8 ms·

SARS-CoV-2 detected in Barcelona sewage water sample from March 2019

110 points by elies 6y ago

cs702 6y ago
Wait, what? The same virus? March 2019? Are we sure that's not an off-by-one typo, or an error? If that date stands up to scrutiny, wouldn't it call into question everything we thought we knew about the origins and history of covid-19?
- Izkata 6y ago
  Not a typo. The abstract explicitly says "long before" the first declared case.
- gallexme 6y ago
  According to the paper : 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.
- bredren 6y ago
  Yes. It would also stand in contrast to everything we know about how quickly it spreads. I am very skeptical of this claim.
  - sudosysgen 6y ago
    It would be very unlikely, but in theory this coronavirus could have spread very weakly for months up to a year before evolving the set of mutations that allow it to spread so rapidly in humans. Indeed, it's exceedingly unlikely that the coronavirus could have had an R0 of >3 right out just after the zoonotic crossing, it's much more likely that it would be significantly lower than one and needed to infect a few people and mutate to adapt to humans. But to such an extent, and in Barcelona? It's still quite unlikely, though in the realm of possibility.
    - tchaffee 6y ago
      > in theory this coronavirus could have spread very weakly for months up to a year The evidence from the study does not support that theory: "All samples from January 2018 to December 2019 came out to be negative for the presence of SARS-CoV-2 genomes with the exception of March 12, 2019."
      - sudosysgen 6y ago
        This is coherent with a weak infection that subsides after a few days, and was weakly transmissible so only infected one or two people.
        tchaffee 6y ago
        Is it? Would it even show up in sewage if it only weakly infected one or two people? I thought only a percentage of Coronavirus infections result in the virus ending up in the feces. And the tests are that sensitive? Do you have a source?
  - thu2111 6y ago
    How much do we really know about that? Recall the apparently 'exponential' increase in cases was in reality an exponential increase in testing - when viewed as a proportion of tests yielding a positive result the virus was spreading not especially fast, and the positive percentage went up quite slowly from a non-zero base.
- elies 6y ago
  This article is a preprint and has not been peer-reviewed. Quote from article: ...”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.”
  - SpicyLemonZest 6y ago
    Green jelly beans cause acne, I guess. I take back anything I ever said about that one XKCD comic making a trivial point.
- tchaffee 6y ago
  I don't think so unless you make a lot of assumptions. That it was a variation that is just as contagious. That it was a variation that could cause as severe symptoms. That it even came from humans. All samples from January 2018 to December 2019 came out to be negative for the presence of SARS-CoV-2 genomes with the exception of March 12, 2019. Why just one month and then nothing for so long before the outbreak? Per the study, sewage includes rainwater from open drains. A highly infected bat could have ended up dead in a sewer. Nature is full of unexpected possibilities. I bet there are other assumptions without which it doesn't call into question what we think we know.
  - mark-r 6y ago
    I don't know how they do things in Barcelona, but in the US the rainwater has its own sewer system. If it didn't the waste water treatment plants would be overrun every time it rains.
    - roywiggins 6y ago
      Combined sewers are common in the US. https://en.m.wikipedia.org/wiki/Combined_sewer https://en.m.wikipedia.org/wiki/Combined_sewer
      - mark-r 6y ago
        My understanding is that combined sewers are being phased out whenever possible for the reason I gave.
        VBprogrammer 6y ago
        I'm not sure how much you know about Barcelona but it's an ancient city who's history can be traced back through to the Neolithic period with very narrow streets designed before motor vehicles. It's not really compatible to any US city.
        roywiggins 6y ago
        They have exactly that problem, but it didn't stop dozens of American cities being built with them.
- wokwokwok 6y ago
  Honestly, its quite problematic. There are vested interests with a great deal to lose if no counter narrative to the origin of the virus turns up... and they’re already seeding all kinds of conspiracy theories all over the place. So, while I’m all for “science”, under the circumstances, the burden of “prove this isn’t a false positive” is overwhelmingly higher than the due diligence taken here. So, yes, it would, but no, it doesn’t.
  - aasasd 6y ago
    > vested interests with a great deal to lose if no counter narrative to the origin of the virus turns up Guess I'm under the rock here—what are those interests? To my knowledge, Trump does the most, ahem, novel hypothesizing, which is pretty much expected routine by now.
- loeg 6y ago
  Yes, it would be an extraordinary result, if it wasn't deeply suspicious for exactly the reasons it's extraordinary.
- vikramkr 6y ago
