While the researchers believe there is no threat to public health, they hope this case holds much-needed answers to treating long COVID.
Molecular virologist Dr. Marc Johnson, a microbiology professor at the University of Missouri’s medical school, spent much of his career studying HIV.
That changed in early 2020 when Missouri health officials asked him to lead the state’s wastewater sampling program to help track COVID outbreaks. At the time, Johnson said there was not much data available on the genetic material of the virus.
“There was no protocol established at that point for sequencing SARS-CoV-2 from wastewater, so I developed my own,” Johnson said.
As the virus evolved into different variants, like Delta and Omicron, sequencing its genetic material helped identify which strains were more prevalent in different areas. That’s when Johnson discovered what he calls “cryptic” strains, or “cryptics.”
“(Cryptics) have certain patterns; there are certain mutations that they regularly accumulate that are not in a circulating lineage,” Johnson said.
Johnson found that these unique versions of the virus would linger in one wastewater system for a period of time and suddenly disappear. At first, he could not understand why these mutated sequences weren’t spreading, even in densely populated areas like New York City.
“I thought it was coming from the rats, simply because I couldn’t think of anything else that…had enough mass in the sewer shed that wouldn’t move around,” Johnson said. “We’ve tested more rat feces than I care to remember.”
The rat fecal tests were negative.
As sequencing became more common in sewer systems across the United States, Johnson started looking at publicly available data. A cryptic in Wisconsin led to Johnson’s next discovery: these sequences might be linked to just one person.
“We started tracking it,” Johnson said. “So, we started from the main treatment plant of over 100,000 people, and sort of like checked all the lines. And all of them, only one of the lines had the lineage. And so we would just keep going, checking… all of the pieces of the web, figuring out, following it up, up the line until we got to a single manhole. That manhole actually only got waste from one place, which was a company (that) had about 30 employees.”
Johnson said the trail went cold after two-thirds of the employees at the Wisconsin company agreed to be tested for COVID with nasal swabs, and all of the tests came back negative. While he and his colleagues spent months studying the cryptic strain and gaining approval to collect stool samples from the employees, the strain vanished.
“We don’t know why,” Johnson said. “Either they left the job, or got better, or is in remission – we don’t know. But we’re still monitoring it. And we’ve actually now gotten started collecting stool samples from the company.”
This spring, Johnson found another cryptic in Columbus’s sewer shed. He said the same sequence appeared in Washington Court House and has a lineage that pre-dates the Delta variant, the strain most prevalent in the summer of 2021.
Johnson believes this indicates that someone has been carrying and shedding the COVID virus for more than two years. He went as far as to predict that this person lives in Columbus and commutes to Washington Court House for work.
“I just know that they regularly shed into both sewer sheds often on the same day,” Johnson said.
The researcher hopes that by sharing this story, that person will come forward to help him answer a lot of important questions.
“How many cases are there like this? What are their symptoms? Is this related to long COVID?” Johnson said. “There are a lot of people who got COVID and never really got over it, and we don’t know why. It’s probable most of them are not chronic infections, but some of them might be, which would actually be good, because that’s theoretically treatable, and they actually get better.”
Johnson stressed that this is not a threat to public health, explaining that the virus is inactive once it passes through the gastrointestinal tract.
If you frequently commute between Columbus and Washington Court House, you can email Johnson at email@example.com.
A spokesperson for the Ohio Department of Health said health officials are not fully convinced that the cryptic strain is linked to only one person, and they are not investigating it because it poses no threat to public health.