Amount of Covid found in the wastewater in Boston
mwra.com
mwra.com
I don't think anyone knows about the kinetics of Omicron yet. I think the increasing prevalence of Omicron may have a lot more to do with its ability to escape immunity from past infection and increased probability of vaccine breakthrough than any inherent higher transmissibility to those who are immunologically naive.
has it ? I've seen this claim made over and over, w/out documentation.
I've seen documentation of higher nasal swab loads, but not higher systemic circulating virus. Higher upper respiratory loads (e.g. mucosal) would also lead to increased transmissibility, but not higher waste water levels.
Very early report on Delta, describing higher loads in oropharyngeal swabs: https://www.medrxiv.org/content/10.1101/2021.07.07.21260122v...
> I've seen documentation of higher nasal swab loads, but not higher systemic circulating virus.
You'll have almost no reports of "systemic circulating virus" load, because there's not really an accepted definition for how this measurement would be taken. Plasma concentrations don't appear to be particularly meaningful except in late stages of critical disease.
> higher waste water levels.
My understanding of the evidence is that fecal loads of Delta are higher than other variants, but not as elevated in comparison to how much throat and nose swabs are elevated. I.e. both statements appear true (higher loading overall, and even higher loading in upper respiratory tissue).
Wait, what? This seems completely at odds with the literal definition of viral load per https://en.wikipedia.org/wiki/Viral_load:
> Viral load, also known as viral burden, is a numerical expression of the quantity of virus in a given volume of fluid, including biological and environmental specimens.
Yes, in a specific fluid. Grandparent doesn't like viral load data coming from upper respiratory swabs-- preferring some kind of "higher systemic load" number.
Well, there's no magical "real systemic" load. You can measure it in the nose; you can measure it (sometimes) in the bloodstream (but this is sporadic and small even in severe cases, though it has prognostic value in critical care). You can measure it in feces, etc.
> To better understand the coronavirus’s journey from one person to another, a team of 50 scientists has for the first time created an atomic simulation of the coronavirus nestled in a tiny airborne drop of water.
> To create the model, the researchers needed one of the world’s biggest supercomputers to assemble 1.3 billion atoms and track all their movements down to less than a millionth of a second. This computational tour de force is offering an unprecedented glimpse at how the virus survives in the open air as it spreads to a new host.
And they look at things like how mucins, water, and calcium atoms interact with the proteins of the virus particle.
> This discovery may help explain how the Delta variant became so widespread. Delta’s spike proteins have a more positive charge than those on earlier forms of the coronavirus. As a result, mucins huddle more closely around them. That attraction could potentially make the mucins a better shield.
Delta undoubtedly has many advantages, and disadvantages, over earlier variants that it outcompeted. That's why I said viral load is "a factor".
One thing that's interesting to me is how the selective pressures on pathogens change. Early on, adaptations that cause higher viral loads are often highly advantageous because they aid transmission-- this tends to be correlated with higher virulence, too. Later, as a smaller portion of the population is susceptible, and adaptations that are less virulent, have longer incubation periods, etc, can win.
It'll be interesting to learn about Omicron virulence and transmissibility. I wouldn't be surprised if it's less, like early reports hint at. However, disentangling this from partial immune escape, etc, is hard.
https://covid.cdc.gov/covid-data-tracker/#variant-proportion...
If we're lucky, it's a mild strain - this doesn't have strong evidence yet. If we're unlucky, and it's similar to other strains, we have around a month before things get very bad indeed.
https://www.kare11.com/article/news/local/breaking-the-news/...
Where it was less useful was when people would cite it day by day. All kinds of examples where it'd contradict what we were seeing in the actual COVID data when using it that way.
Around here we mostly just call it Hopkins or JHU.
Pursuant to IL FOIA, please provide me with records sufficient to show all non-exempt fields of information from the COVID-19 water sampling that's described at: https://mwrd.org/sites/default/files/documents/Sewage%20Surveillance_FS_210119.pdf. The document mentions that MWRD already shares this surveillance information with academic partners, so I believe it should be relatively easy to collect these records.
As the statute allows a requester to specify a file format, please provide me the records in excel format.
Please reach out to me if you have any questions about this request.And there's further, but diminishing gains from fitting the fluorescence curves.
Although, to be fair, last October didn’t look bad, and then there was a massive spike…
What else can our waste tell us?