  The date is very very unlikely to stand up to scrutiny. As others in the thread have pointed out, the data doesn't make much sense, it lacks consistency, they don't show their statistics, and it's very very likely to be a false positive finding that for some reason the authors decided to go ahead and use as the basis for a very out-there claim. Peer review isn't perfect, but it's generally good enough to at least catch something as sloppy as this paper. I'd be very very surprised if it stood up to scrutiny.
- vmception 6y ago
  I think people should remain open to possibilities. People started dropping like flies from AIDS in the 1980s from an otherwise completely benign virus they had for 10-12 years, which we didn't know existed and later identified as HIV. A virus which now we are still tracing further and further back, earliest human infection now being 1909. Everything that happened over the last century co-existed with a virus we didn't know was around and slowly incubating and slowly spreading. The similarity being that we know it is possible, and its really opportunistic infections that cause issues with HIV. With SARS-CoV-2 we have identified A virus and have been trying to trace its origin and are still trying to understand its actual effects. But maybe its not alone and isn't new. So therefore it is a non-negligible possibility that there is an additional opportunistic infection that causes issues with SARS-CoV-2. Or we can dismiss it as a false positive and not mention it at all.
raverbashing 6y ago
It's still a preprint but I would be very wary of such claims. How specific can Sars-Cov-2 tests are (to other coronaviruses)? Maybe it was a less virulent variant.
hprotagonist 6y ago
If you processed archival samples and current samples in the same facility, and on the same machines, your immediate prior should be that your archival samples were contaminated during the assay.
- sjg007 6y ago
  They run controls for this reason. So a known negative sample gets processed through the same workflow using the same machines etc...
elektor 6y ago
The usual reminder for these articles: This article is a preprint and has not been peer-reviewed. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice.
cjbprime 6y ago
It is never worth wasting your time on an unreviewed preprint outside your expertise. There is tremendous pressure to publish exciting results as an academic, and very weak tools for detecting false results, whether dishonest or just statistically unsound.
- myth2018 6y ago
  Indeed. Reminds me of that infamous study about chloroquine ran by scientists of the university of Marseille in March. Despite all the criticism regarding the very small sample and a bunch of huge methodological failures, one of the authors started a campaign claiming that hydroxychloroquine + azithromycin could cure covid-19. That has been used by many politicians in USA and Brazil as a underlying reason for their claims that social distancing measures were unnecessary. The losses in terms of time, money and, worst, lives because of this disinformation campaign are immeasurable and I feel really bad when I think that probably none of those who intentionally spread such false claims will be ever punished.
  - cjbprime 6y ago
    Ugh, yeah. On the other hand, that case is at least a legitimate dilemma -- "ignore every paper when it's published, wait a year for reproductions and meta-analysis" is the right thing to do except for the case where there's a new global pandemic and it's very valuable to be able to stop everyone dying right now if you can.
    - myth2018 6y ago
      Agree, but what we've seen was the extreme opposite of a rigorous protocol. Based on mere six cases or so, authors made an extremely bold claim. That could justify further research, though, and they were in fact made. Within some weeks there were already more thorough studies showing the inefficacy of those drugs, but the politicization was already irreversible at that point.
- vibrio 6y ago
  I agree so much. Frequency at which the popular media is reporting headlines from unreviewed preprints is appalling. There should be much more journalistic discipline, but that cow has probably left the barn with the internet.
koheripbal 6y ago
This is one single frozen sample from March 2019 that was positive. Note that subsequent frozen samples from later in 2019 were negative. Without more data - I'd chalk this up to a false positive or sample contamination.
- cjbprime 6y ago
  Also seems like this could end up being a case of multiple hypotheses -- if the false positive rate is very low but all the large cities are performing this test right now, someone's going to hit what will seem to them to be a very unlucky false positive.
- moralestapia 6y ago
  Hard to define the null hypothesis on this one, to be honest ...
- barbegal 6y ago
  I'd have to agree given the prior probability of finding a positive result only in the March 2019 sample. Extraordinary results need extraordinary proof.
- hedora 6y ago
