Variant of SARS-CoV-2 Found in Southern California Is Spreading Rapidly

A variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) identified in association with a recent surge in coronavirus diseases 2019 (COVID-19) in Southern California is spreading rapidly, new research suggests.

Investigators at Cedars-Sinai Medical Center (CSMC) conducted phylogenetic analysis of 185 samples taken during a surge of COVID-19. The study, published in JAMA, found that the variant, CAL.20C, accounted for about 36% (67 of 185) of samples collected at CSMS between Nov. 22 and Dec. 28.

“The spread of the new CAL.20C strain of the SARS-CoV-2 virus is likely a reflection of increased COVID-19 cases due to social behavior over the winter holidays,” study's co-senior author, Jasmine Plummer, PhD, 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 told Contagion®. “This development is a reminder that social distancing, wearing a mask, washing hands and staying home where possible, plus also getting vaccinated when you are able to, can help curb this pandemic.”

CAL.20C originated from a group of viruses tracked from Europe to New York early in the pandemic and was first detected in California in July. It reemerged in October and became more prevalent, accounting for about 35% of all coronavirus strains in California and 44% of those in Southern California on Jan. 22. CAL.20C is distinct from variants identified in the United Kingdom (B.1.1.7), South Africa (B.1.351), and Brazil (B.1.1.248) and had been detected in 26 states and several other countries by Jan. 22.

“We initially began this research at a time when the hospital was overwhelmed post-holidays with increased COVID-19 positive cases, and the UK variant was reported and spreading,” Plummer said. “So we first looked for the UK variant and instead found the new CAL.20C strain, which was prevalent in Southern California and accounted for almost 40% of cases within our hospital population.”

The variation includes 3 mutations in the spike protein, which is a target of vaccines and monoclonal antibodies, raising concerns about the potential implications for disease severity and infectivity. Functional effects remain uncertain.

“Using the advanced technology known as next-generation sequencing and finding new versions of the SARS-CoV-2 virus can help promote public health surveillance and arm clinicians with information about what may be presented to them as cases emerge in the healthcare system,” Plummer said. “Research like ours allows scientists the opportunity to ensure virus variants have no adverse effects, and if they do, that we can modify vaccines in a way to address this development.”

Functional studies are underway to examine the infectiousness and clinical outcomes of CAL.20C.

Prevalent strains in the United States appear to be sensitive to therapeutics, but emerging variants raise concerns that the virus could develop resistance, an accompanying editorial by John R. Mascola, MD; Barney S. Graham, MD, PhD; and Anthony S. Fauci, MD, of the National Institute of Allergy and Infectious Diseases. They noted that studies have suggested the B.1.1.7 variant is 30% to 80% more effectively transmitted and associated with a 30% increased risk of death.

Surveillance, tracking, and vaccine deployment will be key to addressing these new variants and could benefit from the infrastructure and process used for updating influenza vaccines.

“SARS-CoV-2 will be with the global population for some time and has clearly shown its tendency toward rapid antigenic variation, providing a ‘wake-up call’ that a sustained effort to develop a pan-SARS-CoV-2 vaccine is warranted,” the NIAID authors wrote.

A variant known as B.1.525 first identified in Europe and Africa in December also has made its way to the United States. B.1.525 shares a mutation found in the Brazilian and South African variants that raise concerns about the possibility of resistance to antibodies.

A lineage B.1.2 variant spreading predominantly in the South and Southwest was first identified in October and has spread to account for about 27% of all sequenced SARS-CoV-2 genomes in Louisiana and 11% of those in New Mexico.

The emergence of more transmissible variants highlights the need for improved sequence-based surveillance along with testing and contact tracing to improve prevention measures as the disease evolves, Adam S. Lauring, MD, PhD, told Contagion® in a January interview.