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Tracking Omicron and Other Coronavirus Variants

On Nov. 26, the World Health Organization named the Omicron variant of the coronavirus a new variant of concern.

Local transmission

Omicron detected in a traveler

So far it has been detected in South Africa, Botswana, Zambia and Zimbabwe, as well as in travelers to Argentina, Austria, Brazil, Chile, Czech Republic, Estonia, Fiji, Finland, Ghana, Greece, Hong Kong, Ireland, Italy, Japan, Kuwait, Latvia, Liechtenstein, Luxembourg, Malaysia, Maldives, Mexico, Nepal, the Netherlands, Nigeria, Norway, Réunion, Romania, Russia, Saudi Arabia, Senegal, Singapore, South Korea, Sri Lanka, Sweden, Switzerland, Thailand, Tunisia, Uganda and the United Arab Emirates.

Australia, Belgium, Britain, Canada, Croatia, Denmark, France, Germany, Iceland, India, Israel, Mozambique, Namibia, Norway, Portugal and Spain have also reported cases in people who did not travel internationally.

In the United States, the variant has been detected in 20 states: California, Colorado, Connecticut, Florida, Georgia, Hawaii, Illinois, Louisiana, Maryland, Massachusetts, Minnesota, Mississippi, Missouri, Nebraska, New Jersey, New York, Pennsylvania, Texas, Utah, Washington and Wisconsin.

Omicron detected

The variant was identified by scientists in South Africa. Preliminary tests suggest that it has been spreading rapidly there, but researchers have yet to determine if it truly is more contagious than other variants.

A growing number of countries are restricting travel from southern African countries. Israel, Morocco and Japan are banning all foreign travelers.

The United States announced travel restrictions from eight countries in southern Africa.

Britain announced restrictions from two additional countries. The European Union is also considering restrictions.

AFRICA

Angola

Malawi

Zambia

Mozambique

Zimbabwe

Botswana

Namibia

Eswatini

South

Africa

Lesotho

The United States announced travel restrictions from eight countries in southern Africa.

AFRICA

Malawi

Mozambique

Zimbabwe

Botswana

Namibia

Eswatini

South

Africa

Lesotho

Britain announced restrictions from two additional countries. The European Union is also considering restrictions.

Angola

Zambia

OMICRON’S SPIKE MUTATIONS

Omicron carries about 50 mutations not seen in combination before, including more than 30 mutations on the spike protein that the coronavirus uses to attach to human cells.

Deletions

Mutations

Key mutations in

the Omicron spike

(top view)

Deletions

Mutations

Key mutations in

the Omicron spike

(top view)

Omicron’s spike protein has several mutations that are found in other variants of concern and that are thought to make the virus more infectious, including D614G, N501Y and K417N.

Mutations

Deletions

Key mutations in

the Omicron spike

Mutations

Deletions

Key mutations in

the Omicron spike

More research is needed to determine whether Omicron’s collection of mutations will enable the variant to evade immunity from vaccines or infections. It’s also not clear yet whether the disease it causes is more or less severe than other variants.

RECENT COVERAGE OF OMICRON

Waves of Variants

Over the course of the pandemic, many variants of the SARS-CoV-2 coronavirus have arisen. Some variants have spread around the world and helped to draw out the pandemic, while others have faded away or been supplanted by other variants.

Waves of Variants in the United States

This summer the Delta variant pushed aside other circulating variants in the United States. (For other countries, see CoVariants.)

100%

75%

Earlier variants

of the coronavirus

Alpha

Delta

50%

25%

Epsilon

Mu

Iota

Gamma

Beta

Nov.

2020

Dec.

Jan.

2021

Feb.

March

April

May

June

July

Aug.

Sept.

Oct.

2021

100%

Earlier variants

of the coronavirus

75%

Alpha

Delta

50%

25%

Epsilon

Mu

Iota

Gamma

Beta

Jan.

2021

Feb.

March

April

May

June

July

Aug.

Sept.

Oct.

2021

100%

Earlier

coronavirus

variants

75%

Alpha

Delta

50%

25%

Epsilon

Mu

Gamma

Iota

Beta

Jan.

April

July

Oct.

2021

Currently the Delta variant is dominant around the world, but researchers are monitoring other variants of concern, including the recently announced Omicron variant.