  The study tested 36 samples, from what I can tell (N is well-obfuscated). About ten of those were from before the COVID outbreak. The paper doesn’t talk about the false positive rate of the test they used, and doesn’t compute any sort of P value. ~ 3% is a reasonable false positive rate for a COVID test, so you’d expect 0.3 of those earlier samples to test positive. I doubt it will survive peer review in its current form. In fairness to the authors, the focus of the paper is testing sewage to track diseases. The most interesting result is that they stopped detecting COVID mid-pandemic due to heavy rainfall. Edit: plugging into binomial distribution calculator says there’s over a 25% chance of getting one false positive in the pre-covid samples.
  - pfortuny 6y ago
    (This is not tinfoil-hatting but mere elementary statistics). As long as you keep testing, you will get a false positive (the farther away you test, the more striking it gets). So, it is: if you keep testing, you will find something. It might as well have been "There were SARS-Covid-2 positive samples in June 2018", but it was March 2019.
koeng 6y ago
Until they show full genome sequencing of a novel strain under controlled conditions, I’d assume this is contamination or a crappy primer set. If you’re running a bunch of PCRs, especially of the same thing, there is a good chance of environmental contamination from older sample (shipping containers labs for testing have split partitions because of this). There has also been times reported where there has been primer contamination at the synthesis company because they were also building SARS-CoV-2 controls. Also, there is a very easy way to figure out if it’s real - why didn’t they just Sanger sequence the outputs of the RT-qPCR? Such a simple experiment.
williesleg 6y ago
I'm sure they sneezed immediately before testing.
ortusdux 6y ago
After some early discussion, I've yet to see much about testing sewage. Can it be used to accurately establish a relative infection rate?
devit 6y ago
This is the quote: "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.". And no discussion of the obvious possibility that they screwed up the testing, any discussion of whether they could repeat the test on another part of the sample or on the 2019 April-August samples they didn't test, or any sort of attempt at a Bayesian probability analysis. Pretty ridiculous and shameful, I'd say.
- Ajedi32 6y ago
  Pretty much a textbook case of https://xkcd.com/882/ https://xkcd.com/882/ then?
  - vikramkr 6y ago
    Yep. Except this time, the people asking about the jelly beans are trying to prove they cure acne, and are also selling jelly beans. "This research was supported in part by the REVEAL project, funded by SUEZ Spain." https://www.suez.es/es-es/seccion-comercial/nuestras-referencias/referencias-comerciales/city-sentinel https://www.suez.es/es-es/seccion-comercial/nuestras-referen...
- deleted 6y ago
  [deleted]
- searine 6y ago
  The test from March 2019 wasn't even consistent for a positive result. It found only two of five proteins searched for. Clearly a false positive.
  - dmix 6y ago
    Additionally, it was from a 'frozen archival sample' (they tested frozen samples back to 2018 and daily samples from April-May 2020).
- 6y ago
DangerousPie 6y ago
That's a huge claim without much data to back it up. I am very sceptical.
vikramkr 6y ago
Can there be a [PREPRINT] flag or the like added to titles for posts like these on HN? It's really important to keep in mind that preprints are not peer reviewed, and with the increase in interest in healthcare papers on this forum, it would be really helpful to be able to make that clear. It's more likely that the march 2019 sample is a false positive, not a true finding, and in peer review the statistical validity of that finding would be called into question and further validation would be required. Just posting the headline makes it seem as if this is something that has been conclusively determined without the disclaimer that medrxiv itself puts at the top of each of these publications: that preprints aren't peer reviewed and should not be used to inform clinical decisions etc.
taxicabjesus 6y ago
I recently met someone who claimed the symptoms of their SARS-CoV-2 infection started on December 7, 2019, soon after her friends returned from a trip to China. She said the doctors didn't know what to make of her ("lots of bloody mucus", iirc). By February her doctors realized they should test for SARS-CoV-2, and that she tested positive. Her symptoms mostly resolved by March 2020. The conventional narrative tells us that SARS-CoV-2 started in Wuhan in December 2019 and reached the United States in January 2020 [1]. I think it perfectly reasonable to think this particular weakling virus spread rapidly in China starting in fall 2019, became more virulent as the sun went away and people's vitamin D levels went down. I think the virus blew up in Wuhan, China and northern Italy because of the air pollution [0]. When the medical industry came up with a test and decided to treat the most obvious symptoms of the virus (oxygen saturation levels) instead of the factors that made people vulnerable to the virus, casualties got out of control [2]. Now we've realized that the virus on its own, in a season with adequate sunlight, is basically equivalent to the flue: good at killing old people, not so good for justifying the massive disruptions hoisted upon us all. Casualties have gone down now that doctors aren't ventilating so aggressively. Imagine what would happen if they realized Vitamin D and zinc deficiency and chronic inflammation and concurrent bacterial infections (TB, etc) are treatable conditions that make people vulnerable to the virus. [0] https://news.ycombinator.com/item?id=23085633 https://news.ycombinator.com/item?id=23085633 [1] https://www.cdc.gov/media/releases/2020/p0121-novel-coronavirus-travel-case.html https://www.cdc.gov/media/releases/2020/p0121-novel-coronavi... [2] https://news.ycombinator.com/item?id=22993264 https://news.ycombinator.com/item?id=22993264
