In-Depth: A testing trick with roots in Carlsbad helps screen for omicron

Thermo Fisher's PCR test offers an early warning
Posted at 7:07 PM, Dec 10, 2021
and last updated 2021-12-14 23:43:37-05

SAN DIEGO (KGTV) – Scientists detected the San Diego region’s first case of omicron this week with the help of a testing trick that’s now being used to improve surveillance for the variant around the world.

The sequencing shortcut has a fancy name, S gene dropout, and it has roots in Carlsbad.

Thanks to a chance mutation in the omicron variant’s spike protein, a PCR test made by Thermo Fisher Scientific can quickly flag likely instances of the variant.

The World Health Organization has urged labs to use Thermo Fisher’s widely available test as a screening method to prioritize samples for full-genome sequencing, a more expensive process that can take several days. The U.S. only sequences about 5 to 10 percent of its positive PCR tests.

“PCR happens quickly in a couple of hours in the lab, and so we can straightaway flag if it’s a likely case,” said executive vice president Mark Stevenson.

When Scripps Research Institute came across a positive test this week with an S gene dropout, it prioritized the sample for sequencing. It turned out to be the first confirmed case of omicron in San Diego County. The sample was flagged by a Thermo Fisher TaqPath assay, a lab member confirmed.

Thermo Fisher is a global manufacturing giant with more than 2,200 employees at its satellite offices in Carlsbad. Some of the raw materials for the TaqPath COVID-19 test are made at the Carlsbad campus, Stevenson said.

Shortly after omicron was first detected in South Africa, a lab in Gauteng, South Africa, notified Thermo Fisher that its TaqPath test kit might offer an early warning.

The company first released the TaqPath test in March 2020. While some diagnostic makers opted to develop tests that search for a single region of the virus, Thermo Fisher decided to use multiple targets. Its test searches for separate three genes, a strategy that paid dividends when the virus later mutated.

“We designed this assay knowing that viruses could mutate. Therefore, we had some redundancy present in the design. It was by chance that it turned out a mutation occurred under one of the areas we were detecting,” Stevenson said.

Because of a mutation in omicron, the variant is missing code at the 69th and 70th positions in its sequence. That location, on the virus’ spike protein, just happens to be one of the three areas Thermo Fisher’s test detects.

When scientists process a TaqPath test containing omicron, a distinctive signature appears on their computer screen. Two of the three genes are present. The third gene on the spike protein is missing: what researchers call S gene dropout.

It’s not outright confirmation of omicron, but it tells scientists they’ve come across a sample of the novel coronavirus that is not delta. That’s useful because delta still causes 99 percent of the infections in the U.S.

“Straightaway, we can identify if there’s a traveler coming into the region, if there’s a community spread coming out, and we can take public health action,” said Stevenson.

Thermo Fisher says it has ramped up production to make 20 million TaqPath test kits per week. Its PCR test is the one widely available option to screen for omicron, but other diagnostic companies are racing to release similar products.