- The Omicron variant has been detected in Wisconsin.
- The Omicron variant has a number of mutations occurring on its spike protein that make it more transmissible than previous variants and reduce the effectiveness of some monoclonal antibody treatments.
- COVID-19 vaccines still offer protection against severe illness, hospitalization, and death from COVID-19, including circulating variants.
- With the emergence of the Omicron variant, it is critical to get vaccinated, get your booster, and layer public health practices to prevent further spread.
Find Data from the Wisconsin State Laboratory of Hygiene
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 virus. Viruses, including SARS-CoV-2, naturally change or mutate over time and new variants are expected to occur.
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 better understand how different mutations change the characteristics of the virus, like how easily it spreads from person-to-person.
The Department of Health Services (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 up to date with COVID-19 vaccines.
Why track SARS-CoV-2 variants?
- To understand which strains are spreading in our state.
- To know which variants make up the largest proportion of new cases in Wisconsin.
- To help public health effectively plan COVID-19 prevention measures because some variants can spread more quickly than earlier strains and/or reduce the effectiveness of vaccines or treatments. The Centers for Disease Control and Prevention (CDC) classifies these as variants of concern.
- To understand how common the new strains are in our communities, not to have a real-time number of cases infected with each strain.
The CDC classifies variants into four categories:
- Variants Being Monitored
- Variants of Interest
- Variants of Concern
- 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. Learn more about SARS-CoV-2 variant classifications on the CDC website.
- Variant B.1.1.529, also known as the Omicron variant, was first discovered in South Africa in November 2021.
- On December 1, 2021, the United States detected its first case of the Omicron variant.
- On December 4, 2021, the Omicron variant was first detected in Wisconsin.
- On December 20, 2020, the CDC announced that the Omicron variant became the dominant strain among new COVID-19 cases.
- The Omicron variant continues to change into new sub-lineages. Sub-lineages are newer versions of the same variant. These sub-lineages differ based on mutations in the spike protein, but they still share a lot of the mutations as the original Omicron variant strain, B.1.1.529.
- CDC refers to Omicron variant sub-lineages as BA lineages.
- Attributes of the Omicron variant include:
- Increased transmissibility compared to the Delta variant
- Potential decrease in vaccine effectiveness against preventing SARS-CoV-2 infection compared to the Delta variant. Initial studies show that COVID-19 vaccines still provide protection against severe illness, hospitalization, and death caused by the Omicron variant.
- Reduction in the effectiveness of some monoclonal antibody treatments
- With the emergence of the Omicron variant, it is critical to get vaccinated, get your booster, and layer public health practices to prevent further spread.
Visit the CDC website for more information on the Omicron variant.
- The Delta variant, B.1.617.2, was first discovered in India in October 2020.
- The Delta variant continues to change into new sub-lineages. Sub-lineages are newer versions of the same variant. These sub-lineages differ based on mutations in the spike protein, but they still share a lot of the mutations as the original Delta variant strain, B.1.617.2.
- CDC refers to Delta variant sub-lineages as AY lineages
- Attributes of the Delta variant:
- Increased transmissibility compared to the original strain of SARS-CoV-2
- Decrease in vaccine effectiveness against preventing SARS-CoV-2 infection compared to the original strain.
- Susceptible to monoclonal antibody treatments.
- Available evidence shows that the current COVID-19 vaccines are highly effective against severe illness, hospitalization, and death from the Delta variant.
Visit the CDC website for more information on the Delta variant.
All viruses mutate, or change, over time. Mutation can happen very slowly or more quickly. The longer a virus sticks around, the more time it has to change. When a virus changes, it is called a variant. Many variants are no more harmful than the original virus, however, some can be more infectious or deadly. When our bodies are faced with a new variant, our immune responses built from vaccination or a previous infection may be able to fight it off.
Vaccines reduce a virus's ability to infect people. Vaccines still provide protection against current variants since many of the characteristics of the virus remain the same. The sooner people get vaccinated against COVID-19, the less opportunity we give the virus to keep mutating.
Available in Spanish.
Available in Spanish.
