By Sarah Rubinstein | Bond LSC
When Marc Johnson set out to find the source behind the mysterious combinations of coronavirus mutations he found in wastewater, he had no idea this work could one day be his legacy.
“If there’s anything in my career that’s ever cited in 100 years, it will be this study,” said Johnson, a principal investigator at Bond Life Sciences Center.
The research details how scientists narrowed a search for a cryptic lineage of SARS-CoV-2, the virus that causes COVID-19, from sewer shed sampling in Wisconsin. The work was published in The Lancet Microbe in April, but his first study on cryptic lineages was referenced by Stephen Colbert and Freakonomics Radio featured his new work on their podcast.
Finding the source of a mysterious viral strain in wastewater was like “finding a needle in a haystack,” Johnson said.
Cryptic lineages are sequences of strange viral combinations of mutations contained in one place that don’t spread like prevalent variants of the SARS-CoV-2 virus, like Delta or Omicron. Cryptic lineages have never been identified in a source beforehand, but wastewater testing allows scientists to pick up on these mutants that aren’t otherwise readily detected through more traditional testing.
When Johnson identified these highly divergent cryptic lineages in wastewater sent by the Wisconsin Department of Health Services, he assumed it had come from an animal reservoir or nursing home. Except, he was wrong. By going manhole to manhole, they tested wastewater to track down the source to a small, 30-person company in Wisconsin. Johnson said it likely came from one person.
“I could not believe how much COVID-19 there was in that sample,” he told Freakonomics Radio. “It was 1,000 times higher than anything I’d ever seen.”
This level of virus comes from viral shedding – when an infected person’s cells make new copies of the virus that are then excreted from the body. After narrowing the source to a specific company and even the exact toilet, Johnson offered free employee testing to get to the bottom of it. Since only two-thirds of employees got tested, he could not find the culprit.
However, he did figure out how a single person could shed enough SARS-CoV-2 to be detected in wastewater. It likely comes down to a long-term infection in a person with a compromised immune system.
“It probably means there was someone in that sewer shed that was infected with a variant for two years, and then they suddenly started shedding enough that we could detect it,” he said. “So, the question is, how many more of these people like this are out there?”
Johnson’s next task is to investigate other patients with persistent GI infections since they had COVID-19, or patients who believe they have long COVID-19. To do that, he’s spent the past nine months asking for people from all over to donate their stool samples if they match these characteristics. He infers that many long COVID-19 patients have had ongoing COVID-19 for years without knowing it, some contracting it as early as 2020.
Once he identifies similar people, he wants to learn what symptoms they have in common. Since he hasn’t found the exact person who has caused the cryptic lineage from The Lancet Microbe study, he doesn’t know what the long-term effects would be for persistent infections, but Johnson hypothesized it could involve a GI tract infection that doctors can’t detect from a typical nasal swab test.
Getting participants to donate stool samples is a much harder sell when trying to convince potential subjects why donating samples is important. Since testing isn’t mandatory, he offers it for free, hoping it will encourage participation and ultimately help people, he said.
“The biggest challenge has just been the conflict between public health and individual privacy,” he said.
While the big takeaway is that some people have long-term COVID-19 infections without knowing it, Johnson cautions care must be taken in linking a specific person to an infection because it could open them up to community or workplace scrutiny or retaliation. He estimates that one in every 1,000 infections is persistent, but this level of viral resistance is still potentially harmful, as these individuals could be “a potential source of lineages that could make our hard-fought immunity less useful.”
Johnson and his team were never in it for the recognition, but all the attention has brought awareness to his efforts, and he still hopes to identify and help these long COVID-19 patients.
“I still have some questions; I’m going to keep chipping away at it until we either figure it out or they just go away, but I don’t think they’re going to go away,” he said.