By COVID “Wastewater Surveillance” Continues; Labs Testing for Omicron Variant in California and Elsewhere
(by B.N. Frank | Activist Post) – 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. Read Full Article >
