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Clinical Laboratories and Pathology Groups

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Microbiology team has tracked 37 unique strains of the coronavirus since they began researching lineages two years ago

Microbiologists and clinical laboratory scientists will be interested to learn about the discovery of a new strain of SARS-CoV-2, the coronavirus that caused the COVID-19 pandemic, in wastewater sampled in Ohio. 

Virologist Marc Johnson PhD, a professor of molecular microbiology and immunology at the University of Missouri School of Medicine, discovered the cryptic genetic variant (CVG) while studying the spread of the COVID-19 coronavirus in wastewater, The Columbus Dispatch reported.

According to an article published in Nature Reviews Genetics, a CVG is “a genetic variation that normally has little or no effect on phenotype but that—under atypical conditions that were rare in the history of a population—generates heritable phenotypic variation.”

Johnson tracked the lineage of the cryptic strain to Ohio, where it appears to have originated from one individual who travels regularly between the cities of Columbus and Washington Court House. He believes this person may have a form of long COVID and is unaware that he or she is infected with the coronavirus.

“This person was shedding thousands of times more material than a normal person ever would,” Johnson told The Columbus Dispatch. “I think this person isn’t well. … I’m guessing they have GI issues.”

“If someone has this infection, the chances are nil that they’re going to figure out what it is,” Marc Johnson, PhD, Professor of Molecular Microbiology and Immunology at the University of Missouri School of Medicine, told Insider. Microbiologists and clinical laboratory scientists in the Columbus, Ohio, area may be able to help locate this person. (Photo Copyright: University of Missouri.) 

Other Cryptic COVID-19 Lineages

This isn’t the only “Cryptic COVID” case identified by Johnson and his team. In Wisconsin, another unique strain was discovered and narrowed down to a single facility and about 30 individuals. Two thirds of the employees were tested but, unfortunately, all tests came back negative. The cryptic strain seemed to have disappeared.

“We don’t know why,” Johnson told The Hill. “Either [the infected person] 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.”

In “Tracing the Origin of SARS-CoV-2 Omicron-like Spike Sequences Detected in Wastewater,” which Johnson and his team published on the medRxiv preprint server, the researchers wrote, “These ‘cryptic’ wastewater sequences have harbored many of the same mutations that later emerged in Omicron lineages.

“We systematically sampled [sewer] maintenance holes to trace the Wisconsin lineage’s origin. We sequenced spike RBD [receptor-binding domain] domains, and where possible, whole viral genomes, to characterize the evolution of this lineage over the 13 consecutive months that it was detectable.

“The high number of unusual mutations found in these wastewater-specific cryptic sequences raises the possibility that they originate from individual prolonged shedders or even non-human sources. The Wisconsin lineage’s persistence in wastewater, single-facility origin, and heavily mutated Omicron-like genotype support the hypothesis that cryptic wastewater lineages arise from persistently infected humans.”

Johnson and his team have tracked 37 unique strains of the COVID-19 virus, including one in New York City, The New York Times reported.

In a statement to The Columbus Dispatch regarding the Columbus strain, the federal Centers for Disease Control and Prevention (CDC) noted that, “The virus lineage in question is not currently spreading or a public health threat.

“Unusual or ‘cryptic’ sequences identified in wastewater may represent viruses that can replicate in particular individuals, but not in the general population,” the CDC noted. “This can be because of a compromised immune system. CDC and other institutions conduct studies in immunocompromised individuals to understand persistent infection and virus evolution.”

In identifying these lineages, and the individuals who shed them, scientists can learn more about how COVID-19 mutates and spreads.

Mitigating Consequences of COVID-19 Variants

Although the CDC says that particular strain is not a threat to the public it could pose a long-term health risk for the individual suffering. And this individual may hold clues for the future of how the COVID-19 virus mutates and grows. Therefore, locating these people is a priority.

“The coronavirus will continue to spread and evolve, which makes it imperative for public health that we detect new variants early enough to mitigate consequences,” Rob Knight, PhD, Founding Director of the Center for Microbiome Innovation and Professor of Pediatrics, Computer Science and Engineering at the University of California San Diego (UCSD).

In “Researchers Use Genetic Sequencing and Wastewater Analysis to Detect SARS-CoV-2 Variants and Monkeypox within Communities,” Dark Daily reported on the Knight Lab’s study of San Diego’s wastewater to detect the COVID-19 coronavirus as well as the Monkeypox virus, which was making the rounds at the time.

“Before wastewater sequencing, the only way to do this was through clinical testing, which is not feasible at large scale, especially in areas with limited resources, public participation, or the capacity to do sufficient testing and sequencing,” said Knight in a UCSD press release. “We’ve shown that wastewater sequencing can successfully track regional infection dynamics with fewer limitations and biases than clinical testing to the benefit of almost any community.”

Although tracing the individuals shedding cryptic COVID-19 lineages may not have an immediate effect on public health, it could lead to future discoveries about the SARS-CoV-2 coronavirus that can help shape public health goals in fighting future pandemics.

At the very least, one individual in Columbus may learn how to treat long COVID’s adverse symptoms. Microbiologists and clinical laboratory scientists involved in COVID-19 wastewater research can learn much from following these research investigations.

—Ashley Croce

Related Information:

Scientists Are Trying to Find a Mystery Person in Ohio Who Has a New Kind of COVID and Is Shedding It into the Sewage

A Virologist’s Search for Answers: Curious Case of ‘Cryptic COVID’ Leads to Columbus Area

Cryptic Genetic Variation: Evolution’s Hidden Substrate

In New York City Sewage, a Mysterious Coronavirus Signal

Tracking Cryptic SARS-CoV-2 Lineages Detected in NYC Wastewater

Tracing the Origin of SARS-CoV-2 Omicron-Like Spike Sequences Detected in Wastewater

Tracking SARS-CoV-2 Variants in Wastewater

Marc Johnson Twitter Thread on Discovery of Cryptic Lineage in Ohio Wastewater

Ohio Resident Sought by Scientists May Have Had ‘Cryptic’ COVID Strain for Two Years

CDC: Long COVID or Post-COVID Conditions