The Variant in the Sewer

An Essay on Wastewater Surveillance and the Disappearance of the Patient

Author’s note: This essay engages SARS-CoV-2 surveillance on the establishment’s own terms — accepting, for the sake of argument, the framework of variants, pathogens, and detection. Readers of this Substack will know I do not accept that any virus has been properly isolated or demonstrated to cause disease. The argument here is narrower: even granting every premise the establishment grants, the system that announced BA.3.2 to the world cannot do what it claims to do. Establishment terminology — variant, pathogen, viral RNA — appears throughout because the essay examines the establishment’s own apparatus on its own terms. The deeper question, whether there is anything real to detect at all, has been treated in earlier essays and in my book No Virus.

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On 19 March 2026, the CDC published an entry in the Morbidity and Mortality Weekly Report announcing what it described as the global detection of SARS-CoV-2 variant BA.3.2.¹ The report documented, as of 11 February 2026, the following evidence from the United States: 132 municipal wastewater samples from 25 states, three airplane sewage samples, four self-collected nasal swabs from international travellers, and five clinical specimens from patients.¹

One hundred and thirty-two sewage samples. Five patients.

More than 90 per cent of the evidence for what the CDC called a variant — one that triggered WHO monitoring across 23 countries and dominated headlines from CNN to HuffPost to Newsweek as “highly mutated,” “concerning,” and “spreading quickly” — came from pipes carrying the biological and chemical waste of American cities.¹ ² ³ By late March, as the media cycle expanded, the wastewater count had risen to 260 samples across 29 states. The patient count had risen to 29.⁴

The WHO designated BA.3.2 a “Variant Under Monitoring” not because people were getting sick in unusual numbers, but because the fragment carried 70 to 75 mutations in its spike protein, suggesting a “potential” for evasion of prior immunity.¹ ⁵ The MMWR’s own limitations section states: “the impact of these findings on human health outcomes (e.g., illness severity and health care system impact) remains to be determined.”¹

A global health alert, sustained by sewage, in which the announcing agency acknowledges it does not know whether anyone will be harmed.

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How We Got Here

The use of sewage as a population-level indicator is not new. Wastewater testing for poliovirus began in the 1940s and was incorporated into the WHO Global Polio Eradication Initiative as a complement to clinical reporting.⁶ Through the 1990s and 2000s, the technique expanded to monitor drug consumption and antimicrobial resistance markers in urban centres.⁷ Its application to respiratory illness was largely theoretical until 2020, when three research groups — KWR Water Research Institute in the Netherlands, MIT/Biobot Analytics in Massachusetts, and Arizona State University — reported finding what they identified as SARS-CoV-2 RNA in sewage and proposed the technique as a community-level signal that would supplement clinical reporting.⁸ ⁹ ¹⁰

The original framing was modest. The MIT/Biobot group described wastewater as “a supplementary measure” foreshadowing clinical cases.⁹ The Dutch team called it “a sensitive instrument” that “complements the measurement of COVID-19 in the population.”⁸ The premise was a tool that confirmed what doctors were already seeing in hospitals.

Then clinical sequencing collapsed. As government-funded testing sites closed after 2023 and home antigen tests replaced laboratory diagnostics, the volume of clinical sequence data submitted to genomic databases fell sharply.¹ The MMWR BA.3.2 report acknowledges this: “Limited detection in clinical specimens in the national SARS-CoV-2 genomic surveillance program likely reflects a decline in sequencing submissions since 2023.”¹

The clinical infrastructure became less available. The supplementary tool was promoted to fill the gap. By 2026, the same MMWR report describes wastewater performing the primary surveillance function: “In most states, detections of the variant in wastewater occurred many weeks before detection in clinical specimens from patients; therefore, wastewater surveillance served as an effective early warning system for this SARS-CoV-2 variant.”¹

A niche polio tool through 2019. A supplementary pandemic signal from 2020 to 2022. An emerging primary source as clinical testing fell away from 2023 to 2025. The sole evidentiary basis for variant naming and global alerts in 2026.¹¹ At each stage the change was framed as a gain — earlier detection, broader coverage, cost efficiency — and at each stage the system moved further from the sick human body.

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What the Pipeline Actually Does

A reader who encounters a headline about a new variant detected “across 25 states” reasonably imagines that something was found in 25 states — something identifiable, something discrete, something that exists in the way a blood sample or a throat swab exists. The reality is different.

