Detailed studies of the so-called P.1 variant have revealed how it ravaged a Brazilian city. Scientists now want to know what it will do in other parts of the world.
Two variants of the Coronavirus have become so familiar that you hear their inscrutable alphanumeric names regularly on television.
It has demonstrated a remarkable ability to spread far and fast since it was first detected in Britain. There is a mutant in South Africa called B.1.351 that can dodge human antibodies, reducing the effectiveness of some vaccines.
A third variant that arose in Brazil, called P.1, has also caught the attention of scientists. P.1 research has been slow since its discovery in late December, leaving scientists unsure how serious it is.
“I’ve been holding my breath,” said Bronwyn MacInnis, an epidemiologist at the Broad Institute.
Three studies have now shed light on P.1’s meteoric rise in Manaus, an Amazonian city. Most likely, it arose there in November and triggered a record spike in Coronavirus cases. Researchers found that an increased contagiousness contributed to its dominance in the city.
In addition, it acquired the ability to infect people who had previously been immune to Covid-19. Laboratory experiments suggest that P.1 may weaken the protective effect of a Chinese vaccine currently used in Brazil.
The new studies have not yet been published in scientific journals. The authors note that laboratory findings don’t always translate to the real world, and they are still learning how P.1 behaves.
“This study applies to Manaus, but I’m not sure if it applies elsewhere,” said Nuno Faria, a virologist at Imperial College London.
Despite the mysteries surrounding P.1, experts said it is worth taking seriously. “This data shows why we should be concerned about P.1,” said William Hanage, an epidemiologist at the Harvard T.H. Chan School of Public Health.
There have been reports of P.1 spreading to 24 countries, including the rest of Brazil. The Centers for Disease Control and Prevention has recorded six cases in five states: Alaska, Florida, Maryland, Minnesota, and Oklahoma.
Doctor said it was important to take every measure we can to slow the spread of the Coronavirus in order to reduce the risk of outbreaks and reinfections. A mask and social distancing can be effective against P.1. Vaccination can also reduce transmission and protect those who do contract the disease.
“The main message is to step up vaccination efforts as soon as possible,” he said. The virus must be kept at bay by staying one step ahead.
As soon as the Coronavirus exploded in Brazil last spring, Doctor and his colleagues began tracking it. Manaus, a city of two million in the Brazilian Amazon, was particularly hard hit. In springtime, the cemeteries of Manaus were overrun with bodies.
However, Manaus seemed to have recovered from the worst of the pandemic after a peak in late April. Scientists believed Manaus had gained herd immunity due to the drop.
In June and October, Doctor and his colleagues examined blood samples from a Manaus blood bank for antibodies to Coronavirus. Manaus’ residents were estimated to be infected by roughly three-quarters.
Near the end of 2020, however, new cases began to surge again. Compared to the previous peak of cases in late April, there were far more cases, Doctor said. “We found that very puzzling.”
The resurgence might be partly caused by new variants, according to Doctor and his colleagues. There was a surge in B.1.1.7 outbreaks across Britain, according to researchers.
Doctor and his colleagues started a genome sequencing effort in the city to look for variants. B.1.1.7 had already arrived in other parts of Brazil, but not in Manaus. Instead, they discovered a variant that had never been seen before.
Several variants in their samples shared 21 mutations not found in other viruses circulating in Brazil. “I think I’m seeing something really strange, and I’m quite concerned about it,” Faria said in a text message to a colleague.
Several mutations in particular concerned him, because scientists had already discovered them in either B.1.1.7 or B.1.351. The mutations might make the variants more capable of infecting cells, according to experiments. They can also evade antibodies produced by vaccines or antibodies from previous infections.
Researchers in Japan were making a similar discovery as Doctor and his colleagues analyzed their results. The Coronavirus was detected in four tourists returning from the Amazon on Jan. 4. The same mutations were detected in Brazil by Doctor and his colleagues.
Doctor and his colleagues described P.1 on an online virology forum on Jan. 12. The researchers then investigated why P.1 was so common. The mutations may have made it more contagious, or it might have been lucky. In Manaus, the variant might have appeared just as public health measures were being relaxed.
As a result of its ability to reinfect people, P.1 could also become common. Coronavirus reinfections are rare, since antibodies produced by the body after infection remain active for months. It was possible that P.1 carried mutations that prevented those antibodies from latching onto it, allowing it to slip into cells and cause new infections.
P.1 was tracked from its earliest samples in December to test these possibilities. As of early January, it accounted for 87 percent of samples. In February, it had completely taken over.
By combining genomes, antibodies, and medical records in Manaus, the researchers concluded that P.1 conquered the city because of its mutations, not luck. On average, it infects more people than other variants, like B.1.1.7. Coronaviruses of this lineage are estimated to be two to three times more transmissible than those of other lineages.
However, it also has mutations that allow it to escape antibodies from other Coronaviruses. Between 25 and 61 of 100 people who were infected with non-P.1 lineages in Manaus last year could have been reinfected if they were exposed to P.1.
Using antibodies from Brazilians who had Covid-19 last year, the researchers found support for this conclusion. In comparison with other coronaviruses, their antibodies were sixfold less effective against P.1. This might indicate that some people are susceptible to P.1 infections in the future.
According to Doctor, “an increasing body of evidence” suggests that most cases in the second wave resulted from reinfections.
Currently, Doctor and other researchers are observing P.1’s spread across Brazil. One of the outbreaks occurred in Araraquara, a Brazilian city of 223,000 people that did not have high Covid-19 rates before P.1 arrived, according to an infectious disease expert at the University of So Paulo School of Medicine.
According to her, if people in Araraquara did not have high levels of antibodies before P.1 arrived, it suggests that the variant may be capable of spreading without the extreme history of Manaus. “This could happen anywhere,” she said.
It’s time to pay attention to P.1 in the United States, says Michael Worobey, a virologist at the University of Arizona who wasn’t involved in the research. As it became more common in the United States, it would compete with B.1.1.7, which may soon become the dominant variant.
“It will at least be a contender,” Doctor said.
Doctor and his colleagues also tested antibodies taken from eight Brazilians who received CoronaVac, a Chinese vaccine. The vaccine-generated antibodies were less effective than other types at stopping the P.1 variant.
As Doctor cautioned, these results, derived from cells in test tubes, don’t necessarily imply vaccines will be less effective at protecting real people from P.1. Vaccines could still provide strong protection from P.1 even if their antibodies aren’t as potent. In addition, even if the variant is able to infect vaccinated people, they will probably be protected from a severe Covid-19 infection.
In Doctor view, P.1’s ultimate significance lies in the threat posed by concerning variants when they appear anywhere.
“Just a matter of time and chance,” she said.