- cjbprime 6y ago
  It seems surprising that she could maintain a positive PCR test for eight weeks. I thought the window was much smaller. Here's a paper that says the false negative rate of an RT-PCR test for SARS-CoV-2 increases from 21% on day 9 to 66% by day 21 of symptom onset (and keeps increasing after that). https://www.acc.org/latest-in-cardiology/journal-scans/2020/05/18/13/42/variation-in-false-negative-rate-of-reverse https://www.acc.org/latest-in-cardiology/journal-scans/2020/...
vikramkr 6y ago
The march 2019 finding is almost certainly a false positive. This is the more interesting and potentially more robust finding from the paper: "Unexpectedly, analysis of archival samples revealed the increasing occurrence of SARS-CoV-2 genomes in samples from January 15 to March 4, 2020 (Figure 1, panels D and E). Of note, SARS-CoV-2 was detected in sewage 41 days (January 15) before the declaration of the first COVID-19 case (February 25), clearly evidencing the validity of wastewater surveillance to anticipate cases in the population." This is unfortunately likely to be overshadowed by the march 2019 thing, and I'm surprised that the authors felt comfortable drawing an actual conclusion based off of the 2019 finding and presenting it as "indicating" that widespread circulation was occurring nearly a year before the pandemic hit worldwide circulation. It's not responsible science and might draw doubts on the validity of the other, more interesting conclusion with more evidence to back it up, and rightfully so.
- hn23 6y ago
  You can call it, "economy of attention". Same could be said about the Paris case.
- CodeWriter23 6y ago
  > I'm surprised that the authors felt comfortable drawing an actual conclusion based off of the 2019 finding and presenting it as "indicating" that widespread circulation was occurring nearly a year before the pandemic hit worldwide circulation. “widespread” is your own embellishment.
vikramkr 6y ago
Did a couple cursory google searches. Looks like the people funding this paper (SUEZ Spain) are selling a COVID senteniel service to track covid spread through the wastewater[0]. Nothing wrong with research funded by a for profit firm. However, in light of the, well, surprising claims this article makes, and how the article suggests that wastewater surveillance could have caught it that early and doesn't seem to be discussing the limitations of this approach (such as the apparent propensity for false positives...), it's something to keep in mind. [0]https://www.suez.es/es-es/seccion-comercial/nuestras-referencias/referencias-comerciales/city-sentinel https://www.suez.es/es-es/seccion-comercial/nuestras-referen...
davewritescode 6y ago
Even if it were true, and I'm not even mostly convinced it is. Why would this be surprising and why would anyone immediately jump to the conclusion that it's from humans? I mean Covid-19 didn't just pop out of the air one day, it's been present all along in animals like bats correct? How is it surpising that an animal carcass found it's way into a swage water sample?
- vibrio 6y ago
  One would have to explain how the virus appeared in both china and Spain. Did a bat carrying it make it all that way or did the virus evolve twice independently? Both seem unlikely.
jonplackett 6y ago
This seems almost definitely a false positive, surely.
hnarn 6y ago
Eveything we know about how contagious this virus is would seem to indicate that this has to be a false positive. How would it even be possible for a virus like this to stay "dormant" while circulating for 6+ months before seeing the spread we have now? It seems completely counter-intuitive to me.
abstr 6y ago
I had it in April 2019 in San Francisco, and have medical history to confirm the symptoms and treatment that worked in my case: steroids plus antibiotics. (Steroids stop the autoimmune reaction, antibiotics help to fight off the bacterial infection which can happen because of steroids). Back then doctors said it was a viral bronchitis "because of some strange coronavirus" which rapidly turned into pneumonia. Three different doctors all were quite puzzled. So I've been telling ppl for a while that it's been around for longer than is generally believed. I don't think we can say it was "exactly the same" virus, because it constantly mutates. It might have been that I got less virulent and severe version. I also did self-isolate myself on day one of the symptoms, as I do with any cold or flu, which probably reduced the spread from me. Not saying my experience automatically validates the study, rather that I expect some trustworthy study to eventually confirm that genetically similar strains have been around for almost a year longer. If anyone's curious about the details, comment below and I'll leave info on how to get in touch.