Current variants of concern
Name Lineage Status
Omicron B.1.1.529 Identified in southern Africa in Nov. 2021.
Delta B.1.617.2 Emerged in India in late 2020 and spread around the world.
Delta carries the L452R spike mutation, among others.
Gamma P.1 Emerged in Brazil in late 2020.
Beta B.1.351 Emerged in South Africa in late 2020.
Alpha B.1.1.7 Emerged in Britain in late 2020.


Current variants of interest
Name Lineage Status
Mu B.1.621 Emerged in Colombia in early 2021.
Lambda C.37 Emerged in Peru in late 2020.


Mutations that may help the coronavirus spread
Mutation Lineage Status
D614G B.1 Appeared in early 2020 and spread around the world.
N501Y Several A defining mutation in several lineages, including B.1.1.7 (Alpha), B.1.351 (Beta) and P.1 (Gamma). Helps the virus bind more tightly to human cells.
E484K or “Eek Several Appears in several lineages. May help the virus avoid some kinds of antibodies.
K417 Several Appears in several lineages, including B.1.351 (Beta) and P.1 (Gamma). May help the virus bind more tightly to cells.
L452R Several Appears in several lineages, including B.1.617.2 (Delta).

What Is a Variant?

When an infected human cell assembles new coronaviruses, it occasionally makes tiny copying errors called mutations. Scientists can track mutations as they are passed down through a lineage, a branch of the coronavirus family tree. A group of coronaviruses that share the same inherited set of distinctive mutations is called a variant.

Diagram of the

CORONAVIRUS

GENOME

Spike

CORONAVIRUS

RNA genome

Start of

genome

30,000

RNA letters

Diagram of the

CORONAVIRUS

GENOME

Spike

RNA

genome

Start of

genome

30,000

RNA letters

Spike

RNA

genome

Diagram of the

CORONAVIRUS

GENOME

Start of

genome

30,000

RNA letters

Other Variants of Concern

Coronaviruses that appear to be more infectious or cause more severe disease than other circulating coronaviruses.

Delta: The B.1.617.2 Lineage

Delta is an aggressive variant that emerged in late 2020 and quickly became the most common variant in India. It continued spreading around the world and is currently the dominant variant.

KEY MUTATIONS

The variant emerged with more than a dozen mutations, but was initially called a “double mutant” because of two prominent mutations: L452R and E484Q, which lies at the same location as E484K, the “Eek” mutation.

Deletions

Mutations

Key mutations in

the Delta spike

(top view)

Deletions

Mutations

Key mutations in

the Delta spike

(top view)

As the Delta variant continues to spread around the world, some versions have developed additional spike mutations found in other variants of concern. These modified variants are sometimes referred to as Delta Plus.

Gamma: The P.1 Lineage

Gamma emerged in late 2020 in Manaus, the largest city in Brazil’s Amazon region. It quickly became the predominant variant there and in several other South American cities.

The P.1 lineage is a close relative of the B.1.351 lineage, and it has some of the same mutations on the coronavirus spike protein. It may be able to overcome the immunity developed after infection by other variants.

E5665D

SGF 3675-3677

deletion

Mutations in the

P.1 LINEAGE

L18F

T20N

P26S

D138Y

R190S

P.1

CORONAVIRUS

K417T

E484K

N501Y

H655Y

K1795Q

mutation

T1027I

S1188L

E92K

28269-73

insertion

P80R

Start of

genome

30,000

RNA letters

E5665D

Mutations in the

P.1 LINEAGE

SGF 3675-3677

deletion

L18F

T20N

P26S

D138Y

R190S

K417T

Genome

E484K

N501Y

H655Y

K1795Q

mutation

T1027I

S1188L

E92K

28269-73

insertion

P80R

Start of

genome

30,000

RNA letters

N protein

P80R mutation

28269-73 insertion

E92K

M

E

ORF3a

T1027I

H655Y

Spike

protein

N501Y

E484K

K417T

R190S

D138Y

P26S

T20N

L18F

ORF1b

protein

E5665D

Mutations in the

P.1 LINEAGE

SGF 3675-3677

deletion

ORF1a

protein

K1795Q

S1188L

KEY MUTATIONS

Key mutations in the P.1 spike protein are similar to those in the B.1.351 lineage, although they arose independently:

N501Y, which helps the virus latch on more tightly to human cells. This mutation also appears in the B.1.1.7 and B.1.351 lineages.

