India has been put on the UK’s “red list” for travel as it battles a devastating rise in infections and new variants of coronavirus that have spread to other countries, including the UK. One of these variants is showing a rapid rise in numbers in England and has now been designated a “variant of concern”. What do we know about the variants?
How were the variants discovered?
Scientists in India drew attention to a new variant as it gained ground in the western state of Maharashtra between December 2020 and March this year. On 24 March the Indian health ministry reported that 15-20% of coronavirus sequenced in the region – an early hotspot of the country’s second wave – carried two unusual mutations in the spike protein that are of particular concern: E484Q and L425R. The figure has reportedly risen to more than 60% in the region since then. The variant was named B.1.617. It is now known as B.1.617.1 after two closely related variants were identified: B.1.617.2 and B.1.617.3. These contain a slightly different suite of mutations, with B.1.617.2 lacking the E484Q mutation.
When did it arrive in the UK?
Genomic surveillance in the UK found B.1.617.1 among samples dating back to February, with B.1.617.2 and B.1.617.3 first detected in samples dating from mid to late March.
Cases of these variants, taken together, have risen dramatically in recent weeks. According to data from the Wellcome Sanger Institute’s Covid-19 genomic surveillance, about 2.4% of more than 8,000 Covid genomes in England sequenced in the two weeks around 17 April relate to these variants.
The proportion is even higher in some parts of the country – in Bolton, in that period, 24.1% of genomes sequenced related to the variants, although the actual number of sequences a week was low and scientists warn the data can be “noisy”. This dataset includes genomes sequenced for general surveillance but not from surge testing or travel-related testing.
The key driver of the rise appears to be B.1.617.2. According to the Covid-19 genomics UK consortium database – which may include duplicates and does not record whether sequences of the variants are linked to travel – for sequences up to Saturday 1 May there have so far been 752 sequences of the B.1.617.2 variant, compared with 298 sequences of B.1.617.1 and 11 of B.1.617.3
How dangerous is the variant?
It is hard to tell. Scientists are working to confirm whether or not the variants are more dangerous than others in circulation, for example by spreading more quickly, causing more severe disease, or evading immunity built up from previous infection or vaccination. At first all three of the Indian variants were declared variants “under investigation” by PHE, a label given to potentially worrisome new variants that are not well understood, however B.1.617.2 has now been upgraded to a “variant of concern”. That suggests that at least some laboratory studies, epidemiological analyses and other work have confirmed it to be problematic.
Of the two key mutations in the Indian variants, L452R, could help the virus evade some antibodies from vaccination, while E484Q has similarities to the E484K mutation which helps make the South African variant at least partially resistant to vaccines.
That said, the mutations in the Indian variants are highly unlikely to render vaccines completely ineffective, because the shots induce such broad immune defences.
Early results – yet to be peer reviewed – from the laboratory of Prof Ravi Gupta at the University of Cambridge suggest L452R and E484Q each mean antibodies generated by one dose of the Pfizer vaccine have a fourfold to sixfold lower ability to neutralise the variant compared with the pre-existing form of the virus. But there does not seem to be an additive effect, in other words a similar sized drop is seen even when the mutations appear together.
By contrast, the E484K mutation seen in certain other variants, such as that first detected in South Africa, has been linked to a tenfold reduction. Gupta further said that his team’s data suggested all three variants first detected in India might be more transmissible than the original strain of the coronavirus as they contained a mutation called P681R – similar to a mutation seen in the Kent variant – and which experiments suggested might help the virus to enter cells.
It is unclear whether the new variants are driving the surge in cases in India, but some scientists were keen to see India put on the travel red list in the hope of keeping imported cases at bay.
Are scientists worried?
Some are. Danny Altmann, a professor of immunology at Imperial College London, said that data from Gupta’s lab suggested the variants, including B.1.617.2, could be more transmissible. “I agree it carries some immune evasion, but this seems less pronounced than the E484K mutants, and current vaccines would almost certainly be effective against it,” he said.
Paul Hunter, a professor in medicine at the University of East Anglia, also raised concerns, noting that PHE data, seen by the Guardian, revealed there had been clusters of B.1.617.2 around England, including in care homes.
“The reported cluster linked to a care home where the residents had already had two doses of the AstraZeneca vaccine is particularly concerning,” Hunter said. “Although [it seems that] the second dose was only given a week before the outbreak this does raise concerns about how effective existing vaccines are against these variants. If the rate of growth in cases that we have seen in the past few weeks continue it will not be long before the Indian variants become the dominant variant and possibly triggers an early surge in total cases.”