Okay, it’s all over the news. The UK has pretty much become a Pariah where the rest of the World is concerned with many countries closing their borders to us because of a new variant of SARS CoV2 causing a lot of infections across London, the East and South East. As if that weren’t enough it’s led to the Government effectively banning Christmas… not that I mind too much as I’m working anyway… but I feel sorry for those who were looking forward to a celebration at the end of such a horrible year!
So, what is the new variant and what does it mean for us in the UK?
Essentially the new variant of SARS CoV2 has acquired a number of mutations (23 in total!) that make it possible for it to spread more efficiently than the original SARS CoV2 virus that was first identified in China a year ago (yes, it really has only been 1 year since this all began). But it’s not surprising to see mutations in RNA viruses, they are pretty rubbish at maintaining stability in their genomes, and we have already seen this happen this year.
So, what is the new variant and what does it mean for us in the UK?
Essentially the new variant of SARS CoV2 has acquired a number of mutations (23 in total!) that make it possible for it to spread more efficiently than the original SARS CoV2 virus that was first identified in China a year ago (yes, it really has only been 1 year since this all began). But it’s not surprising to see mutations in RNA viruses, they are pretty rubbish at maintaining stability in their genomes, and we have already seen this happen this year.
Mink-related mutations
Between June and November a number of European countries experienced outbreaks of Covid-19 with new variants of SARS CoV2 associated with mink farms (see the Microbiology Nuts & Bolts Bug Blog for more details). The Netherlands, Denmark and Sweden all had new variants of the virus which occurred after humans working with mink spread the virus to the mink, the virus mutated in the animals and then transferred back to humans.
In Denmark there were 214 human cases associated with the mink variant. You may remember the news story where the Denmark Government wanted to cull the 17 million mink in its farms to control the outbreak… we didn’t close our border to them though… just saying (although hospitals were meant to look out for possible mink-related cases… but none have yet been reported). Don’t forget viruses mutate and migrate this is normal; there is also evidence of a new variant that originated in Spain which was introduced into the UK multiple times due to travel from Spain in the summer, and also a new variant originating in Scotland which is now circulating in Europe! “Many thousands of mutations have already arisen in the SARS-CoV2 genome since the virus emerged in late 2019; …the vast majority of mutations have no apparent effect on the virus” (Covid Genomics UK Consortium)
In the Denmark mink farm outbreak there were two main variants of SARS CoV2. The first variant had a mutation that increased the affinity of SARS CoV2 for the host cell’s ACE2 receptor which allows the virus to “enter the cell”. As the ACE2 receptor in mink is slightly different to that of human’s, the virus mutated to a new variant that then allowed it to better access into the mink’s cells. It is thought that this mutation lead to increased ability for SARS CoV2 to spread in mink. When this mutated variant transferred back to human’s it was also found to be better able to bind to human ACE2 as well, which potentially made this variant more infectious in humans.
The other variant they found in the Denmark mink had 4 mutations. These particular mutations affected the spike protein which helps the virus “bind to host cells”. The new spike protein altered the body’s immune response which may not recognise the new variant as these spike proteins are the main target for both natural and vaccine induced antibodies against SARS CoV2. It was found that in 9 patients who had previously recovered from Covid-19 this variant appeared to make the virus 4 times less susceptible to naturally derived antibodies. There were 12 human cases of this antibody resistant variant identified in people with close contact with mink farming. Fortunately, their disease followed the same course as the original Covid-19 cases, no better no worse.
Returning to the UK
The problem in the UK now is that the new variant has acquired a lot of mutations ALL at the same time in the same variant (23 mutations in total). The details are still sketchy but from what I have been able to piece together this is what we have been told so far.
It is thought that this new variant may have arisen in someone with impaired immunity who had become chronically infected with SARS CoV2 and who therefore had the virus for a long enough time for multiple mutations to occur before passing it on to someone new.
Remember, viruses can only mutate whilst they are reproducing and they can only reproduce inside a host cell not in the environment. In addition, SARS CoV2 mutates very slowly for an RNA virus at about 20 or so mutations per year. So, for SARS CoV2 to mutate 23 times “in one go” it has to have been inside a host cell for a very long time and maybe even up to a year if the normal mutation rate is still correct.
The combination of mutations in the new variant is associated with laboratory evidence of:
There is increasing evidence that the new variant of SARS CoV2 in the UK does have increased ability to cause infection. A figure of “70% more transmissible” is quoted in the media… but who knows what that really means!? Is it that the infectious dose is 70% less, or does an infected person infect 70% more people or is the incubation period 70% shorter? Added to this, whether the new variant is able to escape the immune response in people who have had the infection before or who have been vaccinated is not yet known. However, reassuringly, most laboratory tests use multiple targets for detecting SARS CoV2, not just the spike protein, so most laboratory tests will still detect the new variant of SARS CoV2 including those used in the Lighthouse Laboratories.
At the moment there is a lot we just don’t know about the new variant of SARS CoV2 but there are lot of people looking at what these mutations mean and how they are going to affect the course of the pandemic, clinical disease and the effectiveness of post infection immunity and vaccination. Now I accept that a new mutation may sound alarming, and the media is promoting the story, and France has closed the border (is this a Brexit negotiation strategy?!?!?!) BUT let’s not panic just yet and wait and see where the science takes us… goodness knows we’ve all had enough of “Science by Press Release” this year after all!
