Tracking Omicron and Other Coronavirus Variants

This tracker followed early variants of the coronavirus through May 2022. It is no longer being updated.

The Centers for Disease Control and Prevention regularly updates its variant estimates for the United States.

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

The variant was first identified in South Africa and Botswana, and has been detected in at least 190 nations. In the United States, the variant has been detected in all 50 states and in Washington, D.C.

SUBVARIANTS OF OMICRON

· BA.1: Initially, a subvariant known as BA.1 was the most common circulating version of Omicron.

· BA.2: By April, a genetically distinct subvariant known as BA.2 accounted for more than half of new cases in the United States, and had become the dominant coronavirus variant around the world.

· BA.2.12.1: A newer subvariant, known as BA.2.12.1, has been spreading rapidly and became dominant in the United States in late May. The subvariant was first detected in New York State.

· BA.4 and BA.5: First identified in January and February, these two subvariants of Omicron were linked to a surge of cases in South Africa in May.

OMICRON’S SPIKE MUTATIONS

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

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.

Researchers have also found that 13 of Omicron’s mutations, highlighted below, are extremely rare in other coronaviruses, and represent a large jump in viral evolution. The 13 mutations appear in three clusters on each spike protein:

Waves of Variants

Many variants of the SARS-CoV-2 coronavirus have arisen over the course of the pandemic. Some spread around the world, while others quickly faded away or were supplanted by other variants.

The Delta variant became dominant in the United States during the summer of 2021, but Omicron has now surpassed it as the dominant variant, according to estimates by the Centers for Disease Control and Prevention.

Other variants of interest or concern around the world include:

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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 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.

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.

The E484K Spike Mutation

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

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.

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.

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

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).

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

Tracking the Coronavirus