There's been talk amongst Police Departments in whether investing in wide scale wastewater monitoring could help locate drug dealers/labs. Personally, I think this is a huge invasion of privacy, but since wastewater is a "public good" police currently can do whatever they want with it (source: I work in a wastewater testing facility).
As easy as one bad actor flushing the wrong/right stuff a few times (stuff that is known to be monitored, say a specific infectious agent) in a few public toilets across a city, and waiting for the reports to trickle in. More of a fanning the flames rather than starting a panic, since the threat would have been well-known enough to have been monitored in the first place.
So maybe keep those waste reports on a need-to-know basis, rather than broadcasting a public “daily waste report”.
Because more people are getting sick with COVID19 at this time... it makes sense that more COVID19 samples will be found in wastewater.
Perhaps that's what you meant?
Viruses could literally be affected by the lesser amounts of sun and shorter days. UV-rays kill the virus for instance, and we get less of them in the winter than during the summer.
Without knowing any more details on "why" there's a relationship between COVID and the winter (whether its human behavior that changes, or if its physically something associated with the virus / sun... like day length + UV rays or heat vs humidity), we just have to say the most generic thing possible to remain correct.
In this case: we know that COVID19 seems to spread more in the winter. We have lots of theories why this happens, but I personally haven't seen any "Mythbusters" style study that goes over all the theories and actually proves any of them.
But yes, there was a spike in December 2019, and another spike in December 2020. So we all are expecting a spike in December 2021.
No, just a significant minority:
https://www.webmd.com/cold-and-flu/cold-guide/common_cold_ca...
Corona viruses are a family of viruses that extends far beyond the particular virus responsible for the current pandemic/epidemic.
Corona viruses are the #2 family responsible for the common (viral) cold, behind rhinoviruses (In the ballpark of 10-20% and 50-60% respectively, iirc, but definitely rank #2 & #1).
So there is a great deal of historical knowledge about the corona family of viruses, just not necessarily specific to this corona virus and it's variants.
In the context of looking for seasonal patterns in respiratory viruses, it's the first place you'd look in trying to find common traits.
ETA: WebMD says 10-40% Rhino, 20% Corona, 20% RSV/parainfluenza, and 20-30% "other".
See for example:
"Epidemiology and Clinical Presentations of Human Coronavirus NL63 Infections in Hong Kong Children"
Authors: Ting Fan Leung, Chung Yi Li, Wai Yip Lam, Gary W. K. Wong, Edmund Cheuk, Margaret Ip, Pak Cheung Ng, and Paul K. S. Chan
ASM Journals, Journal of Clinical Microbiology, Vol. 47, No. 11
https://doi.org/10.1128/JCM.00832-09
https://journals.asm.org/doi/10.1128/jcm.00832-09?permanentl...
In my country - where for the last month we've basically had no sun, just clouds - there is a distinct spike around winter, which would follow nicely with the vitamin D theory. However in places like Southern Europe, which still has a good amount of sun during winter, there are similar spikes.
Most respiratory viruses, like influenza and colds have greater prevalence during the local winter. We'd expect COVID to behave similarly. The reasons for that are still debated.
In wastewater collection system, I&I (Inflow & Infiltration) is a constant problem where excess water from the environment enters the waste treatment pipeline. It's costly because all that otherwise clean water has to get the full treatment. So, it's interesting to me, that, unless they have normalized for I&I somehow which is not apparent in their raw data, the true seasonal variation in concentration is actually understated.
Biobot says:
"We normalize the SARS-CoV-2 viral concentration to a fecal indicator, to account for differences in dilution. We use PMMoV as this fecal indicator, which is an RNA virus that is commonly excreted in stool."
So they're effectively reporting on the ratio between SARS-CoV-2 and PMMoV concentration, which should be normalized for seasonal changes in dilution.
https://www.worldometers.info/coronavirus/country/us/
I definitely think there was going to be a major fourth surge that propelled the US death count to 1 million people from the holidays.
Who knows what omicron will do.
I've gotten very conditioned when urls contain a question, to expect a bloated, ad-ridden , 5-page editorial, focusing on a tangentially related long sob story of a guy and their dog, with the answer to the question barely hinted at, buried inconspicuously somewhere around page 4.
Here in Finland they use a N2 PCR test published by the CDC (don't ask me how that works, I am a software developer...). However, the results are presented in millions of RNA copies per 1000 inhabitants per 24 hours.
