Tag Archives: COVID

Virus Detection in Sewage

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With the appearance of COVID and polio the USA, the news has revealed that it is possible to detect and monitor certain viruses in municipal sewage. As a chemist I marvel at this. Sewage is a frightfully complex mixture of biological waste products along with many chemical cleaning products, detergents, grime and pharmaceuticals that go down the drain. How is it that one can collect enough intact virus particles from this fecal hell broth with enough purity to make a positive identification of genetic material?

A recent methodology is given in an article titled Detection of Pathogenic Viruses in Sewage Provided Early Warnings of Hepatitis A Virus and Norovirus Outbreaks and published in Appl Environ Microbiol. 2014 Nov; 80(21): 6771–6781, DOI: 10.1128/AEM.01981-14 by Maria Hellmér,aNicklas Paxéus,bLars Magnius,cLucica Enache,bBirgitta Arnholm,dAnnette Johansson,bTomas Bergström,a and Heléne Nordera,c. As you can see the work is from 2014 so this is not brand-spanking-new technology. It is interesting to note that the material used to sediment the viruses in this article was acidified powdered skim milk proteins. The article was found by a Google search and located at the NIH National Library of Medicine.

Why powdered skim milk? It could be that milk fat interferes with the process or the workers are just removing variables. More likely, it is because the widely available powdered milk that you buy at the grocery store is from skim milk. Dairy fat is too valuable for a business to squander and is used to make more profitable products like ice cream or whipping cream.

A more recent methodology has been reported in PLoS One. 2017; 12(1): e0170199. Published online 2017 Jan 18. doi: 10.1371/journal.pone.0170199. The article, by Mathis Hjort Hjelmsø,#1,* Maria Hellmér,#2 Xavier Fernandez-Cassi,3 Natàlia Timoneda,3,4 Oksana Lukjancenko,1 Michael Seidel,5 Dennis Elsässer,5 Frank M. Aarestrup,1 Charlotta Löfström,2,¤ Sílvia Bofill-Mas,3 Josep F. Abril,3,4 Rosina Girones,3 and Anna Charlotte Schultz2 and titled Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing. The article cites potential sedimentation substances as Iron(III) Chloride, powdered milk flocculation, PEG, and glass wool filtration. More extraction sources can be found online.

In the 2014 article above, the virus particles are extracted from the raw sewage onto acidified powdered skim milk proteins and amplified with quantitative polymerase chain reaction, qPCR. Powdered milk may seem strange but realize that virus particles can be removed by coagulation with metal ions, lime or with other polyelectrolytes, including proteins. The charge distribution on milk proteins will vary with acidity so these methods are very pH dependent. The viruses are naturally coated in proteins and thus will acquire surface charges varying with pH. The coagulation of proteins occurs when dissolved or suspended proteins irreversibly change their secondary structure by unfolding and condense to form a thicker solution or a solid form. The formation of cheese by acidification or solidifying a runny egg with heat are common examples of coagulation.

A 1973 review article by Gerald Berg in Bull World Health Organ. 1973; 49(5): 451–460, reviews methods for the removal of viruses from effluents, so knowledge of the sedimentation, or coagulation, of viruses in sewage has been around for a long while.

These articles are written by specialists in the field and may present considerable difficulty for a few readers. I would urge those so inclined to try to plow through the articles and pick up what you can. This holds true for all scientific papers. See what you can learn.

When future historians view this pandemic

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Some historians in the future will focus on this time period and try to make sense of the social and political turmoil we’re now experiencing in this endemic of COVID-19. Many US citizens are in conflict with knowledgeable authorities who are trying to limit the spread of this viral disease. As of this writing the endemic has not yet fully played out.

There are several particularly good questions that must be investigated- How should we view a culture that can’t bring itself to cooperate internally in the prevention of a communicable disease that has so far caused more than 900,000 deaths? Would one expect that roughly 1/3 of the adult population in a highly advanced culture such as ours would refuse to cooperate with the most minor measures to prevent the spread of contagion? That is, wearing a light weight mask when around others. Standing apart just a little bit and washing your hands a little more. These are simple requests yet they appear to be outrageous forfeitures of liberties to many people in the USA.

What kind of civilization is this where an appreciable fraction of the citizens refuse to act in the direction of self-preservation of the population? When shouting about personal rights to not wear a mask or get vaccinated outweighs the rights of the majority to remain infection free?

As bad luck would have it, the endemic coincides with a far right wing-leaning conservative political movement in the USA. This crowd had issues with the government anyway. They are especially furious that experts within various health agencies have issued instructions and mandates on containment of the disease.

We might have thought it obvious that when presented with a highly infectious virus that is spread through the air, it would be in our self-interest to voluntarily control where infectious breath goes, dial back our movement a bit and increase interpersonal distances temporarily in order to avoid mass infection and mass casualties. One might also think that given the long and highly successful use of vaccines, volunteering to get a shot would seem reasonable and also be in our self-interest.

The US constitution is silent on personal freedoms in a time of contagion as it is on many other things. I interpret that as wiggle room to figure out solutions for the problems of our time that serve to further the cause of survival against a mindless but efficient virus.

One of the purposes of government has always been to protect ourselves from each other. What we’ve experienced when government has tried to intervene is loud hysteria and political pressure from an infectious vocal minority who are actually dying from COVID at a higher rate than the vaccinated public. Aggravating matters greatly, some of the opponents of masking and vaccination have very large commercial platforms from which to broadcast self-serving misinformation. It has been obvious for a long time that this is done to increase viewership and profit from the misinformed. Capitalist organizations are using their broadcasts to increase the bottom line on the backs of the volatile misinformed.

At the moment, it doesn’t look like persuasion with solid information will work with the anti crowd. Do the rest of us have to wait around until these folks, many of whom are fervent authoritarian Trump supporters, just live out their lives and die hoping that they don’t crash democracy along the way?

Is this really the direction that the American experiment goes? What kind of country are we? I thought that I had a good grasp of that. I was wrong.