Coronavirus: Rise of the mutants

Now the COVID-19 virus has circulated worldwide for more than a year, new variants are emerging. A race is on to assess and understand the risk they pose.

As one example of the impact of these variants, the US vaccine manufacturer Moderna announced this week that its COVID-19 vaccine is still  “expected to be protective”.

However, it will investigate using extra booster shots along with a booster shot tailored to a form of the virus seen in South Africa, after studies suggest vaccines were six to nine times less potent and antibodies from recovered patients were six to 200 times less effective at neutralizing that variant.

I talked to Prof Massimo Palmarini, Director of the MRC-University of Glasgow Centre for Virus Research (CVR), where a wide range of studies on COVID-19 are carried out, and includes a £2.5 million science hub  – Crush (Covid-19 Drug-Screening and Resistance Hub)-  to investigate promising drugs and work on mutant viruses.

One UK consortium, COG-UK, is monitoring the “genotype” – genetic code, or genome – of the virus, the leading effort of its kind worldwide. Another consortium, “Genotype-to-Phenotype UK” is complementing this effort by investigating how the differences in the viral genome can change the virus and its behaviour (“phenotype”). Glasgow is a member of both consortia.

Prof Palmarini’s edited responses are in italics.

CAN WE PREDICT HOW A VIRUS WILL BEHAVE FROM ITS GENETIC CODE?

Neither the genetic sequence of a virus by itself, what we call the genotype, nor even if we know the structure of its component proteins, will give you detailed insight into the relevance of a mutation or variant of the virus, notably key characteristics, such as its virulence or how easily it spreads, which is what we call the phenotype.

To put it in a scientific way, it is hard to predict phenotype from genotype beyond making educated guesses.

HOW DO WE KNOW A NEW VARIANT OF THE VIRUS WILL CAUSE A PROBLEM?

To use the Public Health England term Variant of Concern (note that the naming of new variants is somewhat confusing) you need to piece together epidemiological data on the emergence of the variant in question.  

For example, the B.1.1.7 variant, also referred in the press as the “Kent variant,” started to emerge very rapidly in the presence of many other variants that it outcompeted. This was a concern, as it suggested that B.1.1.7 possesses properties that favour its transmission above and beyond other co-circulating variants.

By comparison, what you saw at the start of the pandemic was the so-called founder effect, when – to put it in in terms of market competition– the market was dominated by the first product of its kind to reach the market, rather than the product best suited to that market.   

WE’RE WORRIED ABOUT MUTANTS YET WE WERE TOLD THIS VIRUS DOES NOT MUTATE MUCH.

In a way, both statements are right. All viruses mutate. The SARS-CoV-2 virus is quite large by the standards of similar viruses (the genetic code, written in the form of RNA, consists of 30,000 nucleotides or ‘letters’) and the errors are kept somewhat in check by error correction machinery so the rate of mutation of this virus is roughly half that of influenza and one quarter that of HIV.

Even so, it does mutate, and the relevance of these mutations has to be considered in the context of its environment. When the pandemic started a year ago, it was spreading in a population that had no natural resistance (that is, they had no immunity) and was completely susceptible to SARS-CoV-2 infection. 

Now we are beginning to see some population immunity (roughly 10% in some areas but this increases in others and vaccine roll-out will increase this further). Hence, if a variant has mutations that allows it to flourish despite pre-existing immunity, then that variant with time will overcome other variants that do not have these properties. 

Other coronaviruses of livestock, such as one that causes infectious bronchitis of chickens, do require vaccines to be tweaked over time as the virus changes. It is likely that when it comes to COVID-19 our vaccines will have to be tweaked as the years go by to protect against new variants.

DON’T VIRUSES EVOLVE TO BE LESS HARMFUL?

In general terms, the goal of a virus is to be transmitted, simply to infect a host cell so that it can be transmitted to another cell and then to the cells of another individual. If a mutation makes the virus more lethal, and kills an individual very rapidly, then it will be harder for the virus to be transmitted efficiently to other individuals.

However, there are different angles to this concept. If the increase in virus virulence is associated with an increase in symptoms that facilitate virus transmission, then a more virulent variant could be also selected.

For example, if we are talking about a gastrointestinal virus that causes diarrhoea, a mutation that makes the diarrhoea worse means that more virus in the environment, and the more chance it has to spread and be transmitted.

When it comes to a respiratory virus like SARS-CoV-2, again mutations are favoured that help it to be transmitted.  For example, if a mutation allows higher replication rates in the upper respiratory tract, then it might mean that people shed more virus and transmission is facilitated.  However,  it also may mean that the persons infected with this new variant have worse symptoms. 

