COVID-Variants Tracking Variants

Tracking Variants

Updates as of April 12, 2022:

  • Added information on BA.2 subvariant.


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. On May 10, 2022, the Centers for Disease Control and Prevention (CDC) updated the COVID Data Tracker and projected that BA.2 is the dominant Omicron sublineage in the U.S. [56.4% (49.3-63.3%)] for the week ending May 7, 2022. Similarly, per the CDC COVID Data Tracker, BA.2 is projected to be the dominant Omicron sublineage in Region 9 which includes California [74.7% (69.5-79.3%)] for the week ending May 7, 2022. CDPH data, including the latest modeling estimates and wastewater surveillance trends also suggest that the BA.2 proportion is increasing in most regions of the state. While the BA.2 sublineage is 1.4 times more transmissible than BA.1, it appears to be similar to other Omicron sublineages with respect to severity of illness and vaccine effectiveness.

BA.2 sublineage has been further reclassified into several daughter sublineages, among which, BA.2.12 and BA.2.12.1 are particularly noteworthy. BA.2.12.1 has an estimated growth advantage of 23-27% over BA.2, but there is no evidence yet of increased disease severity due to either BA.2.12 or BA.12.1. As of May 11, 2022, these two sublineages together make up 11.4% of confirmed Omicron cases sequenced in the state in the month of April.            

Please note, that one of the COVID-19 anti-SARS-CoV-2 monoclonal antibodies, sotrovimab, has been shown to be less effective in treating COVID-19 infections due to the BA.2 sublineage. Because of this, the U.S. Food and Drug Administration (FDA) has removed the authorization for sotrovimab in all US states and territories, including California. Providers should prioritize the use of Paxlovid and remdesivir for the treatment of mild to moderate COVID-19 in outpatients at risk for disease progression, as these drugs are effective against all Omicron sublineages. If an anti-SARS-CoV-2 monoclonal antibody is indicated over these two antiviral treatments, providers should use bebtelovimab.


Variants Being Monitored

Variants being monitored are seen at low levels or no longer detected. They do not pose a significant or immediate risk to the public. They are likely to have one or more of the following features:

  • Potential or known effect on treatment
  • More severe symptoms
  • Increased transmission

​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 May 11, 2022, there have been 564,341 samples sequenced in California. In March 2022 17% of 77,641 cases in California had been sequenced, and this percent is expected to increase in coming weeks as more sequence data becomes available. In February 2022 15% of 324,182 cases in California had been sequenced. In January 2022, 2% of 2,546,730 cases were sequenced, and in December 2021, 10% of 700,167 cases 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. Note that although the total number of cases sequenced in January 2022 is similar to previous months, the total number of cases reported was more than 3.5 times that reported in December 2021, hence the percentage sequenced was lower in January 2022.

 

Variant Genetic Sequence Data