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.
Diagram of the
CORONAVIRUS
GENOME
CORONAVIRUS
RNA genome
Start of
genome
30,000
RNA letters
Diagram of the
CORONAVIRUS
GENOME
RNA
genome
Start of
genome
30,000
RNA letters
RNA
genome
Diagram of the
CORONAVIRUS
GENOME
Start of
genome
30,000
RNA letters
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.
| News and updates | ||
|---|---|---|
| Feb. 7 | South Africa stops using AstraZeneca’s vaccine against the B.1.351 variant. | |
| Feb. 7 | The B.1.1.7 variant is doubling every 10 days in the United States. | |
|
Variants of concern |
||
| Lineage | Variant name | Status |
| B.1.1.7 | Variant of Concern 202012/01, or 501Y.V1 | Emerged in Britain in December and is roughly 50 percent more infectious. Now detected in over 70 countries and 33 states. |
| B.1.351 | 501Y.V2 | Emerged in South Africa in December. Reduces the effectiveness of some vaccines. |
| P.1 | 501Y.V3 | Emerged in Brazil in late 2020. Has mutations similar to B.1.351. |
|
Mutations that may help the coronavirus spread |
||
| Lineage | Mutation | Status |
| B.1 | D614G | Appeared in early 2020 and spread around the world. |
| Several | N501Y | A defining mutation in several lineages, including B.1.1.7, B.1.351 and P.1. Helps the virus bind more tightly to human cells. |
| Several | E484K | Appears in several lineages. May help the virus avoid some kinds of antibodies. |
| Several | L452R | Increasingly common in California, but not yet shown to be more infectious. |
|
Other variants in the news |
||
| Lineage | Variant name | Status |
| B.1.427, B.1.429 | CAL.20C | Carries the L452R mutation. Common in California, but not yet shown to be more infectious. |
Variants of Concern
Coronaviruses that appear to be more infectious 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 roughly 50 percent more infectious. 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 35 percent more deadly than other variants. On the other hand, vaccines appear to 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.
SGF 3675-3677
deletion
Mutations in the
B.1.1.7
LINEAGE
H69-V70
deletion
B.1.1.7
CORONAVIRUS
Start of
genome
30,000
RNA letters
Mutations in the
B.1.1.7
LINEAGE
SGF 3675-3677
deletion
Start of
genome
30,000
RNA letters
S235F mutation
Spike
protein
Y144/145 deletion
H69-V70 deletion
Mutations in the
B.1.1.7
LINEAGE
ORF1b
protein
SGF 3675-3677
deletion
ORF1a
protein
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.
Key mutations in
the B.1.1.7 spike
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:
Key mutations in
the B.1.1.7 spike
(top view)
Key mutations in
the B.1.1.7 spike
(top view)
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.
SOUTH
AFRICA
B.1.1.7 detected,
typically in a traveler
Local transmission
SOUTH
AFRICA
B.1.1.7 detected
Local transmission
SOUTH
AFRICA
B.1.1.7 detected
Local transmission
SOUTH
AFRICA
B.1.1.7 detected
Local transmission
B.1.1.7 has now been detected in over 70 countries. It was first reported in the United States in January, and has now reached at least 33 states.
B.1.1.7 detected
More than 100 cases
B.1.1.7 detected
More than 100 cases
B.1.1.7 detected
More than 100 cases
Last month, the Centers for Disease Control and Prevention 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.
SGF 3675-3677
deletion
Mutations in the
B.1.351
LINEAGE
B.1.351
CORONAVIRUS
K1655N
mutation
Start of
genome
30,000
RNA letters
Mutations in the
B.1.351
LINEAGE
SGF 3675-3677
deletion
K1655N
mutation
Start of
genome
30,000
RNA letters
T205I mutation
Spike
protein
Mutations in the
B.1.351
LINEAGE
ORF1b
protein
SGF 3675-3677
deletion
ORF1a
protein
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.
Key mutations in
the B.1.351 spike
(top view)
Key mutations in
the B.1.351 spike
(top view)
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 24 countries.
SOUTH
AFRICA
B.1.351 detected,
typically in a traveler
Local transmission
SOUTH
AFRICA
B.1.351 detected
Local transmission
SOUTH
AFRICA
B.1.351 detected
Local transmission
SOUTH
AFRICA
B.1.351 detected
Local transmission
It has been detected in three states: Maryland, South Carolina and Virginia.
B.1.351 lineage detected
B.1.351 lineage detected
B.1.351 lineage detected
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.
SGF 3675-3677
deletion
Mutations in the
P.1 LINEAGE
L18F
T20N
P26S
P.1
CORONAVIRUS
K1795Q
mutation
28269-73
insertion
Start of
genome
30,000
RNA letters
Mutations in the
P.1 LINEAGE
SGF 3675-3677
deletion
L18F
T20N
P26S
K1795Q
mutation
28269-73
insertion
Start of
genome
30,000
RNA letters
P80R mutation
28269-73 insertion
Spike
protein
ORF1b
protein
Mutations in the
P.1 LINEAGE
SGF 3675-3677
deletion
ORF1a
protein
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.
Key mutation
in the P.1 spike
(top view)
Key mutations
in the P.1 spike
(top view)
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 several countries.
P.1 detected,
typically in a traveler
Local transmission
P.1 detected
Local transmission
P.1 detected
Local transmission
P.1 detected
Local transmission
P.1 has been detected in two states: Minnesota and Oklahoma.
P.1 lineage detected
P.1 lineage detected
P.1 lineage detected
PREVIOUS COVERAGE OF MANAUS AND P.1
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
Start of
genome
30,000
RNA letters
Location of the
D614G
MUTATION
Location of the
D614G
MUTATION
Spike
protein
The D614G mutation is thought to make the coronavirus more infections, but it does not appear to make the disease more severe or help the virus escape vaccines.
The D614G
spike mutation
The D614G
spike mutation
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.
Location of the
N501Y
MUTATION
CORONAVIRUS
Start of
genome
30,000
RNA letters
Location of the
N501Y
MUTATION
Location of the
N501Y
MUTATION
Spike
protein
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 N501Y
spike mutation
(top view)
The N501Y
spike mutation
(top view)
PREVIOUS COVERAGE OF N501Y
The E484K Spike Mutation
The E484K mutation arose independently in multiple lineages, including B.1.351 and P.1. Scientists are also concerned that the mutation was recently found in some samples from the B.1.1.7 lineage from Britain.
Location of the
E484K
MUTATION
CORONAVIRUS
Start of
genome
30,000
RNA letters
Location of the
E484K
MUTATION
Location of the
E484K
MUTATION
Spike
protein
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.
The E484K
spike mutation
(top view)
The E484K
spike mutation
(top view)
WHERE E484K HAS BEEN FOUND
E484K has been found in Brazil, Britain, the United States, Canada 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.
Location of the
L452R
MUTATION
CORONAVIRUS
Start of
genome
30,000
RNA letters
Location of the
L452R
MUTATION
Location of the
L452R
MUTATION
Spike
protein
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.
The L452R
spike mutation
(top view)
The L452R
spike mutation
(top view)
WHERE L452R HAS BEEN FOUND
Roughly 45 percent of current samples in California show this mutation.
RECENT COVERAGE OF L452R
Other Variants in the News
These variants have not yet been shown to be more infectious.
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 listed above. But it’s not yet clear whether it is more infectious.
WHERE CAL.20C HAS BEEN FOUND
By early February, the variant was found in more than half of samples tested in Los Angeles.
PREVIOUS COVERAGE OF CAL.20C
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.
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