Brazil variant of Covid-19 capable of re-infecting recovered Covid-19 patients

The Brazil variant of Covid-19 likely arose in Manaus and then fuelled a record-breaking spike of coronavirus cases.
The Brazil variant of Covid-19 likely arose in Manaus and then fuelled a record-breaking spike of coronavirus cases.PHOTO: AFP

BRAZIL (NYTIMES) - In just a matter of weeks, two variants of the coronavirus have become so familiar that you can hear their inscrutable alphanumeric names regularly uttered on television news.

B117, first identified in Britain, has demonstrated the power to spread far and fast. In South Africa, a mutant called B.1.351 can dodge human antibodies, blunting the effectiveness of some vaccines. Scientists have also had their eye on a third worrying variant that arose in Brazil, called P1.

Research had been slower on P1 since its discovery in late December, leaving scientists unsure of just how much to worry about it. "I've been holding my breath," said Dr Bronwyn MacInnis, a public health researcher at the Broad Institute. Now three studies offer a sobering history of P1's meteoric rise in the Amazonian city of Manaus.

It likely arose there in November and then fuelled a record-breaking spike of coronavirus cases. It came to dominate the city partly because of an increased contagiousness, the research found. But it also gained the ability to infect some people who had immunity from previous bouts of Covid-19, and laboratory experiments suggest that P1 could weaken the protective effect of a Chinese vaccine now in use in Brazil.

The new studies have yet to be published in scientific journals. Their authors caution that findings on cells in laboratories do not always translate to the real world, and they've only begun to understand P1's behaviour.

"The findings apply to Manaus, but I don't know if they apply to other places," said Dr Nuno Faria, a virus expert at Imperial College London who helped lead much of the new research.

But even with the mysteries that remain around P1, experts said it is a variant to take seriously.

"It's right to be worried about P1, and this data gives us the reason why," said Associate Professor William Hanage, a public health researcher at the Harvard T.H. Chan School of Public Health. P1 is now spreading across the rest of Brazil and has been found in 24 other countries.

In the United States, the Centres for Disease Control and Prevention has recorded six cases in five states: Alaska, Florida, Maryland, Minnesota and Oklahoma.

To reduce the risks of P1 outbreaks and reinfections, Dr Faria said it was important to double down on every measure developed to slow the spread of the coronavirus. Masks and social distancing can work against P1. And vaccination can help drive down its transmission and protect those who do get infected from severe disease.

"The ultimate message is that you need to step up all the vaccination efforts as soon as possible," he said. "You need to be one step ahead of the virus."

Dr Faria and his colleagues started tracking the coronavirus when it exploded in Brazil last spring.

Manaus, a city of two million in the Brazilian Amazon, was hit particularly hard. At its springtime peak, the cemeteries of Manaus were overwhelmed by the bodies of the dead. But after a peak in late April, Manaus seemed to have got past the worst of the pandemic. Some scientists thought that the drop meant Manaus had gained herd immunity.

Dr Faria and his colleagues looked for coronavirus antibodies in samples from a Manaus blood bank in June and October. They determined that roughly three-quarters of the residents of Manaus had been infected.

But near the end of 2020, new cases began surging again. "There were actually far more cases than in the previous peak of cases, which had been in late April,"Dr  Faria said. "And that was very puzzling to us."

He and his colleagues wondered if new variants might be partly to blame for the resurgence. In Britain, researchers were finding that B117 was surging across the country. To search for variants, Dr Faria and his colleagues started a new genome sequencing effort in the city.

While B117 had arrived in other parts of Brazil, they didn't find it in Manaus. Instead, they found a variant no one had seen before. Many variants in their samples shared a set of 21 mutations not seen in other viruses circulating in Brazil. Dr Faria sent a text message to a colleague: "I think I'm looking at something really strange, and I'm quite worried about this."

He and his colleagues posted a description of P1 on an online virology forum on Jan 12. They then investigated why P1 was so common. Its mutations may have made it more contagious, or it might have been lucky. By sheer chance, the variant might have shown up in Manaus just as the city was getting more relaxed about public health measures. It was also possible that P1 became common because it could reinfect people.

Normally, coronavirus re-infections are rare because the antibodies produced by the body after infection are potent for months. But it was possible that P1 carried mutations that made it harder for those antibodies to latch onto it, allowing it to slip into cells and cause new infections. The researchers tested these possibilities by tracking P1 from its earliest samples in December. By early January, it made up 87 per cent of samples. By February it had taken over completely.

Combining the data from genomes, antibodies and medical records in Manaus, the researchers concluded that P1 conquered the city thanks not to luck but biology: Its mutations helped it spread. Like B117, it can infect more people, on average, than other variants can. They estimate it is somewhere between 1.4 and 2.2 times more transmissible than other lineages of coronaviruses.

Dr Faria and other researchers are now looking across Brazil to observe P1's spread.

Dr Ester Sabino, an infectious disease expert at the University of São Paulo School of Medicine, said that one of the new outbreaks arose in Araraquara, a Brazilian city of 223,000 people that did not have high rates of Covid-19 before P1 arrived. If people in Araraquara did not have high levels of antibodies before P1's arrivals, she said, that suggests that the variant may be able to spread in places without Manaus' extreme history. "This might happen in any other place," she said.

Professor Michael Worobey, a virus expert at the University of Arizona who was not involved in the research, said it was time to pay attention to P1 in the United States. He expected it would become more common in the US, although it would have to compete with B117, which may soon become the predominant variant in much of the nation. "At the very least, it's going to be one of the contenders," he said.