Local COVID-19 Strain Explained

Cedars-Sinai investigators recently discovered a new strain of the coronavirus that likely contributed to the crisis-level surge in COVID-19 cases in Los Angeles over the holidays. Jeffrey A. Golden, MD, vice dean of Research and Graduate Education at Cedars-Sinai, offers an explanation about the strain—designated as CAL.20C—and whether it is more contagious than the original form of the virus.

"Being aware that new variants can arise, we identified one," said Golden, director of the Burns and Allen Research Institute at Cedars-Sinai. "It is that particular variant, the CAL.20C, that has correlated with the tremendous surge in cases that we have seen here in Los Angeles."

The Cedars-Sinai findings did not indicate whether the strain is more deadly than current forms of the coronavirus.

CAL.20C is distinct from the virus version identified in Britain—known as B.1.1.7—that is spreading in the U.S. and is believed to be highly transmissible. In Southern California, B.1.1.7 has been found in scattered coronavirus cases in Los Angeles, San Diego and San Bernardino counties. In contrast, the CAL.20C strain was identified in 36.4% of cases in the Cedars-Sinai study.

CAL.20C includes a virus variant that the California Department of Public Health reported Jan. 17 based on data submitted by Cedars-Sinai and other investigators. This variant, dubbed L452R, is one of five recurring mutations that constitute the CAL.20C strain, which has propagated across the country, starting in Los Angeles.

Los Angeles County has emerged as one of the nation's COVID-19 hotspots. Through mid-January, the county had reported more than 1 million COVID-19 cases and nearly 14,000 deaths since the start of the pandemic. More than two-thirds of the cases were added since the beginning of November.

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, 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 study was submitted to MedRxiv.org, an online archive for health science manuscripts that are not yet peer-reviewed, while simultaneously submitted for peer-review on Jan 14.

The study's co-corresponding authors are Eric Vail, MD, assistant professor of Pathology and director of Molecular Pathology in the Department of Pathology and Laboratory Medicine at Cedars-Sinai, and 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.

Wenjuan Zhang, PhD, assistant professor in the Department of Pathology and Laboratory Medicine at Cedars-Sinai, is first author on this study.

The study's co-authors, all from Cedars-Sinai, also 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.