Biomedical student and guest writer Luke Wilski interviews evolutionary virologist from Oxford University Emilia Skirmuntt on the connection between bats and the different variants of Covid-19 and the power of vaccines.

Since Covid-19 was declared a pandemic in March 2020 the general public has been receiving daily updates about cases, hospitalisations, deaths, jabs, emerging variants, government decisions, etc. But many questions regarding the origins of the virus, its evolution and how to prevent future pandemics have been left largely unanswered. In light of this, Emilia Skirmuntt, an evolutionary virologist from Oxford University, reveals the latest advances in our knowledge of the virus.

So far, bats have been singled out as the most probable culprit behind the appearance of this coronavirus among humans. The reason behind this assumption lies in the virus’s DNA. Ms Skirmuntt says:

“Mostly it’s genetics, so what the genome looks like. It was 80% similar to a bat coronavirus. This also points to it not being the direct ancestor of SARS-CoV-2.

“It could be that these viruses jumped from bats to another animal and then to humans. This is what happened before with the Middle-East Respiratory Syndrome (MERS) and the Severe Acute Respiratory Syndrome-1 (SARS-1). But it’s hard to say – bats are wild animals and it’s difficult to test them. I’m afraid we may never find this virus’s ancestor or its reservoir. Even now we don’t know where Ebola virus came from and that happened quite a long time ago.”

Bats have been observed to harbour a wide diversity of viruses. Scientists are still bewildered by the fact these animals can carry so many viruses with minimal symptoms. Emilia Skirmuntt says that there may be multiple reasons for this:

“Bats are one of the oldest orders of mammals. Because of this, these viruses could co-evolve with bats for a very long time. It’s not the best strategy for a virus to kill their host, at least not immediately. After a long period of co-evolution, the virus’ pathogenicity could have decreased. Secondly, bats are the only mammals that can fly. The energetic demand of flying generates a lot of chemicals that can damage the DNA. This process is very similar to that of inflammation after infection. Because of this, bats have needed to evolve some ways of preventing their DNA from being damaged all the time. There are some genes that are normally important in inflammation in other mammals, that are no longer found in bats. So, it seems that inflammation is suppressed in bats.

“Furthermore, relics of viruses in the host’s DNA from previous infections, called endogenous viruses, show a higher than expected diversity in the bat’s genome, so another hypothesis is that these might be used by bats to increase their tolerance to viral infections.”

In December 2020, the emergence of the new, potentially more infectious variant of coronavirus was announced, which precipitated the introduction of higher restrictions around the country to combat its spread. Scientists are still assessing the threat of this new variant. Ms Skirmuntt explains that:

“There are 23 changes in the genome of the new coronavirus variant. Nine of these changes are in the gene encoding the spike protein, which is the protein that interacts with the host cell. It is also the protein that vaccines target and which antibodies recognise during infection. The number of these mutations is quite worrying because they might change some characteristics of the virus. Some of these mutations on the spike protein have been shown to change receptor-binding and so they are expected to alter transmissibility. If the virus infects more cells because it can bind to the receptor more easily, it would mean that your organism could produce more viral particles and the virus could be spread more easily. The new variant is now thought to be around 50% more transmissible, but this information is mainly based on mathematical modelling and we are still waiting for some lab work.”

When asked about the possible explanations of the new mutations, Ms Skirmuntt says that: 

“One suggestion is that it evolved in immunocompromised patients. If such patients are infected the virus can stay undetected in the body for longer and accumulate mutations.

“Phylogenetic trees point to the South of the UK as the place of origin. London was in tier 2 at the time, which is not a high restriction level. It is a very densely populated city and schools were open while infections were rising. With each new infection mutations are more probable. So, the emergence of the new variant could have been caused by an accumulation of the virus in schools in September.”

On the other hand, the virologist also suggests that the new variant’s higher transmissibility could point to it being less lethal. Ms Skirmuntt notices that:

“There are more hospitalisations because there is an infection peak and more people from risk groups are being infected. However, the viral load in samples from patients infected with the new variant seem to be higher even though they presented mild symptoms, and some have suggested that this might mean it’s evolving toward lower pathogenicity.”

There have also been fears that Covid-19 could mutate in such a way as to escape the protective effects of the vaccines, now being administered to millions of people around the UK. Ms Skirmuntt, however, provides a reassuring message in this matter and thinks that there is still a long way to go for this virus to achieve this feat: 

“So far, only 9 amino acids have been altered from the 1273 amino acids that comprise the spike protein and the full antigen which is presented by the vaccine. Our antibodies target many sites on the protein.

“I think the changes would have to be much more extensive to allow for vaccine escape. The structure of the protein and how it folds is exactly the same. The biggest challenge for the antibodies generated thanks to the vaccine would be binding to a protein which has its structure changed. If such mutations would occur then we could start to worry, but at the moment the structure is exactly the same and the antibodies can still bind to it.”

A multitude of vaccines have been developed around the world with unprecedented speed in response to the pandemic, perhaps leaving many wondering how it is that the vaccine against Covid-19 was so much ‘easier’ to make than vaccines for other widespread viruses, such as HIV or Epstein-Barr virus. Ms Skirmuntt provides a sound explanation:

“Coronaviruses do not evolve slowly, but they do evolve much slower than, for example, HIV. This is one reason why it has been possible to develop a vaccine. Furthermore, although this is a new pathogen, it belongs to a family of pathogens that we were already trying to develop vaccines against for a while. Vaccines for SARS-1 and MERS were already in clinical trials. Based on that we could simply take the technology which was already shown to work and try to utilise it to make a SARS-CoV-2 vaccine.”

According Ms Skirmuntt, the recent sending of the WHO team to Wuhan to investigate the origin of Covid-19 has most probably more of a diplomatic nature than any other. Ms Skirmuntt remarks that “people have been trying to sequence the genome, find the samples, find the source, etc. since the beginning of this pandemic. I don’t know what they want to do there after such a long time, after more than a year”.

When asked about whether she feels optimistic that the voice of virologists such as herself will be taken more seriously after this pandemic, her answer revealed a feeling of tentativeness and déjà vu:

“I hope so, but I don’t want to be overly optimistic because we have had previous pandemics like the swine flu outbreak and it was very bad. In the beginning people were listening to all recommendations but after a year or so everyone, the public as well as governments, just seemed to forget all about it. So, there were high hopes and big words, but soon after everybody decided that something else was more important than the proper surveillance of pathogens.”

The big question is whether we can stop the next pandemic. Ms Skirmuntt believes so. She says:

“We know that they will happen. Pandemics happen regularly. It has been sped up by development in some countries like China. They are very densely populated and they are destroying natural environments which means people come into contact with pathogens that we have never seen before. Because of this we need global surveillance and cooperation. Countries can’t just sit alone, hoping nothing will happen to them. Hopefully, during this pandemic people have recognised that such a situation can affect everyone and everything. Only by working together can we prevent such situations happening in the future. We also need to offer help to developing countries which cannot do these things on their own.”

Luke Wilski

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