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Wuhan hospital traffic, search engine data indicate virus activity in Fall 2019 (dash.harvard.edu)
457 points by abc-xyz on June 8, 2020 | hide | past | favorite | 304 comments

This just seems so bogus. Suggesting the virus was circulating in China as early as August but was being covered up?

It’s the 21st century. There were many direct flights between Wuhan and the United States every day, as well as with other countries. If the virus were circulating in august that would have given it months to spread to the USA. We know from antibody studies and the lack of deaths that didn’t happen - the virus didn’t spread widely until 2020.

Vietnam has a population of 100 million and a land border with China. They activated their pandemic response in January and have had ZERO coronavirus deaths. Taiwan, again, activated their response on December 31, 2019, and has had only 7 deaths from COVID-19. These numbers are impossible to square with the idea that COVID-19 was in wide circulation in the Chinese population in August or September.

Therefore the idea that it was circulating in human-to-human transmission in China as early as 4 months before 2020 just can’t make sense.

This seems like science in service of politics or publicity - it’s already being breathlessly used as proof that China somehow covered up the virus for months as an attack on western civilization (again, this doesn’t make sense - when Wuhan actually did come under heavy threat from the virus, social media posts and videos did leak out to us in January).

> Suggesting the virus was circulating in China as early as August but was being covered up?

It's a well established fact that the existence of the virus was initially being covered up and local doctors trying to raise the alarm were being silenced. Even mainland Chinese know this (and are angry with the authorities). One of those doctors was Li Wenliang who has become somewhat of a national hero after his death to covid[1]. Him and dozens of others were given a very stern warning to stop talking about the possibility of a new disease outbreak in the weeks prior to covid becoming official when overwhelming evidence made it no longer possible to sweep under the rug.

The only angle here is that the time when the outbreak began is earlier than thought. This isn't even related to the notion of any coverup. It could have been circulating for months in low volumes without anyone really paying attention. Until the outbreak reaches critical mass, all you'll get is micro clusters which appear and disappear without really blowing up - as we're now seeing in countries that got their first wave under control.

The fact that people here still think that the initial coverup is some sort of conspiracy theory, when it's common knowledge even in China, is a bit mind blowing.


I call this intelligentsia-baiting. Where one needs to educate others parroting insights(/memes) from coastal-elite-marking editorials without reading primary sources.

Li Wenliang was neither a whistleblower nor did he have any first-hand novel data to share. He, an ophthalmologist, received a private group message within the hospital from ER department director and he simply re-shared the message to other private groups with his classmates.

The ER director, Ai Fen, was the source of the hypothesis that some patients in the hospital had, incorrectly, SARS and she was the right channel to escalate in the first place. And her escalation was successful when 1 nurse was observed to have been infected on January 11th.

Li never intended to broadcast anything to the public. What he did privately share was far less detailed than was on the official Wuhan government site [1], the Hubei provincial site [2] and just general mainstream social media [3] from the same date anyway.

[1] http://archive.is/s9elD [2] http://wjw.hubei.gov.cn/fbjd/dtyw/201912/t20191231_1822343.s... [3] https://finance.sina.cn/chanjing/gdxw/2019-12-31/detail-iihn...

thx for sharing this!

That “only angle” is precisely the problem, as the parent commenter explains quite clearly. It makes sense that some doctors could be briefly silenced for a few weeks at the very beginning of a large virus outbreak (but as we saw, even that apparently attempt to silence failed). It doesn’t make sense that a virus with these characteristics could be covered up for many months without even international travel restrictions.

But err, that's exactly what's happened. We now know that China locked down domestic flights originating from Wuhan in Jan 23. While at the same time pressuring various world governments and WHO to continue accepting international flights.

I feel like this needs to be unpacked for a lot of people. There are two pieces:

1: This paper claims that the virus was circulating in micro-clusters earlier than currently believed. It makes no claims as to any coverup.

2: There is clear evidence of an aggressive coverup lasting at least several weeks prior to covid becoming official. This makes no claims as to when the virus started circulating. Only when the authorities became aware of it.

These two statements are unrelated. The root parent post poisoned the well by conflating them. This paper is just another step towards tracking down the origin of the virus, it has nothing to do with coverups - whether real or conspiracy theory.

> We now know that China locked down domestic flights originating from Wuhan in Jan 23. While at the same time pressuring various world governments and WHO to continue accepting international flights.

As someone else pointed out, this is not a “now know”, it was public the same day in January that it happened.

Also, international flights mentioned were from other places than Wuhan - the international flights out of Wuhan were stopped at the same time as the domestic flights. https://www.factcheck.org/2020/05/trumps-flawed-china-travel...

> 1: This paper claims that the virus was circulating in micro-clusters earlier than currently believed. It makes no claims as to any coverup.

If the virus were circulating to the point of significantly increasing hospital visits in September, that means the Chinese doctors were covering up/hiding atypical pneumonia cases for months. (This doesn’t actually make sense because a virus doesn’t stop spreading because of a cover-up of course and would have escaped Wuhan much earlier)

> We now know that China locked down domestic flights originating from Wuhan in Jan 23.

They locked down all flights originating from Wuhan. In fact, they completely shut down the airport.

The incorrect claim that international flights continued was invented by Niall Ferguson of the Hoover Institution, and then spread uncritically by various news media, as detailed in The Independent: https://www.pressreader.com/uk/the-independent-1029/20200607...

As far as I can tell, the root parent tried to address the various posts here, but mostly on other (social media) sites that immediately jump to the conclusion that do connect 1 and 2. That this was indeed covered up for months, and that this was all planned by China to hurt the west, and whatnot. I see this a lot. It's like we desperately need to focus on things in other countries that are even worse than all the issues we have here. Too bad that stupid cop killed that black guy, ruined the party and shifted our attention back.

> Too bad that stupid cop killed that black guy

You meant to say "too bad those stupid cops have been killing and stomping on black guys for about a century now".

To put it extremely mildly, it's not a response to that one singular incident. This one just happened to be unambiguously caught on camera.

A rational discourse backed by data is way more useful than meaningless comments trying to fan the flames. I'd recommend having another HN thread if you'd really want to have this discussion, and I will happily participate.

Cops have been intentionally terrorizing 40 million black Americans since forever.

The lockdown happened in Jan 20, and it is public. Not 'we now know', it is 'we knew'. What's wrong with "pressuring various world governments and WHO to continue accepting international flights"? Did any country during this crisis prevent their own people from going out except Wuhan China? Did countries stop receiving European and American when there are cases in those countries?

I like how you generalize everything as 'well established fact', 'even mainland Chinese know', 'common knowledge'. And yes, I don't think there are initial coverup, and the world has both underestimated and overestimated the virus. Try to analyze how guardian covers the virus over a time, you will understand how journalism work in a modern age.

Are you going to shoot people with virus?

Not trying to prove you wrong, but I really don't think anyone has enough facts to claim either way confidently. I don't necessarily agree with all of the data presented, but I think your response to it is emotional and unwarranted—the authors haven't said anything about cover up as far as I can tell.

Also, I think just because it's circulating doesn't necessarily mean that there is a good chance of it being brought to other countries. If it really started off in a wet market, I can imagine that the people who are most susceptible to catching the virus initially are not those who can afford/have the opportunity to travel.

If I'm not mistaken, August is about when people return from summer holiday, and there aren't really holidays until Chinese New Year. There a week of holiday in October for National Day, but people typically travel back to their home town instead of overseas.

It feels possible that the virus could be limited to just transmission within China for a while, which gets spread with every festival between August and late December/January, eventually reaches a critical mass and spread to the rest of the world with people travelling due to Chinese New Year in early 2020.

I honestly don't think I'm right, and you probably spotted logical flaws in the example I have given above. I just want to point out that the problem is extremely complex, and even the facts that you have pointed out are only a small part of the whole picture that just happen to support your views and arguments.

A highly contagious disease like COVID19 simply can’t only spread to people who don’t travel.

The timeline of this disease being spread from August 2019 is incompatible with a lot of what we empirically know about the virus, and should be treated as wrong.

We now know that only a small percentage, maybe single-digit, of infected are responsible for super spreading events. The vast majority infect just one other person. Prof Drosten explained a simplified estimate for this: 1 infects another until the 10th who just by chance infects not 1 but 10.

To expand a little with my basic math skills: There's five, maybe seven days between all those infections and it takes months to snowball into a noticeable epidemic. 10 hops to 10 infections, another 7 to 100 active infections, it probably takes three months just to reach 100, a fourth month for 1000 from which point it should get noticed even in a million people city.

Secondly most people are infections for just a week, those with mild symptoms might be even less: Without coughing, singing or shouting (e.g. sport event) the chances drops even further.

Thirdly: The weather. The warmer it is the more often we open the office window for fresh air, we spend more time outside and are less likely to get into close contact for long enough to spread the virus.

For me August as a start of the local epidemic, even earlier for the initial animal-human transmission sounds very plausible.

> even in a million people city

Wuhan's population is an order of magnitude bigger than that.