Raw sewage contains human excreta, industrial runoff, pharmaceutical metabolites, food waste, degraded cellular material from every organism that contributed to the waste stream, and microbial communities numbering in the billions.¹² From this matrix, laboratories must isolate, concentrate, and identify fragments of RNA — typically degraded to fewer than 500 base pairs — and assign them, through software, to a specific variant of a specific pathogen.¹³

The concentration step alone introduces enormous uncertainty. A 32-laboratory interlaboratory study led by Brian Pecson at Trussell Technologies and Charles Haas at Drexel University, published in Environmental Science: Water Research & Technology in 2021, tested 36 standard operating procedures for quantifying the genetic signal in raw wastewater. The recovery efficiencies separating the methods at the extremes spanned more than seven orders of magnitude — a more than ten-million-fold difference in the ability of different methods to recover the same target from the same wastewater matrix.¹⁴ Even after applying recovery correction, only 80 per cent of replicate measurements fell within a band of plus-or-minus 1.15 log₁₀ — a window of more than fourteenfold.¹⁴ The authors concluded that “the same SOP or laboratory should be selected to track SARS-CoV-2 trends at a given facility” — which is to say that comparing absolute values between laboratories is unsafe.¹⁴

A European interlaboratory comparison published in Science of the Total Environment in 2023 by Alexander Wilhelm and colleagues at the European Reference Laboratory consortium reported mean inter-laboratory variability of 104 per cent in genome copy estimates from spiked samples.¹⁵ The same study found that “not all assays detected the correct variant” — meaning laboratories analysing samples they knew contained a specific variant sometimes identified a different one.¹⁵

Once RNA is extracted and amplified, the fragments must be assigned to a specific variant. This is done not by observing a discrete organism but by feeding sequence data into bioinformatic software. The principal tool is Freyja, developed at UC San Diego, which compares the frequency of detected mutations against a “barcode” library of known clinical variants and uses a constrained regression model to estimate the relative proportion of each lineage in the sample.¹⁶ The barcode library updates daily as variant designations change — which means the same wastewater data file can return different variant proportions depending on when it is analysed.¹⁶ The CDC reports a variant as “present” in a community when it reaches 1 per cent of the total assigned RNA.¹³

A 2024 benchmark study by Sutcliffe and colleagues, published in Science of the Total Environment, tested eight commonly used deconvolution tools — including Freyja — against synthetic control mixtures spiked into wastewater RNA.¹⁷ The tools disagreed. Some produced false-positive identifications of lineages that were not present in the samples. The authors concluded that “deconvolution of SARS-CoV-2 variants from mixed viral samples still presents a challenge.”¹⁷ A separate benchmark from the Mangul laboratory at USC, testing over twenty bioinformatics methods, found that lineage abundance estimates degraded significantly with RNA fragmentation and primer scheme — the routine conditions of wastewater samples.¹⁸

A 2025 review in Genome Biology by Lin and colleagues summarised the technical state of the field: “deconvolution-based quantification methods may yield suboptimal results, and classification-based approaches risk generating higher false positives by misassigning reads.”¹³

Variant proportions from wastewater are model outputs from a statistical fit to incomplete, fragmentary mutation-frequency data, matched against a reference library that changes daily.

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Four Findings the System Cannot Survive

Set aside the broader question — whether the entity these tools claim to detect has been demonstrated to exist at all. Evaluate the system entirely on its own terms, accepting every premise the establishment accepts. It still cannot establish what it claims to establish.

A congregate-living study by Lisa Colosi, Amy Mathers, and colleagues at the University of Virginia, published in Applied and Environmental Microbiology in 2021, found that wastewater assay specificity was 100 per cent when convalescent shedding was treated as a true positive — but dropped to 45 per cent when convalescent shedding was treated as a false positive.¹⁹ The test cannot distinguish between someone the establishment classifies as currently ill and someone who recovered weeks ago but continues to shed degraded RNA fragments. In a population where the vast majority of people encountered the relevant conditions years earlier, the proportion of the signal attributable to old, degraded fragments is unknown and uncontrolled.

