was present in wastewater. It's worth looking in to, but hardly discredits the widely-accepted Wuhan origin yet.

In your poorly fit analogy, the scientific consensus would be the gun to the single, unreviewed paper's knife.

Please don't spew falsehoods and add 'general concesus' to it.

There are reports that the French team that traveled in October in Wuhan for mil. sports games, got infected by it. So, that it was at circulating in Wuhan at least since October, even most probably: early september.

https://www.telegraph.co.uk/news/2020/05/08/covid-19-pandemi...

The Telegraph is not a reliable source for anything connected to covid.

The Telegraph is not a reliable source for anything.

Newspapers are not a reliable source for news.

The Telegraph only qualifies as a newspaper in the loosest of terms, in that it also sometimes reports news and is published in dead tree form.

Whether that's likely or not can be estimated by extrapolating case numbers from January back in time into 2019 and using a reasonable estimate for the R0 value without any measures against the spreading of the disease. Even if you don't trust the Chinese numbers, the estimate should be roughly in the right ballpark, since we certainly didn't have millions of deaths in Wuhan in January. The initial exponential growth phase is similar in all regions with comparable population density.

I haven't crunched these numbers, but a start in early September seems unlikely to me - call it a hunch, based on looking at the initial growth curves.

Why did you quote me 'general concesus' and then misspell the word?

I'm not going to respond to the rest of the comment suggesting the Telegraph should be part of my consideration when judging the science.

I think you were partly right on this, so wanted to update you in case you're interested. Science has a new interview with Zhi Zhengli who also no longer supports the idea that it was probably from the market:

"However, two papers published in late January revealed that up to 45% of the first confirmed patients—including four of the five earliest cases—did not have any ties to the market, casting doubt on the theory that it was the origin. Shi agrees: “The Huanan seafood market may just be a crowded location where a cluster of early novel coronavirus patients were found.”

https://www.sciencemag.org/news/2020/07/trump-owes-us-apolog...

I read the spain paper. They don’t report the false positive rate of the test they used, but if it was one that was commonly available, that paper’s P-value is something like 0.5. They don’t compute a P value.

Until the others make it through peer review, I wouldn’t read anything into their results.

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