New Variant of Virus that Causes COVID-19 Detected
Since November 2020, the United Kingdom (UK) has reported a rapid increase in COVID-19 cases in London and southeast England. This rapid increase in cases has been linked to a different version—or variant—of the virus that causes COVID-19
(SARS-CoV-2). Public health professionals in the UK are evaluating the characteristics of this new variant.
What we know
Viruses constantly change through mutation, and new variants of a virus are expected to occur over time. Sometimes new variants emerge and disappear. Other times, new variants emerge and start infecting people. Multiple
variants of the virus that causes COVID-19 have been documented in the United States and globally during this pandemic.
The virus that causes COVID-19 is a type of coronavirus, a large family of viruses. Coronaviruses are named for the crown-like spikes on their surfaces. Scientists monitor changes in the virus, including changes to the spikes on the surface of the virus.
These studies, including genetic analyses of the virus, are helping us understand how changes to the virus might affect how it spreads and what happens to people who are infected with it.
Recent reports indicate that about 6 in 10 cases reported in London are caused by the new variant. Genetic analysis of the new variant shows changes to the spikes on the virus and to other parts of the virus. Initial studies suggest that the new variant
may spread more easily from person to person. So far, scientists in the UK see no evidence that infections by this variant cause more severe disease.
What we do not know
It is still very early in the identification of this variant, so we have a great deal to learn. More studies on the new variant are needed to understand
- How widely the new variant has spread in the UK and potentially around the world
- How the new variant differs from earlier variants
- How the disease caused by this variant differs from the disease caused by other variants that are currently circulating
What it means
Public health officials are quickly studying the new variant to learn more so that they can control its spread. They want to understand whether the new variant
- Spreads more easily from person to person
- Causes milder or more severe disease in people
- Is detected by currently available viral tests
- Responds to medicines currently being used to treat people for COVID-19
- Affects the effectiveness of COVID-19 vaccines. There is no evidence that this is occurring, and most experts believe this is unlikely to occur because of the nature of the virus.
Some countries have announced travel bans to and from the UK while scientists work to better understand the new variant.
Implications of the Emerging SARS-CoV-2 Variant VOC 202012/01
A new variant strain of SARS-CoV-2 that contains a series of mutations has been described in the United Kingdom (UK) and become highly prevalent in London and southeast England. Based on these mutations, this variant
strain has been predicted to potentially be more rapidly transmissible than other circulating strains of SARS-CoV-2. Although a variant may predominate in a geographic area, that fact alone does not mean that the variant is more infectious. Scientists
are working to learn more about this variant to better understand how easily it might be transmitted and whether currently authorized vaccines will protect people against it. At this time, there is no evidence that this variant causes more severe
illness or increased risk of death. Information regarding the virologic, epidemiologic, and clinical characteristics of the variant are rapidly emerging. CDC, in collaboration with other public health agencies, is monitoring the situation closely.
CDC will communicate new information as it becomes available.
Does this variant have a name?
At present, the variant is referred to as “SARS-CoV-2 VOC 202012/01” (i.e., the first variant of concern from 2020, December), or “B.1.1.7.” The press often uses the terms “variant,” “strain,” “lineage,”
and “mutant” interchangeably. For the time being in the context of this variant, the first three of these terms are generally being used interchangeably by the scientific community as well.
Why has this variant been in the news recently?
Since November 2020, a variant strain of SARS-CoV-2 has become prevalent in the southeast of England, reportedly accounting for 60% of recent infections in London. This variant has a mutation in the receptor binding domain (RBD) of the spike protein at
position 501, where amino acid asparagine (N) has been replaced with tyrosine (Y). The shorthand for this mutation is N501Y, sometimes noted as S:N501Y to specify that it is in the spike protein. This variant carries many other mutations, including
a double deletion (positions 69 and 70).
Why has this variant emerged in the UK?