K417T, which is the same site as the K417N mutation in the B.1.351 lineage. It may also help the virus latch on tighter.

E484K, which may help the virus evade some kinds of antibodies.

K417T

N501Y

E484K

N501Y

E484K

N501Y

K417T

K417T

E484K

Key mutation

in the P.1 spike

(top view)

K417T

N501Y

E484K

N501Y

E484K

N501Y

K417T

K417T

E484K

Key mutations

in the P.1 spike

(top view)

Beta: The B.1.351 Lineage

A variant named Beta, from the B.1.351 lineage of coronaviruses, was first identified in South Africa in December.

Clinical trials of vaccines showed that they offer less protection against B.1.351 than other variants. People who recover from other variants may not be able to fend off B.1.351 because their antibodies won’t grab the viruses tightly.

SGF 3675-3677

deletion

Mutations in the

B.1.351

LINEAGE

L18F

D80A

D215G

R246I

B.1.351

CORONAVIRUS

K417N

E484K

N501Y

A701V

K1655N

mutation

P71L

T205I

Start of

genome

30,000

RNA letters

Mutations in the

B.1.351

LINEAGE

SGF 3675-3677

deletion

L18F

D80A

D215G

R246I

K417N

Genome

E484K

N501Y

A701V

K1655N

mutation

P71L

T205I

Start of

genome

30,000

RNA letters

N protein

T205I mutation

M

P71L

E

ORF3a

A701V

N501Y

Spike

protein

E484K

K417N

R246I

D215G

D80A

L18F

Mutations in the

B.1.351

LINEAGE

ORF1b

protein

SGF 3675-3677

deletion

ORF1a

protein

K1655N

KEY MUTATIONS

Mutations near the tip of the spike protein include:

N501Y, which helps the virus latch on more tightly to human cells. This mutation also appears in the B.1.1.7 and P.1 lineages.

K417N, which also helps the virus bind more tightly to human cells.

E484K, which may help the virus evade some kinds of antibodies.

K417N

N501Y

E484K

N501Y

E484K

N501Y

K417N

K417N

E484K

Key mutations in

the B.1.351 spike

(top view)

K417N

N501Y

E484K

N501Y

E484K

N501Y

K417N

K417N

E484K

Key mutations in

the B.1.351 spike

(top view)

Alpha: The B.1.1.7 Lineage

This group of coronaviruses came to light in Britain, where it was named Variant of Concern 202012/01. The World Health Organization later named it Alpha.

Coronaviruses from the B.1.1.7 lineage are thought to be 30 to 50 percent more infectious than earlier variants. They are also likely to be more deadly, based on studies in Britain. But testing suggests that vaccines still work well against it.

The variant quickly spread in other countries and surged at an exponential rate. It became the dominant variant in the United States before being supplanted by the Delta variant.

Alpha appeared to be more infectious than previous variants thanks to several mutations in its spike protein, which the coronavirus uses to attach to cells.

SGF 3675-3677

deletion

Mutations in the

B.1.1.7

LINEAGE

H69-V70

deletion

Y144/

145

B.1.1.7

CORONAVIRUS

I2230T

N501Y

A570D

P681H

T716I

S982A

A1708D

D1118H

T1001I

Q27stop

R52I

D3L

Y73C

S235F

Start of

genome

30,000

RNA letters

Mutations in the

B.1.1.7

LINEAGE

SGF 3675-3677

deletion

Spike

H69-V70

Y144/

145

Genome

I2230T

N501Y

A570D

P681H

T716I

S982A

A1708D

D1118H

T1001I

Q27stop

R52I

D3L

Y73C

S235F

Start of

genome

30,000

RNA letters

S235F mutation

N protein

D3L

Y73C

R52I

M

Q27stop

E

D1118H

ORF3a

S982A

T716I

P681H

Spike

protein

A570D

N501Y

Y144/145 deletion

H69-V70 deletion

Mutations in the

B.1.1.7

LINEAGE

ORF1b

protein

SGF 3675-3677

deletion

ORF1a

protein

I2230T

A1708D

T1001I

KEY MUTATIONS

Mutations in the spike protein include:

N501Y, which helps the virus latch on more tightly to human cells. But the mutation is not likely to help the virus evade current vaccines.

P681H, which may help infected cells create new spike proteins more efficiently.

— The H69–V70 and Y144/145 deletions, which alter the shape of the spike and may help it evade some antibodies.