It's not unlikely, in fact it's expected.

The hypothesis of a virus circulating in August which eventually evolved into what is now SARS-CoV-2 is probably likely (and surely more convenient), rather than the alternative hypothesis of a virus suddenly emerging perfectly adapted to humans and human-human transmission close to a laboratory that studies and specialises in such viruses.

Anecdata, an old relative of mine died of pneumonia earlier this year. My relative did not test positive for influenza despite having flu like symptoms for two weeks prior. The local hospital’s ICU was overwhelmed with patients having the same symptoms. This was in January. COVID was not on the local radar.

But this was in a senior citizen community town, so overwhelmed hospitals aren’t really newsworthy. And I personally only entertain the idea it was COVID-19, but it doesn’t make sense because the dates are all wrong.

Then articles like this make me wonder, what if it swept by undetected? Were the most vulnerable communities already hit and we didn’t notice? Could that happen?

CDC tracks pneumonia deaths across the entire United States through two separate systems.

It couldn’t sweep by undetected. When we actually got hit by coronavirus hard, alarms starting blaring immediately both in local health department stats and in CDC FluView which tracks “influenza-like illnesses” and pneumonia mortality.

1. CDC FluView data - the coronavirus outbreak in the United States is clearly visible as an historically large spike of pneumonia mortality. https://www.cdc.gov/flu/weekly/index.htm

2. New York city’s own surveillance system “ While only about 100 cases of the coronavirus had been confirmed in the whole state, the city’s surveillance system was, by the end of the first week in March, signaling a spike in influenza-like illnesses at emergency rooms. A few days later, the number of police officers calling out sick jumped noticeably, as did calls to 911 for fever and cough.“ https://www.nytimes.com/2020/04/08/nyregion/new-york-coronav...

Athletes from military world games (Wuhan - October 2019) claim they contracted COVID, spreading the virus when they went back home.

A group of Athletes from Sweden suspected they did, as several had symptoms after returning. However, they now all tested negative. If they had tested positive now, that would have been big news.

For antibodies or the disease?

Antibodies. The test was months later so the chance of finding something in PCR would be small.

Most infected people infect zero other people. A lot of infections can happen that don’t manage to spread far.

There were cases in France in December without connection to China: https://www.google.de/amp/s/www.bbc.com/news/amp/world-europ... and suspected cases in November: https://www.google.de/amp/s/amp.rfi.fr/en/france/20200520-sc...

I would also point out that Thailand received 11M Chinese tourists in 2019. It's reasonable to assume that a good chunk of those came in the second half of the year, and hundreds of thousands were plausibly from the Hubei Province. Yet they recorded their first case in January.

There is evidence that there was already community spread in France in November [1]. Note that the article there also mentioned a study that a case (without connection to China) in France was detected in late December. So there is significant evidence that COVID19 was spreading worldwide at least in December. [1] https://www.scmp.com/news/china/society/article/3083599/fran...

Quoting a professor of Computational Systems Biology at University College London about the OP paper, it's:

"most implausible. The analysis of genomic data consistently and robustly points to the ancestor of SARSCoV2 (i.e. the host jump into humans) dating back to around November 2019, see e.g. https://www.sciencedirect.com/science/article/pii/S156713482... "

(The quote is from here:

https://twitter.com/BallouxFrancois/status/12702949067880980... )

Around november as the earliest month also matches the speed of spread of the virus, which we were able to observe and track all around the world. With that speed, August or September aren't plausible too.

Given the lengthy incubation time, and lack of symptoms in many, it could certainly have taken months to be indistinguishable from any other virus. The first few generations of infected people would likely have been handfuls.

I was looking up "coronavirus" on google trends. What I saw was a flat 0 except for a blip in late august, and a score of 100 on September 21, 2019 coming from Hubei Province specifically.

Those results remained the same for over a month until I posted the above in a hacker news comment. Then I was down voted heavily and the results suddenly changed. I do have a picture of it, because I wanted to share the results with my friend and they dont use social media, so I forwarded a picture.

while I agree with the hacker news downvoters (the downvote, hate, hate, unsubscribe, rage, rage, you must be stupid crowd) that this doesn't prove anything, it is certainly part of the evidence building up.

Why would people from Wuhan (who speak Chinese) search for "Coronavirus" in English on Google (which is blocked in China)?

A plausible explanation is that they had seen the term somewhere and wanted to see what means.

Other could be that integrity search databases was compromised somehow and the term was introduced later. I don't know if this is technically feasible or not, but this shouldn't be discarded as a possibility, for sure.

And other is what is claimed here is faked up and really never happened.

probably the same reason they are doing it now?

Why would you type all that out without sharing the picture?

This reads like someone with paranoia spreading unsubstantiated FUD. Either that or you've been sniffing too much Q Anon.

In this Google trends chart, which unfortunately has no data before January 2020, Coronavirus was not a thing until Mid of January: https://www.regenhealthsolutions.info/2020/03/21/google-laun...

Can you please share that screenshot of the Google trends data after that big build up, really interested to see it!

sure, is there an anonymous place I can put the screen shot?

edit: actually, someone posted a link that had an image that is almost exactly what I had taken: https://www.psychologytoday.com/us/blog/long-fuse-big-bang/2...

I am tired of being downvoted on hn for talking about it though.

Thanks for the link

Can someone enlighten me: with Google being blocked in China, how the heck does one search the term in Wuhan and had it being recorded by Google? I know people in China can use VPN to search Google, but the recorded IP would be the exit node of the VPN wouldn't it?

A few issues with the methodology.

- only 6 small hospitals were included, and far away from the wet market

- Baidu Search Index doesn't match what they claim https://imgur.com/a/UkcUZou

- No test for statistical significance, really?

COVID-like mysterious pneumonia was not that hard to detect, the hospital would be alerted once doctors and nurses got infected.

Can I just add that seasonal influenza varies widely from year to year? [0]

It just so happens that this year was a moderately bad year in the US. I don't know about China. But, they'd have to exclude differences from a bad flu season to have any chance of proving their point rigorously.

It's a very cool analysis though.

0. https://www1.nyc.gov/assets/doh/downloads/pdf/hcp/weekly-sur...

(sorry for the PDF)

I have done more research about the 6 hospitals, my initial claim of "6 small hospitals" is wrong, they at least include the biggest two, Wuhan Union and Tongji.

The claim "far away from the wet market" still holds, these hospitals are not in the Jiangan District, and 5 of them are on the other side of the Yangtze River.

You mean SARS-CoV2, that's the virus. How would they be able to detect it? Would they even know what they were looking for? Would CoV2 trigger the same tests as SARS1 (for non-PCR tests)?

Hospitals are obligated to report to the CDC once they discover pneumonia caused by an unknown virus that can transmit from human to human. SARS or COVID is just a name scientists gave to the sequenced virus.

This is a nit, but SARS and COVID aren't the names of the respective viral agents; they're the names for the diseases that the viruses cause.

The virus that causes SARS is called SARS-CoV, and the virus that causes COVID-19 is SARS-CoV-2

If you don't know then you don't have to report. I don't think initially they knew that human to human transmission was possible.

In addition, google trends limited to China doesn’t match their claim.

Most Chinese people don’t use Google. Not sure if you are aware but it is blocked in China.

The only way to access it is with a VPN, right? Which would put your search outside of China.

IT DID. I posted in another comment, dont want to repeat

Agreed this paper is trash

Here are a couple of anecdotal data points:

I was traveling in Japan and Taiwan in October of 2019. I came down with a weird flu-like illness that persisted for three or four weeks (much longer than a flu would have normally lasted for me). And it wasn't just that the symptoms persisted. I really felt sick for that long (with fever and sweats). The flu-like thing also came after a week or so of diarrhea. Could have just been GI issues related to traveling but who knows? Ever since it was reported that the pandemic may have begun earlier than had previously been thought, I've been wondering if I didn't in fact get this virus very early on.

I also had a colleague with me who was traveling with his wife. His wife was also very sick with some kind of super-flu like thing. She was saying it was basically the worst flu of her life.

I have a similar anecdote, but tested negative for nCoV antibodies. I figure my human brain is just prone to availability bias. There were and still are lot of viruses out there, and many share similar symptoms.

A take it or leave it anecdote for you: I was chatting with an actuary working in life insurance field who is heavily involved in the pandemic industry groups. The actuary told me the antibody test is considered unreliable and has as high as 50% false negative rate.

Anecdotes aren't worth much in this area. There's no conspiracy of silence about problems. We can use actual science. They actually test the quality of these tests. Some are better than others.

For example, the Abbott test has a surprising accuracy [1] "Researchers at the University of Washington School of Medicine found Abbott’s test had a specificity rate of 99.9% and a sensitivity rate of 100%, suggesting very few chances of incorrectly diagnosing a healthy person with the infection and no false negatives."

1. https://www.cnbc.com/2020/05/08/study-suggests-abbott-covid-...