110 points by elies 6y ago

Wait, what? The same virus? March 2019? Are we sure that's not an off-by-one typo, or an error? If that date stands up to scrutiny, wouldn't it call into question everything we thought we knew about the origins and history of covid-19?

Izkata 6y ago
Not a typo. The abstract explicitly says "long before" the first declared case.
gallexme 6y ago
According to the paper : 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.
bredren 6y ago
Yes. It would also stand in contrast to everything we know about how quickly it spreads. I am very skeptical of this claim.
- sudosysgen 6y ago
  It would be very unlikely, but in theory this coronavirus could have spread very weakly for months up to a year before evolving the set of mutations that allow it to spread so rapidly in humans. Indeed, it's exceedingly unlikely that the coronavirus could have had an R0 of >3 right out just after the zoonotic crossing, it's much more likely that it would be significantly lower than one and needed to infect a few people and mutate to adapt to humans. But to such an extent, and in Barcelona? It's still quite unlikely, though in the realm of possibility.
  - tchaffee 6y ago
    > in theory this coronavirus could have spread very weakly for months up to a year The evidence from the study does not support that theory: "All samples from January 2018 to December 2019 came out to be negative for the presence of SARS-CoV-2 genomes with the exception of March 12, 2019."
    - sudosysgen 6y ago
      This is coherent with a weak infection that subsides after a few days, and was weakly transmissible so only infected one or two people.
      - tchaffee 6y ago
        Is it? Would it even show up in sewage if it only weakly infected one or two people? I thought only a percentage of Coronavirus infections result in the virus ending up in the feces. And the tests are that sensitive? Do you have a source?
- thu2111 6y ago
  How much do we really know about that? Recall the apparently 'exponential' increase in cases was in reality an exponential increase in testing - when viewed as a proportion of tests yielding a positive result the virus was spreading not especially fast, and the positive percentage went up quite slowly from a non-zero base.
elies 6y ago
This article is a preprint and has not been peer-reviewed. Quote from article: ...”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.”
- SpicyLemonZest 6y ago
  Green jelly beans cause acne, I guess. I take back anything I ever said about that one XKCD comic making a trivial point.
tchaffee 6y ago
I don't think so unless you make a lot of assumptions. That it was a variation that is just as contagious. That it was a variation that could cause as severe symptoms. That it even came from humans. All samples from January 2018 to December 2019 came out to be negative for the presence of SARS-CoV-2 genomes with the exception of March 12, 2019. Why just one month and then nothing for so long before the outbreak? Per the study, sewage includes rainwater from open drains. A highly infected bat could have ended up dead in a sewer. Nature is full of unexpected possibilities. I bet there are other assumptions without which it doesn't call into question what we think we know.
- mark-r 6y ago
  I don't know how they do things in Barcelona, but in the US the rainwater has its own sewer system. If it didn't the waste water treatment plants would be overrun every time it rains.
  - roywiggins 6y ago
    Combined sewers are common in the US. https://en.m.wikipedia.org/wiki/Combined_sewer https://en.m.wikipedia.org/wiki/Combined_sewer
    - mark-r 6y ago
      My understanding is that combined sewers are being phased out whenever possible for the reason I gave.
      - VBprogrammer 6y ago
        I'm not sure how much you know about Barcelona but it's an ancient city who's history can be traced back through to the Neolithic period with very narrow streets designed before motor vehicles. It's not really compatible to any US city.
      - roywiggins 6y ago
        They have exactly that problem, but it didn't stop dozens of American cities being built with them.
wokwokwok 6y ago
Honestly, its quite problematic. There are vested interests with a great deal to lose if no counter narrative to the origin of the virus turns up... and they’re already seeding all kinds of conspiracy theories all over the place. So, while I’m all for “science”, under the circumstances, the burden of “prove this isn’t a false positive” is overwhelmingly higher than the due diligence taken here. So, yes, it would, but no, it doesn’t.
- aasasd 6y ago
  > vested interests with a great deal to lose if no counter narrative to the origin of the virus turns up Guess I'm under the rock here—what are those interests? To my knowledge, Trump does the most, ahem, novel hypothesizing, which is pretty much expected routine by now.
loeg 6y ago
Yes, it would be an extraordinary result, if it wasn't deeply suspicious for exactly the reasons it's extraordinary.
vikramkr 6y ago
The date is very very unlikely to stand up to scrutiny. As others in the thread have pointed out, the data doesn't make much sense, it lacks consistency, they don't show their statistics, and it's very very likely to be a false positive finding that for some reason the authors decided to go ahead and use as the basis for a very out-there claim. Peer review isn't perfect, but it's generally good enough to at least catch something as sloppy as this paper. I'd be very very surprised if it stood up to scrutiny.
vmception 6y ago
I think people should remain open to possibilities. People started dropping like flies from AIDS in the 1980s from an otherwise completely benign virus they had for 10-12 years, which we didn't know existed and later identified as HIV. A virus which now we are still tracing further and further back, earliest human infection now being 1909. Everything that happened over the last century co-existed with a virus we didn't know was around and slowly incubating and slowly spreading. The similarity being that we know it is possible, and its really opportunistic infections that cause issues with HIV. With SARS-CoV-2 we have identified A virus and have been trying to trace its origin and are still trying to understand its actual effects. But maybe its not alone and isn't new. So therefore it is a non-negligible possibility that there is an additional opportunistic infection that causes issues with SARS-CoV-2. Or we can dismiss it as a false positive and not mention it at all.

