Sewage, Save Us!

Wastewater monitoring in Bay Area, courtesy of

Who knew that effluent could be interesting? Who knew that the poop emoji was grinning for a reason? Who could have foretold, two years ago, that wastewater would be the key to everything? The scientists did.

Scientists have been closely monitoring wastewater and COVID since the start of the pandemic, and their data has helped predict patterns that have proved essential to acting on the spread of the disease. This kind of analysis has saved lives before and may be more common than we knew.

Dr. John Snow, who knew plenty. Photo from wikipedia.

The Intrepid Sewage Scientists of Yesteryear

The year is 1854, London. You’ve read your Dickens, so you can visualize the urchins, the dark and narrow alleys, the choking industrial pollution. And the sewage–open cesspool holes near houses and channels of who-knows-what running near the sidewalks. There’s a cholera outbreak, and cholera has to be one of the nastiest diseases ever invented by that clever bacteria kingdom. I mean, if you’re evil bacteria and you want to spread across your host population as quickly as possible, what better way than to infect a human intestinal tract then produce explosive, watery … uh…. output.

John Snow–not the Game of Thrones guy–was a budding epidemiologist, trying to discount the theory that diseases were caused by “miasma” or bad air that came from rotting food. Snow’s sampling of areas in the Soho streets helped narrow the point of cholera down to a water pump in Broad Street. He insisted that the pump handle be removed, and, afterward, the incidence of disease dropped.

Snow’s map of the 1854 cholera outbreak, based on cesspool testing. Photo from wikipedia.

Polio as a Case Study

Epidemiologists also tracked polio in the 1940s through wastewater, although cell culture sampling methods even in the mid-20th century were fairly crude. Sampling was limited and results were often inconclusive. By the 21st century, methods had improved significantly, enabling environmental scientists to begin using it as an exceedingly important public health tool.

For example, while polio has now nearly been eradicated because of the polio vaccine, alarmed researchers in 2013 saw outbreaks in Israel. As with other diseases, polio is usually recognized when patients report symptoms, typically of severe paralysis (AFP). But paralysis only occurs in a tiny fraction of patients. Like COVID, many carriers of polio are asymptomatic, a smaller percentage show mild symptoms, and only a few are severely afflicted. However, affliction is severe–impairment, paralysis, and death.

Israel’s Bedouin community of Rahat, where a 2013 polio outbreak was detected via wastewater. Photo from Al-Monitor.

Israel had created sewage surveillance in 1989 specifically to look for polio. They narrowed it down to a specific region and a specific population (in the Bedouins of Negev). They noted that for the population most at risk–children under 10–over 56% were infected. Based on molecular analysis, they could tell this strain of the virus started in Pakistan and had traveled to where there were fewer vaccinated people. Now they knew who and where to focus vaccination efforts.

Who’s Got the Biggest AMR Problem?

Another growing concern to scientists has been the expansion of antimicrobial resistance or AMR. A study in The Lancet estimated that some 5 million people died in 2019 from diseases which were resistant to drug treatments. There have been cries for decades to reduce the indiscriminate use of antibiotics. Such drugs are critical when they match the disease. But when an antibiotic is used as a general panacea, it can create resistant strains of viruses. As a result, public health experts for decades have been pushing people not to overuse antibiotics.

I love a good boxplot! From Nature.

When I first read of alarms over a growing “epidemic” of AMR, I assumed it would happen in places like the U.S., where we tend to over-medicate. I was surprised to find, though, that a recent study in the spread of AMR shows it happening across sub-Saharan Africa and a few other developing nations. Medically-advanced areas like New Zealand and Sweden have much smaller incidence rates. The boxplot by continent shows the higher averages in Africa and South America. The spread of high-to-low is also wider (the boxes are taller), but the statistical means (the horizontal lines in the colored boxes) are much higher than those for Europe and North America.

Why? In part, this may be due to a higher incidence of disease in general in poorer countries and a lag in medical practitioners’ behavior. In other words, U.S. doctors have gotten better about not prescribing unnecessary antibiotics, but doctors in places where conditions are poorer and disease incidence is higher are still prescribing the wrong drugs. In places where sepsis or HIV are also high, the greater need for drugs exacerbates the problem.

Also, Be Careful Using Heroin If You’re in Poland

Lest you think that wastewater monitoring is only looking at disease, I direct your attention to another study that suggests otherwise. In March 2020, just as the world went into COVID lockdown and in dire need of sewage samples, researchers in Poland published an analysis that used wastewater for something else: illegal drugs. Leave it to the Eastern Europeans to go there first! And tell you about it!