Last Revised: May 27, 2022
ECDC regularly assesses new evidence on variants detected through epidemic intelligence, rules-based genomic variant screening, or other scientific sources. If a decision is made to add, remove, or change the category for any variant, the tables are updated to reflect this change. The tables are regularly sent for consultation to ECDC and WHO Regional Office for Europe’s joint virus characterisation working group. The rules-based genomic screening is performed using an open source algorithm. The weekly ECDC variant surveillance data report can be found in the weekly COVID-19 country overviews published on ECDC’s website. More information on variants is available on The tables include: Category: variant of concern (VOC), variant of interest (VOI), or variant under monitoring (VUM) (see definition above each table). Note that it is a possible for a VOC, VOI or VUM to also be a part of a broader VOC, VOI, or VUM definition, e.g. B.1.617.2+E484X is also a part of B.1.617.2, this means that there is enough evidence to fulfil the VOC, VOI or VUM criteria for this variant using the broader variant as a reference. For these variants, clear evidence is available indicating a significant impact on transmissibility, severity and/or immunity that is likely to have an impact on the epidemiological situation in the EU/EEA. The combined genomic, epidemiological, and in-vitro evidence for these properties invokes at least moderate confidence. In addition, all the criteria for variants of interest and under monitoring outlined below apply.Description of the tables
Each category is annotated as increased, reduced, similar, unclear, or no evidence depending on the currently available evidence. Increased or reduced means that there is evidence demonstrating that the property is different enough for the variant compared to previously circulating variants that it is likely to have an impact on the epidemiological situation in the EU/EEA. Similar means that there is evidence that demonstrates that the property is not different enough for this variant compared to previously circulating variants that it is unlikely to have an impact. Unclear means that the current evidence is preliminary or contradictory enough to make the assessment uncertain. No evidence means that no evidence has yet been evaluated for this category. The evidence is further annotated with v or m to indicate whether the evidence is available for the variant itself (v) or for mutations associated with the variant (m).Variants of Concern (VOC)
Omicron | BA.1 | South Africa and Botswana | (x) | November 2021 | Increased (v) (1, 2) | Increased (v) (3-5) | Reduced (v) (6-8) | Community |
Omicron | BA.2 | South Africa | (y) | November 2021 | Increased (v) (1, 9) | Increased (v) (3) | Reduced (v) (10, 11) | Dominant |
Omicron | BA.4 | South Africa | L452R, F486V, R493Q | January 2022 | No evidence | Increased (12, 13) | No evidence | Community |
Omicron | BA.5 | South Africa | L452R, F486V, R493Q | February 2022 | No evidence | Increased (12, 13) | No evidence | Community |
x: A67V, Δ69-70, T95I, G142D, Δ143-145, N211I, Δ212, ins215EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F
y: G142D, N211I, Δ212, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
All sub-lineages of the listed lineages are also included in the variant, e.g., BA.1.1 is included in Omicron BA.1 as it is a sub-lineage of BA.1.
Variants of Interest (VOI)
For these variants, evidence is available on genomic properties, epidemiological evidence or in-vitro evidence that could imply a significant impact on transmissibility, severity and/or immunity, realistically having an impact on the epidemiological situation in the EU/EEA. However, the evidence is still preliminary or is associated with major uncertainty. In addition, all the criteria for variants under monitoring outlined below apply.
Omicron | BA.2 + L452X (x) | n/a | L452X | n/a | No evidence | Increased (13) | No evidence | Detected (a) |
x: Any amino-acid substitution
Variants under monitoring
These additional variants of SARS-CoV-2 have been detected as signals through epidemic intelligence, rules-based genomic variant screening, or preliminary scientific evidence. There is some indication that they could have properties similar to those of a VOC, but the evidence is weak or has not yet been assessed by ECDC. Variants listed here must be present in at least one outbreak, detected in a community within the EU/EEA, or there must be evidence that there is community transmission of the variant elsewhere in the world.
Omicron | BA.3 | South Africa | (z) | November 2021 | No evidence | No evidence | No evidence | Detected (a) |
z: A67V, Δ69-70, Δ143-145, N211I, Δ212, G339D, S371F, S373P, S375F, D405N, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, D796Y, Q954H, N969K
n/a: not applicable, no WHO label has been assigned to this variant at this time
De-escalated variants
These additional variants of SARS-CoV-2 have been de-escalated based on at least one the following criteria: (1) the variant is no longer circulating, (2) the variant has been circulating for a long time without any impact on the overall epidemiological situation, (3) scientific evidence demonstrates that the variant is not associated with any concerning properties.
