https://www.sciencedirect.com/science/article/pii/S0013935122013068
Many of you may recall a study from over two years ago which found traces of covid RNA in sewage water in Lombardy, Italy.
This is not that study. This is a study released this month which confirms those earlier findings. A new strain which predates the Wuhan alpha strain was sequenced, labeled proCoV2.
Abstract
As a reference laboratory for measles and rubella surveillance in Lombardy, we evaluated the association between SARS-CoV-2 infection and measles-like syndromes, providing preliminary evidence for undetected early circulation of SARS-CoV-2. Overall, 435 samples from 156 cases were investigated.
RNA from oropharyngeal swabs (N = 148) and urine (N = 141) was screened with four hemi-nested PCRs and molecular evidence for SARS-CoV-2 infection was found in 13 subjects. Two of the positive patients were from the pandemic period (2/12, 16.7%, March 2020–March 2021) and 11 were from the pre-pandemic period (11/44, 25%, August 2019–February 2020).
Sera (N = 146) were tested for anti-SARS-CoV-2 IgG, IgM, and IgA antibodies. Five of the RNA-positive individuals also had detectable anti-SARS-CoV-2 antibodies. No strong evidence of infection was found in samples collected between August 2018 and July 2019 from 100 patients. The earliest sample with evidence of SARS-CoV-2 RNA was from September 12, 2019, and the positive patient was also positive for anti-SARS-CoV-2 antibodies (IgG and IgM).
Mutations typical of B.1 strains previously reported to have emerged in January 2020 (C3037T, C14408T, and A23403G), were identified in samples collected as early as October 2019 in Lombardy. One of these mutations (C14408T) was also identified among sequences downloaded from public databases that were obtained by others from samples collected in Brazil in November 2019.
We conclude that a SARS-CoV-2 progenitor capable of producing a measles-like syndrome may have emerged in late June-late July 2019 and that viruses with mutations characterizing B.1 strain may have been spreading globally before the first Wuhan outbreak.
Our findings should be complemented by high-throughput sequencing to obtain additional sequence information. We highlight the importance of retrospective surveillance studies in understanding the early dynamics of COVID-19 spread and we encourage other groups to perform retrospective investigations to seek confirmatory proofs of early SARS-CoV-2 circulation.
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The paper has serological data, though. PCR contamination wouldn't be enough.
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Yes, that's exactly the issue. They consistently found negative results before a certain date, which makes this kind of contamination unlikely, especially across two different types of test that would require two different types of contamination. And while ELISA is sensitive, it's about 1000x less sensitive than rtPCR, and antibodies are far more fragile than RNA fragments.
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I've mentioned processing time for contamination already and already touched on why it's still unlikely. The problem is that you need this time to concord between different tests
Again, what kind of contamination would work for this? Contamination for both antibodies and RNA is extremely unlikely. You'd need to mix samples or to sneeze on all of the equipment. And it still wouldn't work for the negative controls, as well as for the simply negative samples later on. I can understand RNA contamination because that happens easily enough since RNA fragments are relatively durable, but for simultaneous contamination with both, I don't see it.
They also shipped off an ELISA test to another lab, which gave concordant results. So really there would need to be persistent sample contamination or mixup. It's possible, but it's very unlikely, and this isn't the first study with these results.
Firstly, and I want you to know I'm asking this in good faith because I really am out of my depth entirely here so I'm not at all attempting to be combative, just seeking clarification, but:
Firstly doesn't it simply suggest the first CASE was recorded at the Wuhan market. Like, the crossing into humans doesn't contain anything wuhan specific right? We just up until this point assumed that was the site because it was the first recorded case as far as we know. In fact even that isn't true it seems, according to wikipedia.
Now again my understanding of this is incredibly shallow so I'm not proclaiming to be an expert in any way but it seems kinda weird to proclaim Wuhan was where it crossed into humans because the first cases were there but also earlier cases don't invalidate that because we know Wuhan was where it crossed into people because the first cases were there. If there's some specific marker or evidence that they're from there that doesn't rely on the "first reported case(s)" being the flag pole then fair enough, but if not then it seems to be some kind of orthodox circular justification, to me at least. (Or at least when challenged with alternate data that is just as reasonable if we assume the scientists are competent, which brings me to my next point)
Secondly, if we are just going to assume the samples were contaminated can't we just assume that about literally any sample? Doesn't any case for anywhere rely on us assuming the scientists are controlling for this?
I genuinely am trying to fill gaps in my own knowledge here so I hope I came off as earnestly asking for the sake of knowing and not the sake of debating or invalidating what you're saying in any way. o7
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Hey sorry it took me so long to getting around to reading this between Christmas extended family obligations and a new job I just kinda didn't do anything but look at memes for a few days. Thank you very much for the explanation and that makes a lot of sense to consider it that way from a "It's not so much what X or Y proves it's that the model of best fit has a much larger body of evidence and upending that requires a bit more leverage than is really being pushed here but this might have some interesting implications if it continues to hold." kind of thing. I can very much understand the discussion a bit better from that lens even without specific biology knowledge, and does a decent job of answering that 'burden of proof' situation when you're not just challenging a finding but a lot of the other peripheral shit that only holds true if that finding does too.
I agree that the extra sticky bit of covid is that while I say we're supposed to act like these scientists are controlling for this shit because in my brain yeah, ideally, they would. However, gestures vaguely at the last three years of non stop fucking horse shit that doesn't seem to be the case as you mention at the end haha. It's hard to simultaneously want to give them the benefit of the doubt and know that like societally... nah. Nobody should be with the way we've handled covid, but at the moment that doesn't factor as much into the rest of the body of evidence this paper would be challenging so the first place to look for contamination would be here, not there.
Thanks for your time I appreciate you going the extra mile to re-frame it for me.