I was more inclined to think that trying to distinguish variants via sewage is intrinsically flawed, since the Omicron "swarm" for an entire city could have some 157del mutants or otherwise just prompt false-positive. But their previous studies show stark transitions using dels to distinguish Alpha and Delta. Which potentially means the high cycle count isn't as big a flaw either.
RE the model, the math just seems stupid. Delta is staying level until the end. So the model concludes it has to just keep staying level forever, because (as far as I can make out) their equation concludes it will never go high enough to make enough people immune (even though there's tons of prior immunity to Delta). Ok, so your model is idiotic, fix it.
Detecting viral loads in wastewater is a proven concept. The devil of the detail is that the test used has to be of sufficient accuracy and precision to distinguish among potential variants of concern.
That's where the cycle thresholds present a problem--there's considerable evidence to indicate that at higher cycle thresholds (Ct>34 certainly), positive results from viral fragments and dead nucleotides--remnants of prior infection, which are known to linger for quite some time after symptoms have resolved, and can be shed for quite some time after symptoms have resolved.
If the assay is detecting Delta (or Omicron) remnants, the incidence of Delta (or Omicron) is going to be overstated, as the assay was designed to be a quantitative test. Given the fairly recent displacement of Delta by Omicron as the most prevalent variant, including viral fragments in any assessment of the incidence of either variant within a particular population skews the results, possibly dramatically.
That's the other flaw in their modeling--the lack of a discussion about the ratio of "real" cases based on the viral loads found in the wastewater samples and the confirmed cases according to per-patient PCR testing. Without a justifiable ratio estimate to connect wastewater test results to a likely incidence of disease in the community, the only thing the wastewater sampling can ascertain is that there are (or are not) particular variants, occurring at varying loads within the sample. That can tell you if an outbreak is forming, which is a valuable early warning for any infectious pathogen, but that is the limit of what the surveillance can do.
Thanks for this post. I had a few reservations about that article, as people were far too quick to extrapolate the data to say that this is all because of the vaccinated. The test really just tested for genes in the water, and that's really mostly what we can conclude- it's just present. I commented that if they really wanted to see how much Delta is active then they would do genomic sequencing rather than rt-PCR. I did mention that the difference in tropism may mean that someone could be coinfected, but your idea that different populations may be infected and the wastewater collecting together could be viable.
Dr. Vanden Bossche is an interesting character. I'm halfway through his interview on The Highwire, and I think there are some alarming aspects to his assessment. I think we're seeing that many people are steadfast in their ideas or assumptions that they may not want to be able to examine different perspectives if it may undermine their own ideas.
There is some research that purports to permit an extrapolation of viral load from the cycle count in RT-PCR (which is why the authors describe the test as RT-qPCR, the "q" meaning "quantitative".
From my last readings on that particular topic, the research on using PCR for quantitative analysis is far from certain, and I'm not at all convinced that it has the specificity the Yaniv study imputes to it.
But even if RT-qPCR is that accurate, the modeling they attempt from that data is still off base. Viral evolutionary dynamics are going to occur within a single host--that's where viral replication takes place. Wastewater surveillance by its very nature amalgamates the viral loads from multiple hosts, effectively erasing any correlation between the detected viral load and the level of viral infection within an individual host.
It's like taking one teaspoon of sugar and one tablespoon of sugar, then mixing them both into a single cup of water. There is no way to look backwards from the sugar solution to tell if the sugar was added by one teaspoon and one tablespoon or four teaspoons (1tbsp == 3 tsp).
In order to correlate a level of viral load within a wastewater sample, there needs to be a basis for approximating the number of infected hosts in the community. That's the ratio the Proverbio study highlighted which the Yaniv study apparently ignored.
Of course, using a Ct of 40 for PCR testing likely means most samples were not suitable for sequencing. There is a reason the CDC doesn't do sequencing on samples with a Ct above 28.
Wastewater surveillance can be a useful monitoring tool, as it can lead to early detection of pathogens and of a rise in pathogens (again, assuming the test used is reliable). Knowing a virus is making the rounds of a community is good information to have--it can become a cautionary for people to be more diligent in matters of hand hygiene, vitamin D supplementation, and other low-intensity prophylaxis and mitigation. Trying to bend it into a pathway to predict viral evolution just isn't necessary.