raverbashing 6y ago

It's still a preprint but I would be very wary of such claims. How specific can Sars-Cov-2 tests are (to other coronaviruses)? Maybe it was a less virulent variant.

hprotagonist 6y ago

If you processed archival samples and current samples in the same facility, and on the same machines, your immediate prior should be that your archival samples were contaminated during the assay.

sjg007 6y ago
They run controls for this reason. So a known negative sample gets processed through the same workflow using the same machines etc...

elektor 6y ago

The usual reminder for these articles: This article is a preprint and has not been peer-reviewed. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice.

cjbprime 6y ago

It is never worth wasting your time on an unreviewed preprint outside your expertise. There is tremendous pressure to publish exciting results as an academic, and very weak tools for detecting false results, whether dishonest or just statistically unsound.

myth2018 6y ago
Indeed. Reminds me of that infamous study about chloroquine ran by scientists of the university of Marseille in March. Despite all the criticism regarding the very small sample and a bunch of huge methodological failures, one of the authors started a campaign claiming that hydroxychloroquine + azithromycin could cure covid-19. That has been used by many politicians in USA and Brazil as a underlying reason for their claims that social distancing measures were unnecessary. The losses in terms of time, money and, worst, lives because of this disinformation campaign are immeasurable and I feel really bad when I think that probably none of those who intentionally spread such false claims will be ever punished.
- cjbprime 6y ago
  Ugh, yeah. On the other hand, that case is at least a legitimate dilemma -- "ignore every paper when it's published, wait a year for reproductions and meta-analysis" is the right thing to do except for the case where there's a new global pandemic and it's very valuable to be able to stop everyone dying right now if you can.
  - myth2018 6y ago
    Agree, but what we've seen was the extreme opposite of a rigorous protocol. Based on mere six cases or so, authors made an extremely bold claim. That could justify further research, though, and they were in fact made. Within some weeks there were already more thorough studies showing the inefficacy of those drugs, but the politicization was already irreversible at that point.
vibrio 6y ago
I agree so much. Frequency at which the popular media is reporting headlines from unreviewed preprints is appalling. There should be much more journalistic discipline, but that cow has probably left the barn with the internet.

koheripbal 6y ago

This is one single frozen sample from March 2019 that was positive. Note that subsequent frozen samples from later in 2019 were negative. Without more data - I'd chalk this up to a false positive or sample contamination.

cjbprime 6y ago
Also seems like this could end up being a case of multiple hypotheses -- if the false positive rate is very low but all the large cities are performing this test right now, someone's going to hit what will seem to them to be a very unlucky false positive.
moralestapia 6y ago
Hard to define the null hypothesis on this one, to be honest ...
barbegal 6y ago
I'd have to agree given the prior probability of finding a positive result only in the March 2019 sample. Extraordinary results need extraordinary proof.
hedora 6y ago
The study tested 36 samples, from what I can tell (N is well-obfuscated). About ten of those were from before the COVID outbreak. The paper doesn’t talk about the false positive rate of the test they used, and doesn’t compute any sort of P value. ~ 3% is a reasonable false positive rate for a COVID test, so you’d expect 0.3 of those earlier samples to test positive. I doubt it will survive peer review in its current form. In fairness to the authors, the focus of the paper is testing sewage to track diseases. The most interesting result is that they stopped detecting COVID mid-pandemic due to heavy rainfall. Edit: plugging into binomial distribution calculator says there’s over a 25% chance of getting one false positive in the pre-covid samples.
- pfortuny 6y ago
  (This is not tinfoil-hatting but mere elementary statistics). As long as you keep testing, you will get a false positive (the farther away you test, the more striking it gets). So, it is: if you keep testing, you will find something. It might as well have been "There were SARS-Covid-2 positive samples in June 2018", but it was March 2019.