Or if there is a mutation that makes the virus more stable in the environment, that might aid the spread of a variant and would likely not affect the clinical outcome of infection.

Overall, transmission is the key driver of viral evolution.

HOW UNUSUAL IS IT THAT MANY INFECTED PEOPLE ARE FREE OF SYMPTOMS?

That is true for any virus, even viruses like Ebola. You have a range of clinical outcomes, from showing few symptoms to severe symptoms, and understanding the way different people react to the same virus is a critical question that fascinates biologists in many different ways. 

A variety of factors influence how you respond to infection, from comorbidities (such as diabetes, for example) to pre-exposure to similar viruses, age and genetic makeup.  

HOW MANY STRAINS ARE OF CONCERN?

A fast-spreading SARS-CoV-2 variant was identified in Kent in late 2020 has been called Variant Under Investigation 202012/01 known as VUI 202012 or (using another system of classification)  B.1.1.7, whereas another dubs it 20I/501Y.V1.

Another variant of concern has emerged in South Africa, called 501Y.V2 and B.1.351 which is less susceptible to the antibodies created by natural infection and by current vaccines.

Similarly, there is concern in Brazil after COVID-19 cases began to rise again in Manaus in December despite the fact that up to three-quarters of the city’s inhabitants had already been infected with SARS-CoV-2, enough for herd immunity to develop. The surge was caused by a new viral lineage they called P.1.  Again, this variant contains mutations in the spike protein and raises concern about the potential impact on viral infectivity and ability to evade the immune system.

Even though these variants evolved independently in the UK, South Africa and Brazil, all share the N501Y mutation in the virus’s spike protein, while the Brazilian and the South African variants both have the immune-evading E484K mutation.

Note that experts dislike terms such as ‘the Kent Strain’. A World Health Organisation spokesperson commented: ‘We would like this nomenclature to be easily understood and not include country names, because we want to remove any of the geopolitical issues.’

We are still trying to get a full understanding of what the meaning is of some of these variants. The point is that some of these mutations will be really important and others won’t but when you see they are accompanied by a surge of cases, you really need to do experiments in the laboratory to fully understand the properties of that variant. 

If we were to see a new outbreak occurring in a care home where everyone had been vaccinated, then that would be solid evidence to be concerned about the emerging variant. Overall, though, you need lots of layers of evidence, from the epidemiology to experiments in the lab to have a complete picture of what is going on.

We have the Kent, South African and Brazil-Japan variants as well and they share some mutations in common, which rings alarm bells.

When it comes to the South African variant, some of the mutations it carries, including one named E484K, change its surface protein, (the ‘spike’)  and these changes may result in a decreased susceptibility to the antibodies produced during an immune response against a virus that does not possess these mutations. 

HOW DO YOU SCREEN VARIANTS TO SEE IF THEY COULD CAUSE PROBLEMS?

This is what we do collectively with our ‘genotype to phenotype consortium’, which is formally known as the ‘G2P-UK’ National Virology Consortium.

We isolate a variant of the virus of interest and see if it replicates better than other variants in different cell culture systems. We also look at whether it does escape neutralizing antibodies from vaccinated or infected individuals. We can also see how it replicates or it is transmitted in animal models like hamsters. All of these studies require a special Biosafety level 3 laboratory.

What complicates things is that new variants have several mutations and while we can try to guess which ones are more important for the behaviour of the virus, we still need to do experiments to understand exactly which mutations or group of mutations provide a particular phenotype to a particular variant. So, in these cases, we synthesize a whole virus in the lab, and then study each individual mutation.

You can design the genetic sequence of the virus and study just one mutation (they have arcane names such as N501Y or D614G) in the context of the virus having the same genetic sequence for everything else. That way you can find out what is important and, as time passes and more mutants have been identified, we are better equipped to understand what is going on.

It is important to stress that we conduct these studies only with mutations that have arisen naturally among the population. We study mutations that are already present globally, and not random mutations, where you make a change and see what happens, even if it does not exist in the field. To do that is an ethical minefield that we stay well clear of as you may inadvertently select a virus that has functions that were not present in nature (in particular, there is concern that it may lead to a “gain of function”).

HOW DO YOU DEFINE A STRAIN OR VARIANT?

We have never had the opportunity to work with so many sequences of a single kind of virus generated in real-time  (the genetic sequences are analysed by the COG-UK consortium, which is the biggest effort of its kind in the world, depositing around half of the world’s known sequences.)

So, we have more than 200,000 sequences deposited by the COG-UK consortium and it is important to distinguish them, but at the same time, they are very similar. Given there are 30,000 letters of genetic code in SARS-CoV-2, they may actually change by only a handful, or maybe by 20 or so, mutations. 

