The coronavirus variant originally found in Manaus in Brazil and detected in six cases in the UK was able to infect 25% to 61% of the people in the Amazonian city who might have expected to be immune after a first bout of Covid, researchers say.
The extent to which P1 can evade the immune system, and potentially vaccines, emerged as the UK health secretary said the hunt for one person who tested positive for P1 – but did not leave contact details – had narrowed to 379 households in the south-east of England.
Matt Hancock said five people had quarantined at home. The sixth took a home test but did not fill in the necessary form. “Incidents like this are rare and only occur in around 0.1% of tests,” he told MPs in the House of Commons.
“We’ve identified the batch of home test kits in question, our search has narrowed from the whole country down to 379 households in the south-east of England and we’re contacting each one.”
Hancock also said that a third vaccine might be necessary in the autumn, against P1 and similar variants such as B1351, which was first detected in South Africa. Both have mutations in the spike protein that can help virus variants escape the current vaccines.
“Our current vaccines have not yet been studied against this variant and we’re working to understand what impact it might have, but we do know that this variant has caused significant challenges in Brazil, so we’re doing all we can to stop the spread of this new variant in the UK, to analyse its effects and to develop an updated vaccine that works on all these variants of concern and protect the progress that we’ve made as a nation,” said Hancock.
The international team of scientists that detected P1 in Manuas is calling for more genetic sequencing of emerging variants around the world, saying that only with knowledge of how Sars-Cov2 is mutating can the pandemic be brought under control.
The variant, called P1, not only has potential to evade the immune protection of previous illness or vaccines, but is more transmissible than the original coronavirus. The study in Manaus, which has not yet been published in peer-reviewed form, found it was about 1.4 to 2.2 times more transmissible than the original virus.
The scientists said at a briefing that six cases, detected promptly in the UK, did not presage a significant spread of the variant. It was vital, however, to identify variants emerging throughout the world in countries that had little or no genomic sequencing capacity at the moment, they said.
The research was carried out by the Brazil-UK Cadde project, whose work on genetic sequencing predates the pandemic. It includes the Institute of Tropical Medicine in São Paulo, the London School of Hygiene and Tropical Medicine and universities in Oxford, London and Birmingham.
Manaus, the largest city in the Amazon basin, suffered a first wave of Covid in April/May. Studies of blood donors suggested 66% of people had antibodies against the virus in July and 76% by October, which would have been expected to give them immunity.
But the city suffered a serious second wave. There could have been various explanations, including the possibility that the data on previous infection was wrong, but the team of researchers identified the P1 variant on 6 December. It spread rapidly: within eight weeks, it was implicated in 87% of cases.
Dr Nuno Faria of the MRC Centre for Global Infectious Disease Analysis at Imperial College London, said it had concluded that the variant was causing people who had already suffered from Covid to get it again.
“If 100 people were infected in Manaus last year, somewhere between 25 and 61 of them are susceptible to reinfection by P1,” he said at a briefing. “We caution, however, that our results from analysis should not be generalised to other epidemiological contexts and/or other variants of concern.”
Prof Sharon Peacock, the director of Cog-UK, the consortium responsible for the genomic sequencing of the virus and its variants, said P1 has spread to 25 countries to date. “It is being distributed around the world. But I would say that in terms of the UK, we have just six cases identified, which we heard about yesterday from Public Health England, and from the government,” she said.
Peacock expressed a note of caution about the findings from Manaus. “We need to see whether this is generalisable to other settings, she said. “So I think it would be wise to indicate that this is relevant to where the study was done, but we don’t know how that will pan out in other countries, including the UK.
“The response that we’ve taken in the UK has been very brisk, and is appropriate, but very vigorous.”
Public Health England was investigating the six known cases of people infected with P1, tracing contacts and taking appropriate action, she said.
The research shows that P1 has 17 mutations and many are similar to those found in the spike protein of the variant found in South Africa, called B1351. In particular, a mutation called E484K that they share appears to enable the variants to escape the immune system, which means that vaccines may have reduced efficacy.