How dangerous are the new COVID variants?
Dr Khan explains what we know about variants from Brazil, South Africa and the UK, plus a possible new one in Nigeria; and tells us how he has taken up the fight against misinformation about the COVID vaccine on the internet.
Vaccination programmes around the world have been shown to be reducing COVID-19 transmission rates and hospital admissions. But news of COVID variants emerging – and spreading fast – is still a concern.
Viruses mutate; this is to be expected. And, as the coronavirus spreads and infects more people, it will be given more opportunity to do so, particularly in countries that have been slow to lock down, enforce social distancing or close borders.
Mutations are random changes in the DNA of the virus that can alter its shape and the way it behaves. When a virus infects a human cell, its main job is to replicate and then spread. The virus instructs the infected cell to start making more copies of itself that then go on to infect other cells and are eventually coughed, sneezed or breathed out, enabling them to infect other people.
Replication of the virus occurs at a relatively quick rate, however, which means errors can occur. Most of these errors are either harmful to the virus or have no effect, but as time goes on, the chances of an “advantageous error” – one that might make the original virus more powerful or infectious – occurring increases.
Here are the new variants the experts are keeping an eye on.
Something terrible is happening in Brazil. The country, which suffered horrific losses during a painful first wave of COVID-19, now finds itself entangled in an even worse second wave.
After the US, Brazil (population 213 million) has one of the worst COVID-19 death tolls in the world, with more than 11 million people testing positive and more than 270,000 dead. Brazil’s leader, President Jair Bolsanaro, appears to have his head buried firmly in the sand and, in the past, has dismissed COVID-19 as a “little flu”. He has also repeatedly appeared in public without a face mask.
Recently he went to the midwestern state of Goiás, where nearly 9,000 people have died, and told people to “stop whining” about the coronavirus outbreak, a move that was widely condemned by other countries. Furthermore, the roll-out of vaccines in the country has been beset by supply problems and bottlenecks in the delivery process, as well as by false rumours such as one claiming the vaccine will turn people into animals.
To make matters worse, a new variant – known as the P1 variant – has now emerged. It was first identified in the Amazonian city of Manaus in December and is thought to be more infectious than the original virus, enabling it to become the dominant strain. There is not any evidence that this variant will make you more unwell, but as the virus is likely to infect more people this, inevitably, will result in more deaths. More than 2,000 deaths a day are already being recorded in Brazil, largely as a result of this new strain.
It is spreading fast. Since December, the World Health Organization (WHO) has identified it in other countries, including Canada, the United States, the United Kingdom, France, Germany, Spain, Japan, Mexico, India, Italy and the Republic of Korea.
The new variant has overwhelmed hospitals in Brazil. Within weeks of identifying the new variant, Manaus saw cases begin to surge exponentially, including in people who had previously been infected by the original virus. Such were the numbers of people becoming sick that the city ran out of oxygen, leaving doctors with agonising decisions to make over who to give what oxygen they had left to and patients dying of asphyxiation.
The P1 variant has been caused by a number of mutations, but three, in particular, are of concern to scientists.
The first is the E484K mutation, which has also been identified in the South African variant. It is being called an “escape” mutation as it changes parts of the spike protein of the virus that our immune systems rely on to recognise and initiate our immune response. These changes may mean it can evade an immune response triggered by the vaccine or previous infection. More research is needed to fully understand this.
The spike protein lies on the outer surface of the virus. When the virus enters a human host, it has to get inside cells to infect them. It does this by connecting its spike protein to receptors on the outer surface of human cells, called ACE2 receptors.
The E484k mutation has changed the spike protein of the original virus so that it binds more readily and forms a stronger connection to the host cells, making it more infectious. The same mutation also means the virus can evade the neutralising antibodies that a previous coronavirus infection has created more effectively. This may explain some of the reinfections in Manaus.
The second is the N501Y mutation, which is also present in the UK variant. This mutation also affects the spike protein of the coronavirus, but specifically its “receptor-binding domain”. This is the part of the spike protein which makes contact with human cells, clasps onto them and then allows the virus to enter. Not only does this mutation make the virus bind more tightly to the human cells, but it also makes it more likely to stay bound to them, thus increasing the likelihood of infection. This mutation has allowed the UK variant to become the dominant strain in the UK and is most likely what helped the Brazil variant become dominant in Manaus.