Independent testing of the Abbott assay found lower sensitivity, 94%. The blood samples used to establish sensitivity are also from patients who got sick enough to seek medical care, who likely have higher levels of antibodies than milder cases. It's still one of the better tests, just not as perfect as their marketing numbers imply.


Look at the 95% confidence intervals on those results.

I wouldn't take a study with N=256 (103 positive, 153 negative) seriously in claiming the specificity is a couple percentage points lower than the manufacturer's standard. That's simply too low of a cohort to draw that conclusion.

Even the conclusion from that study you linked was actually that the test wasn't that accurate in the first 14 days of infection (which is already known for ab tests), not that test specificity is lower.

First, the original question was about false negatives, and therefore about the sensitivity (positive rate on true positives), not the specificity (negative rate on true negatives). So perhaps you wrote specificity by mistake? By definition, the sensitivity can be calculated only from true positive cases, so the relevant N is just the positives. There were 103 positive samples from 48 patients, and the independent paper did their math using N = 48.

Abbott's marketing referred to a study of 125 patients confirmed positive by PCR, linked below. So it's more, but not dramatically so. The affiliated study doesn't report a confidence interval, but the binomial 95% confidence interval is [97.1%, 100%]. That barely overlaps with the independent study's [82.8%, 98.7%]. So perhaps the affiliated researchers just got lucky and the independent ones got unlucky, or perhaps too many of the independent paper's >=14 day samples were <17 days and they should have waited longer; though depending how cynical your priors are you might also conclude the groups were different (not to allege any misconduct, just to say there's a lot of reasonable judgment in what patients you select that could push the result around by this small amount).

Regardless, the sensitivity of the test is definitely not an unqualified 100%. Even disregarding the independent study completely, that would still be a somewhat misleading claim, given the small sample size in the affiliated study and that patients with mild illness probably develop lower titers than the average patient who sought medical care over the last few months.


I'm still suspicious there's something going on that we don't understand with those tests. Someone I know was seriously ill for several weeks starting in late March with 9 out of the 11 listed symptoms for COVID-19. She eventually recovered and then tested negative on the Abbott SARS-CoV-2 IgG antibody assay. We can't definitively rule out some other virus but based on the timing and symptoms what else could it have been? It certainly didn't present like influenza.

I think the public is simply unaware of how bad the "regular" flu can be... it's a long tail but every year otherwise apparently young healthy people die of the flu. Not to mention confounding factors of latent conditions and concurrent diseases.

The implication of conspiracy theories is that the Chinese government:

* Perfectly covered up the initial outbreak

* Took no further action

* Utterly failed to cover the "second leak" that led to the pandemic

Seems unlikely?

An alternative theory is social media now disproportionately focuses on the regular bell-curve extremes of our normal flu season.

>I think the public is simply unaware of how bad the "regular" flu can be.

It seems that everyone says they have the flu when they become unwell, until they actually get the flu. The difference is quite clear when you get it.

My wife and I visited Iceland last July. 5 days of the trip were spent trekking in the backcountry with a group from 4 different continents. When we got home, my wife came down with a terrible case of the flu that led to pneumonia. She never needed to be hospitalized but it was close for a couple days.

Eventually, it spread to my son and myself. It's the sickest I've ever been in my 40+ years of life. We didn't return to anything resembling normal until early October. It can't have been COVID but there must have been at least one really nasty flu bug going around last year.

It always annoys me that anytime anyone has a minor cold, it's "I had the flu". That lack of understanding is why more people don't get flu shots.

Occam's razor says she had the flu and not Covid-19.

Influenza isn't one thing and the flu can have severe symptoms. Swine flu is also still going around. My wife's coworker (large tech company in the Bay Area) was positive for swine flu around March.

> Occam's razor says she had the flu and not Covid-19.

And, in most places, test positivity rates.

For months in my area covid-19 tests were only available for people with symptoms matching covid-19 - and those people were still testing 95%+ negative for covid-19.

Perhaps, but I've had the flu several times myself and seen many cases in others. This sure didn't look like a flu. I should add that in this particular case the patient's doctor diagnosed her with Covid-19 on a video call based on symptoms. And the patient had a current flu immunization (I know the flu shot isn't completely effective but even when it doesn't exactly match the viral strain it usually mitigates the symptoms).

I also had weird flus this year and last fall. Still tested negative. There are hundreds of viruses and many mutations that give similar symptoms. It's not unusual that you get unusual one for you this one time

It's always possible it was something else, but lack of (testable) antibodies does not rule out COVID-19 infection, as they are not always developed and/or expressed after some time. Seems like that may even be common.

Since T-cell immunity is rather hard to test, you may never know.

I was also pretty sick in early March but not sick enough to get a test then (they were in short supply of course). I recently got the Abbott blood-based anti-body test and I was quite surprised that I hadn't had covid-19 either.

COVID test accuracy is very similar to condom effectiveness: they're both high in theory, but surprisingly low in practice, not because of the science but user error. I've seen estimates as high as 10-30% for false negatives, largely due to poor swabbing practices:


First, if you're talking about swabbing, then I think you're talking about the test to see whether a person is currently infected with the virus. That's what the article you linked was regarding.

The antibody tests are a different animal. They test to see whether you might have been infected in the past, by looking for antibodies in your blood. So these are blood tests, and, I expect, have less chance for user error.

But also, I think lots of covid antibody tests are not high accuracy even "in theory". It seems the FDA relaxed oversight on companies producing antibody tests: ". . . after being criticized for the fumbled rollout of diagnostic tests during the start of a global pandemic, the FDA swung hard in the other direction, waiving its usual requirements and letting firms rush self-validated [antibody] tests into the market."[1]

So there are antibody tests from over 200 companies out there. Some of these antibody tests are quite accurate, high sensitivity and specificity. Others, not so much.

[1] https://khn.org/news/hype-collides-with-science-as-fda-tries...

The Abbott test mentioned above is blood drawn from serum (not a fingerprick blood test!).

This is not the nasal swab test that sometimes misses positive people, as you mentioned.

To avoid confusion over this issue: There is an Abbott nasal swab test, that gives results 15 minutes after being swabbed, and without "special equipment". That specific Abbott test (the instant nasal swab) has experienced dubious results in practice, even compared to more standard nasal swab tests.

That's not the sort of test under discussion here. The Abbot test and other antibody tests are blood based. I'm sure there are things in the pipeline that can go wrong, but they're much less susceptible to error.

What is important is that antibodies are a sufficient but not necessary indication of past infection. There seem to be plenty of people who don't develop them when exposed, possibly due to effective T-cell immunity.

FWIW I think most if not all of the antibody tests are done on blood

There are different tests out there, many are pretty bad. Some are pretty good, for example Abbott's clears 90% in both specificity and sensitivity. That said, given a low prevalence of the disease, this is actually fairly likely to give false positives. 93.8% sensitivity suggests the false negative rate should be pretty low with that test.


Not to mention the PCR tests and the antibody tests got combined into "total cases" in several data sets, mucking the numbers:


Neither being an actuary or insurance adjuster makes you an expert on clinical lab tests.

My guess is the person you were chatting with heard some hyperbolic statistic about ELIZA tests and is repeating it.

Not so anecdotal: There is an Oncology professor in the UK who tested his staff of 200 and got ~10% for antibodies. A month later he expected 30%, but still got around 10% (https://unherd.com/thepost/professor-karol-sikora-fear-is-mo...)

There is a chance antibodies for this simply do not last very long, or that many people fight it off before it reaches the adaptive immune system and requires antibodies (there are many layers that have evolved in our immune systems).

There are many other viruses that don't produce long lasting immunity as well. Hepatitis B vaccines require 3 shots within a few months and even then, the take rate for it is only around 60%.

That link is rather dubious. eg "When the history books are written, the fear will have done much more damage than the virus". This is easy to say when you're one able to read the history book. It's all going to depend on what ones acceptable death rate is, and that gets dark pretty fast.

The author also has a history of controversy which definitely makes me want to take anything with a grain of salt:


There’s likely a reason why that’s on a conservative business’s vanity site and not a scientific journal.

Influenza this year was also particularly nasty. Most people who have anecdotes about feeling terrible October-December in western countries simply had the flu.

New Zealand ordered extra doses early in the season this year as someone predicted that this year would be rough. This is looking rather wise. And when combined with yesterday's eradication of covid, things look rather brighter than seemed possible. https://www.psnz.org.nz/Story?Action=View&Story_id=110 https://www.rnz.co.nz/news/covid-19/418524/prime-minister-ja...

I initially did not think it was the flu, because I get the flu shot every year (but yes, I know there are multiple strains which it might not protect from)

My understanding is that the flu shot for 2019-2020 wasn't as effective as in other years (which even then is only 40-60%).

I was positive for COVID and have no antibodies. Don’t assume you didn’t have it if you don’t have antibodies.

How long after the illness did you have the antibody test taken? My wife was tested positive in April, had all the symptoms, so it is almost 100% sure that she actually had COVID-19. THe antibody test two weeks after the symptoms were gone was negative. The second antibody test a few days later was ambigous. She is planning to take a third antibody test next week.

