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Novel SARS-CoV-2 Variant From California Spreading Widely

TUESDAY, Feb. 16, 2021 -- In a research letter published online Feb. 11 in the Journal of the American Medical Association, researchers describe the emergence of a novel variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), CAL.20C, which originated in Southern California.

Wenjuan Zhang, Ph.D., from Cedars-Sinai Medical Center (CSMC) in Los Angeles, and colleagues sequenced and analyzed a random sample of patients who tested positive for SARS-CoV-2 from Nov. 22 to Dec. 28, 2020, at CSMC. On Jan. 11, 2021, a phylogenetic analysis was conducted with samples and globally representative genomes using Nextstrain.

The researchers selected 192 samples at CSMC and 185 underwent the phylogenetic analysis, together with 1,480 representative genomes using Nextstrain. A diverse set of lineages was identified with two main clusters: The larger cluster (67 of the samples; 36 percent) comprised a novel variant descended from cluster 20C, defined by five mutations, designated CAL.20C. In an analysis of 10,431 samples from California, CAL.20C was first observed in July 2020 in one of 1,247 samples from Los Angeles County and was not detected again in Southern California until October 2020. The variant's prevalence increased thereafter, accounting for 35 and 44 percent, respectively, of all samples collected in January in California state and Southern California. CAL.20C has been detected in 26 states and other countries as of Jan. 22, 2021.

"We are interested in the CAL.20C strain because three of its five variants involve the so-called spike protein, which enables the SARS-CoV-2 virus to invade and infect normal cells," a coauthor said in a statement.

One author disclosed receipt of personal fees from Illumina.

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Posted: February 2021

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