Brazilian Covid variant: what do we know about P1?

Is the P1 coronavirus variant a major threat to the world?

The P1 variant is causing devastation in Brazil, where an uncontrolled Covid pandemic is raging. P1, behind the terrible scenes of hospital overload in Manaus with patients’ relatives pleading for oxygen cylinders, is now the dominant form of coronavirus in many of Brazil’s cities and partly responsible for the high death toll. Other Latin American countries have closed their borders and restricted travel to and from Brazil but P1 is now in at least 15 countries in the Americas, according to the Pan American Health Organization (PAHO).

P1 is highly transmissible. Jesem Orellana, an epidemiologist at Fiocruz, the renowned Brazilian scientific research institution, said on 10 March that because of its epidemic, Brazil was “a threat to humanity”.

As of 6 April, there were 356 cases of P1 in the US, spread across 25 jurisdictions, according to the Centers for Disease Control. The first case arrived in Minnesota in early January. There are far more cases of the UK variant – 16,275 – which like P1 spreads easily, but is very susceptible to vaccines. There were 32 cases of P1 in the UK as of 31 March.

What do we know about the P1 variant?

It is one of two coronavirus variants that have been detected in Brazil, or in people who have travelled from Brazil, called P1 and P2. The P1 variant has more changes – three mutations to the spike protein instead of one – and is causing the most concern.

P1 was first detected in Japan, in people who had travelled from Manaus in Brazil. Investigations confirmed the variant in Manaus, the city on the Amazon that suffered an intense first wave of coronavirus that peaked in April last year. A survey of blood donors in October suggested that 76% of the population had antibodies, so were presumed at least temporarily immune. But in January, there was a resurgence among people who had previously recovered from Covid, suggesting that P1 is capable of infecting people who thought they had natural immunity.

P2 is widespread in Brazil but has fewer worrying mutations.

The UK’s New and Emerging Respiratory Virus Threats Advisory Group (Nervtag) has designated P1 a “variant of concern”, as has the CDC in the US. Not only is it more transmissible – like the “Kent” variant B117 – but may also be capable of antigenic escape. In other words, the vaccines designed to stop coronavirus may not work so well against it.

How is it different from other variants and will vaccines work?

Nervtag says P1 “contains 17 unique amino acid changes, three deletions, four synonymous mutations and one 4nt insertion”. A variant is a virus with mutations, which sometimes have little effect. However, P1 has three that cause concern: K417T, E484K, and N501Y.

E484K is the most worrying. It is in the so-called South African variant too, which has almost identical changes in its spike protein. There are also a few cases where B117, the Kent variant, known for its rapid spread, has gained the E484K mutation. This is the mutation thought to give the variants some ability to escape the vaccines.

Lab tests have suggested so far that the major approved vaccines will work against P1, but with reduced efficacy. A study from Oxford University, published on 30 March in the peer reviewed journal Cell, looked at the antibody response in blood samples from people with P1 elicited by the AstraZeneca and also the Pfizer/BioNTech vaccines. They showed nearly a threefold reduction in neutralisation, so efficacy is reduced – but not as much as it is against the South African variant. The Chinese CoronaVac vaccine, which is being widely used in Brazil, also appears to have some efficacy, according to a separate, non-peer-reviewed study.

What are the chances of P1 becoming widespread in Europe, the UK or US?

It will depend on genomic sequencing of the samples of virus given by people taking Covid tests – and thorough follow-up contact tracing to find anyone else who may have picked up P1.

The UK has become good at this. It is surge testing wherever cases of variants are found, whether P1 or B1351, which originated in South Africa. The UK does more genomic sequencing of viral samples than any other country so is in a good position to know what is going around. When six cases of P1 were picked up in February in the UK, a major search was launched to find one person who had not left contact details when he took his test. Forty people were involved over five days. Eventually the person came forward.

Other countries are stepping up their genomic sequencing as the threat of the variants becomes clear. Even in highly vaccinated countries, P1 could pose problems. Controlling its spread will become ever more difficult as people resume foreign travel.