COVID “Wastewater Surveillance” Continues; Labs Testing for Omicron Variant in California and Elsewhere

By B.N. Frank

In 2020, scientists in the U.S. started collecting and analyzing sewage to track COVID-19 infections (see 1, 2, 3).  Now that the Omicron variant has been identified, labs are testing wastewater for it as well.

From Gov Tech:

California Labs Are Testing Wastewater for Signs of Omicron

California has built up a substantial network of labs to look for concerning coronavirus variants over the past year, and now the scientists in those labs are developing new strategies to quickly identify omicron.

(TNS) — California has built up a substantial network of laboratories to look for concerning coronavirus variants over the past year, and now the scientists running those labs are developing creative new strategies to quickly identify omicron.

At UCSF, one team is studying wastewater — including effluent from San Francisco International Airport — for signs of the newest variant, which has not yet been found in the United States but is likely already here. The head of the Stanford Clinical Virology Laboratory hopes to narrow the search for omicron by focusing on one mutation that it happens to be missing. Some scientists plan to use a simple diagnostic test to speed up the hunt.

Across the state, many public health laboratories are prioritizing viral samples from people who have recently traveled from southern Africa — where the highly mutated variant was first spotted — for further genomic sequencing.

“We have not yet detected omicron at Stanford. But as you might imagine, we are looking for it,” said Dr. Benjamin Pinsky, who runs the Stanford Clinical Virology Laboratory, which has helped track variants for several Bay Area counties. “And so is everyone else in the United States and across the globe.”

This time last year, California’s ability to track new variants hinged on a patchwork of public and private genomic sequencing laboratories that couldn’t begin to keep up with pace of the virus, which was accumulating new mutations much more quickly than scientists had anticipated.

Before January, fewer than 1% of all coronavirus cases underwent sequencing — a process that provides the genetic blueprint of a virus, and captures the mutations that differentiate variants. Infectious disease experts say a state or country needs to sequence more like 5% to 10% of all cases to capture the types of variants that may be spreading, and possibly more than that to quickly identify new variants.

California ramped up its sequencing capacity as more concerning variants began to spread — alpha and epsilon last December, then delta in the summer. The state now sequences roughly 20% of its cases.

Nationally, about 15,000 to 20,000 samples are screened every week in public health labs, according to the Association of Public Health Laboratories. That’s a vast improvement from the roughly 60,000 samples that were sequenced in the U.S. for all of 2020.

“Certainly we are in a much better position than we were a year ago,” said William Lee, vice president for science at Helix, a San Carlos genomic sequencing company. “We are much better prepared for understanding what we need to do to detect these variants as quickly as possible and hopefully do something about them.”

But even in an environment with much more sequencing being done, it’s still important to develop strategies for quickly detecting new variants like omicron, scientists say. The actual sequencing process takes only a few days. But between various reporting and processing delays, a typical sample might take two to three weeks from the day a person gets tested to when the sequencing is complete. That time lag could delay public health responses and give a new variant opportunity to gain traction in a community.

So it’s useful to find ways to speed up the process.

Stanford screens every positive case that comes through its internal laboratories for mutations associated with variants, and then performs genomic sequencing on a subset of those samples. “That’s worked quite well over the last year. We were able to detect early on kappa and beta variants, and also delta,” said Pinsky. The entire process takes seven to 10 days — shorter than average.

Now, almost all of the samples that come to his laboratory are delta. Conveniently, omicron is missing one mutation — known as L452R — that is found in delta, and the Stanford scientists use that knowledge for screening. Any samples that don’t have that mutation will be sequenced right away, Pinsky said.

“We’re prioritizing everything that’s not delta for sequencing,” he said. “So we should be able to identify any omicron variant within days of getting a positive result.”

At UCSF, Dr. Charles Chiu is leading a team that has begun doing viral surveillance of wastewater out of two San Francisco collection locations, including one that’s connected to the airport — “which is what I’m really interested in, because most of the (omicron) cases are imported from other countries,” he said.

Wastewater surveillance can’t identify specific coronavirus cases. But it can allow scientists to quickly analyze a large group of samples for signs of a variant, instead of waiting for an individual to have symptoms and get tested and then running a positive result through genomic sequencing.

Chiu, who heads the UCSF-Abbott Viral Diagnostics and Discovery Center, said his group started surveillance a month or two ago and had been analyzing weekly collections of wastewater. But with a new variant to look out for, “we’ve moved to daily collections,” Chiu said. “The goal is to look for omicron and see evidence in wastewater before appearances in human cases.”

Nationally, an option to speed up detection of omicron may involve diagnostic tests that detect specific genetic material in the virus. One particular test detects three genetic targets, including a target that, in omicron, is so heavily mutated that it doesn’t register.

A positive coronavirus test result that’s negative for that target could be a signal that the person is infected with omicron, and that the sample should be prioritized for sequencing. A similar strategy was used last year to identify alpha, which also showed up negative for that target.

The problem is that some labs, including major ones in California, have moved away from that particular diagnostic test. “A year ago with alpha, that was a tool we used pretty extensively,” said Lee at Helix. “It’s no longer a tool at our disposal.”

But scientists at Helix, which does sequencing in collaboration with the Centers for Disease Control and Prevention, are not concerned about being first to identify omicron, Lee said. Rather, they want to ensure that they’re doing enough sequencing to capture trends with that variant and others that will help public health leaders understand the trajectory of the pandemic.

“For us, it’s more a matter of making sure the CDC and local public health have the data they need in a timely way. We are trying to be part of a coordinated national response,” Lee said.

© 2021 the San Francisco Chronicle. Distributed by Tribune Content Agency, LLC.

In other COVID infection news, last month millions of COVID tests were recalled due to inaccuracies.  Despite an increase in Americans taking the jab, a significant number of vaccine recipients are also still getting the virus.


In the meantime, side effects, injuries, and deaths also continue to be blamed on the COVID jab.  Despite all of this, there is growing pressure for children and adults to take it which has led to numerous lawsuits (see 1, 2, 3, 4, 5).

Activist Post reports regularly about COVID-19.  For more information, visit our archives.

Image: Pixabay

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