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Clinical Laboratories and Pathology Groups

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News, Analysis, Trends, Management Innovations for
Clinical Laboratories and Pathology Groups

Hosted by Robert Michel
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Advances in genome sequencing give virologists and microbiologists new tools for tracking SARS-CoV-2 variants to their sources

Wastewater surveillance has emerged as an essential tool in the detection and tracking of the SARS-CoV-2 coronavirus within communities. Though COVID-19 infections are decreasing in the United States—and clinical laboratories are performing fewer diagnostic tests for the disease—researchers continue to monitor populations for the presence of the coronavirus and its variants to be prepared for the next outbreak.

Genetic sequencing of samples extracted from sewer systems throughout the country have revealed dozens of strains of the coronavirus containing multiple mutations in unusual combinations called cryptic genetic variants (CVG), also known as cryptic lineages. A recent study has indicated that wastewater may also provide answers to questions about long COVID as these mutations can be traced back to individuals who are living with chronic COVID-19 infections. 

That study, “Tracing the Origin of SARS-CoV-2 Omicron-like Spike Sequences Detected in Wastewater,” which was published on medRxiv preprint server for health sciences research, aimed to understand the origin of those cryptic lineages.

“Because increases in wastewater [viruses] generally occur before corresponding increases in clinical cases, wastewater surveillance serves as an early warning system for the emergence of COVID-19 in a community,” said Amy Kirby, PhD (above), CDC program lead for the National Wastewater Surveillance System, during a media telebriefing. Wastewater testing for viruses and bacteria may eventually lead to the implementation of systems to alert clinical laboratories in a region whenever infectious agents are detected in wastewater. (Photo copyright: Center for Global Safe Water, Sanitation, and Hygiene.)

Humans Found to Be Primary Source of Cryptic Lineages

To conduct their study, scientist at the University of Wisconsin-Madison and the University of Missouri School of Medicine examined the evolution of a SARS-CoV-2 Omicron subvariant found in wastewater coming from a single facility in Wisconsin that employed about 30 people. The researchers discovered the mutation had been present in the wastewater for more than a year.

Dark Daily originally covered their findings in “New, Cryptic COVID-19 Lineage Found in Ohio Wastewater by Molecular Virologist Tracking Spread of SARS-CoV-2 Variants.” We reported how scientists had tracked the lineage of the cryptic strain to Ohio, where it appeared to have originated from one individual who travels regularly between the cities of Columbus and Washington Court House. They believed the person had a form of long COVID and was unaware that he or she was infected with the coronavirus.

According to Marc Johnson, PhD, Professor of Microbiology and Immunology at the University of Missouri and one of the authors of the study, the individual who shed the mutations had been shedding at least a thousand times more COVID-19 virus than an average infected person sheds. The scientists examined other wastewater monitoring data and identified 37 related cases in the US. They concluded that humans are the main source of the cryptic lineages. 

“The fact that someone can have this kind of infection—and there’s every indication that they are still an active member of society and not just lying in the hospital—it’s just amazing,” Johnson told CNN.

Wastewater Surveillance Not an Exact Science, CDC Says

Although not directly involved in this study, through its National Wastewater Surveillance System (NWSS) the US Centers for Disease Control and Prevention (CDC) has been tracking wastewater surveillance programs. The federal agency believes cryptic lineages do not pose a threat to public health. 

“The signal we really look for is specific variants increasing in frequency in a community, because that’s what happens at the beginning of a variant surge,” Amy Kirby, PhD, Health Scientist, National Wastewater Surveillance System Lead for the CDC, told CNN. “And it’s not what we’re seeing with these cryptic lineages.”

Kirby also noted that wastewater surveillance is not an exact science and that many factors can impede the interpretation of the data. The mutations observed for this study could be from people with long COVID or even from an infected animal. To be certain of the results, she said, researchers would have to directly link the genetic sequence from a clinical test to a specific wastewater sample.

“Best-case scenario is you find the person, they have long COVID but had no idea they had this infection, and you get them with a doctor who can get them on medicines that will actually give their immune system a bit of an upper hand, and they get better,” Johnson told CNN. “But we only know about the ones we can find, and we don’t know what the implications are, because we still don’t know who those people are.”

Public health messaging in local communities is needed to raise awareness. But though tracking down specific infected individuals could help them receive medical attention, it may not be the most desirable course of action.

“Part of the power of wastewater surveillance is that it is inherently anonymous. It’s a community-level surveillance method,” Kirby said. “And so, tracking back through the wastewater system to identify a person is not what the system is intended for.”

Clinical Laboratories Play Key Role in Public Health

The cryptic lineage that Johnson and his team identified was a mutation that appeared in two watersheds in Ohio—one located in southern Columbus and one in the town of Washington Court House, which is about 40 miles south of Columbus. The researchers hypothesized that an individual living in that area had COVID for more than two years and did not know it, was most likely asymptomatic, and lives in one area and spends a lot of time (perhaps working) in the other area.

“There is almost zero chance the patient in Ohio knew about their infection. There is almost zero chance their doctor would figure it out. It is very likely the infection is causing long term damage,” Johnson wrote in a Twitter tweet. “I’m glad that there is a chance now that they might get appropriate care.”

Wastewater surveillance has materialized as a common method of identifying and monitoring strains of COVID-19 and other infectious diseases. And clinical laboratories play a key role in that process. With genetic sequencing technologies becoming more advanced, lower in cost, faster and more accurate, it’s feasible that those technologies will be utilized more to direct public health initiatives.    

—JP Schlingman

Related Information:

Mysterious COVID-19 Lineages in US Sewers Could Offer Clues to Chronic Infections

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

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

Scientist Say “Longest COVID Patient Ever” Lives in Washington Court House and is Dangerous

New, Cryptic COVID-19 Lineage Found in Ohio Wastewater by Molecular Virologist Tracking Spread of SARS-CoV-2 Variants

Researchers Use Genetic Sequencing and Wastewater Analysis to Detect SARS-CoV-2 Variants and Monkeypox within Communities

CDC, HHS Create National Wastewater Surveillance System to Help Monitor and Track Spread of COVID-19

CDC National Wastewater Surveillance System Locates and Tracks SARS-CoV-2 Coronavirus in the Public’s Wastewater