This is neatly defined by Corum and Zimmer in the New York Times.
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. These mutations can be tracked 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 in SARS-CoV-2 have arisen.
Some of these have worrying features as they may draw out the pandemic or possibly make vaccines less effective.
The variants of concern are ones 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 a variant of concern on 1st December 2020.
Coronavirus is from this lineage are thought to be 30 to 50% 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 now doubling in the United States every 10 days and preliminary evidence suggests that the B.1.1.7 is about 55% more deadly than other variants but testing suggests that vaccines still work well against it.
The reason B.1.1.7 appears to be more infectious is owing to several mutations in the spike protein, which the coronaviruses uses to attach to cells.
These 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 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.
The B.1.1.7 has now been detected in over 90 countries and is thought to become the most predominant source of all infections in the United States by March.
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.
Researchers are concerned about the variant because clinical trials of vaccines are showing that they offer less protection against the B.1.351 than other variants.
People who recover from other variants may not be able to fend off the B.1.351 because their antibodies will not grab the viruses tightly.
Vaccine manufacturers are preparing plans to update their vaccines.
The key mutations are near the tip of the spike protein and 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 kind of antibodies.
This variant has spread from South Africa into neighbouring countries and has since spread to at least 48 countries.
The P.1. Lineage
The 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 late 2020 in Manaus, the largest city in Brazil’s Amazon region. It very quickly became the predominant there and several other South African cities.
P.1 is a close relative of the B.1.351 lineage and has some of the same mutations on the coronavirus spike protein. It may possibly 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 in those to the B.1.351 lineage, although they arose independently:
- N501Y, which helps the virus latch on more tightly to human cells. This mutation also appeared 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 kind of antibodies. It has now spread to at least 25 countries.
Mutations of Concern
Single mutations that may make the coronavirus more infectious and help it avoid antibodies.
The D614G spike mutation.
The D614 gene 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.
It is thought to make the Coronavirus more infectious but does not appear to make the disease more severe or help the virus escape vaccines.
The mutation is widespread throughout the world.
The N501Y spike mutation arose in several variants of concern independently including the B.1.1.7, the B.1.351 and P.1 lineages.
This 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.
This mutation arose independently in multiple lineages including the B.1.351 and P.1. It has been found in samples of the B.1.1.7 lineage in Britain and also in Oregon.
The mutation occurs near the top of the coronavirus spike where it alters the shape of the protein.
This change helps the spikes evade some types of coronavirus antibodies and has been found in Brazil, Britain, the United States, Canada, Japan and Argentina.
The L452R spike mutation has recently spread into California, especially in the Los Angeles area but was not common in the United States before.
It was first observed in Denmark in March and it is possible that it gives the Coronavirus an advantage of spreading over other variants, but the results of experiments are yet to be published.
45% of current samples in California show this mutation.
The K417 spike mutation appears in several lineages including the B.1.351 discovered in South Africa and P.1, which arose in Brazil.
The mutation gets its name from the 417th amino acids in the spike protein changing from lysine K to either asparagines N or threonin T.
This mutation appears on the tip of the Coronavirus spike and helps the virus bind more tightly to human cells.
The Q677 Spike Mutation
This has arisen in at least seven Coronavirus lineages that are spreading in the United States but it is unknown whether the mutation makes the variants more contagious.
The mutation’s location on the side of the spike protein suggests that it might help the Coronavirus enter more easily and infect human cells.
This mutation has been noticed in New Mexico and Louisiana and it appears scattered across the United States.
It has also spread abroad and has arisen independently in other countries.
The CAL.20C variant discovered in California surged in late 2020.
This carries the L42R mutation.
Studies suggest that the variant may be more contagious than earlier forms of Coronavirus but it does not appear to be spreading as quickly as variants like B.1.7.
It has been found in more than half of samples tested in Los Angeles.
The B.1.526 lineage is a group of coronaviruses which are spreading rapidly in New York City and accounted for 27% of New York City sequences.
These variants likely evolved over the course of several months in infected people within weakened immune systems.
If variants do originate in people with long lasting SARS-CoV-2 infections, vaccination efforts should prioritise people whose immune systems are compromised and these should include people with blood related cancers, diabetes or rheumatoid arthritis as well as patients undergoing chemotherapy or taking immune suppressing drugs.
However, these patients may need additional protection from SARS-CoV-2 as these people do not mount a strong immune response to the virus and vaccines might not well work in them, so it is suggested that they may be requiring treatment with cocktails of monoclonal antibodies as well.
Dr Paul Ettlinger
BM, DRCOG, FRCGP, FRIPH, DOccMed