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 acquired similar mutations that are associated with immune evasion and resistance to treatments. One specific mutation at position 346 in the receptor binding domain has appeared in many variants such as BA.2.75.2 and XBB (BA.2 sublineages), 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.

Current Sublineage Proportions

As of May 31, 2023, for the month of May, XBB.1.5 (67.2%), XBB.1.9.1 (9.7%), XBB.1.16 (9.1%), XBB.1.9.2 (4.5%), XBB.2.3 (3.7%), FD.2 (2.3%), BA.2.75 (1.7%), and CH.1.1 (1.2%) make up the confirmed Omicron cases sequenced in California. Since there is a known delay in the availability of sequencing results, CDPH models provide estimates of sublineage proportions for the most recent weeks. Models are updated weekly on Thursdays. Based on CDPH model estimates, variants with highest proportions in California are XBB.1.5 (66.0% (41.6-77.6%)),  XBB.1.16 (12.6% (6.7-23.7%)), XBB.1.9.1 (7.6% (3.1-17.0%)), XBB.2.3 (5.3% (1.7-15.9%)), XBB.1.9.2 (4.4% (1.8-10.7%)), BN.1 (2.9% (0.1-34.4%)), XBB (2.5% (0.8-7.2%)), and FD.2 (2.0% (1.1-3.0%)).​​


Sublineage Proportions and Clinical Decision-Making

Providers should prioritize use of nirmatrelvir/ritonavir (Paxlovid) and remdesivir for treatment of mild to moderate COVID-19 in outpatients at risk for disease progression as these drugs continue to be effective against all Omicron sublineages. If neither of these are clinically appropriate, please see the NIH COVID-19 Treatment Guidelines for additional, effective options.

Please note that monoclonal antibodies are not currently authorized for pre-exposure prophylaxis or treatment of COVID-19 in any region of the United States due to increasing prevalence of sublineages that have been associated with resistance to ​these agents.​​


​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 SARS-CoV-2 Variant Classifications and Definitions (cdc.gov)​.

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

California Sequencing 

​​As of May 31, 2023, there have been 897,527 samples sequenced in California. In April 2023, 18% of 37,734 cases in California were sequenced, and this percent is expected to increase in coming weeks as more sequence data becomes available. In March 2023, 18% of 59,280 cases were sequenced, and in February 2023, 13% of 82,110 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 

​​​