According to information from the UK Government, this mutation can make the virus up to 50 percent more infectious than the original virus.
The third is the K417T mutation, which is not as well understood as the other two. It also occurs in the receptor-binding domain of the spike protein and may make it easier for the virus to bind to human cells, increasing its infectivity. More research is needed on this mutation, but there is a school of thought that suggests this, combined with the N501Y mutation, will increase the binding capacity of the virus to human cells significantly, making the Brazil variant especially dangerous.
Scientists are working hard to find out if the current approved vaccines will be effective against this last mutation. So far, it has been shown that all the vaccines offer some level of protection against serious disease but this protection is lower when compared to variants without this mutation.
Thankfully, the vaccine manufacturers say that if this variant becomes the dominant strain of the virus generally, then their vaccines can be adjusted quickly to accommodate this. The time it takes for these adjustments to be made will vary from vaccine to vaccine. The Pfizer and Moderna ones, which use messenger RNA technology, can be done more quickly – within six weeks according to Pfizer-BioNTech. The Oxford-AstraZeneca vaccine, which uses DNA technology, will take longer and the manufacturer has said it hopes to have a vaccine adjusted for the South African variant in the second half of the year.
Ramping up the roll-out of vaccinations in Brazil is now key to solving this crisis because, although the vaccines are not completely effective against this variant, anything that can reduce severe illness from COVID-19 and reduce the burden on overwhelmed hospitals will help.
Other countries, where the variant has been identified, are scrambling to contain it by identifying and isolating those infected and their close contacts. It remains to be seen if these measures will be enough.
As much as the UK has been applauded for its quick vaccine roll-out, it has also been criticised for its failure to implement lockdown and social distancing measures quickly enough last year. Compounded by problems with its Test and Trace system, this has led to the UK (population nearly 67 million) seeing one of the worst death rates in the world – the current death toll stands at more than 125,000 and, at its peak in January when the vaccine programme had only just got under way, the daily death toll was 1,300.
The new UK variant (also called the B.1.1.7 variant) was first identified in September last year when it accounted for just one in four new diagnoses of COVID-19. By mid-December, however, this had increased to almost two-thirds of new cases in London, and the southeast of England was struggling with a surge in new cases. Since its discovery, the UK variant has also been detected in the US, Canada, Denmark, France, Belgium, Spain, Finland, Nigeria, Ghana, Jordan, Australia and Singapore.
A total of 17 mutations were identified in this variant, with the N501Y mutation (also present in the Brazil variant, above) being the most significant. This mutation allows the virus to form tighter bonds with human cells allowing the virus to enter cells more easily.
As more people became infected with this new variant across the southeast of England, it quickly became the dominant version of the virus.
The good news is that the immune response triggered by the vaccines does appear to be effective against this variant. A study by Pfizer demonstrated good immune responses in people who had been given the Pfizer vaccine and then exposed to the N501Y mutation. It is still researching the precise level of protection it provides against this mutation, however. A study by Oxford University showed the Oxford-AstraZeneca vaccine to be at least 75 percent effective against this variant.
South Africa variant
The South Africa variant is more concerning to scientists. It not only has the N501Y mutation (the same one as is in the UK and Brazil variants, above) which makes it more likely to bind to human cells and hence more infectious, it also contains the E484K mutation (as found in the Brazil variant) which means it may be able to evade some of the antibody response triggered by the vaccines or a previous infection.
The vaccines have been found to be less effective against this variant, but can be adjusted to tackle it if needed. As well as in South Africa, this variant has been identified in a number of countries across the world including Austria, Belgium, Kenya, the United Arab Emirates and Japan.
As time goes by, we are likely to see more variants appear. Because of this, it is widely believed that, in the longer term, we will require annual booster shots that are designed to trigger an immune response to the most common circulating variants in that particular area, much like the annual flu vaccine which is adjusted to the variants that are predicted to cause flu epidemics each year.
Progress Report: A new variant from Nigeria as well?