N501Y

Y144/145

Y144/145

H69–V70

H69–V70

P681H

P681H

Key mutations in

the B.1.1.7 spike

N501Y

Y144/145

Y144/145

H69–V70

H69–V70

P681H

P681H

Key mutations in

the B.1.1.7 spike

It takes three spike proteins to form one spike, so each mutation appears in three places:

Y144/145

Y144/145

N501Y

N501Y

N501Y

Key mutations in

the B.1.1.7 spike

(top view)

Y144/145

Y144/145

Y144/145

N501Y

N501Y

N501Y

Key mutations in

the B.1.1.7 spike

(top view)

Y144/145

For more on the B.1.1.7 mutations, see: Inside the B.1.1.7 Coronavirus Variant.

Mutations of Concern

Single mutations that may make the coronavirus more infectious, or help it avoid antibodies.

The D614G Spike Mutation

The D614G mutation emerged in eastern China early in the pandemic and then quickly spread around the world, displacing other coronaviruses that did not have the mutation.

Location of the

D614G

MUTATION

CORONAVIRUS

D614G

Start of

genome

30,000

RNA letters

Location of the

D614G

MUTATION

Genome

D614G

Location of the

D614G

MUTATION

N protein

M

E

ORF3a

Spike

protein

D614G

The D614G mutation is thought to make the coronavirus more infectious, but it does not appear to make the disease more severe or help the virus escape vaccines.

D614G

The D614G

spike mutation

D614G

The D614G

spike mutation

D614G is so widespread that it has been omitted from other graphics on this page.

The N501Y Spike Mutation

The N501Y mutation arose independently in several variants of concern, including Alpha, Beta and Gamma.

Location of the

N501Y

MUTATION

CORONAVIRUS

N501Y

Start of

genome

30,000

RNA letters

Location of the

N501Y

MUTATION

Genome

N501Y

Location of the

N501Y

MUTATION

N protein

M

E

ORF3a

Spike

protein

N501Y

The mutation is near the tip of the coronavirus spike, where it seems to change the shape of the protein to be a tighter fit with human cells.

N501Y

N501Y

N501Y

The N501Y

spike mutation

(top view)

N501Y

N501Y

N501Y

The N501Y

spike mutation

(top view)

The E484K Spike Mutation

The E484K mutation arose independently in multiple lineages, including Beta and Gamma. The mutation is nicknamed “Eek” among some scientists.

Location of the

E484K

MUTATION

CORONAVIRUS

E484K

Start of

genome

30,000

RNA letters

Location of the

E484K

MUTATION

Genome

E484K

Location of the

E484K

MUTATION

N protein

M

E

ORF3a

Spike

protein

E484K

The mutation occurs near the top of the coronavirus spike, where it alters the shape of the protein. This change may help the spikes evade some types of coronavirus antibodies, as at least one trial has shown.

E484K

E484K

E484K

The E484K

spike mutation

(top view)

E484K

E484K

E484K

The E484K

spike mutation

(top view)

The L452R Spike Mutation

The L452R mutation appears in several lineages. It was first observed in Denmark in March, 2020, and was later found to be spreading in California, especially in the Los Angeles area.

Location of the

L452R

MUTATION

CORONAVIRUS

L452R

Start of

genome

30,000

RNA letters

Location of the

L452R

MUTATION

Genome

L452R

Location of the

L452R

MUTATION

N protein

M

E

ORF3a

Spike

protein

L452R

It’s possible that the L452R mutation gave the variant an advantage at spreading over previous variants.

L452R

L452R

L452R

The L452R

spike mutation

(top view)

L452R

L452R

L452R

The L452R

spike mutation

(top view)

The K417 Spike Mutation

The K417N or K417T spike mutation appears in several lineages, including Beta and Gamma.

The mutation gets its name from the 417th amino acid in the spike protein changing from lysine (K) to either asparagine (N) or threonine (T).

Location of the

K417

MUTATION

Spike

K417N

or

K417T

Genome

Location of the

K417

MUTATION

N protein

M

E

ORF3a

Spike

protein

K417N or K417T

The mutation appears on the tip of the coronavirus spike, and may help the virus bind more tightly to human cells.

K417

K417

K417

The K417

spike mutation

(top view)

K417

K417

K417

The K417

spike mutation

(top view)

Tracking the Coronavirus