It is possible to overcome the virus without antibodies. I forgot the name for the process, but I'll try to track it down.

I think what you are referring to is that it is apparently possible, in some patients, for the innate immune system to stop the infection before adaptive immunity kicks in, which would leave you both without antibodies and subject to reinfection at a later point. This can also reduce the adaptive response level.

Yep. Cytotoxic T-Cells can wipe out a viral infection, especially with the help of interferons, before the B-Cells can develop an effective antibody response. Keep in mind that viruses are incredibly tiny and have small antigenic surface areas compared to bacteria.

It also means you are likely to get infected again.

T lymphocytes defend against covid. Immunity can be the product of previous flu exposure.

mucosa antibodies in the nose and the back of the throat


Interested. Please do.

It's also possible the antibody test is inaccurate. TWIV (This Week in Virology) reported a big double-digit false negative rate.

Sorry, what's TWIV?

It's This Week in Virology, and a reminder to everyone that acronyms are not as well known as you think they are, please spell them out unless they're very common or have already been defined.

Yep, my wife had the same story. She thought she had Covid-19 back in December when she was sick with flu-like symptoms. We both tested negative for the covid-19 PCR and antibody test this past week.

I'm guessing this is a common trend for people who are over analyzing their symptoms in the past year.

I didn't think the antibody tests were reliable enough yet to be taken very seriously?

What’s the sensitivity of the test you took?

100% ...according to the one limited study that it was the subject of.

There are a lot of illnesses out there.

Some of my friends where making regular trips to central China in the late 90’s and described how anyone joining them got horrifically sick at least once. Though regulars tended to have fewer issues. Presumably, they where in contact with a range of local diseases most of which never spread widely enough to become a pandemic.

It’s surprisingly difficult to track the this stuff in part because many diseases make the jump but then simply die out without gaining a major foothold in the human population.

> It’s surprisingly difficult to track the this stuff in part because many diseases make the jump but then simply die out without gaining a major foothold in the human population.

I was wondering about this the other day. How can we know if some other zoonotic coronavirus spread to a only single rural household somewhere? Is there any way to estimate this? Is there any literature on the subject?

Have you had the opportunity/availability to get an antibody test?

Everyone I've heard with such an anecdote has received multiple negative antibody tests, anecdata! (Only two people I've known)

My Brother was in China in November and got pretty sick with back to back to back colds/flu like bugs, I also was very sick for late Nov. - late December, didn't have a fever but had a hard time breathing than normal for a cold/flu, I asked my Doctor and a friend at Stanford and both of them said the antibody tests they have are not accurate. I really want piece of mind if I had covid-19 but am still waiting for a decent antibody test.

I’m waiting on these antibody tests as well. My symptoms weren’t as bad as yours but I too had an illness around that time, and so did a fair number of people around me, I remember joking with my drinking buddy that I probably got whatever it was from her. I’m still mostly convinced that whatever it was, it wasn’t COVID-19, but I can’t ignore the sheer number of stories that I keep hearing from people about a strange illness in that time frame. Some medical professionals who I’ve heard on various podcasts addressed these anecdotes and say it probably wasn’t COVID-19, and let’s be fair, it most likely wasn’t.

I would still like a way to prove or disprove it though, and same as you, anyone I’ve talked to about it says the antibody tests just aren’t good enough yet to prove anything conclusively.

Even the data we do have available sucks. There’s a bunch of States and counties which still aren’t reporting or aren’t reliably reporting recoveries which is artificially inflating the active case count in the United States.

For your situation, existing antibody tests are fine. They are not accurate enough to do mass testing to find out how prevalent SARS2 is in the population. This is because the base rate in the population is pretty low. If you are reasonably sure that you've had it, a false negative/false positive for you is still pretty unlikely (in the 5% order of magnitude range for lateral flow antibody tests, better for ELISA lab tests).

A positive test result for antibodies is a strong indicator for having been exposed to covid, but a negative test result doesn't say much because 80% of people exposed to covid don't produce antibodies, even if they get sick and recover. It doesn't matter how good the test is if seropositivity is the exception rather than the rule.

> because 80% of people exposed to covid don't produce antibodies

Are there any data available to support this claim? That would mean that the virus is cleared by the innate immune system and not the adaptive, but it is still a pretty bold statement.

The last I read (a Nature Genetics study, if I recall) was that the antibody quantity was lower in milder cases (but with a large inter-person variability).

Yes, I linked to a relevant paper in this thread. (And I think it's what you would expect for a disease that is non-symptomatic for many young/healthy people.)

> That would mean that the virus is cleared by the innate immune system and not the adaptive

Not necessarily, because adaptive antibodies produced through previous exposure to coronaviruses can also bind to covid19.

At least the abstract says something different:

> Nevertheless, rare but recurring RBD-specific antibodies with potent antiviral activity were found in all individuals tested, suggesting that a vaccine designed to elicit such antibodies could be broadly effective.

Very low levels, but still produced. (Note that I still have to dig through the paper.)

My understanding is that those RBD-specific antibodies are not necessarily produced as a response to covid19, but I could be mistaken.

In addition:

> Plasmas collected an average of 39 days after the onset of symptoms had variable half-maximal neutralizing titers ranging from undetectable in 33% to below 1:1000 in 79%

Of course this is only a single study and more research is needed, but I notice people draw way too strong conclusions from studies that show low seropositivity prevalence.

It looks like another preprint found antibodies in the airways mucosa instead of blood. That would perhaps explain why some were undetectable.

That was exactly my point (and a reason why getting an antibody test is still useful in the context of a single person). Thanks for explaining it better than I did.

A bunch of people in my office got sick about two weeks after chinese new year returnees returned to the office. A few people got very, very sick, unlike any kind of flu they'd had before and a bunch of the rest got a sort of dry cough.

On a whim, I decided to go get the abbott antibody test to see if it was Covid-19, because it sure seemed like it might have been. But no, negative.

Recent finding: 80% of people exposed to covid produced only a minimal amount of antibodies. Our immune system protects against millions of diseases, and we don't require specific antibodies for most of them.


And yet somehow 57% of citizens of Lombardia have covid19 antibodies.

No, it's only in the province of Bergamo and there is selection bias because people that chose to take the test presumably has symptoms before.

As a counter-anecdote, I know two people from a less hit area, both of whom had fever, and none of them had any antibodies (like, the test said 0.0 for both IgM and IgG).

True. Just Bergamo. Which changes nothing in my argument. But there's a claim that results were from sufficiently large and random sample: https://www.google.com/amp/s/www.thejakartapost.com/amp/news...

If that's true then my argument still holds. How can 80% not get antibodies if they were detected in 57% of large random sample of some population?

Because of dosage. If you are exposed to a small amount of viral mass your natural immune system can deal with it before the virus has multiplied to the point where you get sick. If you're confined to a small space where the virus is prevalent you're getting a big dose and your immune system has to kick into high gear and produce antibodies.

> How can 80% not get antibodies if they were detected in 57% of large random sample of some population?

I agree with that part, even if the sample was not random.

I think randomness matters. If it was not random, but heavily skewed towards more symptomatic cases it might have been showing more people having antibodies because heavier symptoms could correlate with strength of immune response and more antibodies.

Are you sure about this claim? I live there and I didn't hear such region wide figures, only local city data.

In Bergamo it's closer to that from early data, but for example in Milano it might be from 4 to 10 (but in this case the sample was blood donors, so skewed towards younger and healthy).

Super helpful, thanks, I'll read up some more.

That happened to me in South America in 2009. These individual data points are not meaningful.

Maybe it was covid... but it just doesn't tell us anything since there's obviously a reporting bias here.

The flu literally kills people. If it doesn't put someone in the ICU or the ground, i'm not sure "super" flu is the appropriate term. What would normal flu that kills people be called then? It's not diminishing someone's experience to simply say the flu.

Also, I was sick three separate times in the first three months of the year. Very different symptoms each time. There were nasty colds going around.

You do realise that the `normal` flu kills people, right?

I don't follow. That's literally what I said. >"What would normal flu that kills people be called then?"

I misread your comment

I heard a handful of first hand accounts of weird, extra-severe flu-like illnesses from coworkers/friends over last 9 months, but what gets me is that mortality anomalies only started in what, late Feb? That's what I can't square away with the anecdotes.

How good is your memory of first-hand accounts of weird, extra-severe flu-like illnesses from coworkers and friends in previous years? One possibility is that people get weird severe flu-like illnesses fairly regularly (perhaps every few years for most people), and they recount those experiences to their coworkers and friends, and no one thinks much of it until there is a global pandemic of a respiratory illness.

I can only recall one such illness that I experienced. I was in college living on campus, and I felt like I had been hit by a truck for 2 days before I made it to the campus clinic. I tested positive for influenza, but if I hadn’t, and this pandemic had happened 6 months later, I almost certainly would have been tempted to attribute it as one of these supposed extremely early cases.

How do you know that they weren't attributed to the flu or complications thereof?

Because when you look at the excess deaths charts [1], there's nothing at all surprising before mid-March. Then from mid-March onwards, deaths (from all causes) go through the roof.