I guess that leads to results unaffected by water consumption habits or rainfall (if the rains drains to the same system as household sewers, some location have dual systems).
https://www.thl.fi/episeuranta/jatevesi/jatevesiseuranta_vii...
https://web.archive.org/web/20170814094625/http://www.bipm.o...
The first random picture seems to confirm that in the US a capital L is used.
https://murraybrand.com/wp-content/uploads/2015/07/crystal_o...
> Since 1979, the litre may exceptionally be written using either an uppercase "L" or a lowercase "l", a decision prompted by the similarity of the lowercase letter "l" to the numeral "1", especially with certain typefaces or English-style handwriting. The American NIST recommends that within the United States "L" be used rather than "l".
In European measurement contexts I've sometimes seen ℓ (with a script l), but I'm not sure I've seen plain l. (However, I live in the U.S. and might not have as much exposure to European references to liters.)
In 1979 the capital L was recognized by SI (as non-SI unit), too. (I don't know whether the script form was recognized at the same time). According the German Wikipedia capital L is used mainly in English speaking countries. Which makes sense because in handwriting the American (not so sure about the British) digit 1 and small letter l cannot really be distinguished. So 1 liter written as 1 l would be hard to read. In Germany the digit 1 nearly unviversally has a rising stroke on the left in handwriting, so 1 l is not a problem. German Wikipedia says capital L is not used by ISO.
I wonder if this could be an effective way of determining COVID prevalence in areas where they are not doing enough testing?
And yes! Our testing represents every individual in the community that has used a toilet connected to a sewer, independent of where they live, whether they experience symptoms, or whether they have the time, money or access to clinical testing. It's helped public officials stay informed and make decisions even with limited or inconsistent individual testing data.
We can look at excess deaths (https://www.cdc.gov/nchs/nvss/vsrr/covid19/excess_deaths.htm) and the speed and locations it spread around the world and be fairly certain that if the virus were here in significant quantities in 2019 we'd have seen signs of it.
But it's not really necessary most of the time.
It's often done more for political reasons than technical ones, because it's easier for the public to understand and trust UV disinfection than the other, much more complex processes that are typically used.
Cobb County GA is an example of a plant that has large scale UV treatment right before discharge into the Chattahoochee River. But it's effluent is cleaner than the water getting pumped into their water supply.
This paper discusses treatment and emergent pathogens:
"The Role of Wastewater Treatment in Protecting Water Supplies Against Emerging Pathogens"
https://www.jstor.org/stable/23803199
I thought direct chlorination played a larger role, it seems it doesn't.
(Heavy chlorination of water does result in post-treatment chlorine compounds being present, these are themselves an environmental concern. The bulk of the chlorine evaporates or is reacted relatively quickly. Chlorine also negatively impacts "digestors" which process residual organic matter in wastewater.)
UV, oxygenation, sunlight, filtration, and dilution are all utilised as well.
Viruses tend not to survive long periods of environmental exposure outside a host in most circumstances, though I'm not knowledgeable on specifics or exceptions.
I wouldn't be too worried about catching COVID from the water.
Eg, in the uk there’s less than 300 cases of it
SOURCE: I work in a leading U.S. wastewater testing lab.
Currently, labs have two main tools available - RT-qPCR and tiled amplicon sequencing. RT-qPCR provides cycle threshold (Ct) values which quantify the amount of virus RNA in a sample. RT-qPCR is not practical for finding and quantifying de novo variants as it relies on standard primer sets. Sequencing based approaches are less quantitative but provide more insight into the diversity of RNAs and mutations present in a sample - and thus which variants are present.
https://www.gisaid.org/hcov19-variants/ has a variant dashboard based on sequencing data, including Omicron. It's not as quantitative qPCR, but still may be of interest.
Some labs quantify amount of variant by running multiple RT-qPCRs using primers specific to mutations unique to each variant (see https://www.promega.com/products/pcr/qpcr-and-rt-qpcr/sars-c...).
Both of these strategies leave much to be desired. For one, it's terribly costly to run multiple RT-qPCRs in parallel. It also fails to account for any novel variants whose mutations lie outside your primer binding region(s).
From what I've gathered, RT-qPCR is useful for quantifying what is already known while sequencing helps you discover what is unknown.
I guess if you had unlimited time and money you could order new primer/probe sets from IDT every time a new variant comes into play...kind of like a home-brew microarray? Honestly, I'm kind of surprised there aren't SARS-CoV-2 variant microarrays on the market yet...we're all just spitballing here.