More than 30 extremely mutant never-before-seen strains of Covid lurk in several US states, DailyMail.com can reveal.
A team of scientists from the University of Missouri has tracked these so-called “cryptic” variants by testing sewage samples across the country.
They have so far detected 32 tribes in 13 states – including New York, California and Florida – but say these cases are just the “tip of the iceberg”.
The viruses are harbored by people known as “long-distance riders,” patients struggling for months or even years to clear the Covid infection, giving the virus an unusually long window of opportunity to mutate.
dr Marc Johnson, the Missouri virologist leading the research, warned that the strains have mutated in a way that if they spread, they would be immediately classified as “variants of concern.”
Hover over the map to see how many cryptic lineages have been discovered in your state!
Scientists have uncovered 32 cryptic lineages in 13 states in the past two years. That includes 10 cases in New York City alone and four in California
dr Marc Johnson (pictured), a virologist at the University of Missouri, told DailyMail.com that searching for people with cryptic lineages can provide a better understanding of the virus and what causes it to cause ‘Long Covid’.
“I suppose the cryptic lineages are the tip of the iceberg,” said Dr. Johnson.
“When there are so many long-term infections [we have found]how many do we not discover.’
He believes more resources should be invested in finding these strains, saying “It would be worth finding out who has the infection and why.”
The scientist isn’t sure if the patients shedding the novel variants are contagious or how they managed to stay infected for so long.
dr Johnson doesn’t think they’re contagious. But he warns that if patients continue to harbor the viruses, they risk acquiring a mutation that allows them to spread quickly through the population.
None of the patients with a cryptic lineage have been identified, and little is known about each of them.
In a report last year, Dr. Johnson: “The simplest explanation for the appearance of cryptic lines in the sewage is that they are excreted by immunocompromised patients with persistent infections.”
Patients who harbor viruses for an exceptionally long time often have compromised immune systems, meaning their bodies have trouble clearing the virus.
Many scientists believe that the Alpha, Delta, and Omicron variants all arose in this way.
They probably all share some sort of genetic mutation that allows the virus to bypass their immune systems for so long.
“I suspect there is something similar in these patients, but it may not be obvious,” he said.
He believes that one in 4 million people carries or has had in the past one of these strains. This would mean that there are about 80 cryptic lineages in circulation.
So far, ten have been spotted in New York City — more than double the number in any single state.
The virologist said that’s because the city is so densely populated that wastewater samples from the Big Apple included more people than other areas.
As a result, these tribes are easier to spot in the Big Apple than anywhere else.
Four have been discovered in California, and one to three lineages have been found in 11 other scattered states.
These include: Colorado, Florida, Kentucky, Missouri, Montana, New Jersey, Ohio, Oklahoma, Texas, Virginia and Wisconsin.
“I wasn’t looking for them; We just started sequencing things that didn’t add up,” said Dr. Johnson on his first encounters with the lines.
Wastewater sequencing is a tool used by virologists and public health experts to collect data on the prevalence of various viruses in a local community.
Scientists will collect and test samples of sewage to look for different strains.
Because a person sheds the virus in stool before experiencing symptoms, this type of surveillance can allow public health experts to forestall some outbreaks.
One such strain was found in central Ohio, where Dr. Johnson believes he has found a person who has been infected with the virus for at least two years.
This person commutes regularly between Columbus – the state’s largest city – and Washington Court House, a small town of 15,000 people 40 miles southwest.
Researchers have found the same cryptic line that has been circulating between the two cities since at least March 2021.
The same lineage has not been discovered anywhere else, to the scientists’ knowledge.
This specific pattern likely means the person lives in the Washington Court House and is commuting to Columbus.
It could be for work, but the patient could also be a college student, as Columbus is home to Ohio State University — with more than 66,000 students.
It’s unclear how the person harbored the virus for so long, but it’s likely that the virus mutated inside him to cause minor complications.
Overall, there are probably only a few thousand people who meet these guidelines, a relatively small group to sift through.
In the spring of 2022, Dr. Johnson in Wisconsin a cryptic tribe. The affected person lost viral load at an exorbitant rate.
His team tested water in nearby wells and were able to determine where the cargo was coming from.
In the late summer of 2022, they linked the exposure to a toilet in a particular building that employed many people who came to work every day. One of those employees carries the cryptic burden, believes Dr. Johnson.
A person in Ohio has been infected with Covid for over two years. Researchers found they regularly commute from the small town of Washington Court House about 40 miles northeast to Columbus, Ohio. It is likely that they live in Washington and work or go to school in Columbus
The man’s Covid strain evolved significantly differently than existing strains such as the Omicron and Delta variants known to the general public. Pictured: A viral ‘tree’ showing how different versions of Covid have evolved. Grouped in the center (blue arrow) are known variants that are distributed around the world. Within these strains there are thousands, if not millions, of mutations that differentiate them. However, the strain of the unknown Ohio person (red line) mutated entirely separately. Its viral makeup is very different from other versions of the virus, and its evolutionary chain is linear – with no thousands of branching pathways. This indicates that the tribe only circulates in a single person.
The company has agreed to Dr. Johnson to allow stool samples to be taken from some employees to determine who bears the burden.
The typical Covid case lasts just a few days – and the maximum time anyone should expect to be sick is two weeks.
dr Johnson hopes that finding the people harboring these cases can allow scientists to learn more about the virus itself and whether these cryptic lineages are linked to the “long Covid” phenomenon.
“I suppose the cryptic lineages are the tip of the iceberg. If there are so many long-term infections, how many more do we not realize,” he explained.
“It would be worth finding out who has these infections and why.”
In March 2021, Dr. Johnson first pointed to a mysterious lineage while sequencing sewage in Missouri.
His team discovered a strain of Covid they had never seen before. Within a month, they discovered 12 samples of a strain with up to six mutations distinct from the typically circulating strains.
Expanding their research over the coming months, scientists would find six unidentified lineages circulating in New York City, one in California and a second in Missouri.
They dubbed them “cryptic lineages” and went on a quest to determine where they came from.
At first, the virologists thought that the strains circulated in animals. Rats were an easy answer because so many infest New York City’s sewers.
However, some strains displayed RNA incompatible with rodent infection, and the mutations picked up by the viruses were human “immune escape mutations,” meaning they would help evade a person’s immune system.
If rats housed the strains, they wouldn’t mutate to evade the human immune system.
Patients probably don’t know they have Covid. Instead, they are either asymptomatic or suffer from symptoms resembling a stomach infection.
These include diarrhea, nausea, vomiting, and other relatively manageable symptoms.
In many cases, the person is still able to carry out everyday activities such as going to work or caring for their children.
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