Marc Johnson’s group at the University of Missouri-Columbia — Johnson is a co-author on the BA.3.2 MMWR itself — has documented persistent lineages in Missouri sewage that have never been observed in any clinical specimen, anywhere in the world.²⁰ These “cryptic lineages” show evolutionary convergence toward mutations associated with established variants, all in sewage with no patient correlate. The authors state: “a non-human source for some of the cryptic lineages observed in wastewater cannot be ruled out.”²⁰ The system that claims to track human illness produces sequences whose origin its own developers cannot identify.

The disagreement between laboratories is fundamental. The Pecson interlaboratory study documents recovery efficiencies separated by more than seven orders of magnitude across the methods tested.¹⁴ The Wilhelm European comparison documents 104 per cent inter-laboratory variability and misidentification of known variants.¹⁵ The Sutcliffe benchmark documents false-positive lineage calls from established deconvolution tools.¹⁷ These are not marginal discrepancies between near-equivalent measurements. They describe disagreements about what is in the sample and how much of it is there.

The PCR step itself, the foundation of the entire detection chain, amplifies material that is not the target. The Lancet Microbe review by Levy and colleagues in 2024 — generally favourable toward wastewater surveillance — concedes that quantitative and digital PCR “can show non-specific amplification for RNA extracted from wastewater surveillance samples, given the abundance of off-target but similar templates.”²¹ Sewage contains too many similar sequences from too many biological sources for the assay to be specific.

These findings come from researchers working within mainstream institutions: the University of Virginia, Drexel, the University of Missouri, the European Reference Laboratory consortium, UC San Diego. Each is published in peer-reviewed journals the establishment considers authoritative. Together they describe a system that cannot reliably distinguish its target from background, cannot agree with itself across laboratories, cannot differentiate active illness from old biological debris, and produces sequences whose origin it cannot identify.

The CDC’s own NWSS interpretation page acknowledges: “Whether individual(s) are infectious or symptomatic cannot be determined from wastewater surveillance data… The minimum number of individuals shedding SARS-CoV-2 into the system needed to detect a viral RNA signal in wastewater is not known at this time.”²²

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The Headlines and the Footnotes

The media cycle that followed the BA.3.2 MMWR was uniform. Within seven days, coverage had appeared in Fox News, Reuters, Newsweek, TIME, CNN, NBC/TODAY, PBS NewsHour, HuffPost, the Washington Times, USA Today, JAMA Medical News, and Gavi’s Vaccines Work platform, among others.² ³ ⁴ ²³ ²⁴ ²⁵ ²⁶ ²⁷ ²⁸ The variant acquired the nickname “Cicada” — coined by evolutionary biologist T. Ryan Gregory at the University of Guelph — to evoke an organism that remains underground before emerging.²⁹

The same descriptors recurred across outlets: “highly mutated,” “concerning,” “spreading,” “immune escape,” “alarming.”² ³ ²⁵ ²⁶ The accompanying images — grey spheres bristling with red protrusions against dark backgrounds — descend almost without exception from a single rendering produced by Alissa Eckert and Dan Higgins for the CDC’s Public Health Image Library in January 2020.³⁰ The illustrators have spoken openly about the design choices. They were asked to create “an identity” for the virus, “something to grab the public’s attention.” They worked in 3D rendering software and made a series of decisions about colour, lighting, and texture, with what one of them later described as “dramatic lighting to give the image its ominous look.” The shadows cast by the spikes — central to the image’s visual force — were, as the New York Times later reported, “pure fiction,” added to “convey symbolically the gravity of what this virus represents.” Higgins acknowledged: “We took artistic license on the color.”³¹ None of these images are derived from BA.3.2 sequence data. None are microscopy. They depict a discrete, photographable entity that has been visually designed for emotional impact. The data underneath is a statistical deconvolution of RNA fragments from sewage.

Below these headlines, the qualifications appeared. The WHO stated that “BA.3.2 has not shown a sustained growth advantage over any other co-circulating variant.”²⁶ PBS quoted Robert Hopkins Jr. of the National Foundation for Infectious Diseases describing it as “currently a minority strain.”²⁷ Gavi’s explainer noted that “despite its many mutations, BA.3.2 does not appear to have a clear edge over other currently circulating variants.”²⁸ PolitiFact recorded: “No published clinical or immunological data is available as of this update.”²⁴

In Western Australia, where BA.3.2 comprised 20 per cent of wastewater samples, health officials admitted that overall incidence was “not substantially higher” than in previous years.³²

Andrew Pekosz of the Johns Hopkins Bloomberg School of Public Health, quoted across multiple outlets, supplied the most candid assessment: “It looks scary on paper, but it hasn’t really made a big impact in terms of disease in most places yet.”²⁵

No mainstream outlet questioned the evidentiary basis of the announcement — whether 132 wastewater detections and five patients warranted the language being deployed. Pekosz’s qualification was the strongest reservation any major outlet published.

