All you need to know about the new UK variant of COVID-19

Genome sequencing is a technique that allows scientists to read the entire genetic make-up of an organism. Doing this helps to keep track of changes in the organism’s genome, and to develop therapies and vaccines where necessary.

A WHO release says that UK health authorities had already been running the genome sequence of 5-10% (4% in South-east England) of viral samples collected from COVID-19 patients when England saw a sudden rise in infection rate. Between 5 October and 13 December, the 14-day reporting rate in South East England shot up by more than 300%. Genome sequencing showed that more than half the patients in this part of the UK had contracted a new variant of the SARS-CoV-2.

Retrospective analysis tracked the first identified case of this variant back to 20 September 2020, in the Kent area of South East England.

So far, most of the people who have contracted this variant of COVID-19 are under 60 years of age.

It is early days in the study of the new variant, and scientists are still trying to gauge if and how the variation will affect people. For example,

• Will the variation make the disease more or less severe? (The UK public health experts have said that so far there are no indications that the variant causes more severe disease.)
• Will it have an impact on the effectiveness of the therapies developed so far?
• Questions have also been raised over whether the current vaccines in development will be able to prevent this form of the infection.

What we do know so far can be summarised as follows:

• Human to human transmission of the variant may be easier and faster than before. Experts peg the increase in transmissibility at 40-70%, based on initial findings
• There are at least 14 mutations or changes in the variant, including three deletions and changes in amino acids. Deletions in the gene sequence can have a cascading effect in terms of how the virus behaves, and how to defeat it.
• Some of the mutations have been seen before in some countries; for example, N501Y—a mutation that has changed an amino acid in the receptor binding domain (RBD) which the virus uses to lock into healthy human cells—was previously reported in South Africa and Australia. Based on sequence analysis, WHO says this mutation in the UK seems to be independent of the change that occurred in South Africa and Australia
• Some of the mutations may necessitate small changes in how we diagnose this coronavirus infection. Importantly, public health experts say that one of the three deletions in the variant will reduce the efficacy of (only those) RT-PCR tests that look for the S (spike protein) gene of SARS-CoV-2.
• RT-PCR tests for COVID-19 mostly look for structural proteins including the envelope (E) protein, the spike (S) protein, the nucleocapsid (N) proteins or specific genetic material (open reading frame). According to a WHO release, “the impact of the variant on diagnostics is not anticipated to be significant”.
• VUI-202012/01 has also been observed in Australia, Denmark, Italy, Iceland and the Netherlands.
• A mutation called P681H has been found, and marked as biologically important, by public health researchers. This change, too, is reflected in the receptor binding domain or RBD.

The UK response to the new Covid variant comprises public health and virological studies, to:

• Assess how quickly and widely this variant of the virus can spread
• Determine if the variant virus has different biological features; if yes, what they are
• Check if these changes affect disease severity in any way
• Check if these changes might alter the effectiveness of vaccines for COVID-19
• Check if there’s any change in the antibody response to this new variant

As of 19 December 2020, UK authorities have also put more restrictions on movement and gatherings in affected areas. The government is also asking people in affected areas to work from home as much as possible and close non-essential businesses.

The WHO in its release on 22 December 2020 explained that this mutation is nothing unusual. “All viruses, including SARS-CoV-2, change over time, but most of these mutations or changes do not have a direct benefit to the virus or may even be detrimental to its propagation,” the WHO release said.

Studies are on to understand the effects of these particular mutations on the virus, the illness it causes—COVID-19—and on the medicines and vaccines being developed/administered to fight it. Scientists have found that the virus may spread more easily, especially among people under 60, but so far there are no indications of it causing more severe illness. The effect of the mutation on vaccines is not known yet.

The UK has shared the genome sequence of this variant with the WHO, and the WHO SARS-CoV-2 Virus Evolution Working Group is working with the UK to analyse the effect of this variant.

The WHO has also advised that countries increase routine sequencing of the SARS-CoV-2 virus, and sharing sequencing data, to find and study any concerning mutations as quickly as possible.