Alpha | B.1.1.7 | United Kingdom | N501Y, D614G, P681H | September 2020 | Increased (v) (14) | Similar | Increased (v) (15, 16) | Drastically reduced circulation in the EU/EEA following the emergence of Delta; little evidence of impact on vaccine induced immunity | |
n/a | B.1.1.7+E484K | United Kingdom | E484K, N501Y, D614G, P681H | December 2020 | Increased (v) (14) | Increased (v) (17, 18) | Increased (v) (15) | Very low levels of circulation in the EU/EEA | |
Epsilon | B.1.427/B.1.429 | USA | L452R, D614G | September 2020 | Unclear (19) | Increased (v) (19) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA and available data indicating that vaccines and treatments are effective against such variant | |
n/a | B.1.616(c) | France | V483A, D614G, H655Y, G669S | February 2021 | Detection (c) (20) | No evidence | No evidence | Not detected since 2021-04-23 (26) | |
Eta | B.1.525 | Nigeria | E484K, D614G, Q677H | December 2020 | No evidence | Increased (m) (17, 22) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
Theta | P.3 | The Philippines | E484K, N501Y, D614G, P681H | January 2021 | Increased (m) (14) | Increased (m) (17) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
Kappa | B.1.617.1 | India | L452R, E484Q, D614G, P681R | December 2020 | Increased (v) (23) | Increased (v) (24-27) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | B.1.620 | Unclear (b) | S477N, E484K, D614G, P681H | February 2021 | No evidence | Increased (m) (17, 28) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | B.1.617.3 | India | L452R, E484Q, D614G, P681R | February 2021 | Increased (m) (14) | Increased (m) (17, 19) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | B.1.214.2 | Unclear2 | Q414K, N450K, ins214TDR, D614G | December 2020 | No evidence | No evidence | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | A.23.1+E484K | United Kingdom | V367F, E484K, Q613H | December 2020 | No evidence | Increased (m) (17) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | A.27 | Unclear (b) | L452R, N501Y, A653V, H655Y | December 2020 | Increased (m) (14) | Increased (m) (19) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | A.28 | Unclear (b) | E484K, N501T, H655Y | December 2020 | No evidence | Increased (m) (17) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | C.16 | Unclear (b) | L452R, D614G | October 2020 | No evidence | Increased (m) (17) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | B.1.351+P384L | South Africa | P384L, K417N, E484K, N501Y, D614G, A701V | December 2020 | Increased (v) (29) | Increased (v) (30, 31) | Unclear (32) | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | B.1.351+E516Q | Unclear (b) | K417N, E484K, N501Y, E516Q, D614G, A701V | January 2021 | Increased (v) (29) | Increased (v) (30, 31) | Unclear (32) | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | B.1.1.7+L452R | United Kingdom | L452R, N501Y, D614G, P681H | January 2021 | Increased (v) (14) | Increased (m) (19) | Increased (v) (15) | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | B.1.1.7+S494P | United Kingdom | S494P, N501Y, D614G, P681H | January 2021 | Increased (v) (14) | Increased (m) (33) | Increased (v) (15) | No longer detected or detected at extremely low levels in the EU/EEA | |
Iota | B.1.526 | USA | E484K, D614G, A701V | December 2020 | No evidence | Increased (m) (17) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | B.1.526.1 | USA | L452R, D614G | October 2020 | No evidence | Increased (m) (19) | No evidence | Lineage withdrawn from Pango | |
n/a | B.1.526.2 | USA | S477N, D614G | December 2020 | No evidence | No evidence | No evidence | Lineage withdrawn from Pango | |
Zeta | P.2 | Brazil | E484K, D614G | January 2021 | No evidence | Increased (m) (17) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | B.1.1.519 | Mexico | T478K, D614G | November 2020 | No evidence | Increased (m) (19) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | AV.1 | United Kingdom | N439K, E484K, D614G, P681H | March 2021 | No evidence | Increased (m) (17) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | AT.1 | Russian Federation | E484K, D614G, N679K, ins679GIAL | January 2021 | No evidence | Increased (m) (17) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | C.36+L452R | Egypt | L452R, D614G, Q677H | December 2020 | No evidence | Increased (m) (19) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | P.1+P681H | Italy | D614G, E484K, H655Y, K417T, N501Y, P681H | February 2021 | No evidence | Unclear (34, 35) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