So there simply wasn't any death toll before mid-March that suggests at all that the virus could have been spreading much earlier.

Likewise, we would have seen the hospitals becoming overwhelmed earlier.

Any unchecked spread in the fall or January would have caused those charts to have started spiking much earlier. There's no evidence for earlier community spread, and good evidence against it. You can't have a virus that can spread widely, and only later turn on its lethality.

1. https://www.nytimes.com/interactive/2020/04/28/us/coronaviru...

There are more than one major flu strands in the wild now and depending on which we got first will tell us how we react to the other. Or, so I'm told.

Here's a video on the flu from 1918 that killed many. It's a few years old and talks about our responses to virus and how they trace them. It's enlightening.... https://www.youtube.com/watch?v=48Klc3DPdtk

In any case, it could have been a bad flu infection. An antibody test would really help. I know several people who had a bad flu that was detected as influenza.

After visiting my brother in Las Vegas the first week of February I came down with a fever, sweats, and extremely bad cough with wheezing in my chest for over a week. I saw a doctor two weeks in and she thought I had bronchitis and prescribed me an inhaler. The Rx failed to treat the cough or wheezing. I emailed the doctor after over a week and she was surprised the medication wasn't working. It ran it's course for about a month exactly. Now I don't actually think I had COVID-19, but the chance is non-zero for sure. I wish it was cheap/easy to get an antibody test in the U.S. so I won't need to worry as much in the small chance I did actually have it.


It’s $10 with insurance with one caveat that your state may not allow self testing without seeing a doctor.

I believe it's $10 without insurance and without a doctor too, they say they bill the government if you're uninsured, and that the $10 fee is for them to have a physician rubber stamp it for you.

Thank you. I did not know about this. I've signed up and have an appointment.

It is free and easy (drive thru) in some parts of the US. Check with your local health resources.

Unfortunately the free and easy ones in my county are diagnostic only.

> Unfortunately the free and easy ones in my county are diagnostic only.

Exactly, I just got tested for antibodies, and since my insurance has lapsed as my Industry was the worst hit in this pandemic I had to pay out of pocket. It was $99 for the visit, and $50 for the lab results.

They said there was a program where the State would pick up the tab but they'd need my credit card on file in case it doesn't get processed etc... I just opted to pay for it instead and keep the State out of this and pay those people who are currently risking their lives working at hospitals and clinics.

They were super busy, too. They said it would be a 30 min affair and turned into nearly 2 hours. I'm glad I opted for antibody test and not the swab (I'm no longer showing symptoms) because I can see why Human error is one of the biggest reasons its yielding less than ideal validity.

I had horrible sickness (was tested for flu, but it wasn't, doctors assumed pneumonia) in end of September, that led to me being part OOO for entire October, after returning from my European vacation. I'm joking to my wife that I'm patient 0 or close: part of the vacation was in Italy (worst hit), then I went to Zurich, then to Seattle (I live close to Kirkland, where first covid cluster started).

p.s. No, it wasn't COVID, at least I recently tested and was said that I don't have it. I haven't asked if I have antibodies though.

In the past five years I've had three multi-week overseas vacations where I've had to take a week or more off sick from work immediately on returning home. Each of those years, that was my only time that year getting sick. I assume travelling just exposes us to more people, more unsanitary situations, and more opportunities to wear down our immune systems.

Were you tested for antibodies?

I know at least half a dozen people who have the exact same theory - a couple got tested and it came out negative

I took a domestic flight on Saturday and have had GI issues starting today. I procured a COVID-19 test kit before I flew just in case, and am thinking of administering it tomorrow or the day after. :\

Many respiratory tract viruses are also gastro intentional track viruses.

It makes sense because the thing they’re getting in to is mucous membranes, which the GI is lined with.

Have you taken an antibody test? Been sick since you got over that illness in 2019? You could help add a datapoint to this Fall 2019 mystery.

Same thing happened to me November 2018. I wonder if it started back then?

There's also the "mystery respiratory illness" that was never identified in July 2019 which could potentially point to an even earlier start. Does anyone know if they've looked into it being related?


> Three people have also died, but Dr. Benjamin Schwartz of the Fairfax County Health Department said Wednesday afternoon that those who died were "older" and had complex health problems. Officials don't yet know the extent to which the respiratory illness contributed to their deaths, he said.

Culture negative pneumonia is a relatively common phenomena. It's also quite difficult to get adequate sputum cultures, but in this case where n=60 I'm skeptical that was the issue. There could be a lot of potential causes for this, but COVID is low on the differential.

I want to say that spillover events, or a virus jumping from X host to humans, happens all the time. COVID became a pandemic because human to human transmission was possible from genetic mutation. Usually with spillover events humans are a dead end host and the person infected will be an n=1.

> It's also quite difficult to get adequate sputum cultures

Heck yes. PNA cx will come back negative a good 2/3 of the time. Doesn't mean an awful lot.

It's one of thousands mystery respiratory illnesses caused by a virus/bacteria/fungus/chemicals/bad food/bad water/bad air.

Its saddening to see the way we are responding to this pandemic. I understand that finding the source of the pandemic is important, however it seems like we are highly politicizing a world wide problem and trying to blame each other for cover ups. If the pandemic started in august and given the rate of transmission we are seeing world wide, we should have had a ridiculous spike in the number of deaths by now. Furthermore, there are many international flights coming out of Wu Han, the rest of the world should have detected the virus earlier then. The fact is none of us were prepared and we were all too complacent about things. Towards the end of February I made a trip from Singapore to Seattle. At the time the virus was peaking in China. I recall that the flight was extremely empty and already most countries in Asia had begun temperature screening at airports and started conducting quarantines. On the other hand as I walked through the immigration and customs in US there was not even the slightest trace of preparation for the virus. Not once was I asked "did you travel to China?" and for a country with such a large expenditure on defense I cannot see how much it would cost to place thermal cameras at the customs exit.

In all honesty I would love to see a study done on how this virus came to be but this study should be conducted on a purely scientific stand point. In fact it'd be best if we took politics out of the picture and ask

- what was the chain of transmission from its original animal source?

- what type of mutations took place?

- how in future can we come up with a robust international/interspecies virus surveillance program such that we can flag animal viruses which are likely to mutate to infect humans?

As of now all I can see is that both US and China are misbehaving and taking shots at one another. Our global supply chains have come to a halt. There are countries like US and India which overproduced food yet out of fear of lack of food these countries have halted export causing problems for other countries dependent on them for food. Yet, farmers in these countries are having to throw away crop because they cant sell there produce domestically. As a human race can we really stoop any lower?

> While queries of the respiratory symptom “cough” show seasonal fluctuations coinciding with yearly influenza seasons, “diarrhea” is a more COVID-19 specific symptom and only shows an association with the current epidemic.

Since when is diarrhea a COVID-19 specific symptom? Using Baye's the probability of Covid-19 given diarrhea is:

prevalence of covid in general pop (medium low) * probability of diarrhea given Covid-19 (very low, given we only recently found out this was a symptom at all) / prevalence of diarrhea in general pop (the prevalence of diarrhea in general is definitely higher than Covid-19).

Which lends to a very small probability. Pre-print publications like this based off of shaky data should be taken with a large handful of salt.

This is very interesting but the date significantly precedes my (layman's!) understanding of TMRCA estimations of mid November (earliest cases examining the existing genetic evidence and extrapolating backwards through genetic drift calculations).

How do the scientists here account for the disagreement - beyond the fact they are using completely different methods?

Alternatively, I'd be interested in somebody explaining why my understanding of the TMRCA is incorrect - like I said, its not my field.

TMRCA relies on accurate information about when specific strains were identified.

There is ample reason to believe Chinese authorities lied about when they observed specific strains.

Can you provide some evidence to back up your claim here?

The TMRCA calculations would have ample information to provide a statistically accurate date without a single Chinese genome at this point. Those early Chinese genomes merely act as a validation that the genetic clock is "ticking" how the model(s) estimates that it did.

Just rampant misinformation in this thread - a mid-November start date is still by far the most probably and you are pretty much guaranteed to have had some other disease than SARS-Cov-2 in October 2019.

The TMRCA calculations need to know approximately how many people were infected to calculate the time.

Mutation rate is essentially based on how many people the virus passes between not really time.

So if China is lying about the number of infections early on (or even simply doesn't know the true number) then the calculated time of first infection would be off.

*TMRCA (Time to Most Recent Common Ancestor)

Thanks, corrected. I must have typed that two different ways several times in the last 20 minutes...

Regarding the year-over-year comparison of cars in parking lots, have these researchers considered that perhaps car ownership is just growing that fast[1] in China?

A highly contagious disease would hardly be not noticed during a time of free travel. You could also do the reverse math knowing what we know about its R-naught.

[1] https://www.researchgate.net/publication/311910366_Cities_of...