Re: coinfection -- that possibility would tend to support classifying Omicron as a distinct serotype from original SARS-CoV-2/Alpha/Delta. If there is a prevalence of coinfection I tend to agree with the Institut Pasteur that Omicron should be considered a different serotype from Delta.
as they say in software development: shit in, shit out. bwaahahahahahaha
I was more inclined to think that trying to distinguish variants via sewage is intrinsically flawed, since the Omicron "swarm" for an entire city could have some 157del mutants or otherwise just prompt false-positive. But their previous studies show stark transitions using dels to distinguish Alpha and Delta. Which potentially means the high cycle count isn't as big a flaw either.
RE the model, the math just seems stupid. Delta is staying level until the end. So the model concludes it has to just keep staying level forever, because (as far as I can make out) their equation concludes it will never go high enough to make enough people immune (even though there's tons of prior immunity to Delta). Ok, so your model is idiotic, fix it.
Detecting viral loads in wastewater is a proven concept. The devil of the detail is that the test used has to be of sufficient accuracy and precision to distinguish among potential variants of concern.
That's where the cycle thresholds present a problem--there's considerable evidence to indicate that at higher cycle thresholds (Ct>34 certainly), positive results from viral fragments and dead nucleotides--remnants of prior infection, which are known to linger for quite some time after symptoms have resolved, and can be shed for quite some time after symptoms have resolved.
If the assay is detecting Delta (or Omicron) remnants, the incidence of Delta (or Omicron) is going to be overstated, as the assay was designed to be a quantitative test. Given the fairly recent displacement of Delta by Omicron as the most prevalent variant, including viral fragments in any assessment of the incidence of either variant within a particular population skews the results, possibly dramatically.
That's the other flaw in their modeling--the lack of a discussion about the ratio of "real" cases based on the viral loads found in the wastewater samples and the confirmed cases according to per-patient PCR testing. Without a justifiable ratio estimate to connect wastewater test results to a likely incidence of disease in the community, the only thing the wastewater sampling can ascertain is that there are (or are not) particular variants, occurring at varying loads within the sample. That can tell you if an outbreak is forming, which is a valuable early warning for any infectious pathogen, but that is the limit of what the surveillance can do.
Thanks for this post. I had a few reservations about that article, as people were far too quick to extrapolate the data to say that this is all because of the vaccinated. The test really just tested for genes in the water, and that's really mostly what we can conclude- it's just present. I commented that if they really wanted to see how much Delta is active then they would do genomic sequencing rather than rt-PCR. I did mention that the difference in tropism may mean that someone could be coinfected, but your idea that different populations may be infected and the wastewater collecting together could be viable.
Dr. Vanden Bossche is an interesting character. I'm halfway through his interview on The Highwire, and I think there are some alarming aspects to his assessment. I think we're seeing that many people are steadfast in their ideas or assumptions that they may not want to be able to examine different perspectives if it may undermine their own ideas.
There is some research that purports to permit an extrapolation of viral load from the cycle count in RT-PCR (which is why the authors describe the test as RT-qPCR, the "q" meaning "quantitative".
From my last readings on that particular topic, the research on using PCR for quantitative analysis is far from certain, and I'm not at all convinced that it has the specificity the Yaniv study imputes to it.
But even if RT-qPCR is that accurate, the modeling they attempt from that data is still off base. Viral evolutionary dynamics are going to occur within a single host--that's where viral replication takes place. Wastewater surveillance by its very nature amalgamates the viral loads from multiple hosts, effectively erasing any correlation between the detected viral load and the level of viral infection within an individual host.
It's like taking one teaspoon of sugar and one tablespoon of sugar, then mixing them both into a single cup of water. There is no way to look backwards from the sugar solution to tell if the sugar was added by one teaspoon and one tablespoon or four teaspoons (1tbsp == 3 tsp).
In order to correlate a level of viral load within a wastewater sample, there needs to be a basis for approximating the number of infected hosts in the community. That's the ratio the Proverbio study highlighted which the Yaniv study apparently ignored.
Of course, using a Ct of 40 for PCR testing likely means most samples were not suitable for sequencing. There is a reason the CDC doesn't do sequencing on samples with a Ct above 28.
Wastewater surveillance can be a useful monitoring tool, as it can lead to early detection of pathogens and of a rise in pathogens (again, assuming the test used is reliable). Knowing a virus is making the rounds of a community is good information to have--it can become a cautionary for people to be more diligent in matters of hand hygiene, vitamin D supplementation, and other low-intensity prophylaxis and mitigation. Trying to bend it into a pathway to predict viral evolution just isn't necessary.
Re: coinfection -- that possibility would tend to support classifying Omicron as a distinct serotype from original SARS-CoV-2/Alpha/Delta. If there is a prevalence of coinfection I tend to agree with the Institut Pasteur that Omicron should be considered a different serotype from Delta.