We do not know. By chance alone, viral variants often emerge or disappear, and that may be the case here. Alternatively, it may be emerging because it is better fit to spread in humans. This rapid change from being a rare strain to becoming a common strain
has concerned scientists in the UK, who are urgently evaluating the characteristics of the variant strain and of the illness that it causes.
Have we seen this variant in the United States?
The VOC 202012/01 variant has not been identified through sequencing efforts in the United States, although viruses have only been sequenced from about 51,000 of the 17 million US cases. Ongoing travel between the United Kingdom and the United States,
as well as the high prevalence of this variant among current UK infections, increase the likelihood of importation. Given the small fraction of US infections that have been sequenced, the variant could already be in the United States without having
What do we know already about variants containing N501Y?
Prior work on variants with N501Y suggests they may bind more tightly to the human angiotensin-converting enzyme 2 (ACE2) receptor. It is unknown whether that tighter binding, if true, translates into any significant epidemiological or clinical differences.
In one laboratory study of transmission of the virus between ferrets, this mutation (and one other) spontaneously arose in the ferrets during the experiment. The significance of this observation remains to be elucidated. VOC 202012/01 so far has no
known association with animals or animal contact.
What about the other mutations in this variant of SARS-CoV-2?
SARS-CoV-2 mutates regularly, acquiring about one new mutation in its genome every two weeks. Many mutations are silent (i.e., cause no change in the structure of the proteins they encode) because they produce a three-letter codon that translates to the
same amino acid (i.e., they are “synonymous”). Other mutations may change the codon in a way that leads to an amino acid change (i.e., they are “non-synonymous”), but this amino acid substitution does not impact the protein’s
VOC 202012/01 has 14 non-synonymous (amino acid [AA] altering) mutations, 6 synonymous (non-AA altering), and 3 deletions, notably including
69/70 deletion: this double deletion has occurred spontaneously many times, and likely leads to a change in the shape of (i.e., a conformational change in) the spike protein.
P681H: near the S1/S2 furin cleavage site, a site with high variability in coronaviruses. This mutation has also emerged spontaneously multiple times.
ORF8 stop codon (Q27stop): This mutation is not in the spike protein but in a different gene (in open reading frame 8), the function of which is unknown. Similar mutations have occurred in the past. In Singapore, one strain with this type of mutation
emerged and disappeared.
What implications could the emergence of new variants have?
Among the potential consequences of these mutations are the following:
Among these possibilities, the last—the ability to evade vaccine-induced immunity—would likely be the most concerning because once a large proportion of the population is vaccinated, there will be immune pressure that could favor and accelerate
emergence of such variants by selecting for “escape mutants.” There is no evidence that this is occurring, and most experts believe escape mutants are unlikely to emerge because of the nature of the virus.
Is this new variant related to the newly emergent variant in South Africa?
On December 18, 2020, the South African government announced that it had also seen the emergence of a new strain in a scenario similar to that in the UK. The South African variant also has the N501Y mutation and several other mutations but emerged completely
independently of the UK strain and is not related to it.
What is CDC doing to track emerging variants of SARS-CoV-2?
In November 2020, CDC officially launched the National SARS-CoV-2 Strain Surveillance (NS3) program to increase the number and representativeness of viruses undergoing characterization. When fully implemented in January 2021, each state will send CDC
at least 10 samples biweekly for sequencing and further characterization. In addition, CDC’s COVID-19 response is actively seeking samples of interest, such as samples associated with animal infection and, in the future, samples from vaccine-breakthrough
infections. Data from these efforts are continuously analyzed at CDC, and genomic data are rapidly uploaded to public databases for use by researchers, public health agencies, and industry. To coordinate US sequencing efforts outside of CDC, since
early in the pandemic, CDC has led a national coalition of laboratories sequencing SARS-CoV-2 (SPHERES). The SPHERES coalition consists of more than 160 institutions, including academic centers, industry, non-governmental organizations, and public
health agencies. Of the approximately 275,000 full-genome sequences currently in public databases, 51,000 are from the United States. (The UK currently has the most sequences, with 125,000).
Information gathered from CDC website