Link to a prior post of mine:


China reports infectious disease counts and deaths each month. The numbers from December '19 were insane compared to '18

Except that we already know that the strain of flu around this winter was particularly bad, much worse than recent years, so a jump in deaths like that is actually not surprising. After all the number is about 700k even in a typical year. This could also help explain the hospital traffic data.

I just don’t buy it. If Covid-19 was in wide circulation, affecting hundreds of thousands of people as early as September and October, how come it wasn’t all over China? Or the rest of the world for that matter. What was keeping it in Wuhan?

There’s no way it could have grown within the wuhan population, to affect that many people that early, without it being propagated all over the place. People just travel too much these days in China.

We also know that China is willing and able to lock down whole swathes of the country to prevent viral spread. If it appeared earlier on the scale of what happened in Wuhan, and local politicians didn't fuck up, the Party would have locked down wherever that was.

> We also know that China is willing and able to lock down whole swathes of the country to prevent viral spread.

They may have boarded up Wuhan, only after dissapearing journalists and citizens showing the severity of it as the CCP lied about its transmission, but the rest of the Mainland were free to rush into Hong Kong despite local opposition and Medical workers warning of spreading the virus. They overwhelmed the medical system and on were recorded on social media platforms sneezing and coughing directly into often touched areas in public spaces.

It is seriously not hyperbole that the CCP should face Crimes Against Humanity for biological warfare.

>It is seriously not hyperbole that the CCP should face Crimes Against Humanity for biological warfare.

It sure sounds like hyperbole. Hong Kong has had a bit over 1100 cases so far, which is frankly trivial.

> It sure sounds like hyperbole. Hong Kong has had a bit over 1100 cases so far, which is frankly trivial.

And that is because of their personal efforts, not the CCP who forcefully kept the borders via Carrie Lam's legislation open against Public outcry.

Hong Kong had already learned the lesson from SARS outbreak, and understood what they needed to do to lessen the contagion and they quarantined and limited human contact--they even stopped protesting despite it being in full swing in late November to early December.

There medical system was still overwhelmed and PPE was scarce while they were still treating mainlanders who came in droves and continued to abuse the system and foment violence amongst Hong Kong citizens. Many mainlanders were supposed to quarantine but violated the 2 week mandatory period and were out in public and going into restaurants with their armbands indicating they were supposed not leave their home/hotel. If I had the time I'd go look for the videos and pictures, but I'm sure you'd try to rationalize that away some how, too.

You can look at the numbers and try to draw erroneous conclusions, but that doesn't tell the entire story; you know what does? The CCP violently enforcing the Security Law Bill, beating and killing protestors that have eventually led to Hong Kong citizens now having to flee to Taiwan and the UK now.

No, I agree that there is horrible oppression in Hong Kong. It is terrible, and China should be punished for that warcrime. I disagree about the biological warcrimes bit. I think China did enough to try and halt the spread, even if they did it only out of self-interest.

Thanks for a detailed and careful response, lack of agreement doesn't mean we can't build bridges of understanding :)

> lack of agreement doesn't mean we can't build bridges of understanding :)

Granted, but as a fellow biologist myself (Cellular, Molecular by schooling but excelled in Mircobiology) you have to see forcing a separate country, that you've had violent conflict with since 2014, to keep its borders open while virulent vectors are coming in and overwhelming a population's medical system [1] as well as Society for what it is: Biological Warfare. All while withholding critical information of its severity, and then using the WHO as a mouthpiece to spread propaganda and mislead the Global Community about what is occurring all while suppressing your own citizen's and physician's who do not fall in line with that narrative and continued to post the horrible medical conditions, arrests, and deaths happening in real time in Wuhan on social media.

Then, quite likely because of their State sanctioned conditioning, are let loose on the street breaking quarantine requirements in Hong Kong and are then caught on camera purposelessly coughing and sneezing into elevators, stairways, railways etc... all of which are used by the public in daily Life in what seems like a way to propagate the the virus into other hosts in Hong Kong. What other motive would there be to do so?

Hong Kong being, as I mentioned before, victims of politically influenced and targeted violence by the CCP over the violation of the Sino-British Joint pact agreement that stipulated HK's 2 systems, 1 country conditions must be honored in order for China to be given Hong Kong.

How is this not biological warfare in your view? Moreover, the fact that you really think that China did anything to 'halt the spread' shows just how quickly even trained biologists are to buy into this false narrative. Its simply not true and shows how effective the CCP's propaganda is and for anyone involved with the HK protests its very clear how overtly they tried to spread the disease.

1: https://www.businessinsider.com/coronavirus-wuhan-hospital-w...

There seem to be at least one case older than Wuhan. The new trend is just to consider the market has a spreading place, not precisely the source.

Do you accept that America with ~350m people has ~20k deaths from the flu each year, while china with ~1.5b people only has ~18?

No, I'm sure they severely under-report it, mainly because I doubt they have the data. Most people don't go near hospitals if they can possibly avoid it because it's so expensive. Still, assuming a consistent recording methodology, changes in recorded case numbers should still serve as a useful indicator of trends.

> Most people don't go near hospitals if they can possibly avoid it because it's so expensive. Still, assuming a consistent recording methodology, changes in recorded case numbers should still serve as a useful indicator of trends.

In china? The difference is that outside of china, if you die, it's reported as something like "died of heart attack bought on by influenza virus", or "died of complications caused by influenza virus", etc.

In china, if you have /any/ underlying condition, the reported death is the underlying condition, not influenza.

Wouldn't there be higher genetic diversity of the virus if this were the case?

There doesn't seem to be any real evidence for this theory in the genetic data we have.

From https://www.wsj.com/articles/so-where-did-the-virus-come-fro...:

> New re­search has deep­ened, rather than dis­pelled, the mys­tery sur­round­ing the ori­gin of the coro­n­avirus re­spon­si­ble for Covid-19. Bats, wildlife mar­kets, pos­si­bly pan­golins and per­haps lab­o­ra­to­ries may all have played some role, but the sim­ple story of an an­i­mal in a mar­ket in­fected by a bat that then in­fected sev­eral hu­man be­ings no longer looks cred­i­ble.

> A study pub­lished in early May by sci­en­tists at the Broad In­sti­tute in Cam­bridge, Mass., and at the Uni­ver­sity of British Co­lumbia has un­cov­ered an un­usual fea­ture of the virus’s re­cent de­vel­op­ment: It has evolved too slowly. The genomes of viruses sam­pled from cases dur­ing the SARS epi­demic of 2002-2003 showed rapid evo­lu­tion­ary change dur­ing the early months of the epi­demic, as the virus adapted to its new host, fol­lowed by much slower change later. By con­trast, sam­ples taken from re­cent cases of the new coro­n­avirus, SARS-CoV-2, have com­par­a-tively few ge­netic sub­sti­tu­tions com­pared with an early case from De­cem­ber.

> The au­thors, Shing Hei Zhan, Ben­jamin De­v­er­man and Yu­jia Alina Chan, write: “We were sur­prised to find that SARS-CoV-2 ex­hibits low ge­netic di­ver­sity in con­trast to SARS-CoV, which har­bored con­sid­er­able ge­netic di­ver­sity in its early-to-mid epi­demic phase.” This im­plies, they ar­gue, that “by the time SARS-CoV-2 was first de­tected in late 2019, it was al­ready pre-adapted to hu­man trans­mis­sion to an ex­tent sim­i­lar to late epi­demic SARS-CoV.” This is po­ten­tially very good news: Be­cause the virus is rel­a­tively sta­ble ge­net­i­cally, a vac­cine that works against it, if we’re able to de­velop one, will be more likely to work against all strains.

> The same study seems to rule out the pos­si­bil­ity that in­fected an­i­mals at the Hua­nan Seafood Mar­ket in Wuhan trans­mit­ted the virus to sev­eral hu­man be­ings, as some have sug­gested as a point of ori­gin. The Chi­nese au­thor­i­ties have now con­firmed that no an­i­mal sam­ples from the mar­ket were in­fected. This sug­gests that a sin­gle per­son brought a virus that was al­ready adept at hu­man trans­mis­sion to the mar­ket and in­fected oth­ers.

It's weird that no one mentions Fauci was funding and promoting bat to human coronavirus research in Wuhan in 2019.


Is it just a coincidence?

Additionally, it is possible to accelerate virus gain of function by exposing it directly to the target host.

However, this is even stranger than the Chinese lab conspiracy theory, since this particular research is US funded.

This type of pandemic is heavily predicted. It’s not a coincidence that it is being researched. It’s no more coincidence than studying earthquakes near a fault line.

That's a very good point. So it is that Dr. Fauci anticipated the outbreak, and that is why he is advising the president.

> So it is that Dr. Fauci anticipated the outbreak, and that is why he is advising the president.

I believe Dr. Fauci is advising the administration because he is the director of the National Institute of Allergy and Infectious Diseases, and been an advisor on epidemics to every president since Reagan.

Yes, and I haven't seen him show up in previous epidemics like swine flu, so I made the connection that his recent gain of function funding might have given him special insight for this particular pandemic.

