US labs preparing for omicron, sequencing 80K positive test samples per week

With the COVID-19 omicron variant expected to be detected in the U.S. soon, public health labs are ramping up testing efforts and prioritizing sequencing of positive samples with an "s-gene dropout," a marker absent in the delta strain, according to a Nov. 30 Politico report.

"I am expecting it any day now. I’ve said that for the last two days," Association of Public Health Laboratories CEO Scott Becker said at a briefing, according to the report.

The U.S. is sequencing about 80,000 positive samples per week, or 1 in 7 lab-based PCR positive cases, according to the report. That level of testing, more robust than what was mustered for earlier strains, should be able to pick up any variant that accounts for a hundredth of a percent of total cases.

Home testing kits, a key innovation that bolstered nationwide testing rates, could pose problems for public health officials in the omicron detection effort because the results often aren't reported.

"Unfortunately, we don't have a system in place in our country yet to automatically triage some of those rapid tests — positive samples — to get sequenced," Rick Bright, former director of the Biomedical Advanced Research and Development Authority, told Politico.


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