Insights into the new B.1.1.7 coronavirus lineage

A new lineage of coronavirus was first identified in the UK, but why is it spreading much more rapidly within the population?

The UK finds itself in a third lockdown in an attempt to slow the spread of a new, more transmissible strain of coronavirus. With the number of cases remaining high during the first weeks of January 2021, many scientists have expressed concern that lockdown restrictions must remain in place to contain the spread of the virus. 

Two studies, one conducted by researchers at EMBL’s European Bioinformatics Institute (EMBL- EBI) and the Wellcome Sanger Institute, the other by researchers at Imperial College London, have provided insight into how a new SARS-CoV-2 lineage (also called a variant) termed B.1.1.7 can transmit more readily between people. While it’s still debated whether those contracting the B.1.1.7 lineage display stronger COVID-19 symptoms, the accelerated spread of this lineage is a growing global concern. 

First identified in September 2020, the B.1.1.7 lineage has since spread rapidly across the UK, and cases have been identified in other countries. Moritz Gerstung, Research Group Leader at EMBL-EBI, and his team are trying to monitor the spread of the new strain and what can be done to stop it. Here, Moritz gives his opinion on why this lineage is more transmissible, and shares his thoughts on how to reduce its spread. 

What is different about the new B.1.1.7 coronavirus lineage?

The B.1.1.7 lineage has 23 new mutations in its genome. This is a lot of mutations to have appeared all at once; it is quite unusual. Viral proteins are altered by 17 of these mutations, giving rise to new biological characteristics. In this case, the mutations give rise to a new lineage which is more transmissible than the old one. This is probably because some of these mutations alter the structure of the spike protein used by the virus to adhere to our cells. 

When did the new B.1.1.7 coronavirus lineage first appear? 

Cases of the new B.1.1.7 lineage can be traced back to September 2020. When you first look at the effect of the second lockdown in the UK in late autumn 2020, it appears to have worked. Overall, the number of new infections in the UK noticeably fell. However, what we found was that, while cases of the original SARS-CoV-2 variants – which were dominant at the time – were falling, cases of the new lineage had spread unnoticed during this second lockdown.

How much more transmissible is the new lineage compared to the original strain? 

It’s been shown that the R value of the new lineage is around 1.5 times greater than that of the old one, meaning it is approximately 30–50 percent more transmissible. What we observed in the second UK lockdown was that the number of cases with the old lineage more than halved after a month, but the number with the new lineage roughly tripled at the same time, meaning that the new lineage can result in six and perhaps even eight times as many new cases as the old one in the same space of time. 

What data did you use in your study to research the new lineage?

We used a combination of daily local SARS-CoV-2 incidence data and weekly genomic surveillance data from the COVID-19 Genomics UK Consortium (COG-UK) to investigate the infection dynamics of the B.1.1.7 lineage. We used this data to address the question: did the B.1.1.7 lineage spread during the lockdown due to a general failure of viral containment or because of a biological advantage specific to the new lineage? Our study suggests that the latter is most likely to be true. 

Are UK lockdown restrictions enough to stop the spread of this lineage?

So far we have seen a decrease in the total number of diagnosed cases of approximately 50–60%, and the good news is that this involves both old and new lineages. However, the rate of decline appears to be somewhat uneven, with a faster decline of old variants. This is in line with what one would expect based on the experience of the past two months. A consequence of the slower decline is that one needs a longer lockdown and the risk remains that cases surge quickly as soon as restrictions are loosened. For comparison, daily reported cases had jumped from roughly 10,000 to 60,000 throughout December, while now after four weeks of lockdown they’re still well above 20,000 per day. 

What advice would you give to other countries to prevent the spread of B.1.1.7?  

It’s very possible that the new virus lineage is already spreading unnoticed in other populations. It’s a very threatening situation because, if it only becomes apparent from the increasing number of cases that the new lineage is in the country, it’s already too late. If possible, pre-empting this with a tougher lockdown first could help reduce the spread of B.1.1.7. The clock is ticking: we must act fast to stop the spread of this new lineage. 

This post was originally published on EMBL-EBI News

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Tags: bioinformatics, coronavirus, covid-19, embl-ebi, sars-cov-2