The most important thing we all need to remember is that the simple things work. It doesn’t matter that the virus has become a bit easier to transmit; we can still stop it transmitting if we do the basics well:
Try and have a good Christmas, whatever restrictions you are under, and we’ll see what the New Year brings us….
Between June and November a number of European countries experienced outbreaks of Covid-19 with new variants of SARS CoV2 associated with mink farms (see the Microbiology Nuts & Bolts Bug Blog for more details). The Netherlands, Denmark and Sweden all had new variants of the virus which occurred after humans working with mink spread the virus to the mink, the virus mutated in the animals and then transferred back to humans.
In Denmark there were 214 human cases associated with the mink variant. You may remember the news story where the Denmark Government wanted to cull the 17 million mink in its farms to control the outbreak… we didn’t close our border to them though… just saying (although hospitals were meant to look out for possible mink-related cases… but none have yet been reported). Don’t forget viruses mutate and migrate this is normal; there is also evidence of a new variant that originated in Spain which was introduced into the UK multiple times due to travel from Spain in the summer, and also a new variant originating in Scotland which is now circulating in Europe! “Many thousands of mutations have already arisen in the SARS-CoV2 genome since the virus emerged in late 2019; …the vast majority of mutations have no apparent effect on the virus” (Covid Genomics UK Consortium)
In the Denmark mink farm outbreak there were two main variants of SARS CoV2. The first variant had a mutation that increased the affinity of SARS CoV2 for the host cell’s ACE2 receptor which allows the virus to “enter the cell”. As the ACE2 receptor in mink is slightly different to that of human’s, the virus mutated to a new variant that then allowed it to better access into the mink’s cells. It is thought that this mutation lead to increased ability for SARS CoV2 to spread in mink. When this mutated variant transferred back to human’s it was also found to be better able to bind to human ACE2 as well, which potentially made this variant more infectious in humans.
The other variant they found in the Denmark mink had 4 mutations. These particular mutations affected the spike protein which helps the virus “bind to host cells”. The new spike protein altered the body’s immune response which may not recognise the new variant as these spike proteins are the main target for both natural and vaccine induced antibodies against SARS CoV2. It was found that in 9 patients who had previously recovered from Covid-19 this variant appeared to make the virus 4 times less susceptible to naturally derived antibodies. There were 12 human cases of this antibody resistant variant identified in people with close contact with mink farming. Fortunately, their disease followed the same course as the original Covid-19 cases, no better no worse.
Returning to the UK
The problem in the UK now is that the new variant has acquired a lot of mutations ALL at the same time in the same variant (23 mutations in total). The details are still sketchy but from what I have been able to piece together this is what we have been told so far.
It is thought that this new variant may have arisen in someone with impaired immunity who had become chronically infected with SARS CoV2 and who therefore had the virus for a long enough time for multiple mutations to occur before passing it on to someone new.
Remember, viruses can only mutate whilst they are reproducing and they can only reproduce inside a host cell not in the environment. In addition, SARS CoV2 mutates very slowly for an RNA virus at about 20 or so mutations per year. So, for SARS CoV2 to mutate 23 times “in one go” it has to have been inside a host cell for a very long time and maybe even up to a year if the normal mutation rate is still correct.
The combination of mutations in the new variant is associated with laboratory evidence of:
- Increased affinity for the ACE2 receptor – making it better able to bind to ACE2 which may allow more virus to get into cells to cause an infection and/or may result in needing less virus to cause an infection in the first place as small numbers of virus become more efficient at setting up infections
- Immune evasion – making it less recognisable to pre-existing immune responses such as antibodies and reactive T cells
- False negative laboratory tests – the mutated spike protein is not detected in a few assays that only target the spike protein
- Escape from some monoclonal antibodies – some manufactured monoclonal antibodies that have been trialled in the treatment of Covid-19 do not recognise the new variant spike protein and so do not have any treatment benefit
- Faster growth – the virus appears to replicate faster in cells and therefore could have a shortened incubation period
There is increasing evidence that the new variant of SARS CoV2 in the UK does have increased ability to cause infection. A figure of “70% more transmissible” is quoted in the media… but who knows what that really means!? Is it that the infectious dose is 70% less, or does an infected person infect 70% more people or is the incubation period 70% shorter? Added to this, whether the new variant is able to escape the immune response in people who have had the infection before or who have been vaccinated is not yet known. However, reassuringly, most laboratory tests use multiple targets for detecting SARS CoV2, not just the spike protein, so most laboratory tests will still detect the new variant of SARS CoV2 including those used in the Lighthouse Laboratories.
At the moment there is a lot we just don’t know about the new variant of SARS CoV2 but there are lot of people looking at what these mutations mean and how they are going to affect the course of the pandemic, clinical disease and the effectiveness of post infection immunity and vaccination. Now I accept that a new mutation may sound alarming, and the media is promoting the story, and France has closed the border (is this a Brexit negotiation strategy?!?!?!) BUT let’s not panic just yet and wait and see where the science takes us… goodness knows we’ve all had enough of “Science by Press Release” this year after all!
The most important thing we all need to remember is that the simple things work. It doesn’t matter that the virus has become a bit easier to transmit; we can still stop it transmitting if we do the basics well:
- Strict attention to hand hygiene
- Isolation of patients with suspected or confirmed Covid-19
- Limiting contacts and crowds (no mixing outside of support bubbles)
- Physical (“social”) distancing (2 metres)
- Face masks in indoor spaces
Try and have a good Christmas, whatever restrictions you are under, and we’ll see what the New Year brings us….
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