Coronavirus Variants and Mutations

Each coronavirus contains nearly 30,000 letters of RNA. This genetic information allows the virus to infect cells and hijack them to make new viruses.

As an infected cell builds new coronaviruses, it occasionally makes tiny copying errors called mutations. Scientists can track mutations as they are passed down through a lineage, which is a branch of the viral family tree.

A group of coronaviruses that share the same inherited set of distinctive mutations is called a variant. If enough mutations accumulate in a lineage, the viruses may evolve clear-cut differences in how they function. These lineages come to be known as strains. Covid-19 is caused by a coronavirus strain known as SARS-CoV-2.

Over the course of the pandemic, a number of variants of SARS-CoV-2 have arisen. Some of them are raising worries that they may draw out the pandemic or make vaccines less effective.

Variants of Concern

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

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 variant is also known as 20I/501Y.V1, or simply called B.1.1.7.

Coronaviruses from the B.1.1.7 lineage are thought to be 30 to 50 percent more infectious than other variants in circulation today. They are also likely to be more deadly, based on studies in Britain.

After its discovery in December, it quickly emerged in other countries and surged at an exponential rate. It is doubling in the United States every ten days. Preliminary evidence suggests that B.1.1.7 is about 55 percent more deadly than other variants. But testing suggests that vaccines still work well against it.

B.1.1.7 appears to be more infectious thanks to several mutations in its spike protein, which the coronavirus uses to attach to cells.

KEY MUTATIONS IN B.1.1.7

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.

WHERE B.1.1.7 HAS BEEN FOUND

The variant was first detected in the United Kingdom in December, and a look back at previous samples found it as early as Sept. 20.

B.1.1.7 has now been detected in over 90 countries. It was first reported in the United States in January, and has now reached at least 49 states.

The Centers for Disease Control and Prevention has warned that B.1.1.7 could become the predominant source of all infections in the United States by March.

RECENT COVERAGE OF B.1.1.7

The B.1.351 Lineage

A variant known as 20H/501Y.V2, from the B.1.351 lineage of coronaviruses, was first identified in South Africa in December.

Scientists are concerned about the variant because clinical trials of vaccines are showing 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. The F.D.A. is preparing a plan for updating vaccines if the variant surges in the United States.

KEY MUTATIONS IN B.1.351

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.

WHERE B.1.351 HAS BEEN FOUND

The variant spread from South Africa into neighboring countries, and was detected in the United States in January. It has since spread to at least 48 countries.

It has been detected in at least 25 states, including in a Connecticut resident who was hospitalized in New York City:

RECENT COVERAGE OF B.1.351

The P.1 Lineage

A variant known as 20J/501Y.V3 is from the P.1 lineage, an offshoot of the larger B.1.1.28 lineage.

The variant was first reported in Japan, in four people who contracted P.1 on a trip to Brazil. The lineage 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.

P.1 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 IN P.1

Key mutations in the 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.

WHERE P.1 HAS BEEN FOUND

P.1 was discovered in December and reached the United States in January, but it may have been circulating as early as October in Manaus, Brazil. It has now spread to at least 25 countries.

P.1 has been detected in at least 18 states.

PREVIOUS COVERAGE OF MANAUS AND P.1

The CAL.20C Variant

A variant discovered in California, called CAL.20C, surged in late 2020. The variant spans the B.1.427 and B.1.429 lineages, and carries the L452R mutation described below.

Two studies suggest the variant may be more contagious than earlier forms of the coronavirus, but it does not appear to be spreading as quickly as variants like B.1.1.7.

WHERE CAL.20C HAS BEEN FOUND

By early February, the variant was found in more than half of samples tested in Los Angeles.

RECENT COVERAGE OF CAL.20C

Variants of Interest

Coronaviruses with mutations that may help it evade antibodies or bind more tightly to human cells. They have not yet been shown to be more infectious.

The B.1.525 Lineage

A variant from the B.1.525 lineage has been spreading in New York. The variant carries some of the same mutations as the B.1.1.7 lineage, including E484K and the H69–V70 deletion. It also carries the Q677H mutation described below.

WHERE B.1.525 HAS BEEN FOUND

The variant first appeared in December, 2020.

The B.1.526 Lineage

A group of coronaviruses known as B.1.526 has been spreading rapidly in New York City. The variant appears in two forms: one with the E484K spike mutation, which may help the virus evade antibodies, and one with the S477N mutation, which may help the virus bind more tightly to human cells.

WHERE B.1.526 HAS BEEN FOUND

The variant first appeared in samples taken in November, and by mid-February it accounted for about 27 percent of New York City sequences.

RECENT COVERAGE OF B.1.526

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.

PREVIOUS COVERAGE OF D614G

The N501Y Spike Mutation

The N501Y mutation arose independently in several variants of concern, including the B.1.1.7, B.1.351 and P.1 lineages.

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.

RECENT COVERAGE OF N501Y

The E484K Spike Mutation

The E484K mutation arose independently in multiple lineages, including B.1.351 and P.1. The mutation is nicknamed “Eek” among some scientists, and has recently been found in samples of the B.1.1.7 lineage from Britain and from Oregon.

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.

WHERE E484K HAS BEEN FOUND

E484K has been found in Brazil, Britain, the United States, Canada, Japan and Argentina.

RECENT COVERAGE OF E484K

The L452R Spike Mutation

The L452R mutation is not common in the United States, but it has recently spread in California, especially in the Los Angeles area.

The mutation appears in several lineages, and was first observed in Denmark in March. It’s possible that the L452R mutation gives the coronavirus an advantage at spreading over other variants, but the results of experiments that will demonstrate that have yet to come.

WHERE L452R HAS BEEN FOUND

Roughly 45 percent of current samples in California show this mutation.

RECENT COVERAGE OF L452R

The K417 Spike Mutation

The K417N or K417T spike mutation appears in several lineages, including B.1.351, discovered in South Africa, and P.1, which arose in Brazil.

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.

The Q677 Spike Mutation

The Q677 mutation has arisen in at least seven coronavirus lineages that are spreading in the United States, but it’s unclear whether the mutation makes the variants more contagious.

In some lineages the mutation was Q677H, where the 677th amino acid of the spike protein changed from glutamine (Q) to histidine (H). In other lineages it was Q677P, where the same amino acid changed to proline (P).

The mutation’s location on the side of the spike protein suggests that it might help the coronavirus more easily enter and infect human cells.

WHERE Q677 HAS BEEN FOUND

The mutation was noticed in New Mexico and Louisiana in late 2020. It seems to be scattered across the United States, but the country does not perform enough genetic sequencing to determine the full spread.

Some of the seven lineages have spread abroad, and the Q677 mutation has also arisen independently in other countries.

RECENT COVERAGE OF Q677

Additional reporting by Matthew Kristoffersen.

Sources: Bedford Lab, University of Washington; Andrew Rambaut et al. and Nuno R. Faria et al., Virological; Houriiyah Tegally et al., medRxiv; Paul A. Offit et al., Journal of the American Medical Association; Centers for Disease Control and Prevention; GISAID; SARS-CoV-2 lineages. Spike protein model from Ward Lab, Scripps Research. Cahill-Keyes map projection by Gene Keyes.

Tracking the Coronavirus