At the start of the year, infectious disease experts across California were, in their own words, stumbling around in a blind frenzy.
A new variant of the coronavirus was raging across the United Kingdom, causing unprecedented spikes in cases and deaths. California was similarly overwhelmed by a surge in winter cases — but here, very little high-tech testing was being done to identify the source of those infections. When California scientists finally discovered a locally bred variant, it was almost by accident. The mutant virus had long since gained a foothold and spread widely.
That experience raised alarms, statewide and nationally, and spurred fresh efforts and funding for genomic sequencing, the main tool scientists use to hunt for variants.
As a result, sequencing has exploded since January in California. It jumped sixfold in California in April alone, when nearly 20,000 genomic sequences from the state were deposited in a global database — more than from all but four countries. Across the U.S., sequencing increased more than fourfold in May from January.
California is now sequencing up to 10% of all coronavirus cases, a huge improvement from less than 0.5% at the start of the year. That means the state is now, finally, doing enough sequencing that infectious disease experts say they have a good grasp of the types of variants spreading here, and they are confident that scientists will be able to spot any new mutations quickly.
“We’ve got enough visibility to feel comfortable that we know which variants are emerging and how quickly they’re moving and whether they’re getting a foothold,” said Dr. Sara Cody, the Santa Clara County health officer.