Prevalence of this variant has increased. The variant now makes up nearly half of COVID-19 cases in Southern California.
Biological characteristics of this new variant, such as infectivity, are still unknown. It is unclear whether the surge of this variant is due to the enhanced transmissibility or human behavior, including local travel, time spent indoors, close contacts, mask wearing, and behavior during the symptom-onset period.
This variant has also been found in 26 states, Washington D.C., and six countries. However, it’s not clear how common it is outside of California.
One person who tested positive for CAL.20C in January of this year had previously been infected with a different SARS-CoV-2 virus, in July 2020.
The variant is defined by 5 mutations: I4205V in ORF1a; D1183Y in ORF1b: S13I, W152C and L452R in S.
L452R mutation in the S protein locates in the receptor binding domain. L452R was first detected in Denmark in March 2020, from an epidemics in minks.
L452R mutation has been found to be resistant to certain monoclonal antibodies against the S protein, but did not alter the sensitivity to the convalescent sera. This needs to be confirmed by testing with this variant
It is not clear whether this variant enhances the disease severity.
The efficacy of currently available vaccines against this variant has not been reported.
The efficacy of currently available therapeutics against this variant has not been reported.
The current molecular tests detect most of the variants and thus are able to diagnose COVID-19 infection by such variants. Yet, the fine identification of the type of variants is still based on sequence analysis although multiplex PCR test are being evaluated.
Indeed, the current variants of concern show distinctive mutations in the spike protein. Due to such mutations, most diagnostic tests for COVID-19 have been designed by targeting not only the spike protein but also other conserved proteins. For example, molecular tests designed to detect multiple SARS-CoV-2 genes (i.e., multiplex reverse transcription polymerase chain reaction targeting ORF1ab, N, and E genes) are less susceptible to the effects of genetic variation than tests designed to detect a single gene. The FDA is also monitoring the potential effects of genetic variation in molecular tests that have received Emergency Use Authorization and provides information about the tests.
Overall, the precise characterization of the variants still relies on genomic sequencing analysis. For instance, CDC is currently increasing sequence surveillance to more than 6000 samples per week to efficiently monitor the variants of concerns and other emerging variants. COVID-19 caused by variants in the U.S. can be found here.