When Kauai first learned that BA.2 was present on the island, the news did not come from a local laboratory, but from one more than 4,000 miles away at the University of Missouri.

The detection of the omicron subvariant of the coronavirus did not come from a nasal swab collected from a patient, but a wastewater sample from Kauai’s sewer system.

Marc Johnson, professor of molecular microbiology and immunology at the university, had requested wastewater samples from Hawaii and dozens of other states to analyze as part of a project searching for unknown viral lineages using “targeted deep sequencing.”

“At the beginning of the year, when omicron hit, we figured out we could do a sequencing but exclude the major omicron variant, which is BA.1,” said Johnson. “We basically take a sample, ask what is in there besides BA.1 and see if there are any low- lying lineages that don’t match.”

Johnson’s lab received three samples from Hawaii, including one from Kauai, and found no “cryptic lineages,” which appear at least superficially similar in structure but exhibit genetic differences.

But the lab was quickly able to confirm the presence of BA.2 weeks before the state Department of Health’s variant report — which shares data from whole genome sequencing of test specimens from humans — confirmed it March 29.

In the latest variant report, released Wednesday, DOH found BA.2 now makes up 70% of new coronavirus cases in Hawaii, and confirmed a new omicron subvariant, XE, detected on Oahu.

A growing number of studies show the value of wastewater monitoring not only as an early detection system for trends in coronavirus cases in a community, but for the presence of variants such as BA.2. and other potential mutations on the horizon.

A good percentage of people infected with the coronavirus shed viral RNA in their feces even if they are asymptomatic, according to the U.S. Centers for Disease Control and Prevention.

Thus, wastewater provides a collective snapshot of what’s going on, regardless of whether people have developed symptoms or been tested.

A rise in coronavirus levels in wastewater offers about a week’s advance notice of where case counts are headed, according to Natalie Exum, assistant scientist of environmental health and engineering at Johns Hopkins Bloomberg School of Public Health in Baltimore.

It could be more cost- effective than the clinical testing of every person — and more efficient.

The time it takes for an infected person to flush their feces down the toilet and for it to reach a wastewater system for analysis, she said, is generally less than it takes for someone who starts developing symptoms to realize they might have COVID-19 and then get a test with confirmed results.

Sequencing of wastewater samples can detect variants of concern, allowing health officials to respond with mitigation strategies ahead of time.

“I think omicron in December and January was the best example of this,” Exum said. “In my opinion, wastewater was certainly the canary in the coal mine.”

This played out during the surge in many places, including the San Francisco Bay Area and New York City.

Wastewater monitoring is also a tool for tracking the virus’ evolution and potentially finding new mutations.

Johnson’s project, a multi-institutional collaboration, is doing exactly that by analyzing and comparing the virus in wastewater samples from various regions.

Recently, the team detected four cryptic variants of the virus in wastewater samples from New York City and published its findings in the peer-reviewed scientific journal Nature Communications. Johnson thinks they are linked to rats that frequent the city’s sewer system, but more study is needed to verify that.

Monitoring delays

Hawaii’s Health Department does not have a statewide wastewater-monitoring system for the coronavirus yet, but has been working on it and expects it to be fully operational sometime this summer, officials said.

Early in the pandemic, Edward Desmond, DOH State Laboratories Division administrator, said he envisioned collecting wastewater from specific nursing homes and prisons to help detect COVID-19. By detecting it early, infected cohorts could be separated from others to prevent further spread.

But there was a six-month wait for shipment of the sample-collection machines, which were back-ordered due to high demand. By then the coronavirus had already spread to those facilities.

The focus shifted to testing wastewater from treatment plants, which DOH worked on with assistance from Priscilla Seabourn, a postdoctoral fellow from the Association of Public Health Laboratories.

Seabourn, who has since completed her time at DOH, set up infrastructure and a molecular biology lab to process wastewater samples.

The monitoring equipment, at a cost of about $100,000, covered by federal funds, is now in place, as are protocols.

