Manuela Andreoni, Ernesto Londoño and Letícia Casado
RIO DE JANEIRO:
COVID-19 has already left a trail of death and despair in Brazil, one of the worst in the world. Now, a year into the pandemic, the country is setting another wrenching record.
No other nation that experienced such a major outbreak is still grappling with record-setting death tolls and a health care system on the brink of collapse. Many other hard-hit nations are, instead, taking tentative steps toward a semblance of normalcy.
But Brazil is battling a more contagious variant that has trampled one major city and is spreading to others, even as Brazilians toss away precautionary measures that could keep them safe.
On Tuesday, Brazil recorded more than 1,700 COVID-19 deaths, the highest single-day toll of the pandemic.
“The acceleration of the epidemic in various states is leading to the collapse of their public and private hospital systems, which may soon become the case in every region of Brazil,” the national association of health secretaries said in a statement.
“Sadly, the anemic rollout of vaccines and the slow pace at which they’re becoming available still does not suggest that this scenario will be reversed in the short term.”
And the news just got worse for Brazil — and possibly the world.
Preliminary studies suggest that the variant that swept through the city of Manaus is not only more contagious, but it also appears able to infect some people who have already recovered from other versions of the virus. And the variant has slipped Brazil’s borders, showing up in two dozen other countries and in small numbers in the United States.
Although trials of a number of vaccines indicate they can protect against severe illness even when they do not prevent infection with the variant, most of the world has not been inoculated. That means even people who had recovered and thought they were safe for now might still be at risk and that world leaders might, once again, be lifting restrictions too soon.
“You need vaccines to get in the way of these things,” said William Hanage, a public health researcher at Harvard T.H. Chan School of Public Health, speaking of variants that might cause reinfections. “The immunity you get with your cemeteries running out of room, even that will not be enough to protect you.”
That danger of new variants has not been lost on scientists around the world. Rochelle Walensky, director of the U.S. Centers for Disease Control and Prevention, pleaded with Americans this week not to let their guards down. “Please hear me clearly,” she said. “At this level of cases with variants spreading, we stand to completely lose the hard-earned ground we’ve gained.”
Brazilians hoped they had seen the worst of the outbreak last year. Manaus, capital of the northern state of Amazonas, was hit so hard in April and May that scientists wondered if the city might have reached herd immunity.
But then in September, cases in the state began rising again, perplexing health officials. An attempt by Amazonas Gov. Wilson Lima to impose a new quarantine ahead of the Christmas holiday was met with fierce resistance by business owners and prominent politicians close to President Jair Bolsonaro.
By January, scientists had discovered that a new variant, which became known as P.1, had become dominant in the state. Within weeks, its danger became clear as hospitals in the city ran out of oxygen amid a crush of patients, leading scores to suffocate to death.
Dr. Antonio Souza remains haunted by the horrified faces of his colleagues and relatives of patients when it became clear his Manaus hospital’s oxygen supply had been exhausted. He thinks about the patient he sedated, to spare her an agonizing death, when the oxygen ran out at another clinic.
“Nobody should ever have to make that decision,” he said. “It’s too terrible.”
Maria Glaudimar, a nurse in Manaus, said she felt trapped in a nightmare early this year with no end in sight. At work, patients and their relatives pleaded for oxygen, and all the intensive care beds were full. At home, her son caught tuberculosis after contracting COVID-19, and her husband shed 22 pounds as he fought the virus.
“No one was prepared for this,” Glaudimar said. “It was a horror film.”
Since then, the coronavirus crisis has eased somewhat in Amazonas but worsened in most of Brazil.
Scientists have scrambled to learn more about the variant and to track its spread across the country. But limited resources for testing have kept them behind the curve as they try to determine what role it is playing.
Anderson Brito, a Brazilian virus expert at Yale University, said his lab alone sequenced almost half as many coronavirus genomes as all of Brazil had. While the United States has done genetic sequencing on roughly one in 200 confirmed cases, Brazil sequences about one in 3,000.
The variant spread quickly. By the end of January, a study by government researchers found it was present in 91% of samples sequenced in the state of Amazonas. By the end of February, health officials had reported cases of the P.1 variant in 21 of 26 Brazilian states, but without more testing it is hard to gauge its prevalence.
Throughout the pandemic, researchers have said that COVID-19 reinfections appear to be extremely rare, which has allowed people who recover to presume they have immunity, at least for a while. But that was before P.1 appeared and doctors and nurses began to notice something strange.
João Alho, a doctor in Santarém, a city in Pará, a state that borders Amazonas, said that several colleagues who recovered from COVID-19 months ago had fallen ill again and tested positive.
Juliana Cunha, a nurse in Rio de Janeiro who has been working at COVID-19 testing centers, said she assumed she was safe after catching the virus in June. But in November, after experiencing mild symptoms, she tested positive again.
“I couldn’t believe it,” Cunha, 23, said. “It must be the variants.”
But there is no way to be sure what is happening to people who are reinfected, unless both their old and new samples are kept, genetically sequenced and compared.
One way to tamp down the surge would be through vaccinations, but the rollout in Brazil, as in so many countries, has been slow.
