Efforts to detect variants step up but are still far behind,

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Mon, 2021-04-12 10:52 — mike kraft

As variants surge, efforts in a patchwork of surveillance have ramped up to detect them Though variant hunting has improved, experts say it’s not enough to stay ahead of dangerous new forms of the virus. Erin Cox, Jenna Portnoy Washington Post

The nation dramatically stepped up its surveillance for coronavirus variants in recent weeks, but experts say there’s much further to go if the Washington region — and the rest of the country — wants to stay ahead of new and potentially dangerous versions of the virus.

Conducting the genetic sequencing to detect for variants is far more expensive, time-consuming and sophisticated than testing whether people have contracted the coronavirus, leading to a patchwork system with some states aggressively seeking out variants and others lagging behind.

“There are definitely states where they really champion this,” said Duncan R. MacCannell, chief science officer for the Centers for Disease Control and Prevention’s Office of Advanced Molecular Detection. “But, you know, there’s also a lot of blanks [on the map], dark spots, places where we just don’t have regular sequence data.”

... Nationwide, sequencing volume has tripled since early February, but the country had been so far behind in its efforts that CDC and public health experts say nearly all states still need far more sequencing to create an accurate picture of variants already circulating.

The uneven information about variants circulating in the country comes as states race to vaccinate residents ahead of a potential fourth surge in cases fueled by more contagious and potentially more deadly variants. The Biden administration has put nearly $2 billion into helping the CDC ramp up variant surveillance efforts nationwide, including $1.75 billion included in the rescue package Congress passed last month.

MacCannell’s division leads the consortium to coordinate the country’s knowledge about variants, as well as recruits private labs and universities to surveil for them. Part of the challenge, he said, is that not all public health labs have the expertise to decode the genetic sequences deposited into the national database and then connect them to community outbreaks. ...

Some states, such as Oklahoma and South Dakota, have sequenced less than 0.25 percent of their positive tests since the pandemic began, according to CDC data. In places with low rates, those efforts are largely done by private commercial companies such as Quest Diagnostics and LabCorp that have contracts with the CDC to do 6,000 sequences a week nationwide. ...

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