I'm trying to make sense of the odd correlation between his involvement with the administration and that he was also instrumental in research about the very zoonosis the experts think occurred.

Perhaps it is all a coincidence. I don't know all the background probabilities involved.

He's been there though, even if you haven't seen him. Here's a C-SPAN interview from 2009 about H1N1 for example: https://www.c-span.org/video/?288279-6/h1n1-virus

Yes, I saw that. But he doesn't seem to have been front and center like he is with the current pandemic. I chalk that up to the remarkable fact he was able to predict both the vector and location with his funding prior to the outbreak. Fauci's got his ear to the ground!

I seriously doubt that Fauci is doing any research himself, given that he directs NIAID. Where are you getting the idea that he did gain-of-function research? I'm actually interested in where this misinformation is getting generated.

For some reason your most recent comment is dead, and I cannot reply to it, so I'll reply here.

It looks like the funding did cover the WIV research, from what I understand the article to say.

"The NIH research consisted of two parts. The first part began in 2014 and involved surveillance of bat coronaviruses, and had a budget of $3.7 million. The program funded Shi Zheng-Li, a virologist at the Wuhan lab, and other researchers to investigate and catalogue bat coronaviruses in the wild. This part of the project was completed in 2019."

Here's the 2015 paper co-authored by Zheng-Li Shi detailing a chimeric coronavirus that uses the SARS backbone to target ACE2, very similar to how covid-19 operates.


"Using the SARS-CoV reverse genetics system2, 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 enzyme II (ACE2), replicate efficiently in primary human airway cells and achieve in vitro titers equivalent to epidemic strains of SARS-CoV."

It makes me confused regarding the recent debunking article that claims there is no way humans can have engineered the covid-19 spike that targets ACE2, and there is no known backbone used in the covid-19 genome. Seems in contradiction to this 2015 paper.

That gain-of-function research was done by Ralph Baric in the US, not in Wuhan.

You say that the virus in the experiment is similar to SARS-CoV-2. That just shows how little you understand what you're talking about. A little knowledge is a dangerous thing. You know just enough to find these conspiracy theories, but not enough to realize why they're ridiculous.

From the newsweek article I posted in the parent comment.


Fauci is not personally conducting gain of function research, but he is both funding and promoting such research. Particularly, he funded the Wuhan lab to research bat to human coronavirus gain of function in 2019 before the outbreak. One of the lead researchers successfully created a chimeric virus that is similar to how covid-19 theoretically became so good at infecting humans.

Obviously, there is good reason for this research, since that's where SARS, MERS and swine flu came from, so Fauci's foresight got him a few months ahead of the covid-19 pandemic. It is quite impressive that he picked both the vector and location prior to the pandemic outbreak. Seems like we should be giving him much greater recognition for this achievement.

> he is both funding and promoting such research

You mean the US NIAID is funding it? Fauci doesn't personally review and approve every (or even any) grants issued by NIAID. The NIAID director is far too busy to do that. I think it's done by scientists who volunteer their time.

> Particularly, he funded the Wuhan lab to research bat to human coronavirus gain of function in 2019 before the outbreak.

The grant doesn't appear to say anything about gain-of-function research at the WIV. Are you getting this claim from Newsweek, or have you seen it elsewhere?

> One of the lead researchers successfully created a chimeric virus that is similar to how covid-19 theoretically became so good at infecting humans.

Really? Which researcher did that, and can you cite the publication in which they describe that chimeric virus?

> It is quite impressive that he picked both the vector and location prior to the pandemic outbreak. Seems like we should be giving him much greater recognition for this achievement.

It sounds like you're saying that Fauci engineered SARS-CoV-2, but I may be misinterpreting you. Is that indeed what you're suggesting? Where did you get this claim from?

What is going on with your account, everything you post is dead?

Yes, I see that the WIV associated researcher Shi Zheng-Li just provided the genetic materials, and the experiment itself was carried out by Baric.

I don't believe the lab origin theory. As you point out, all the scientists believe it is ludicrous. I am just trying to make sense of this weird connection between Fauci and the WIV with an experiment that to my uninformed mind looks like it contradicts the official debunking article's claims that recently appeared in Nature. If nothing else, I hope to improve my bioinformatics knowledge through this research :)

There's no connection between Fauci and the WIV. He heads a massive organization, the NIAID. He doesn't personally manage every grant.

I don't even think the grants in question go directly to the WIV. They go to an American organization that works together with the WIV on certain projects.

I think the implication of the article is that Fauci likely was aware of this research since he promoted such studies, and it was approved by a secret panel at the NIH, along with him being the head of the organization that funded the research.

What do you mean by "secret panel"? I think the internal deliberations of almost all funding committees are confidential. But once they decide to fund a project, that information is out in the open. The grant was online, and the research is published in scientific journals.

The actual scandal with the grant in question is that it was canceled for political reasons, despite being highly ranked by the scientific reviewers (and how obviously critical such research is, given what the pandemic has shown us about the dangers of emerging diseases).

From the article:

"The NIH established a framework for determining how the research would go forward: scientists have to get approval from a panel of experts, who would decide whether the risks were justified.

The reviews were indeed conducted—but in secret, for which the NIH has drawn criticism."

From what you are saying, it sounds like the author is making a big deal out of standard procedure.

Not really.

(1) Genetic diversity increases with both time and size of the infected population. You'll get a lot more diversity if it's mutating in 4 million individuals than in 4000.

(2) For a virus this young especially, genetic diversity is not at all precise measures.

I'm taking about genetic diversity over time. From there you can extrapolate back to when to common ancestor existed. To within a limited number of generations.

This calculation shows this common ancestor existed between mid November to December.

This is not responsive to the parent at all.

The current phylogenetic data go as far as October as the farthest estimate, as far as I can see.

Seems like 28-Oct-2019 was the early limit of the confidence interval.


There's a recent paper that analyzed about 7,000 sequences of known isolates and tried to give an estimate, whose lower limit is close to that date, IIRC.

This paper is a trainwreck. Could be a case of scientific fraud.

Gist of this paper:

The authors look for circumstantial evidence of community transmission of COVID-19 within Wuhan for dates substantially prior to the seafood market outbreak. They do this by attempting to triangulate* web search volume data with satellite mapping of Wuhan hospital parking lots.

*suggestively gesture back and forth between

In the parking lots, they're looking for more vehicles than expected based on prior years' imagery.

In the web search trends, they're looking for "disease signals".

Specifically, they're looking at two terms: a symptom of sufficient specificity to be useful for differential diagnosis of COVID-19 vs. influenza ("diarrhea"), and a more generic term representing influenza-like illness ("cough").

Here's the teardown:

1. "We developed a comprehensive list of hospitals in Wuhan (using Google Maps, Wikipedia and PubMed)."

List not provided.

2. Search terms are given in English even though they were actually input in Mandarin.

You can verify this by trying to search the English terms yourself. By process of elimination and the shape of their graphs, the terms had to have been:

"cough" → 咳嗽

"diarrhea" → 腹泻

Live link below. Requires signup. Make sure to select Hubei → Wuhan (湖北 → 武汉).


3. "We extracted the relative search volumes of the terms “cough” and “diarrhea” using WebPlotDigitizer, v4.215."

What? The values are provided on tooltip hover. This data is written into the page. You can just pull the real data out of the html.

Based on a cursory glance at WebPlotDigitizer, the vague method quote above appears to be tantamount to saying "we made up the data from screenshots".

4. They're looking at seasonal trends.

This is clearly visible from basic inspection. This is not interesting.

5. Their Relative Search Volume scale doesn't agree with Baidu.

Their numbers are wrong. Just look at Figure 2b's y-axis.


Maxima: It shouldn't go to 600. The actual values peak on Baidu at 711.

Minima: None of their data should be plotting near 0. The minimum volume in their date range is 76.

6. The uptick for "diarrhea" (腹泻) that they claim exists doesn't.

Again, this is Figure 2b. The red line is the problem here.

This appears to be deliberate fabrication. No competent researcher can miss the discrepancy between what this graph depicts and what the source depicts.

咳嗽 ("cough" / blue line on harvard preprint) was following a completely normal-looking seasonal cycle during the period under discussion.

腹泻 ("diarrhea" / red line on harvard preprint) was, again, following a completely normal-looking seasonal cycle, with a slightly elevated baseline.

The red line is mis-plotted to trend up in a sudden surge right where the researchers would need this to occur for their argument to hold any value at all. Then, rather than declining substantially prior to the January 2020 cluster, this plot depicts the trend holding through to 2020.

This information is simply false. That's not what Baidu reports.

Here's a side-by-side of the discrepancy:


Here's a superimposed version, for charitable reading of Figure 2b. I've stretched it to fit. Red should overlay green.


7. Screw the sat mapping, frankly.

If you can't be trusted to screenshot a graph without us having to arrive at this point, there's no point even assessing the content of your claims about something orders of magnitude more complex.

The sat mapping doesn't constitute evidence so much as it constitutes having paid for the visuals needed to launder this preprint into mainstream news. The only thing that can currently be done with this information is a data dump for other researchers to use.