Mu | B.1.621 | Colombia | R346K, E484K, N501Y, D614G, P681H | January 2021 | Increased (m) (14) | Increased (m) (14) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
Lambda | C.37 | Peru | L452Q, F490S, D614G | December 2020 | No evidence | Increased (v) (36, 37) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | AY.4.2 | United Kingdom | L452R, T478K, D614G, P681R, A222V, Y145H | June 2021 | Increased (v) (38) | Similar (v) (38, 39) | Similar (v) (38) | Delta sub-lineages will continue to be monitored within Delta VOC | |
n/a | B.1.1.318 | Unclear (b) | E484K, D614G, P681H | January 2021 | No evidence | Increased (m) (17) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | B.1.617.2 + K417N | United Kingdom | L452R, T478K, D614G, P681R, K417N | June 2021 | No evidence | No evidence | No evidence | Delta sub-lineages will continue to be monitored within Delta VOC | |
n/a | C.1.2 | South Africa | D614G, E484K, H655Y, N501Y, N679K, Y449H | June 2021 | Increased (m) (14) | Increased (m) (17) | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | B.1.617.2 + E484X (d) | India | L452R, T478K, D614G, P681R, E484X (d) | April 2021 | No evidence | No evidence | No evidence | Delta sub-lineages will continue to be monitored within Delta VOC | |
n/a | B.1.617.2 + Q613H | India | L452R, T478K, D614G, P681R, Q613H | April 2021 | No evidence | No evidence | No evidence | Delta sub-lineages will continue to be monitored within Delta VOC | |
n/a | B.1.617.2 + Q677H | India | L452R, T478K, D614G, P681R, Q677H | April 2021 | No evidence | No evidence | No evidence | Delta sub-lineages will continue to be monitored within Delta VOC | |
Beta | B.1.351 | South Africa | K417N, E484K, N501Y, D614G, A701V | September 2020 | Increased (v) (29) | Increased (v) (30, 31) | Increased (v) (16, 32) | No longer detected or detected at extremely low levels in the EU/EEA | |
Gamma | P.1 | Brazil | K417T, E484K, N501Y, D614G, H655Y | December 2020 | Increased (v) (7) | Increased (v) (40) | Increased (v) (16) | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | B.1.640 | The Republic of Congo | D614G, F490R, N394S, N501Y, P681H, R346S, Y449N, 137−145de | September 2021 | No evidence | No evidence | No evidence | No longer detected or detected at extremely low levels in the EU/EEA | |
n/a | XF | United Kingdom | Omicron-like | January 2022 | No evidence | No evidence | No evidence | No longer detected. | |
n/a | France | NTD Delta-like; remaining Omicron-like | January 2022 | No evidence | No evidence | No evidence | No longer detected. | ||
Delta | B.1.617.2 | India | L452R, T478K, D614G, P681R | December 2020 | Increased (v) (41) | Increased (v) (42-44) | Increased (v) (43, 45) | Detected at extremely low levels in the EU/EEA |
n/a: not applicable, no WHO label has been assigned to this variant at this time
All sub-lineages of the listed lineages are also included in the variant, e.g., B.1.429.1 is included in B.1.427/B.1.429 as it is a sub-lineage of B.1.429.
(a) No assessment of transmission is given for variants in the monitoring category, only detected/not detected.
(b) The earliest detections from several different countries are close in time and there is no clearly demonstrated travel link to a specific country that explains the detections.
(c) The property of concern for this variant was the fact that there are reports of difficulties associated with detecting it in upper respiratory tract samples. These difficulties were not caused by primer-template mismatch but rather by the virus not being present in sufficient quantities in the upper respiratory tract.
(d) Any amino acid substitution
See changes from previous weeks
Geographic scope of the tables
The tables are based on genomic, phenotypic, and epidemiological evidence available on a global scale, but focus on the potential impact for the European region. For this reason, the list may deviate slightly from the global variants of concern and interest list and labels produced by WHO and published in the WHO weekly epidemiological update.
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