COVID-19: Emerging SARS-CoV-2 Variants

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What are SARS-CoV-2 variants and how do they occur?

A variant is a new strain of the SARS-CoV-2 virus, the virus that causes COVID-19. Variants occur through mutations, which are changes in the genetic code of a virus. Variants have specific gene mutations that make them unique and different from the original SARS-CoV-2 virus. Viruses, including SARS-CoV-2, naturally change or mutate over time and the new variants are expected to occur.

This webpage will be updated as we learn more about emerging SARS-CoV-2 variants in Wisconsin.

Understanding our data: What does this chart mean?

This chart shows the total number of specimens that have been sequenced using whole genome sequencing by laboratories in the state of Wisconsin. The Wisconsin State Laboratory of Hygiene, along with other laboratory partners, uses data from whole genome sequencing to detect variant cases of SARS-CoV-2, the virus that causes COVID-19. This sequencing is performed on a proportion of positive COVID-19 test specimens. This chart also shows the total count of variant cases that have been detected in Wisconsin. DHS displays case counts for notable variants identified by the Centers for Disease Control and Prevention (CDC). See emerging variant cases in the U.S. here.

Please note that the variant cases identified in this table likely represent a fraction of how many cases of SARS-CoV-2 variants are circulating in Wisconsin. DHS, along with the Wisconsin State Laboratory of Hygiene and other laboratory partners are working to expand efforts to sequence SARS-CoV-2 specimens and identify variants.

About our data: How do we measure this?

Data source:  GISAID.

The Wisconsin State Laboratory of Hygiene, along with other laboratory partners, identifies variant cases of SARS-CoV-2, the virus that causes COVID-19, through whole genome sequencing. Routine analysis of genetic sequence data allows us to identify new variant strains in Wisconsin.

We plan to update our data each Thursday by 4 p.m.

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    Understanding our data: What does this chart mean?

    This chart shows the proportion of specimens, characterized by variant type, that are present in each Health Care Emergency Readiness Coalition (HERC) region of the state. The Wisconsin State Laboratory of Hygiene, along with other laboratory partners, uses data from whole genome sequencing to detect variant cases of SARS-CoV-2, the virus that causes COVID-19. See emerging variant cases in the U.S. here.

    'Other lineages' refers to all other common SARS-CoV-2 lineages and variants detected through surveillance that do not meet the CDC's criteria for variants of concern. These variants are expected to arise as the pandemic continues.

    Please note that the variant cases identified in this table likely represent a fraction of how many cases of SARS-CoV-2 variants are circulating in Wisconsin. DHS, along with the Wisconsin State Laboratory of Hygiene and other laboratory partners are working to expand efforts to sequence SARS-CoV-2 specimens and identify variants.

    About our data: How do we measure this?

    Data source: GISAID.

    The Wisconsin State Laboratory of Hygiene, along with other laboratory partners, identifies variant cases of SARS-CoV-2, the virus that causes COVID-19, through whole genome sequencing. Routine analysis of genetic sequence data allows us to identify new variant strains in Wisconsin.

    We plan to update our data each Thursday by 4 p.m.

      Back to a list of charts on this page.


      What We Know About Variants of Concern

      The Centers for Disease Control and Prevention (CDC) classifies variants into three categories: variants of interest, variants of concern, and variants of high consequence. A variant's classification is based on its attributes, including how easily it spreads, how sick it makes people, and whether COVID-19 treatments and vaccines can prevent it. The classification of a particular variant might change based on new research.

      The CDC reports on the different variants that are circulating nationally, which includes many different variants and several variants of concern. At this time, there are no variants of high consequence. Learn more about SARS-CoV-2 variant classifications on the CDC's website.

      Variants of Concern

      Using the CDC's classifications, DHS tracks variants of concern through whole genome sequencing. Variants of concern identified by the CDC are listed below.

      Variant B.1.1.7

      • Variant B.1.1.7 was first discovered in England in November of 2020. The variant was first reported in the United States in December 2020 and was first identified in Wisconsin in January 2021.
      • Researchers believe this new strain spreads more rapidly and easily than the original strain of SARS-CoV-2. B.1.1.7 may also be associated with an increased risk of death but more studies are needed to confirm this.

      Variant B.1.351

      • Variant B.1.351 was first discovered in South Africa in samples dating back to October 2020. 
      • Researchers have found that this strain also spreads more rapidly and easily than the original SARS-CoV-2 virus. It is not yet known if this variant has any impact on disease severity. There is some evidence that this variant may affect how vaccine induced antibodies respond to this virus.