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Explain It To A 6-Year-Old

Imagine a town where everyone gets their water from a big lake. The town wants to know if the lake is safe.

There are two ways to find out. The first way: ask the people drinking the water how they feel. If they feel fine, the water is fine. If they get sick, find out why.

The second way: take a bucket of water from the storm drain — water mixed with mud, leaves, oil from the road, rubbish from gardens — and run it through a machine that looks for tiny pieces of things. The machine finds some fragments. A computer programme compares those fragments to a long list and guesses what they might be from. The programme says: 1 per cent of these tiny pieces match something on the list called “the dangerous fish.”

Nobody has seen the dangerous fish. Nobody has caught the dangerous fish. Nobody who drinks from the lake feels any worse than they did last year. The machine cannot tell whether the fragments came from a fish that swam in the lake yesterday, a fish that died years ago, or something that was never a fish at all.

The news announces that the dangerous fish has been found across 25 states. The news shows a picture of the fish — a picture an artist drew six years ago, before anyone said the fish existed, with shadows added to make it look frightening. Twenty-three countries put up warning signs around their lakes.

The townspeople, meanwhile, are fine.

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The Inversion

In 2020, wastewater was offered as a leading indicator that confirmed and anticipated what doctors were observing in hospitals. In 2026, with clinical sequencing collapsed, the CDC’s own report states that wastewater “served as an effective early warning system” because there were not enough patients to track.¹

The methodology that produced the BA.3.2 announcement is, by the establishment’s own published account, characterised by recovery efficiencies separated by more than seven orders of magnitude across tested methods,¹⁴ inter-laboratory variability exceeding 100 per cent,¹⁵ bioinformatic tools that disagree among themselves and produce false-positive lineage calls in benchmark tests,¹⁷ assay specificity that collapses by more than half depending on how degraded RNA is classified,¹⁹ persistent “cryptic” sequences whose own discoverers cannot attribute to a human source,²⁰ non-specific PCR amplification from off-target templates,²¹ and an absence of standardised international protocols acknowledged in the MMWR’s own limitations section.¹

One hundred and thirty-two sewage samples. Five patients. A global monitoring designation. The announcing agency’s own footnotes state it does not know whether any of it matters to human health.

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References

1. Shakya M, Ma KC, Hughes LJ, et al. “Early Detection and Surveillance of the SARS-CoV-2 Variant BA.3.2 — Worldwide, November 2024–February 2026.” MMWR Morb Mortal Wkly Rep 2026;75:130–137. DOI: 10.15585/mmwr.mm7510a1.

2. HuffPost. “What To Know About BA.3.2, The Highly Mutated COVID Variant Spreading Through The World Right Now.” March 2026.

3. Newsweek. “Map Shows New COVID ‘Cicada’ Variant BA.3.2 Spread Across US.” March 2026.

4. TODAY / NBC News. “A New, Highly Mutated COVID Variant Called ‘Cicada’ Is Spreading in the US.” Updated 13 April 2026.

5. World Health Organization. BA.3.2 designated Variant Under Monitoring, 5 December 2025.

6. World Health Organization. Global Polio Surveillance Action Plan 2025–2026. Environmental surveillance listed as complementary to clinical AFP surveillance.

7. Choi PM, Tscharke BJ, Donner E, et al. “Wastewater-based epidemiology biomarkers: Past, present and future.” TrAC Trends in Analytical Chemistry 2018;105:453–469.

8. Medema G, Heijnen L, Elsinga G, et al. “Presence of SARS-Coronavirus-2 RNA in Sewage and Correlation with Reported COVID-19 Prevalence in the Early Stage of the Epidemic in The Netherlands.” Environ Sci Technol Lett 2020;7(7):511–516.

9. Wu F, Xiao A, Zhang J, et al. “SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases.” mSystems 2020;5(4):e00614-20.

10. Hart OE, Halden RU. “Computational analysis of SARS-CoV-2/COVID-19 surveillance by wastewater-based epidemiology locally and globally: Feasibility, economy, opportunities and challenges.” Sci Total Environ 2020;730:138875.

