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The first detailed studies of the so-called P.1 variant show how it devastated a Brazilian city. Now scientists want to know what it will do elsewhere. 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. B.1.1.7, 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 concerning variant that arose in Brazil, called P.1. Research had been slower on P.1 since its discovery in late December, leaving scientists unsure of just how much to worry about it. “I’ve been holding my breath,” said Bronwyn MacInnis, an epidemiologist at the Broad Institute. Now three studies offer a sobering history of P.1’s meteoric rise in the Amazonian city of Manaus. It most likely arose there in November and then fueled 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 P.1 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 P.1’s behavior. “The findings apply to Manaus, but I don’t know if they apply to other places,” said Nuno Faria, a virologist at Imperial College London who helped lead much of the new research.
But even with the mysteries that remain around P.1, experts said it is a variant to take seriously. “It’s right to be worried about P.1, and this data gives us the reason why,” said William Hanage, an epidemiologist at the Harvard T.H. Chan School of Public Health. P.1 is now spreading across the rest of Brazil and has been found in 24 other countries. In the United States, the Centers for Disease Control and Prevention has recorded six cases in five states: Alaska, Florida, Maryland, Minnesota and Oklahoma. To reduce the risks of P.1 outbreaks and reinfections, Dr. Faria said it was important to double down on every measure we have to slow the spread of the coronavirus. Masks and social distancing can work against P.1. 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 gotten 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.”
Dr. Faria and his colleagues wondered if new variants might be partly to blame for the resurgence. In Britain, researchers were finding that B.1.1.7 was surging across the country.
To search for variants, Dr. Faria and his colleagues started a new genome sequencing effort in the city. While B.1.1.7 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.” A few mutations in particular worried him, because scientists had already found them in either B.1.1.7 or B.1.351. Experiments suggested that some of the mutations might make the variants better able to infect cells. Other mutations let them evade antibodies from previous infections or produced by vaccines. As Dr. Faria and his colleagues analyzed their results, researchers in Japan were making a similar discovery. Four tourists returning home from a trip to the Amazon on Jan. 4 tested positive for the coronavirus. Genome sequencing revealed the same set of mutations Dr. Faria and his colleagues were seeing in Brazil. Dr. Faria and his colleagues posted a description of P.1 on an online virology forum on Jan. 12. They then investigated why P.1 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....