This creates some problems when it comes to nomenclature. For example, when you see how all these variants are related to each other, they are actually far more related than if you were taking a bunch of closely related hepatitis C viruses or HIV.

Although the terms mutation, variant, and strain are often used interchangeably even by virologists, the distinctions are important. Mutations are the actual changes in the virus genome. We use the term variants when the viral genomes sequences are different from the others. These changes can be even for a few nucleotides.

Usually, the term “strain” refers instead to a given variant with well-defined and demonstrated phenotypic characteristics. For example, there may be a given strain of a virus that is more “virulent” (that is, causes more severe clinical symptoms in infected individuals than others).  

The variants of concern at the moment are: B.1.1.7 (also known as 501y.V1, or the Kent strain); B.1.351 (also known as 501Y.V2, or the South African strain) and P.1 (also known as 501Y.V3, or the Brazilian strain).

They have 23, 21 and 17 mutations, respectively. However, the mutations that are of most interest are those in the spike protein that the virus uses to invade human cells. There are 8, 9 and 10 mutations in the spike, respectively.

We already know that the ‘Kent variant’ transmits up to 40 per cent more easily and preliminary data suggest that it is more lethal too, such that if 1,000 60-year-olds were infected with the old variant, 10 of them might be expected to die.

But this rises to about 13 with the new variant.

HOW DO THESE MUTANTS OCCUR?

Viruses possess two kinds of genetic material, DNA and RNA, and SARS-CoV-2 relies on the latter. Mutations arise naturally when viruses reproduce.

Though RNA viruses typically have higher mutation rates than DNA viruses, coronaviruses make fewer mutations than their RNA peers because they encode an enzyme that corrects some of the errors. Most mutations do little, some make the virus sickly and less able to compete with the established variants but occasionally a mutation can emerge that gives the virus an advantage over other variants, whether how quickly it reproduces, how easily it transmits or how nimbly it evades the body’s immune system.

It is inevitable that new variants will arise. Viruses vary randomly all the time and they also respond to their environment or selection pressure. As we vaccinate more people, it could be that puts pressure on the viral population for strains to emerge that flourish in these circumstances.

When a lot of people have less well functioning immune systems, as in care homes, they do not clear the virus so efficiently, the infection may go on for longer and that may encourage new strains. And so on.

DO YOU BELIEVE COVID-19 WAS CREATED OR HONED BY HUMANS?

No. When it comes to building a virus that nobody knows anything about and synthesizing it from scratch, it would take decades and decades of secret research and even with that, I doubt that it would be possible. It is similar enough to bat viruses to be confident that is where the virus came from.

HOW DO THESE MUTATIONS CHANGE THE VIRUS’S BEHAVIOUR?

We are all focusing on the spike protein and receptor binding domain (the part of the spike that binds with receptors, proteins on human cells, like a key in a lock) because of the interest in whether mutations in the spike could allow the virus to escape from host antibodies and compromise vaccine effectiveness (the spike is used in the current crop of vaccines to train the body to recognise the virus).

Because current vaccines provoke an immune response to the entire spike protein and not just the part that changes because of a mutation, it is hoped that effective protection may still occur despite a few changes at the sites in SARS-CoV-2 variants linked with antibody production.

We’re all focused on the spike for good reasons, but there are other proteins in the virus that might mutate to change its behaviour. The virus relies on an enzyme called polymerase to replicate so of mutations allow it to replicate that little bit faster that might make it able to escape the immune system that bit more easily and give it more chance to be transmitted.  

IS THERE EVIDENCE OF RESISTANCE TO TREATMENTS OR VACCINES?

Currently, there are not very effective drugs to target the virus itself and therefore no evidence of drug-resistant variants of the virus. 

In terms of vaccines, the key worry reported with the South African variant (we have not seen the data yet) is that roughly half of the convalescent sera – the antibody responses – from individuals that were infected by other variants of this virus were unable to neutralize this South African variant.

We have another paper being published looking at another variant that emerged some time ago carrying the N439K mutation which again is a mutation in the receptor binding domain of the spike. We have seen that this mutation confers on the resulting variant the ability to be less effectively neutralized by antibodies from people who had recovered from infection from different variants.

But there might be antibodies against parts of the virus other than the spike and immunity is more than just antibodies –   many kinds of white blood cell play a role in immunity too, which we also need to understand fully with respect to their action against different variants.

HOW CAN YOU TELL IF A VACCINE WON’T PROTECT AGAINST A GIVEN MUTATION?

First of all, you can take blood from vaccinated people (or better the serum fraction of the blood, which does not contain blood cells) and then measure its ability to neutralize the virus variant in the laboratory.

You can also do T cell assays (T cells are one kind of white blood cell) and see how the cellular immunity function against different variants.

