COVID-Variants Tracking Variants

Tracking Variants

Variants Are a Normal Part of Viruses 

Viruses change through mutations that create new strains of virus over time. This is a normal process that happens with most viruses. We call these strains variants.

Some variants rise and then disappear. Other variants become common. Most variants do not have a meaningful impact. 

Why Are We Tracking Variants?

Scientists and public health officials are studying variants to learn more about how to control their spread. They want to understand whether the variants:

  • Spread more easily from person-to-person
  • Cause milder or more severe disease in people
  • Are detected by currently available viral tests
  • Respond to medicines currently being used to treat people for COVID-19
  • Change the effectiveness of COVID-19 vaccines

Variants We Are Tracking  

Variants of Concern

Variants of concern are likely to have one or more of the following features:

  • More contagious
  • Likely to cause more severe symptoms
  • Resistant to treatment
  • More resistant to vaccines

​Variant

​Known differences

​​Delta

  • 200% increased transmission compared to other variants

  • Reduced antibody treatment effectiveness

​Omicron

The California Department of Public Health is working with the CDC to gather up-to-date information about the Omicron variant.

  • At least 2 to 4 times more transmissible than the Delta variant

  • Reduced effectiveness of certain antibody treatments

The Omicron variant (Pango Lineage B.1.1.529) has been classified into the following sublineages: BA.1, BA.1.1, BA.2, BA.3, BA.4, and BA.5. Each sublineage is further classified into several distinct sublineages due to accumulation of additional mutations. 

Of note, several sublineages of BA.2, BA.4, and BA.5 have been acquiring similar mutations that have been associated with immune evasion. One specific mutation at position 346 in the receptor binding domain has appeared in many variants such as BA.2.75.2 (BA.2 sublineage), BA.4.6 (BA.4 sublineage), BF.7 and BQ.1.1 (BA.5 sublineages). Mutations at other locations on the receptor binding domain are also common and have been shown to be antigenically significant in prior variants of concern.   

As of November 23, 2022 for the month of November, BA.2.75 (2.6%), BA.4.6 (2.9%), BF.7 (6.5%), BQ.1 (16.5%), BQ.1.1 (13.2%), and BA.5 (46%) sublineages make up the confirmed Omicron cases sequenced in California. However, there is a known delay in sequencing results being available; thus, CDPH models projections for the most recent weeks for which sequencing data are not yet available. Based on this, updated CDPH models estimate that 26.8 (0.4%-84.3%) of cases in California are currently BA.5. However, the proportion of BA.5 cases in the state are declining whereas proportion of BQ.1 (29.9% (0.2%–82%)) and BQ.1.1 (29.1% (0.3%–84.1%)) cases are increasing.

As noted by the National Institutes of Health (NIH), "the subvariants BQ.1 and BQ.1.1 are likely to be resistant to bebtelovimab, and the subvariants BA.4.6, BA.2.75.2, BA.5.2.6, BF.7, BQ.1, and BQ.1.1 are likely to be resistant to tixagevimab plus cilgavimab (Evusheld).The decision to administer tixagevimab plus cilgavimab to a given patient should be based on the regional prevalence of the resistant subvariants, the individual patient’s risks, the available resources, and logistics.  Bebtelovimab should only be used when the majority of circulating Omicron subvariants in the region are susceptible to bebtelovimab." Based on CDPH model estimates above, >50% of circulating variants in most California regions are likely resistant to bebtelovimab and tixagevimab plus cilgavimab.




​Variant

​Known differences

​Alpha

  • ​Increased transmission

  • Potential increased disease severity and risk of death

  • Minimal impact on antibody treatment effectiveness

​Beta

  • Increased transmission

  • Reduced antibody treatment effectiveness

​Gamma

  • ​Reduced antibody treatment effectiveness

​Epsilon

  • Increased transmission

  • Significantly reduced antibody treatment effectiveness

​Eta

  • ​​Moderately decreased antibody treatment effectiveness

​Iota

  • ​Significantly reduced antibody treatment effectiveness

​Kappa

  • ​Moderately decreased antibody treatment effectiveness

​Zeta

  • ​Moderately decreased antibody treatment effectiveness

Mu

  • Moderately decreased antibody treatment effectiveness


California follows the CDC's variant classifications and definitions.

CDC and CDPH do not consider variants being monitored as variants of concern at this time.

California Sequencing 

As of November 23, 2022, there have been 782,207 samples sequenced in California. In October 2022 11% of 84,529 cases in California were sequenced, and this percent is expected to increase in coming weeks as more sequence data becomes available. In September 2022 15% of 124,482 cases were sequenced, and in August 2022 10% of 297,227 cases in California were sequenced. This is the number of sequences submitted to the data repository GISAID and is not a complete list of sequences completed to date.



Variant Genetic Sequence Data