As we talk about new variants emerging, scientists in the UK have identified yet another new variant with potentially worrying mutations. Thought to have originated in Nigeria, the B1525 variant has now been found in Denmark, Australia and the US. This variant also possesses the E484K mutation which may mean it can elude our immune response. Scientists are studying this new variant urgently to see what the likelihood is of it spreading and becoming a dominant strain.
In the Doctor’s Surgery: Tackling misinformation on the internet
The coronavirus pandemic has been difficult for everyone. As well as the physical health implications, it has taken a toll on many people’s mental health. This has clearly spilled over onto social media, where those people who are vehemently opposed to lockdowns and social distancing measures clash with those who understand that these restrictions are necessary to prevent further deaths.
As a doctor who has a social media presence, I feel it is my duty to challenge any misinformation I see about the pandemic and the virus itself.
Having the correct information is key if people are going to be able to keep themselves safe. When the vaccination programme began in the UK in late December, I took to social media to actively encourage those who were being offered the vaccine because of their age, or because they were front line workers, to take it. Misinformation about the vaccines was rife, so tackling this was an important part of my job.
Now, I am used to receiving derogatory comments on social media; I am not so naïve that I have not come to expect it. But the sheer volume of personal abuse and threatening messages I have received for promoting the vaccines has taken me by surprise.
These abusive missives have varied from overt racism to accusations that I am part of a global organisation that stands to profit from vaccine uptake. To be clear, I do not profit from people taking up the vaccine, my only goal is to protect the patients I care for and I know that the vaccine will do that.
Vaccine hesitancy is understandable – it’s not particularly pleasant to be jabbed with a needle – and asking questions about your concerns is welcomed. But it is vital that the answers to those questions come from reputable sources.
Sadly, “anti-vaxxers” who are suspicious of vaccines for a wide array of reasons, have been able to get their voices heard on social media like never before.
They are able to peddle outright lies and misinformation that could put vulnerable people off having the vaccine and potentially put them at risk of contracting the coronavirus and dying as a result. It is fine if you do not want the vaccine – that is your choice. But it is not right to frighten other people with misinformation.
To all those who send me such messages, I want to say: I will not stop, I will keep on promoting the vaccines, I will keep on challenging misinformation. I have seen too much death in the past year and comforted too many bereaved families to let some ill-informed keyboard warriors stop me.
And Now, Some Good News: COVAX rolls out vaccines in Ghana
COVAX, the organisation set up by the World Health Organization to ensure equitable access to vaccines across the world, has begun distributing vaccines. At the end of February, an aircraft carrying 600,000 doses of the Oxford-AstraZeneca vaccine, sent by the Serum Institute of India in Pune, landed in Accra where jabs are now being administered to front-line health workers, who COVAX is prioritising in all countries in the first instance. This is just the first batch to be shipped and delivered within Africa by the COVAX Facility as part of an unprecedented effort to deliver at least two billion doses of COVID-19 vaccines to poorer countries all over the world by the end of 2021.
“We will not end the pandemic anywhere unless we end it everywhere,” said Dr Tedros Adhanom Ghebreyesus, WHO Director-General, in a statement in late February. “Today is a major first step towards realising our shared vision of vaccine equity, but it’s just the beginning. We still have a lot of work to do with governments and manufacturers to ensure that vaccination of health workers and older people is underway in all countries within the first 100 days of this year.”
This is a bold but necessary vision from an organisation that understands the pandemic will continue to be a problem even for the richest of countries with wide-scale vaccination programmes, if it is not brought under control in the poorest ones as well.
Reader’s Question: Is the vaccine really safe for all ethnic groups?
This is a question I get asked a lot. The first thing to say is there is no evidence that the vaccines will work differently for different ethnic groups. The efficacy rates you see published for each vaccine apply to all ethnicities. The trials for each vaccine included people from different ethnic backgrounds: 9.6 percent of the Pfizer study participants across several different countries were from Black African backgrounds and 3.4 percent were from Asian backgrounds. For the Oxford-AstraZeneca vaccine, 10.1 percent of trial participants, again from several different countries, were Black and 3.5 percent were from Asian ethnic groups. The overall effectiveness was found to be the same across all ethnic groups and there is no reason to believe this will change as the vaccines are rolled out across the world.