H5N1 Is Messing with Texans

A taboo hypothesis nobody’s willing to entertain

A key lesson of the pandemic is that viruses we have traditionally thought of as respiratory pathogens often also replicate in the gut. I don’t find the lesson surprising. The few times I’ve had flu it came with diarrhea so bad I ended up shitting crystal clear water for a little while.

Last week, a team spearheaded by a brilliant former colleague of mine, Mike Tisza, posted a preprint reporting the detection of substantial amounts of bird flu (H5N1) in samples of wastewater from nine Texas cities.

The preprint cautiously reports:

A variant and SNP analysis found mutations consistent with either avian or cattle origin; mainly, the presence of a glutamic acid, instead of a lysine, in position 627 of the PB2 gene supports a non-human source.

I appreciate the team’s reluctance to risk stirring up false alarms, but this timid description of the results is so “cautious” it crosses over into the territory of being a scientifically unsupported claim. Flu researchers have a pretty good catalog of the hallmark mutations (e.g. E627K) that occur when flu shifts from birds to mammals, but the pattern of mutations associated with transition from cattle to humans isn’t well worked out. In other words, glutamic acid at position 627 is just as consistent with a possible human source as it is with a possible cattle source!

There are a lot of cattle in Texas, but seeing these levels of H5N1 in nearly every sewer system in the survey doesn’t smell like bull shit to me. Humans are obviously the simplest explanation for these results. The specific hypothesis nobody seems willing to speak out loud is that many Americans currently have H5N1 replicating in their gut and the infection simply isn’t bothering them enough to send them to the hospital. If true, it would basically be good news… unless further adaptation increases pathogenicity [1].

I’m reminded of Marc Johnson’s heroic work tracing the source of an exotic Covid variant to a single office building in Ohio. Nearly all of the building’s occupants agreed to give a nasal swab but none of the nasal swabs were positive for Covid. A lesson is that tracing studies should include anal swabs. Assuming things along the lines of the new Lucira flu/Covid kit can detect H5N1, the socially awkward swabbing could easily be done as a home self-test.

Ignoring scientifically valid hypotheses that make easily testable predictions actually isn’t very cautious.

•Update 1: H5N1 monitoring programs routinely swab bird anuses. Why not humans?

•Update 2: Now found on the anuses of cats, bears, dolphins, seals, canids, ferrets, squirrels, mice, raccoons, skunks, and possums! Is anybody seriously imagining that primate anuses are so unique and special that we need not bother checking them?

•Update 3: This past weekend (June 9), a vendor at my local farmers market was proudly advertising raw milk “for pets”[2]. This quote from Celine Gounder refers to cows, but her thinking is equally applicable to humans:

“Unfortunately, not testing does not mean that something does not exist. It means you’re just not looking for it,” Gounder said.

Update 4: Shared farmworkers may be causing the spread of bird flu among cattle and poultry in Michigan

Update 5: Wastewater collected at sites far from any dairies or chicken farms contains H5N1.

[1] Jessica Wildfire offers excellent coverage of an important history lesson:

The plague emerged in two phases. In late spring of 1918, the first phase, known as the “three-day fever,” appeared without warning. Few deaths were reported. Victims recovered after a few days. When the disease surfaced again that fall, it was far more severe. Scientists, doctors, and health officials could not identify this disease which was striking so fast and so viciously, eluding treatment and defying control. Some victims died within hours of their first symptoms. Others succumbed after a few days; their lungs filled with fluid and they suffocated to death.

Sounds like the butts of people with unexplained three-day fevers would be a good place to look?

[2] Song of the day: “Eye for an Eye” by UNKLE. This song gets my nod for the greatst virus-hunting lyrics of all time. Warning, the video has horror movie levels of disturbing cartoon gore.

Disclaimer: this friendly public peer review is intended as constructive criticism. It does not represent the views of my employer or the authors of the preprint.