In addition, we can also use animal models too, such as hamsters which are a reasonable model. You can immunize an animal with ‘variant x’ and then see how they are susceptible to ‘variant y’, how transmissible the variant is and so on.  The hamsters don’t get the more lethal disease but are a reasonable model.

I would normally say that we need to study the virus in its natural host – in this case, humans – but SARS-CoV-2 seems quite plastic and flexible in terms of which species they can infect.

As one example of how easily this virus can jump species, another variant of COVID-19 emerged on mink farms in the Netherlands and Denmark in late spring and early summer last year and by November, Danish authorities reported that more than two hundred cases of human coronavirus disease that were linked with mink farms.

Many SARS-CoV-2 sequences from the Netherlands and Danish outbreaks had a Y453F mutation in a key part of the spike that binds to human cells, again in the receptor binding domain.

The way the virus adapted to mink worried scientists because the continued evolution of the virus in an animal reservoir could potentially lead to spill-over events of novel SARS-CoV-2 from mink to humans and other mammals. For this reason, many countries carried out large-scale culls of mink on farms.

WILL THE WORLD EVER GET RID OF COVID-19?

We’re not going to eradicate the virus. Nobody can say anything is an absolute certainty in science, but I would be extremely surprised if we ever rid ourselves completely of SARS-CoV-2 and COVID-19.

However, when I say that we will not get rid of the disease we are not going to continue to live with social distancing, travel restrictions and lockdowns.

As the vaccination will be successfully rolled out, I imagine that COVID will become a disease to be managed like influenza, where there is a vaccine and the population as a whole will be protected but, unfortunately, there will still be a number of susceptible individuals who may die.

It is not going to stay like this for many years…that would be depressing for everybody, even a virologist!

HOW DO YOU SCREEN FOR COVID-19 DRUGS?

One of the bottlenecks for these studies is that you need to carry them out (or at least most of them) in special laboratories (“biosafety level three facilities”).

To find an antiviral drug, we can screen for different things, using just part of the virus or measuring the enzymatic activity of the virus to do the initial screens of potential drugs.

Once you have found ones that seem to work, then you need to test the drug on an assay in cells that are infected with live virus, moving on to types of cell that are known to be vulnerable to the disease, such as airway epithelial cell types. Then you can test the efficacy of the drugs in animal models.  

You also want to see how easily drug resistant variants can arise in cells. We have set up a facility to do just that, not to develop drugs ourselves but to work with academia and industry to facilitate an antiviral drug discovery programme.    

WHY IS IT EASIER TO DEVELOP VACCINES THAN DRUGS?

Vaccines rely on existing platforms – using viruses, such as adenovirus, to present spike proteins or RNA and so on – that have already been tested to some extent and are well understood in general terms. All the safety and efficacy data are within a well-known context.

For drug development also the initial approach is to “re-purpose” existing drugs that may work with other viruses but not much came out of that.

So now the next step is to look at libraries of new chemical compounds or to rationally develop inhibitors of specific stages of the viral replication cycle. Finding new drugs and pushing them through clinical trials is a very expensive process that can take several years to put in the market.

What in many ways what is depressing is that we use Remdesivir as a passive control in our tests since it blocks the virus really well in tissue culture, but in the clinic, there is only a narrow window of opportunity to use it, at the very beginning, if it is to work. Some of the larger trials of this drug have failed.

WHAT HAS STRUCK YOU ABOUT COVID-19?

SARS-CoV-2 has really pushed scientists to work together. We could look at the variants from the beginning to end just in our centre but to do it at scale and speed, different centres have to work together to maximise returns as the field is moving so fast and there is so much to do. I think scientists in the UK have really come together well. 

When we were writing the proposal for our G2P-UK consortium we were worried about variants.  Then a week or so before we were interviewed about the funding, there was news of the mink variant, soon after the UK Health Secretary talked about the Variant of Concern in England, then came the South African and Brazilian variants, and we are only going to officially start our work in February.

When we started to write our proposal there were just above 1 million deaths worldwide and now we have moved up to two million. That’s when the enormity of the challenge hits you. It is mind-blowing.

How can I find out more?

The latest picture of how far the pandemic has spread can be seen on the Johns Hopkins Coronavirus Resource Center or Robert Koch-Institute website.

You can check the number of UK COVID-19 lab-confirmed cases and deaths along with figures from the Office of National Statistics.

There is much more information in our Coronavirus blog series (including some in German by focusTerra, ETH Zürich, with additional information on Switzerland), from the UKRI, the EU, US Centers for Disease Control, WHO, on this COVID-19 portal and Our World in Data.

The Science Museum Group is also collecting objects and ephemera to document this health emergency for future generations.