COVID-Variants Tracking Variants

Tracking Variants

What is a variant? 

Viruses constantly change through mutations that create new strains of virus (called variants) over time. Some virus variants emerge and then disappear, while others persist or become common. Most variants do not have a meaningful impact. Public health becomes concerned about a SARS-CoV-2 variant when it affects COVID-19 transmission, severity, testing, treatment, or vaccine effectiveness. 

How are variants identified? 

Multiple variants of the virus that causes COVID-19 have been identified globally during the COVID-19 pandemic. Variants are determined by their genetic sequences. It's important to understand that genetic mutations of the virus that causes COVID-19, SARS-CoV-2, are expected, and that there are many strains of the virus.  Public health, academic, and clinical partners are working together to sequence the genetic material of the virus in California. The term variant of interest (VOI) is used to describe a newly emerging variant for which the medical and public health importance is not yet known. If a variant is thought to be more contagious or likely to cause greater illness or severe disease, or may impact treatment or vaccine response, then it is considered a variant of concern (VOC).  

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

Which variants are being tracked in California? 

CDPH collects data on variant sequences from a variety of different sources to assemble a picture of the different strains currently circulating in California. The variant strains shown in the tables below are those CDC has designated a variant of concern or a variant of interest. CDC maintains a listing of these variants and displays the prevalence of the variants of concern circulating in the United States by state.   

What effect do variants have on vaccine effectiveness?

CDPH is working with federal, local and academic partners to better understand how variants might impact Californians, including if they have any differences in their response to vaccination.

The immune response resulting from either COVID-19 infection or vaccine targets several parts of the SARS-CoV-2 spike protein. Even if a virus has one or more mutations in the spike protein, vaccines and natural infection would still be expected to provide valuable protection.

What do we know about the variants of concern?

  • B.1.1.7 (Alpha) variants are associated with approximately 50% increased transmission, and likely with increased disease severity and risk of death. Appears to have minimal impact on the effectiveness of treatments with antibodies.
  • B.1.351 (Beta) variants are associated with approximately 50% increased transmission. May have moderately decreased response to antibody treatments.
  • P.1 (Gamma) variants may have moderately decreased response to some antibody treatments.
  • B.1.617.2 (Delta) variants are associated with approximately 200% increased transmission. May have moderately decreased response to antibody treatments. (Delta totals include Delta sub-lineages AY.1 and AY.2)

What do we know about the Variants of Interest?

  • B.1.526 (Iota) is associated with significantly reduced efficacy of some antibody treatments.
  • B.1.525 (Eta), and P.2 (Zeta) variants may have moderately decreased response to some antibody treatments.
  • B.1.617.1 (Kappa) may have moderately decreased response to some antibody treatments.
  • B.1.427 and B.1.429 (Epsilon) are associated with approximately 20% increased transmission. There is significantly reduced efficacy of some antibody treatments.

How much sequencing is being done in California?

As of September 15th 157,168 samples have been sequenced in California. In August 2021, 8% of cases in California were sequenced, and this percent is expected to increase in coming weeks as more data becomes available. In July 2021, 16% of 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.

Known Variants of Concern in California

As of September 15, 2021

​Variant
​WHO Label
​Number of Cases Caused by Variant
​B.1.1.7*
​Alpha
​16,178
​B.1.351
​Beta
​171
​P.1
​Gamma
​3,168
​B.1.617.2*
Delta 
​60,573

* includes all sublineages (Q for B.1.1.7 and AY for B.1.617.2)

CDPH is also monitoring the variants of interest shown in the table below. Since their clinical and epidemiologic significance is not yet known, CDC and CDPH do not consider them variants of concern at this time. 

Known Variants of Interest in California

As of September 15, 2021

​Variant
​WHO Label
​Number of Cases Caused by Variant
​B.1.427 and B.1.429
Epsilon
31,055
​P.2
Zeta
112
​B.1.525
​Eta
​67
B.1.526
​Iota
1304
​B.1.617.1
Kappa
​75

How has the proportion of variants of concern and variants of interest in California changed over time?

The table below shows the percent of specimens sequenced that are variants of concern or variants of interest.

Specimen
Collection
Month
Alpha
Beta
Gamma
Delta
Epsilon
Zeta
Eta
Iota
Kappa
​21-Sept
​0.0%
​0.0%
​0.0%
​100.0%
​0.0%
​0.0%
​0.0%
​0.0%
​0.0%
​21-Aug
​0.2%
​0.0%
​0.3%
​98.5%
​0.0%
​0.0%
​0.0%
​0.0%
​0.0%
​21-Jul
​2.4%
​0.0%
​1.7%
​93.2%
​0.0%
​0.0%
​0.0%
​0.1%
​0.0%
​21-Jun
27.2%
0.1%
10.0%
50.3%
0.9%
0.0%
0.0%
2.0%
0.0%
​21-May
54.1%
0.4%
10.6%
6.2%
5.5%
0.0%
0.1%
4.9%
0.1%
21-Apr
49.2%
0.6%
7.9%
2.1%
17.7%
0.1%
0.3%
4.5%
0.4%
21-Mar
21.6%
0.4%
2.1%
0.0%
49.5%
0.3%
0.1%
1.5%
0.1%
21-Feb
5.1%
0.0%
0.0%
0.0%
58.5%
0.2%
0.0%
0.3%
0.0%
21-Jan
1.1%
0.0%
0.0%
0.0%
45.3%
0.1%
0.0%
0.0%
0.0%
20-Dec
0.6%
0.0%
0.0%
0.0%
23.9%
0.1%
0.0%
0.0%
0.0%
20-Nov
0.0%
0.0%
0.0%
0.0%
10.5%
0.0%
0.0%
0.0%
0.0%
20-Oct
0.0%
0.0%
0.0%
0.0%
3.2%
0.0%
0.0%
0.0%
0.0%
20-Sep
0.0%
0.0%
0.0%
0.0%
1.1%
0.0%
0.0%
0.0%
0.0%
20-Aug
0.0%
0.0%
0.0%
0.0%
0.2%
0.0%
0.0%
0.0%
0.0%
20-Jul
0.1%
0.0%
0.0%
0.0%
0.4%
0.0%
0.0%
0.0%
0.0%
20-Jun
0.0%
0.0%
0.0%
0.0%
0.0%
0.0%
0.0%
0.0%
0.0%
20-May
0.0%
0.0%
0.0%
0.0%
0.0%
0.0%
0.0%
0.0%
0.0%
20-Apr
0.1%
0.0%
0.0%
0.0%
0.1%
0.0%
0.0%
0.2%
0.0%
20-Mar
0.0%0.0%0.0%0.0%0.1%0.0%0.0%0.0%
​​0.0%

Note: The cases identified above are based on a sampling of SARS-CoV-2-positive specimens and do not represent the total number of infections due to the strains that may be circulating in California. The number of California samples sequenced is the number of sequences submitted to the international GISAID database and is not a complete list of all sequences completed to date. Numbers are updated on Thursdays by noon but reflect data posted on GISAID the day prior.