What’s CAL.20C? New Covid-19 strain in LA may be behind dramatic rise in Southern California cases: Study
Researchers are yet to determine whether the local variant is more deadly than current forms of the coronavirus
Researchers have discovered a new coronavirus variant that has been found in over one-third of the cases in Los Angeles. This local strain, designated as “CAL.20C,” may be contributing to the massive increase in Covid-19 cases across Southern California over the last two months, according to Cedars-Sinai scientists.
“The recent surge in Covid-19 positive cases in Southern California coincides with the emergence of CAL.20C,” confirms Dr Eric Vail, assistant professor of Pathology and director of molecular pathology in the Department of Pathology and Laboratory Medicine at Cedars-Sinai. The paper, which is yet to be peer-reviewed, has been submitted to MedRxiv.org, an online archive for health and science manuscripts. Los Angeles County has emerged as one of the coronavirus hotspots in the US. The county has reported more than 1 million coronavirus cases and over 14,000 deaths since the start of the pandemic. More than two-thirds of the cases were added since the beginning of November 2020.
What do we know about this variant?
CAL.20C is distinct from B.1.1.7, the variant that is believed to be highly transmissible and was first identified in the UK. 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 detected in 36.4% of cases in the Cedars-Sinai study.
CAL.20C includes a virus variant that the California Department of Public Health reported on January 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.
The analysis does not reveal whether the strain is more deadly than current forms of the coronavirus. The authors believe the new strain is likely more infectious, but they have to conduct more research to determine whether CAL.20C is more contagious than other forms of the virus. However, experts emphasize that the identification of this novel strain of SARS-CoV-2, like strains arising in Britain and South Africa, is significant to the frontline and global surveillance of the constantly evolving Covid-19 pandemic.
First author Dr Wenjuan Zhang, assistant professor in the Department of Pathology and Laboratory Medicine at Cedars-Sinai, notes that the 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.”
When did it first appear?
According to the investigators, the emergence of the newly detected strain tracks to a time at or before the onset of the current spike in Southern California. Using publicly available databases, they have identified the CAL.20C strain in multiple recent patient samples in Northern California, New York, Washington, DC and even abroad in Oceania.
The team examined SARS-CoV-2 virus samples from 192 patients at Cedars-Sinai who tested positive for coronavirus between November 22 and December 28, 2020. Using a 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 2020, it just exploded or took over the local population in November and December and this coincided with a big spike in cases in Los Angeles and Southern California. Results show that by December, 36.4% of virus samples from Cedars-Sinai patients were determined to be the strain. It was also found in 24% of all samples from Southern California, which includes Imperial, Kern, Los Angeles, Orange, Riverside, San Bernardino, San Diego, San Luis Obispo, Santa Barbara, and Ventura counties. In January 2021, it was identified in almost 50% of the samples.
“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,” writes Dr Jasmine Plummer, a research scientist at the Cedars-Sinai Center for Bioinformatics and Functional Genomics, and associate director of the Applied Genomics, Computation & Translational Core at Cedars-Sinai.