11. Kirby AE, Walters MS, Jennings WC, et al. “The National Wastewater Surveillance System (NWSS): From inception to widespread coverage, 2020–2022, United States.” PMC11103741.

12. CDC National Wastewater Surveillance System. Pre-analytical processing protocols describe centrifugation at 24,000 × g for 30 minutes with Bovine Coronavirus spike controls and Zymo OneStep PCR Inhibitor Removal purification.

13. Lin et al. “SARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities.” Genome Biology 2025. DOI: 10.1186/s13059-025-03927-6.

14. Pecson BM, Darby E, Haas CN, et al. “Reproducibility and sensitivity of 36 methods to quantify the SARS-CoV-2 genetic signal in raw wastewater: findings from an interlaboratory methods evaluation in the U.S.” Environ Sci Water Res Technol 2021;7:504–520. DOI: 10.1039/d0ew00946f.

15. Wilhelm A, Schoth J, Meinert-Berning C, et al. “Interlaboratory comparison using inactivated SARS-CoV-2 variants as a feasible tool for quality control in COVID-19 wastewater monitoring.” Sci Total Environ 2023;903:166540. PMID 37634730.

16. Karthikeyan S, Levy JI, De Hoff P, et al. “Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission.” Nature 2022;609:101–108. DOI: 10.1038/s41586-022-05049-6.

17. Sutcliffe SG, et al. “A gold standard dataset and evaluation of methods for lineage abundance estimation from wastewater.” Sci Total Environ 2024.

18. Mangul S, et al. “A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater.” arXiv 2309.16994 (2023).

19. Colosi LM, Barry KE, Kotay SM, et al. “Development of Wastewater Pooled Surveillance of SARS-CoV-2 from Congregate Living Settings.” Appl Environ Microbiol 2021;87(13):e00433-21. DOI: 10.1128/aem.00433-21.

20. Gregory DA, Rushford C, Hunter T, et al. “Continued selection on cryptic SARS-CoV-2 observed in Missouri wastewater.” PLoS Pathog 2023;19(12):e1011688. DOI: 10.1371/journal.ppat.1011688. See also Gregory et al. “Genetic Diversity and Evolutionary Convergence of Cryptic SARS-CoV-2 Lineages Detected Via Wastewater Sequencing.” PLoS Pathog 2022;18(10):e1010636.

21. Levy JI, et al. “Global wastewater surveillance for pathogens with pandemic potential: opportunities and challenges.” Lancet Microbe 2024. DOI: 10.1016/S2666-5247(24)00192-7.

22. Centers for Disease Control and Prevention. “Public Health Interpretation and Use of Wastewater Surveillance Data.” NWSS archived interpretation page. archive.cdc.gov.

23. Fox News. “CDC detects new COVID-19 variant across 25 US states via wastewater samples.” March 2026.

24. PolitiFact. “What we know about the new COVID-19 variant ‘cicada’ or BA.3.2.” 26 March 2026.

25. The Washington Times. “Highly mutated ‘cicada’ COVID variant detected in 25 states.” 27 March 2026. Pekosz quotation sourced here.

26. TODAY / NBC News, updated 13 April 2026. WHO quotation sourced here.

27. PBS NewsHour. “What we know about the new ‘cicada’ COVID-19 variant.” March 2026.

28. Gavi Vaccines Work. “8 things you need to know about the BA.3.2 ‘Cicada’ variant of COVID-19.” gavi.org.

29. T. Ryan Gregory (University of Guelph) coined the “Cicada” nickname on 6 December 2025.

30. Eckert A, Higgins D. SARS-CoV-2 illustration. CDC Public Health Image Library, ID 23311; 30 January 2020.

31. Eckert and Higgins quotations and design history sourced from interviews and reporting in: University of Georgia Magazine (2020), Dezeen (”Covid-19 images were designed to create ‘feeling of alarm’”, 14 May 2020), The New York Times (April 2020, characterising the spike shadows as “pure fiction”), and Artnet News (”Why the Centers for Disease Control’s Creepy Illustration of the Coronavirus Is Such an Effective Work of Biomedical Art”, 2 April 2020).

32. Western Australian Department of Health reporting, 2025–2026. BA.3.2 comprising approximately 20% of wastewater samples in Perth region with health officials stating overall COVID-19 incidence “not substantially higher” than prior years.