Brazil began vaccinating priority groups, including health care professionals and the elderly, in late January. But the government has failed to secure a large enough number of doses. Wealthier countries have snapped up most of the available supply, while Bolsonaro has been skeptical both of the disease’s impact and of vaccines.
Just over 5.8 million Brazilians — roughly 2.6% of the population — had received at least one dose of a COVID-19 vaccine as of Tuesday, according to the health ministry. Only about 1.5 million had received both doses. The country is currently using the Chinese-made CoronaVac — which laboratory tests suggest is less effective against P.1 than against other variants — and the one made by British-Swedish pharmaceutical company AstraZeneca.
Margareth Dalcolmo, a pulmonologist at Fiocruz, a prominent scientific research center, said Brazil’s failure to mount a robust vaccination campaign set the stage for the current crisis.
“We should be vaccinating more than a million people per day,” she said. “That is the truth. We aren’t, not because we don’t know how to do it, but because we don’t have enough vaccines.”
Other countries should take heed, said Ester Sabino, an infectious disease researcher at the University of São Paulo who is among the leading experts on the P.1 variant.
“You can vaccinate your whole population and control the problem only for a short period if, in another place in the world, a new variant appears,” she said. “It will get there one day.”
Health Minister Eduardo Pazuello, who called the variant a “new stage” of the pandemic, said last week that the government was ramping up its efforts and hopes to vaccinate roughly half of its population by June and the rest by the end of the year.
But many Brazilians have little faith in a government led by a president who has sabotaged lockdowns, repeatedly downplayed the threat of the virus and promoted untested remedies long after scientists said they clearly did not work.
Just last week, the president spoke dismissively of masks, which are among the best defenses to curb contagion, claiming that they are harmful to children, causing headaches and difficulty concentrating.
Pazuello’s vaccine projections have also been met with skepticism. The government last week placed an order for 20 million doses of an Indian vaccine that has not completed clinical trials. That prompted a federal prosecutor to argue in a legal filing that the $286 million purchase “puts millions of lives at risk.”
Even if it proves effective, it will be too late for many.
Tony Maquiné, a 39-year-old marketing specialist in Manaus, lost a grandmother, an uncle, two aunts and a cousin in the span of a few weeks during the latest surge of cases. He said time has become a blur of frantic efforts to find hospitals with free beds for the living, while arranging funerals for the dead.
“It was a nightmare,” Maquiné said. “I’m scared of what lies ahead.”
Virus variant in Brazil infected many who had already recovered from Covid
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, a public health researcher at the Broad Institute.
Now three studies offer a sobering history of P.1’s meteoric rise in the Amazonian city of Manaus. It 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 virus expert 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, a public health researcher 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, 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.”
Faria and his colleagues started tracking the coronavirus when it exploded in Brazil in the spring. Manaus, a city of 2 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.
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,” Faria said. “And that was very puzzling to us.”
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, 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. 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 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 Faria and his colleagues were seeing in Brazil.
Faria and his colleagues posted a description of P.1 on an online virology forum 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.
It was also possible that P.1 became common because it could reinfect people. Normally, coronavirus reinfections are rare, because the antibodies produced by the body after infection are potent for months. But it was possible that P.1 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 P.1 from its earliest samples in December. By early January, it made up 87% of samples. By February it had taken over completely.
Combining the data from genomes, antibodies and medical records in Manaus, the researchers concluded that P.1 conquered the city thanks not to luck but biology: Its mutations helped it spread. Like B.1.1.7, 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.
But it also gets an edge from mutations that let it escape antibodies from other coronaviruses. They estimate that in 100 people who were infected with non-P.1 lineages in Manaus last year, somewhere between 25 and 61 of them could have been reinfected if they were exposed to P.1 in Manaus.
The researchers found support for this conclusion in an experiment in which they mixed P.1 viruses with antibodies from Brazilians who had COVID-19 last year. They found that the effectiveness of their antibodies dropped sixfold against P.1 compared with other coronaviruses. That drop might mean that at least some people would be vulnerable to new infections from P.1.
Faria said “an increasing body of evidence" suggests that most cases in the second wave were the result of reinfections.
Faria and other researchers are now looking across Brazil to observe P.1’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 P.1 arrived.
If people in Araraquara did not have high levels of antibodies before P.1’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.
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 P.1 in the United States. He expected it would become more common in the United States, although it would have to compete with B.1.1.7, 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,” Worobey said.
In their experiments, Faria and his colleagues also tested antibodies from eight people who received CoronaVac, a Chinese-made vaccine that has been used in Brazil. They found that the vaccine-generated antibodies were less effective at stopping the P.1 variant than other types.
Faria cautioned that these results, derived from cells in test tubes, don’t necessarily mean that vaccines will be less effective at protecting real people from P.1. Vaccines may very well provide strong protection from P.1 even if the antibodies they generate aren’t quite as potent. And even if the variant manages to infect vaccinated people, they will likely remain shielded from a severe bout of COVID-19.
For Sabino, the ultimate importance of P.1 is the threat that concerning variants pose when they can pop up anywhere in the world.
“It’s just a matter of time and chance,” she said.