California urgently needs to ramp up genomic sequencing to look for coronavirus variants. But it won’t be easy

Santa Clara County had been lucky: A resident who’d traveled out of the country and returned home infected with a worrying new coronavirus variant had only exposed one other person to the mutated virus.

From the time the resident came down with symptoms to the confirmation Wednesday that a new variant from South Africa was the source of infection, more than two weeks had passed. But the individual had been “exquisitely compliant” with local health orders that mandated post-travel quarantine, said county health officer Dr. Sara Cody.

There was no risk of the variant spreading in the community — not from this case, at least.

But the discovery of that case — plus a second infection with the same variant in an Alameda County resident, also announced last week — rang fresh alarms over the urgent need to detect mutations to the virus that may hinder efforts to control the pandemic.

California’s ability to hunt down these variants relies on widespread and rapid genomic sequencing. But the state, like the rest of the country, is not close to doing enough sequencing. Expanding that effort will require state and national leadership, unprecedented collaboration among laboratory scientists, creative shortcuts and dedicated funding, infectious disease experts say.

Only about 0.4% of California’s 3.4 million cases have undergone genomic sequencing, far below the minimum 5% most experts believe is necessary to quickly identify new variants and understand how widespread they are in communities. And the results almost always come out a week or more after the person is past the most infectious stages of disease, limiting public health officials’ ability to contain it.

“This reminds me of our early days of testing, when we had very little testing. A year ago I remember the very uncomfortable feeling that there had to be cases out there, we’re just not seeing them,” said Cody at a news conference last week.

Research associate Paula Serpa processes process samples at the Chan Zuckerberg Biohub in San Francisco in July.

Research associate Paula Serpa processes process samples at the Chan Zuckerberg Biohub in San Francisco in July.

Josie Norris / Special to The Chronicle 2020

She gets the same disconcerting vibe about variants now. Santa Clara County is doing more sequencing than most California counties — it’s one of only a handful that does sequencing its own public health labs — but “it’s still just a small fraction” of cases, Cody said. “The capacity just isn’t what it needs to be in order to rapidly identify and track emerging variants.”

The United States is 34th in the world in the percent of cases sequenced, according to an international database of coronavirus sequences called GISAID. And California ranks 22nd among U.S. states in percent of samples sequenced, according to the Centers for Disease Control and Prevention. The state is second only to Texas for the total number of sequences done, but far below places like Hawaii, Maine and Washington state that sequence more than 2% of all cases.

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