8. Proofread your paper. 2019 → 2020 below:

> Both search query terms show a large increase approximately 3 weeks preceding the large spike of confirmed COVID-19 cases in early 2019 (Figure 2, c, purple). There is a large decrease in hospital volume and search query data following the public health lockdown of Wuhan on January 23, 2019 (Figure 2, third annotation).

9. No stats anywhere.

Can't do time series analysis without math. Spinning a yarn / telling a just-so story shouldn't be the level of reporting expected of academics in this context.

10. No attempt to build a keyword list or other reference information of continuing utility.

So the analysis dies with this one paper, essentially. There's nowhere to go from here.

According to European surveillance data [1], diarrhea is also a very rare symptom. The authors don't have a convincing argument why this should be a good indicator for COVID-19.

[1] bottom row in this picture (I couldn't find an English source): https://www.rki.de/SharedDocs/Bilder/InfAZ/neuartiges_Corona...

And even then you have to assume that COVID-19 could be the only cause for an uptick in diarrhea. Not impossible, but extremely unlikely.

Judging from my discussions with my MD and peer-group, I'm under the impression that in Germany, at least in my region, virii with that symptom are circulating every few years. Would expect something similar for China.

Kind of glad you weren't on my dissertation committee.

The graph looks even worse when substituting colloquial 拉肚子 for diarrhea.


I saw this on the national evening news today, and was flabbergasted at its insinuation.

The immediate thing that baffled me was why they thought, a year-over-year count of cars in a hospital parking lot, was an indication of an early coronavirus outbreaks, which again, China was concealing from the world.

The news report only said they analyzed 1 year. Did they do it over several months? Or did they do it over 60 months, which might be a better sampling over time. Who knows. But that evidence is rather circumstantial.

Did they also consider that Wuhan doesn’t have as many local clinics, so when someone gets sick, they all go to the same central hospitals, for everything. This is also what added to the problems in Wuhan with the initial outbreak.

Then, regarding the increases in search queries for diarrhea and cough, two symptoms of the virus. But I’m sure searches for coughs go up annually during flu season anyways. I don’t think internet searches from random people over the internet, is a very good signal for anything, and may just be adding noise to the data anyways.

They include an arbitrary choice of parameters from very noisy sources over a really short timespan to find "an upward trend".

Looks like a fishing expedition to me.

I'm curious, how did they get access to location data and Baidu search volumes for just Wuhan?

Search query data Baidu’s database (http://index.baidu.com/) contains logs of web and mobile search query volume in China. User confidentiality is maintained, since only the relative term frequency data is available. We obtained daily data for symptom-related searches likely associated with COVID-19 illness in Wuhan from April 2017 to May 2020. We extracted the relative search volumes of the terms “cough” and “diarrhea” using WebPlotDigitizer, v4.215.

wow just searching 'cough' on google trends seems to be pretty accurate just birds-eye view

would be cool to read similar research using US data, and the implications on policymaking.


It's interesting - tho I've just plugged in China and various periods down to the last 5 years, and there's not an obvious jump beyond the seasonal ones until after December this year.

google in china is less than 5% of the search market

yeah, I considered that - but its still presumably a large enough sample for the phrases listed in the parent comment to stand out.

This always goes up during winter, you also have to control for all the media attention that COVID-19 is getting. People are searching just to be safe even if their symptoms are weak. It might not reflect growing infections, just growing fear.

The spike in the timeframe of the link I put is in mid March and the decreasing rapidly. Plus I think it's also cool at least intuitively the 'trending' states make sense - though I have no idea if they are weighted by population or not.

As interesting as this is, but my understanding was that the genetic evolution / development of the virus can be used to determine when it started spreading. Or jumped from animal to human.

Or did I understand that wrong? Not saying this study is wrong (no way for me to tell), it just seems a very indirect, and thus error prone, way to look at it.

I've asked that question as a separate thread above, I think its an important one, at least for lay people like me.

There is a suggested reason for the discrepancy (Chinese dishonesty about timelines) tho not an answer (yet) from the researchers who've commented elsewhere here or others with a strictly scientific explanation.


The Chinese government and Chinese firms are often willing to share tons of data with researchers. One of my professors was able to get data on cell phone locations, metadata on all text messages sent and received, and occupations of cell phone holders from the largest telecom co in China for a paper on networks and job mobility.

Well, considering the all-seeing Chinese government practically owns Baidu and most other Chinese brands it is not very surprising that they're able to track individual users across multiple platforms. Location data is merely one tiny point on the vast graph of data they have access to.

But this isn't PRC but Harvard.

It's a little surprising the PRC would let this unflattering data be available.

The official line now is that the virus didn't start in the seafood market. The bats that carry the closest viruses to SARS-CoV-2 are located 1000 miles south of Wuhan, and were in hibernation in November. For the theory that the virus was transmitted from a bat to a human in Yunnan to work, it needs to have happened earlier in the year.

If the virus jumped from bat to some other animal 50 years ago, then the 1000 miles of distance is not hard to explain, and doesn't tell us anything about the time-scale of initial human infection.

We need to find the close relative of Covid19 (TMRCA < 1 year) in a non-human host.

There are a lot of points of data to scrub in such a large system, it's not surprising that they would miss numerous of them in the wild. Watch to see if this one disappears or not.

I caught a flu on Dec 23rd. Tested negative for A/B. Continued to have it. Went back in January still with the flu. Tested negative again for A/B and still had effects from it past Jan 20th.

I felt like I was dying and my lungs were full of really bad stuff.

Around the time I would have showed antibodies you could not get a test in the US.

Needless to say, I believe the virus was around before it had been noticed.

That time frame of late Dec is normal flu season. Many people could have been walking around with covid and no one would have noticed.

There was a sizeable group of folks visiting from Wuhan in CES. Several folks I know fell ill after the event. I've been trying to figure out if CES magnified it, but there is very little information available on this.

Sorry but the methodology just sounds laughably stupid on its face. It would baffle me if this kind of analysis would meet the bar to identify any kind of epidemic, let alone a novel and possibly evolving virus.

Not to accuse the authors of anything, but I think the level of bias and wishful thinking in some public and political realm, when it comes to the origin of this virus, is bordering on hysteria. Does anyone still remember the evidence that Trump and Pompeo were seeing about the lab leak theory? Why is there no update coming from any "intelligence" source?

I think the fact of the matter is, the origin question won't be scientifically and satisfactorily answered until at least a few years from now, and only with teams of international scientists. In any case, it would be impossible to achieve that in such a politically charged environment.

Without being emotional and having any sources to back me up, I just believe this virus has been around for a little bit longer than we have initial been told. It seems reasonable taking into consideration that a lot of countries has had a slow infection curve.

But no matter how you spin this, IMO, the chineese is the source of this mess. And frankly it doesn't matter when it happened. It happened.

The key is to have open data and not let Chinese to have world data whilst they close theirs for themselves or not used it for fear of political consequences. Close an area and let china choose to do it or not is not the human right answer. You need to force them to join the world in a meaningful way. We cannot study photos or things like that like study Soviet Union politics.

Seems like virus activity is going on all the time even without Coronavirus. Did the data indicate that virus activity in Fall 2019 was in excess of what would be expected from observing other years?

This seems like low-value data that doesn't mean anything by itself.

What could be inferred from this? Does it mean the fatality could be lower than believed? Or that it takes longer than previously thought to spread? Or Asian countries could have had experienced it earlier leading to some level of immunity?

I would use Autumn here for clarity for sure

If you want to be clear, use the name of a month or a quarter number.

Seasons are opposite in the Southern Hemisphere, and it is always confusing to read American or European information that references a season (I am in New Zealand).

Please Don’t marginalise those of us that are down under (we are already marginalised by physics causing long ping times to servers in the Northern Hemisphere, which is harder to change).

Since they looked primarily at the month of October - I'd just say October.

There is another report that suggested mobile data indicated the Wuhan lab “was closed from Oct. 7 through Oct. 24, 2019, and that there may have been a "hazardous event" sometime between Oct. 6 and Oct. 11.” [0]

As far as I know, no federal agency has been willing to vouch for this conclusion.

I recognize there is skepticism about it coming from the lab, though I thought this is related enough due to how the indicating data was collected to share.

[0] https://www.nbcnews.com/politics/national-security/report-sa...

I guess the point is that Fall doesn't mean Autumn in some places, and the way this is phrased it seems to imply something about the rate of infection, that is, they are falling or something but that isn't what this is about at all.

Agreed. And capitalizing the word 'Fall' (in an attempt to clarify) is problematic too - it's not usually a proper noun.

...of 2019

I thought that was pretty obvious, fall 2020 hasn't happened yet.

except in the Southern Hemisphere... :)

Southern hemisphere English dialects call it Autumn. Might not be a knockdown argument but it's pretty rare to read Americans talking about seasons in the southern hemisphere without clarifying, so I had no doubt we were talking about northern hemisphere seasons.

Wuhan is in the northern hemisphere ;)

I think it's a fair point. You are both correct.

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