      Variant P.1

      • Variant P.1 was first discovered in four travelers from Brazil who were tested at an airport near Tokyo, Japan in early January 2021.
      • Researchers have found this strain also spreads more rapidly and easily than the original SARS-CoV-2 virus. The P.1 variant also has unique genetic mutations that may affect the body's ability to recognize and fight off the virus. Typically antibodies developed through previous COVID-19 infection or through vaccination can fight off the SARS-CoV-2 virus. However, if the virus has mutated, antibodies may not recognize it and leave you exposed to COVID-19 infection by this strain.

      Variant B.1.427

      • Variant B.1.427 was first discovered in California in samples dating back to May 2020. B.1.427 cases increased significantly between September 2020 and January 2021.
      • Researchers have found that this strain also spreads more rapidly and easily than the original SARS-CoV-2 virus. However, it is thought to be less transmissible than B.1.1.7 and B.1.351. Therapeutics, such as monoclonal antibody treatments, may be less effective on B.1.427 variant cases because of its unique mutations.

      Variant B.1.429

      • Variant B.1.429 shares many attributes with variant B.1.427, the main difference is found in its spike protein mutations.
      • Variant B.1.429 was first discovered in California in samples dating back to May 2020. B.1.429 cases increased significantly between September 2020 and January 2021.
      • Researchers have found that this strain also spreads more rapidly and easily than the original SARS-CoV-2 virus. However, it is thought to be less transmissible than B.1.1.7 and B.1.351. Therapeutics, such as monoclonal antibody treatments, may be less effective on B.1.429 variant cases because of its unique mutations.

      Public Health Surveillance

      Variants are identified through a process called whole genome sequencing. Whole genome sequencing takes a sample of the virus from a positive SARS-CoV-2 test specimen and reads its genetic code. Genomic sequencing allows scientists to identify how virus samples from different people might have different genetic characteristics. This way, they can look out for new variants of the virus and understanding changes in the characteristics of the virus, like how easily it spreads from person-to-person.

      DHS, the Wisconsin State Laboratory of Hygiene, and other laboratory partners regularly perform whole genome sequencing on a portion of positive tests. DHS has also requested that clinicians identify cases that may be good candidates for genome sequencing, such as individuals who have traveled internationally or individuals who may have tested positive after being fully vaccinated.

      Sequencing of SARS-CoV-2 is not a diagnostic (Clinical Laboratory Improvement Amendments (CLIA) validated) test. It is performed strictly for public health surveillance purposes and is not meant to advise patient care. Results will not be reported to the submitter or patient.

      By sequencing SARS-CoV-2 genomes in Wisconsin, we improve our understanding of emerging variants and use this information to inform public health decision-making.

      What This Means for the COVID-19 Pandemic

      With emerging strains of SARS-CoV-2 circulating in Wisconsin, including those that may spread more rapidly and easily, it is essential to continue public health practices and prevent the spread of COVID-19. Wear a mask, practice physical distancing, stay home whenever you can, wash your hands frequently, get tested if you have symptoms or are a close contact, and get vaccinated when you are eligible.

      We are still learning about how these variants and how they affect: 

      • Transmissibility: How easily the virus spreads from one person to another.
        • Gene mutation D614G was found in all three notable variants. This mutation allows these variants to spread more quickly than the original SARS-CoV-2 virus.
      • Disease outcome: How ill people get with COVID-19.
        • Emerging evidence suggests that B.1.1.7 may be associated with an increased risk of death compared to the other variants. More studies are needed to confirm this. 
        • More studies are needed to determine if P.1 and B.1.351 are associated with more severe illness.
      • Response to COVID-19 treatments: How well therapies and medicines work.
        • Therapies and medicines for people with COVID-19 use specific antibodies to target regions of the virus and block infection. These treatments may become less effective at helping people recover as new variants emerge.
      • Change in effectiveness of COVID-19 vaccines: How well vaccines work.
        • The SARS-CoV-2 virus would likely need to have multiple, significant mutations to affect the level of immunity provided by vaccination.
        • Based on initial evidence, all three authorized vaccines effectively reduce the risk of COVID-19 for all of the circulating variants.

      How can I download DHS COVID-19 data?

      All DHS COVID-19 data is available for download directly from the chart on the page. You can click on the chart and then click "Download" at the bottom of the chart (gray bar).

      To download our data visit one of the following links:

      You can find more instructions on how to download COVID-19 data or access archived spatial data by visiting our FAQ page. The data dictionary (PDF) provides more information about the different elements available in the data above.

      Last Revised: April 29, 2021