In Urban wastewater analysis as an effective tool for monitoring illegal drugs, researchers Anna Maria Sulej-Suchomska, Agnieszka Klupczynska, Paweł Dereziński, Jan Matysiak, Piotr Przybyłowski & Zenon J. Kokot revealed a large-scale testing process for psychoactive drugs. (I just wanted to paste all those wonderful Polish names to give my spellchecker a migraine.) They’re looking for heroin. They’re looking for marijuana. I can only imagine if they tested the wastewater in the Bay Area, particularly over in the Oakland/Berkeley neighborhoods. I don’t know where that graphic spike in the lower right corner is from, but youths near that WWTP (Waste water treatment plant) in Poland might want to curtail their public giggling.

Polish inspection of sewage for illicit drug use, in Nature, March 2020.

My Favorite Graph in COVID Times Right Now

So wastewater treatment isn’t new, and its use ranges from monitoring public health to other things. Surveillance might become a problem later. Right now, we need it. My son, the budding physicist, first mentioned the extensive use of wastewater analysis at the University of California, San Diego early in the outbreak. Back in the May 2020, when nasal swabs weren’t even widely available, the university quickly began using effluent testing to pinpoint outbreaks. He told me that within a few months of the lockdown, they could tell which building had COVID spikes. Where the monitors saw outbreaks, residents or employees were told to get tests, which let them identify COVID carriers before the people themselves knew they had it.

Fast-forward two years and wastewater analysis has been instrumental in predicting outbreaks. Even now, when testing is far more available than it was, testing still lags weeks behind the outbreaks. And, because many people are symptomatic, testing doesn’t catch all the carriers. But wastewater does because the measure of virus in the sewage is indifferent to symptoms.

Looking through recent wastewater graphs in the Bay Area is especially revealing. The graphs show the omicron variant spikes, and the different paths that our counties are facing. Some locales have turned the corner, with omicron and COVID now dropping. Others have not.

The scoop on poop near me! From

The article in today’s SFGate noted concern for the El Sobrante, San Pablo, San Rafael, and Antioch areas. Those are more rural parts of our sprawling seven-county region. But Alameda County, the heavily populated and suburban spot where I live, might show the blissful relief we’ve been waiting for. The graph started to plateau around New Year’s and is slowly edging downward.

I was never so excited for a graph hit the fan.

Cal Football’s COVID problem: Go Stay Home, Bears!

I am 99% certain that this story won’t surprise any of you. I am 99.5% sure that college football has too many players. And I am 100% disappointed in the stupidity of the behavior of players for my alma mater, which has had to cancel its upcoming game against USC because of a COVID outbreak.

The Bears had 24 players out with COVID on 11/6 that their opponents broke a 20-game losing streak. Getty photo from

The back-and-forth finger-pointing between the Cal sports program and local health officials started before the previous week’s game, when 24 players couldn’t travel to Arizona due to “COVID protocols.” Players, alumni, and sports fans weren’t bashful in criticizing the City of Berkeley Health Services and the university for being overly cautious. However, the dam broke this week, when so many players and staff tested positive that the team had to cancel their next upcoming game. As it turns out, the facts matter, especially when the whole picture is revealed. And, for most of you, who I suspect don’t care about Cal or college football, there are also lessons to be learned.

The Sequence of Events

A few days before the Cal-Arizona football last Saturday, the team announced that 24 players were required to stay home due to COVID protocols. This included starting players, such as quarterback Chase Garber. News reports later clarified that they weren’t staying home just because of exposure to someone with COVID but because they had tested positive themselves.

Continue reading “Cal Football’s COVID problem: Go Stay Home, Bears!”

Opening Up

We are tip-toeing into the future. Conditions are a little spartan, a little unfamiliar. This is good; this is scary. Caution, patience, and gratitude are the watchwords.

Beware: Lots of People Ahead

I took my first flight in a year last week, just a hop up north to see family. Y’all… there are a LOT of people in airports!

Pre-pandemic Hong Kong, photo Wall St Journal

It was like when you are away from home for a long time, like a summer or when you first go to college, then you are back. It is both strange and familiar. Your primitive brain remembers. Crowds of people are back. Can’t say I really liked that. But we have 8 billion people in the world, so we must share it with each other.

If you haven’t done this in a while, never fear (as long as you are vaxxed A.F, as the kids say today). The airplane wasn’t actually that bad although that was the longest wearing a mask nonstop that I have done in a while. And airplane are always late aren’t they? A little late coming in? Early to the arrival gate, which means you sit on the tarmac. Mechanical something or other, flight crew’s not there. That is all oh-so familiar, too. If we have learned nothing from this experience, it ought to be patience.

But that six feet of space thing? People in airports seem to have thrown that out the window already. Be vaxxed or stay masked.

Masks aren’t strange any more. Photo by Vladimir Vladimirov.
Continue reading “Opening Up”
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