Out of a random selection of 185 virus samples collected from patients between November 22 and December 28, in a genomic sequencing study, none matched B.1.1.7, the so-called UK variant. The smaller 2 main clusters was the predominant SARS-CoV-2 strain. But the larger cluster, making up 36% of the samples, was something different, “a new variant that is homegrown California,” said Eric Vail, MD, the director of molecular pathology at Cedars-Sinai Medical Center in Los Angeles.
The nature of these findings speaks to the sporadic way that virus variant detection has operated in the US for most of the COVID-19 pandemic. Until late last fall, public health departments had no federal mandate or additional funding to sequence samples and viral sequencing was limited and unequally distributed, providing only a patchy understanding of circulating and emerging strains. Now that variant surveillance is in the spotlight, experts say that increasing local sequencing capacity is a critical priority.
In a press briefing on February 8, CDC Director Rochelle Walensky, MD, MPH, said “I think once we have more sequencing, we’ll have a better idea as to how many variants there are and what proportion are out there.”
The CDC has contracted with large commercial laboratories to sequence at least 6000 samples per week, and 7 academic institutions are receiving funding to assist public health departments in their efforts.
We are not out of the woods yet, maybe not for a while so stay well, mask up, and stay tuned!