Desmond said it also took months to approve a new staff position for a wastewater microbiologist, also covered by federal funds, who is slated to begin this summer.

CDC testing 12 sites

Meanwhile, the CDC is conducting testing in Hawaii as part of its National Wastewater Surveillance System set up in September 2020 to help communities track the coronavirus.

DOH has enrolled 12 wastewater sites across Kauai, Oahu and Hawaii island in the program but has yet to establish one in Maui County.

LuminUltra Technologies is contracted to collect and test wastewater samples from up to 500 U.S. sites, including those in Hawaii, for COVID-19 as well as genetic mutations associated with the omicron and delta variants.

Wastewater data is posted on the CDC’s COVID Data Tracker online, denoted by dots on a U.S. map, but none is available for at least a dozen states, including Hawaii.

A CDC spokesperson said more than 30 states have been funded to participate, but some are still getting their collection efforts up and running.

“We expect even more states to be represented on COVID Data Tracker in the coming months,” said CDC spokesperson Nick Spinelli in an email.

Data from Hawaii is available, said Spinelli, but not posted yet due to “a technical glitch being resolved with how the points are displayed on the map.”

Also, although 12 sites were enrolled, only three from Kauai and Honolulu counties have data in the dataset received from the contractor, he said. CDC hopes to resolve this soon.

“Also, when Hawaii’s Health Department is able to submit their own data, we will gladly display them as well,” he said.

Campus sampling

More than 200 universities and colleges around the globe have sampled wastewater for signs of corona­virus infections on campus, including individual dorms and student housing.

Many work in collaboration with their respective county or state health departments to analyze the wastewater and provide data to the community. These were actually the grassroots efforts that inspired CDC’s national program.

Since spring 2020 the University of Missouri has worked with the Missouri Department of Health and Human Services to help monitor wastewater, with weekly samples from over 100 sites statewide.

In mid-December the state’s health department announced omicron was detected in wastewater at two treatment facilities, and was able to alert the public of its presence in those areas.

Data on trends and variants detected is shared publicly with color-coded symbols on a map online.

This data is valuable alongside other indicators, according to Exum, and should be shared in an understandable way so decision-makers can respond accordingly.

Hawaii health officials have yet not determined how they will share local wastewater data, but say it will not be available by ZIP code because some treatment plants serve multiple areas.

Earlier efforts

The City and County of Honolulu participated in wastewater monitoring efforts as early as April 2020, according to Department of Environmental Services Deputy Director Michael O’Keefe.

In 2020, Honolulu worked with BioBot Analytics for about four months by providing wastewater samples for the firm in Massachusetts, which provided shipping boxes with labels.

Honolulu sent BioBot samples from nine treatment plants, including the one on Sand Island, the largest serving Oahu.

After that the city also provided wastewater samples for the University of Hawaii, which received a National Science Foundation grant to conduct a study.

That partnership ended in November 2020, and UH does not have any updates on its projects at this time.

“We jumped at the opportunity to participate in these sampling efforts whenever we were asked,” said O’Keefe, explaining that the city department recognized the value of wastewater monitoring. “We’d be happy to continue to participate.”

Hawaii is not the only state with delays in getting a state wastewater-monitoring program up and running.

According to Politico, numerous states have yet to do so, and two — North Dakota and Wyoming — do not plan to participate.

Once set up, wastewater monitoring has potential beyond COVID-19, according to Exum. It also can be used to monitor other viruses, markers of antibiotic resistance and levels of opioid use in a community.

“I think the possibilities far exceed the way we are using the tools right now,” she said. “This is a very powerful tool that needs more development, more participation from wastewater facilities and more infusion of government funding that trickles down to the states.”

She is concerned about gaps on CDC’s Data Tracker, which currently seems to offer only a patchwork of wastewater data.

Some limitations include coverage of rural areas in the U.S., including those in Hawaii, that are not connected to a wastewater system.

Hawaii is still home to about 88,000 cesspools — underground holes for the disposal of human waste — that by state law must be replaced by 2050.