koeng 6y ago

Until they show full genome sequencing of a novel strain under controlled conditions, I’d assume this is contamination or a crappy primer set. If you’re running a bunch of PCRs, especially of the same thing, there is a good chance of environmental contamination from older sample (shipping containers labs for testing have split partitions because of this). There has also been times reported where there has been primer contamination at the synthesis company because they were also building SARS-CoV-2 controls. Also, there is a very easy way to figure out if it’s real - why didn’t they just Sanger sequence the outputs of the RT-qPCR? Such a simple experiment.

williesleg 6y ago

I'm sure they sneezed immediately before testing.

ortusdux 6y ago

After some early discussion, I've yet to see much about testing sewage. Can it be used to accurately establish a relative infection rate?

devit 6y ago

This is the quote: "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.". And no discussion of the obvious possibility that they screwed up the testing, any discussion of whether they could repeat the test on another part of the sample or on the 2019 April-August samples they didn't test, or any sort of attempt at a Bayesian probability analysis. Pretty ridiculous and shameful, I'd say.

Ajedi32 6y ago
Pretty much a textbook case of https://xkcd.com/882/ https://xkcd.com/882/ then?
- vikramkr 6y ago
  Yep. Except this time, the people asking about the jelly beans are trying to prove they cure acne, and are also selling jelly beans. "This research was supported in part by the REVEAL project, funded by SUEZ Spain." https://www.suez.es/es-es/seccion-comercial/nuestras-referencias/referencias-comerciales/city-sentinel https://www.suez.es/es-es/seccion-comercial/nuestras-referen...
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searine 6y ago
The test from March 2019 wasn't even consistent for a positive result. It found only two of five proteins searched for. Clearly a false positive.
- dmix 6y ago
  Additionally, it was from a 'frozen archival sample' (they tested frozen samples back to 2018 and daily samples from April-May 2020).
6y ago

DangerousPie 6y ago

That's a huge claim without much data to back it up. I am very sceptical.

vikramkr 6y ago

Can there be a [PREPRINT] flag or the like added to titles for posts like these on HN? It's really important to keep in mind that preprints are not peer reviewed, and with the increase in interest in healthcare papers on this forum, it would be really helpful to be able to make that clear. It's more likely that the march 2019 sample is a false positive, not a true finding, and in peer review the statistical validity of that finding would be called into question and further validation would be required. Just posting the headline makes it seem as if this is something that has been conclusively determined without the disclaimer that medrxiv itself puts at the top of each of these publications: that preprints aren't peer reviewed and should not be used to inform clinical decisions etc.

taxicabjesus 6y ago

I recently met someone who claimed the symptoms of their SARS-CoV-2 infection started on December 7, 2019, soon after her friends returned from a trip to China. She said the doctors didn't know what to make of her ("lots of bloody mucus", iirc). By February her doctors realized they should test for SARS-CoV-2, and that she tested positive. Her symptoms mostly resolved by March 2020. The conventional narrative tells us that SARS-CoV-2 started in Wuhan in December 2019 and reached the United States in January 2020 [1]. I think it perfectly reasonable to think this particular weakling virus spread rapidly in China starting in fall 2019, became more virulent as the sun went away and people's vitamin D levels went down. I think the virus blew up in Wuhan, China and northern Italy because of the air pollution [0]. When the medical industry came up with a test and decided to treat the most obvious symptoms of the virus (oxygen saturation levels) instead of the factors that made people vulnerable to the virus, casualties got out of control [2]. Now we've realized that the virus on its own, in a season with adequate sunlight, is basically equivalent to the flue: good at killing old people, not so good for justifying the massive disruptions hoisted upon us all. Casualties have gone down now that doctors aren't ventilating so aggressively. Imagine what would happen if they realized Vitamin D and zinc deficiency and chronic inflammation and concurrent bacterial infections (TB, etc) are treatable conditions that make people vulnerable to the virus. [0] https://news.ycombinator.com/item?id=23085633 https://news.ycombinator.com/item?id=23085633 [1] https://www.cdc.gov/media/releases/2020/p0121-novel-coronavirus-travel-case.html https://www.cdc.gov/media/releases/2020/p0121-novel-coronavi... [2] https://news.ycombinator.com/item?id=22993264 https://news.ycombinator.com/item?id=22993264

