The emergence of the newly detected strain tracks to a time at or before the onset of the current spike in Southern California. Of further concern, the investigators, using publicly available databases, have detected the CAL.20C strain in multiple recent patient samples in Northern California, New York, Washington, D.C., and even abroad in Oceania.
To identify the CAL.20C strain, the Cedars-Sinai investigators examined SARS-CoV-2 virus samples from 192 patients at Cedars-Sinai who tested positive for coronavirus between Nov. 22 and Dec. 28, 2020. Using an advanced technique known as next-generation sequencing, they analyzed the genes of the viruses. They combined this data with 4,337 gene profiles of SARS-CoV-2 viruses obtained from patients throughout Southern California, also using publicly available databases.
While the CAL.20C strain was almost nonexistent in October, by December, 36.4% of virus samples from Cedars-Sinai patients were determined to be the strain, as were 24% of all samples from Southern California (defined by Imperial, Kern, Los Angeles, Orange, Riverside, San Bernardino, San Diego, San Luis Obispo, Santa Barbara and Ventura counties).
“The double-digit prevalence of the CAL.20C strain in November and December was striking given that it was first observed in July 2020 in just one of 1,230 virus samples in Los Angeles County and had not again been detected in Southern California until October,” said Jasmine Plummer, PhD, research scientist at the Cedars-Sinai Center for Bioinformatics and Functional Genomics, associate director of the Applied Genomics, Computation & Translational Core at Cedars-Sinai and the other co-corresponding author.
Wenjuan Zhang, PhD, assistant professor in the Department of Pathology and Laboratory Medicine at Cedars-Sinai, said the research team is “not sure what the new findings mean in terms of the infectivity and antibody resistance of the CAL.20C strain, which is important for follow-up studies that will need to be completed.” Zhang is first author on this study.
The study’s co-authors, all from Cedars-Sinai, include Brian Davis, BS, and Stephanie Chen, BS, both from the Center for Bioinformatics and Functional Genomics; and Jorge Sincuir Martinez from the Department of Pathology and Laboratory Medicine.
“The identification of this novel strain of SARS-CoV-2, like strains arising in Britain and South Africa, is highly significant to frontline and global surveillance of the constantly evolving COVID-19 pandemic,” said Jeffrey Golden, MD, vice dean of Research and Graduate Education and director of the Burns and Allen Research Institute at Cedars-Sinai. “We are delighted that the California Department of Public Health was able to use our data to also identify one of the variants included in this new strain. The pioneering research of our Cedars-Sinai investigators is part of our ongoing drive to discover new ways to identify, treat and prevent COVID-19.”