COVID-19: What do we know about the viral mutations being reported in the UK, South Africa and Brazil?

Written by Dr David Owens

Updated on February 1st, 2020

All viruses have a tendency to evolve over time. Random change in genetic structure is the basis of evolution. COVID-19 is caused by an RNA virus. RNA viruses have a tendency to evolve rapidly. Some RNA viruses, such as influenza, change their surface proteins such that they escape historical immunity and require new vaccinations. Other RNA viruses, such as Measles, mutate regularly but do not change protein structure, so the vaccine does not require updating. The term used to describe this natural evolutionary change is Antigenic drift. The SARS-COV-2 virus has already undergone many thousands of such mutations, indeed almost every single infection in Hong Kong has its own 'genetic fingerprint'.

What is special about the UK, South Africa and Brazil mutations?

In the UK approximately 10% of positive cases of COVID-19 have genetic sequencing undertaken. This is an enormous scientific effort and results are shared internationally. Recently, researchers have identified a new variant (501Y.V1) which has been noted to have 23 mutations some of which are on the gene that codes for the spike protein. A different variant (501Y.V2) has also been recognised in South Africa and a third variant (501Y.V3) in Brazil. Whilst the exact position of the mutations are different they share a number of characteristics including change around the spike protein and a suggestion of increasing transmission rates. There has recently been a relatively steep increase in cases of COVID-19 in the UK, South Africa and Brazil. This has been associated with an increase in the number of infections being caused by the new, more infectious variants. The rapid expansion of 501Y.V1 from the South East of England throughout the rest of the country is dramatically demonstrated in the video below. The darker colours represent the percentage of cases caused by the new variant over time.




The new variants have now been identified in many other countries worldwide. It seems very likely that these variants will lead to accelerations of the epidemic in the regions in which they seed. As so often, more data and time will give us a better idea of what is happening. So far, epidemic modelling of the variant infections suggests an increase in the R0 values, an increase in the viral load and an effective increase in the rate of transmission for the UK and South Africa variants of around 50%. Early data from Brazil also suggest high transmission rates. It is possible that by chance, as any virus changes, it may acquire the ability to spread more easily. It is also possible that a viral mutation can lead to more serious disease, although statistically it is more likely that antigenic drift leads to attenuation. That is to say that the natural order of evolution more typically makes new viruses less severe over time. There have been some reports that the UK variant may be associated with an increase in disease severity but the data set was small and more data is needed.

We have previously explained the important distinction between the severity of a disease and the severity of an epidemic. COVID-19 has the potential to overwhelm health systems because of the rapid increase in numbers. The graph below demonstrates this issue. It compares a disease which is 50% more severe, continuing with slightly higher fatality rates, versus a disease which is 50% more infectious, producing a significant increase in mortality due to the rapid increase in the number of infected cases.

This is the reason that public health doctors continue to advocate for nonpharmacological interventions such as test, trace, isolate, mask wearing and social distancing. When dealing with the inevitable frustrations of social distancing measures, it is easy to lose sight of how well the epidemic has been managed in our densely populated city. COVID-19 is a mild disease in the majority of circumstances, but it has the potential to overwhelm health systems because of a potentially rapid increase in the numbers of infected patients. Avoiding excessive strain on the hospital system is one of the main goals of the public health controls. In a recent Podcast we interviewed a frontline emergency doctor about his experiences of the pandemic in London.

Whether SARS-COV-2 will act more like an influenza virus, requiring an update in vaccine structure over time, or whether it will be more stable like measles, is one area of ongoing research. It is too early to be certain what will happen. The fact that some recent mutations are occurring around the area which codes for the spike protein (the area of RNA code used to build vaccines) suggests a possibility that COVID-19 may behave more like Influenza. There is already some early data to suggest that the South Africa variant may be less susceptible to current COVID-19 vaccines. One potential advantage of the new mRNA vaccines is that it is possible to change the structure of mRNA vaccines relatively quickly once the infrastructure is in place.

In summary, we already knew that some mutations of the SARS-COV-2 virus appeared to make it more infectious. As we have previously explained, COVID-19 is not a serious disease in the majority of circumstances but rather it is the nature of the epidemic and particularly the tendency to overwhelm health systems which causes harm. Fortunately, we have very good evidence that public health measures in Hong Kong, in particular test, trace, isolate in association with social distancing and masks are highly effective and there is no reason to believe that they will not continue to be so.

We will update this information as further evidence accumulates.


1. NERVTAG meeting minutes on SARS-CoV-2 variant under investigation: 18 December. Retrieved December 23, 2020, from

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