Since the emergence of the new coronavirus, called SARS-CoV-2, several researchers have proposed that there is more than one strain, and that mutations have led to changes in how infectious and deadly it is.
Mutations in the coronavirus are common; over 4,000 mutations have been detected in the spike protein alone.
Researchers analyzed 103 sequenced genomes using strains from China, and found that 70% of strains were one type, which they called "L." The "L" strain was more aggressive than the remaining 30% of strains, which were dubbed "S." The first strain was more common at the beginning of the outbreak, in Wuhan, China, but its frequency decreased after early January. That drop-off could be a result of the strict measures China put in place to try and stem the spread of the virus.
Scientists note that viruses mutate regularly, including COVID-19, as they spread. The L strain is virtually gone.
VUI – 202012/01 Variant
VUI – 202012/01 is a variant of SARS-CoV-2, reported in the United Kingdom in December 2020. This variant is correlated with a rise in COVID-19 cases in England, leading some to hypothesize a mutation in the viral genome region encoding the spike protein may be facilitating human transmission.
The variant was quickly named VUI-202012/01, the first "Variant Under Investigation" in December 2020, and is defined by a set of 17 mutations the most significant being an N501Y mutation in the spike protein that the virus uses to bind to the human ACE2 receptor. Changes in this part of spike protein may, in theory, result in the virus becoming more infectious and hence fast spreading.
As of December 13, 2020, 1,108 cases with this variant had been identified in the UK in nearly 60 different local authorities. These cases were predominantly in the southeast of England. The strain has also been identified in Wales and Scotland.
On December 20, 2020, the World Health Organization (WHO) had said that the new strain had also been detected in the Netherlands, Denmark, and Australia.
Contagiousness and Virulence
VUI-202012/01 was discovered in September 2020. The new variant could be up to 70% more transmissible than previous strains. There is no evidence that the new variant caused higher mortality, or was affected differently by vaccines and treatments.
There is currently no evidence that this strain causes more severe illness, although it is being detected in a wide geography, especially where there are increased cases being detected.
As of late 2020, several COVID-19 vaccines were being deployed or under development. While the new variant has mutations to the spike protein targeted by the three leading vaccines, the immune system produces antibodies to several regions of the protein in response to the vaccine, so it is thought to be unlikely that a single mutation would make the vaccines less effective.
However, as more mutations occur, the vaccines may need to be altered. The SARS-CoV-2 virus does not mutate as quickly as the flu virus, and the new vaccines that have so far proved effective are types that can be adjusted if necessary.
Control
England, Wales, Scotland all imposed travel restrictions in reaction to the increased spread, at least partly attributed to VUI – 202012/01, of COVID-19, effective on December 20, 2020. The Netherlands, Belgium, France, and Italy had imposed travel bans on flights from the UK by December 20, 2020.
Genetic Mutations
Genetic mutations are a natural, everyday phenomenon. They can occur every time genetic material is copied. When a virus replicates inside the cell it has infected, the myriad of new copies will have small differences.
When mutations lead to changes in how a virus behaves, it can have significant consequences. These do not necessarily have to be detrimental to the host, but in the case of vaccines or drugs that target specified viral proteins, mutations may weaken these interactions.
The initial genome of COVID-19, consisting of 30,000 letters, was revealed in January 2020. Since, then mutations - consisting of a letter change in the genome - have been reported all over the world. More than 13,000 of these changes are now found in the 100,000 Sars-CoV-2 sequenced to date. But any two viruses from any two patients anywhere in the world differ on average by only 10 letters, meaning Sars-CoV-2 is part of a single clonal lineage.
The term mutation tends to conjure up images of dangerous new viruses with enhanced abilities sweeping across the planet. Mutations are a perfectly natural part of any organism, including viruses. The vast majority have no impact on a virus’s ability to transmit or cause disease.
Why are Mutations Significant?
SARS-CoV-2 is an enveloped RNA virus, which means that its genetic material is encoded in single-stranded RNA. Inside a host cell, it makes its own replication machinery. In fact, the virus mutates roughly every week.
RNA viruses have exceptionally high mutation rates because their replication enzymes are prone to errors when making new virus copies.
If a particular genetic alteration changes the target of a drug or antibody that acts against the virus, those viral particles with the mutation will outgrow the ones that do not have it.
Mutations in the region of the SARS-CoV-2 genome that encodes the spike protein have made the virus more transmissible in some cases. This protein is crucial for infection, as it helps the virus bind to the host cell.
The idea of a mutating virus, breaking out into new strains, is enough to scare most people, but there's no need to fear.
Most mutations that change the properties of a protein, as in COVID-19, are more likely to weaken the virus than strengthen it.
Slowly Mutating
It will take some time for the virus to acquire substantial genetic persity. Sars-CoV-2 mutates fairly slowly for a virus, with any lineage acquiring a couple of changes every month; two to six-fold lower than the number of mutations acquired by influenza viruses over the same period.
Most commonly mutations will render a virus non-functional or have no effect whatsoever. Yet the potential for mutations to affect the transmissibility of Sars-CoV-2 in its new human hosts exists. As a result, there have been intense efforts to determine which, if any, of the mutations identifiable since the first Sars-CoV-2 genome was sequenced in Wuhan may significantly alter viral function.
D614G Variant
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein substitution D614G became dominant during the COVID-19 pandemic. The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity.
Recent analyses of the fine-scale sequence variation of SARS-CoV-2 isolates identified several genomic regions of increased genetic variation. One of these variations encodes an S-protein mutation, D614G. This mutation with glycine at the residue 614 (G614) was previously detected to increase with an alarming speed.
The G614 genotype was not detected in February and observed at low frequency in March, but increased rapidly by April and May, indicating a transmission advantage over viruses with D614.
Faster Spread?
D614G was first spotted in viruses collected in China and Germany in late January; most scientists suspect the mutation arose in China. It’s now almost always accompanied by three mutations in other parts of the SARS-CoV-2 genome — possible evidence that most D614G viruses share a common ancestor.
D614G had a rapid rise in Europe before March — when much of the continent went into lockdown — both unmutated ‘D’ viruses and mutated ‘G’ viruses were present, with D viruses prevalent in most of the western European countries that geneticists sampled at the time. In March, G viruses rose in frequency across the continent, and by April they were dominant.
Increased Infectivity
A study from earlier this year showed that viruses carrying G614 mutation are more infectious in cell cultures growing in the laboratory. People with this variant had more virus particles in their upper respiratory tracts than people with other variants. Despite this extra viral load, their illness appeared to be no more severe. An analysis of more than 25,000 viral sequences in the U.K. suggests that viruses with this mutation transmitted slightly faster and caused larger clusters of infections.
The latest study sequenced the genomes of 5,085 strains of the virus from the two COVID-19 waves in Houston.
At the time of diagnosis, people with the G614 variant had significantly more virus particles in their noses and throats, possibly as a result of its increased infectivity.
The Variant 20A.EU1
The Variant 20A.EU1 is a coronavirus strain that emerged in Spain in June has spread across Europe and now makes up a large proportion of infections in several countries, researchers said, highlighting the role of travel in the pandemic and the need to track mutations.
The variant 20A.EU1, which has not been found to be inherently more dangerous, was first identified among farmworkers in the eastern Spanish regions of Aragon and Catalonia. Over the last two months, it has accounted for close to 90% of new infections in Spain. The strain has crossed borders and accounted for 40-70% of new infections in Switzerland, Ireland, and the UK in September, they found. “Its frequency in the UK has continued to increase even after quarantine-free travel was discontinued. The rapid rise of these variants in Europe highlights the importance of genomic surveillance.
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