cjbprime 6y ago
It seems surprising that she could maintain a positive PCR test for eight weeks. I thought the window was much smaller. Here's a paper that says the false negative rate of an RT-PCR test for SARS-CoV-2 increases from 21% on day 9 to 66% by day 21 of symptom onset (and keeps increasing after that). https://www.acc.org/latest-in-cardiology/journal-scans/2020/05/18/13/42/variation-in-false-negative-rate-of-reverse https://www.acc.org/latest-in-cardiology/journal-scans/2020/...

vikramkr 6y ago

The march 2019 finding is almost certainly a false positive. This is the more interesting and potentially more robust finding from the paper: "Unexpectedly, analysis of archival samples revealed the increasing occurrence of SARS-CoV-2 genomes in samples from January 15 to March 4, 2020 (Figure 1, panels D and E). Of note, SARS-CoV-2 was detected in sewage 41 days (January 15) before the declaration of the first COVID-19 case (February 25), clearly evidencing the validity of wastewater surveillance to anticipate cases in the population." This is unfortunately likely to be overshadowed by the march 2019 thing, and I'm surprised that the authors felt comfortable drawing an actual conclusion based off of the 2019 finding and presenting it as "indicating" that widespread circulation was occurring nearly a year before the pandemic hit worldwide circulation. It's not responsible science and might draw doubts on the validity of the other, more interesting conclusion with more evidence to back it up, and rightfully so.

hn23 6y ago
You can call it, "economy of attention". Same could be said about the Paris case.
CodeWriter23 6y ago
> I'm surprised that the authors felt comfortable drawing an actual conclusion based off of the 2019 finding and presenting it as "indicating" that widespread circulation was occurring nearly a year before the pandemic hit worldwide circulation. “widespread” is your own embellishment.

vikramkr 6y ago

Did a couple cursory google searches. Looks like the people funding this paper (SUEZ Spain) are selling a COVID senteniel service to track covid spread through the wastewater[0]. Nothing wrong with research funded by a for profit firm. However, in light of the, well, surprising claims this article makes, and how the article suggests that wastewater surveillance could have caught it that early and doesn't seem to be discussing the limitations of this approach (such as the apparent propensity for false positives...), it's something to keep in mind. [0]https://www.suez.es/es-es/seccion-comercial/nuestras-referencias/referencias-comerciales/city-sentinel https://www.suez.es/es-es/seccion-comercial/nuestras-referen...

davewritescode 6y ago

Even if it were true, and I'm not even mostly convinced it is. Why would this be surprising and why would anyone immediately jump to the conclusion that it's from humans? I mean Covid-19 didn't just pop out of the air one day, it's been present all along in animals like bats correct? How is it surpising that an animal carcass found it's way into a swage water sample?

vibrio 6y ago
One would have to explain how the virus appeared in both china and Spain. Did a bat carrying it make it all that way or did the virus evolve twice independently? Both seem unlikely.

jonplackett 6y ago

This seems almost definitely a false positive, surely.

hnarn 6y ago

Eveything we know about how contagious this virus is would seem to indicate that this has to be a false positive. How would it even be possible for a virus like this to stay "dormant" while circulating for 6+ months before seeing the spread we have now? It seems completely counter-intuitive to me.

abstr 6y ago

I had it in April 2019 in San Francisco, and have medical history to confirm the symptoms and treatment that worked in my case: steroids plus antibiotics. (Steroids stop the autoimmune reaction, antibiotics help to fight off the bacterial infection which can happen because of steroids). Back then doctors said it was a viral bronchitis "because of some strange coronavirus" which rapidly turned into pneumonia. Three different doctors all were quite puzzled. So I've been telling ppl for a while that it's been around for longer than is generally believed. I don't think we can say it was "exactly the same" virus, because it constantly mutates. It might have been that I got less virulent and severe version. I also did self-isolate myself on day one of the symptoms, as I do with any cold or flu, which probably reduced the spread from me. Not saying my experience automatically validates the study, rather that I expect some trustworthy study to eventually confirm that genetically similar strains have been around for almost a year longer. If anyone's curious about the details, comment below and I'll leave info on how to get in touch.