A new emerging variant of SARS-CoV-2, called CAL.20C or lineage B.1.429, was recently reported in California (USA). Identified by researchers at Cedars-Sinai Medical Center in July 2020, the variant was initially reported as rare only to resurface later that year (October). The most recent reports indicate that CAL.20C is rapidly replacing the old 20G lineage, the dominant variant of the region until then.
Unpublished data suggest that this variant may account for nearly half of the virus genome samples collected in the Los Angeles region alone during January 2021. Furthermore, scientists suspect that this lineage is responsible for a resurgence of cases. The new strain is characterized by multiple mutations in the spike protein. Although the impact of these mutations on person-to-person transmissibility and the severity of the disease is still unknown, experts have urged international authorities to closely monitor their spread.
CAL.20C is characterized by the presence of five non-synonymous amino acid changes: one observed within the receptor-binding domain (RBD) -L452R; two other mutations detected outside of RBD – S13I and W152; and the remaining mutations in ORF1ab (I4205V and B1183Y). So far, the strain has only shown sustained spread in California (primarily Southern California), with only a few genomes reported in Australia, New Zealand, and the United Kingdom.
The L452R mutation in RBD is of particular concern because it is found at a key amino acid residue. Although this mutation has not yet been shown to impact affinity for human ACE2, it has already been shown that it makes the virus more resistant to some neutralizing monoclonal antibodies. Therefore, it is highly likely that the L452R amino acid change enhances the ability of SARS-CoV-2 to evade the human immune response. At the moment, the impact of this mutation on the efficacy of the vaccine is being investigated.