New COVID-19 strain found in more than one-third of Los Angeles patients

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In a new study, researchers found that a new strain of the coronavirus was found in more than one-third of COVID-19 cases in Los Angeles.

This may be contributing to the acceleration of the recent surge of cases across Southern California.

The strain, which the investigators designated as CAL.20C, is believed to be in part responsible for the dramatic increase in cases over the last two months.

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

The research was conducted by a team from Cedars-Sinai.

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 current 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 is propagating across the country, starting in Los Angeles.

Los Angeles County has emerged as one of the nation’s COVID-19 hot spots.

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 researchers, 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 team 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 the 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 identification of this novel strain of SARS-CoV-2, like strains arising in Britain and South Africa, is very important to the frontline and global surveillance of the constantly evolving COVID-19 pandemic.

One author of the study is Eric Vail, MD, an assistant professor of Pathology and Director of Molecular Pathology.

The study is published on MedRxiv.

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