Ramifications of the omicron coronavirus variant pushed a peak in cases in the United States Some scientists believe that clues to how these subvariants emerge can be found in wastewater, and their research could help prevent the next dangerous strain of the virus.
Mark Johnson, a professor of molecular microbiology and immunology at the University of Missouri, is one of the researchers leading the hunt for bizarre mutations in SARS-CoV-2, the virus that causes COVID-19. His lab receives more than a hundred wastewater samples each week from places as far apart as California and New York.
Johnson’s lab screens samples for the virus. They then extract its genetic material and sequence it to look for oddities.
“The part of the genome that we’re focusing on is called the receptor-binding domain,” Johnson said. “This is where most mutations accumulate.”
By focusing on the part of the virus that allows it to infect our cells, Johnson can search for mutations that could help it bypass our immune system. Until now, each dangerous variant, such as delta and omicron, had significant mutations in this area.
Sewage tests allow researchers to get an idea of how the virus is spreading – without having to sequence a bunch of individual tests. They can even see warning signs of a power surge based on what’s going on underground.
Beyond finding strange new variants, Johnson and his colleagues are trying to figure out where exactly the variants come from: essentially, the family history of the virus.
“Whenever we’ve had a new line, it’s usually not derived from the previous one,” Johnson said. “So omicron is not derived from delta, delta is not derived from alpha, and so on.”
But to track these the so-called cryptic lines, they must reduce the source of the virus. Instead of sampling a sewage treatment plant that could contain materials from hundreds of thousands of people, Johnson can sample a specific manhole.
To do this, he and other scientists are increasingly using a surprising but practical tool: tampons.
Kendra Maaswho directs the Microbial Analysis, Resources and Services Laboratory at the University of Connecticut, has used the technique to monitor COVID outbreaks on the campus. It was she who shared the approach with Johnson.
“It’s so easy! When I say we tie a fishing line to a pad and throw it down the drain, that’s literally all it is,” Maas said.
Meuse did some research comparing the technique to other sampling methods that require expensive machinery and found it more than delivers. This means that researchers can sample in remote areas or places where it would not be practical; like a busy street in New York City.
New York is exactly where one of Johnson’s colleagues, a Queen’s College virologist Jean Dennehyworked to track down bizarre SARS-CoV-2 mutations.
“We were able to narrow our variation down to a small area of Brooklyn,” Dennehy said. “Unfortunately, in this area there are still hundreds of thousands of people.”
Finding where these cryptic lineages come from is important, he said, because it could help avoid the next dangerous variant at the source.
The researchers believe that these variants could develop in immunocompromised people who have been infected for a long time. Since their body cannot cope with the virus quickly, the virus has the ability to mutate to bypass their immune response.
David O’Connora professor of pathology and laboratory medicine at the University of Wisconsin who worked on the sequencing of SARS-CoV-2, observed patterns that could support this hypothesis.
“[The viruses] have all those characteristics that appear to be under selective pressure from a host’s immune system,” O’Connor said. “They are changing in exactly the way you would expect potentially worrisome viruses in the future to change. “
If viruses mutate in immunocompromised people, finding and treating them could nip the problem in the bud. But researchers aren’t the ones who can quarantine someone with one of these mutated viruses and get them treated. That’s up to officials to decide, and Dennehy fears they don’t know.
“I kind of wonder how aware public health authorities are that these cryptic variants are a potential source of a concerning new variant,” Dennehy said.
A highly mutated omicron variant – BA 2.121 – is now contributing to a new COVID spike in the US
There is as yet no evidence that the subvariant causes more severe disease than the earlier forms. But Johnson said omicron has outperformed previous variants when it comes to producing offshoots, and tracking them will be key to potentially controlling them.
This story comes from a reporting collaboration that includes KBIA and Side Effects Public Media – a public health information initiative based at WFYI. Follow Sebastian on Twitter: @sebastiansings.