Science

The New York Times
Brazil's COVID Crisis Is a Warning to the Whole World, Scientists Say
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. Sign up for The Morning newsletter from the New York Times 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.” This article originally appeared in The New York Times. © 2021 The New York Times Company
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The New York Times
A Virus Variant by Any Other Name ... Please
20H/501Y.V2. VOC 202012/02. B.1.351. Sign up for The Morning newsletter from the New York Times Those were the charming names that scientists proposed for a new variant of the coronavirus that was identified in South Africa. The convoluted strings of letters, numbers and dots are deeply meaningful for the scientists who devised them, but how was anyone else supposed to keep them straight? Even the easiest to remember, B.1.351, refers to an entirely different lineage of the virus if a single dot is missed or misplaced. The naming conventions for viruses were fine as long as variants remained esoteric topics of research. But they are now the source of anxiety for billions of people. They need names that roll off the tongue, without stigmatizing the people or places associated with them. “What’s challenging is coming up with names that are distinct, that are informative, that don’t involve geographic references and that are kind of pronounceable and memorable,” said Emma Hodcroft, a molecular public health researcher at the University of Bern in Switzerland. “It sounds kind of simple, but it’s actually a really big ask to try and convey all of this information.” The solution, she and other experts said, is to come up with a single system for everyone to use but to link it to the more technical ones scientists rely on. The World Health Organization has convened a working group of a few dozen experts to devise a straightforward and scalable way to do this. “This new system will assign variants of concern a name that is easy to pronounce and recall and will also minimize unnecessary negative effects on nations, economies and people,” the WHO said in a statement. “The proposal for this mechanism is currently undergoing internal and external partner review before finalization.” The WHO’s leading candidate so far, according to two members of the working group, is disarmingly simple: numbering the variants in the order in which they were identified — V1, V2, V3 and so on. “There are thousands and thousands of variants that exist, and we need some way to label them,” said Trevor Bedford, an evolutionary biologist at the Fred Hutchinson Cancer Research Center in Seattle and a member of the working group. Naming diseases was not always so complicated. Syphilis, for example, is drawn from a 1530 poem in which a shepherd, Syphilus, is cursed by the god Apollo. But the compound microscope, invented around 1600, opened up a hidden world of microbes, allowing scientists to start naming them after their shapes, said Richard Barnett, a historian of science in Britain. Still, racism and imperialism infiltrated disease names. In the 1800s, as cholera spread from the Indian subcontinent to Europe, British newspapers began calling it “Indian cholera,” depicting the disease as a figure in a turban and robes. “Naming can very often reflect and extend a stigma,” Barnett said. In 2015, the WHO issued best practices for naming diseases: avoiding geographic locations or people’s names, species of animal or food, and terms that incite undue fear, like “fatal” and “epidemic.” Scientists rely on at least three competing systems of nomenclature — Gisaid, Pango and Nextstrain — each of which makes sense in its own world. “You can’t track something you can’t name,” said Oliver Pybus, an Oxford evolutionary biologist who helped design the Pango system. Scientists name variants when changes in the genome coincide with new outbreaks, but they draw attention to them only if there is a change in their behavior — if they transmit more easily, for instance (B.1.1.7, the variant first seen in Britain), or if they at least partly sidestep the immune response (B.1.351, the variant detected in South Africa). Encoded in the jumbled letters and digits are clues about the variant’s ancestry: The “B.1,” for instance, denotes that those variants are related to the outbreak in Italy last spring. (Once the hierarchy of variants becomes too deep to accommodate another number and dot, newer ones are given the next letter available alphabetically.) But when scientists announced that a variant called B.1.315 — two digits removed from the variant first seen in South Africa — was spreading in the United States, South Africa’s health minister “got quite confused” between that and B.1.351, said Tulio de Oliveira, a geneticist at the Nelson Mandela School of Medicine in Durban and a member of the WHO’s working group. “We have to come up with a system that not only evolutionary biologists can understand,” he said. With no easy alternatives at hand, people have resorted to calling B.1.351 “the South African variant.” But de Oliveira pleaded with his colleagues to avoid the term. (Look no further than the origins of this very virus: Calling it the “China virus” or the “Wuhan virus” fed into xenophobia and aggression against people of East Asian origin all over the world.) The potential harms are grave enough to have dissuaded some countries from coming forward when a new pathogen is detected within their borders. Geographical names also quickly become obsolete: B.1.351 is in 48 countries now, so calling it the South African variant is absurd, de Oliveira added. And the practice could distort science. It is not entirely clear that the variant arose in South Africa: It was identified there in large part thanks to the diligence of South African scientists, but branding it as that country’s variant could mislead other researchers into overlooking its possible path into South Africa from another country that was sequencing fewer coronavirus genomes. Over the past few weeks, proposing a new system has become something of a spectator sport. A few of the suggestions for name inspiration: hurricanes, Greek letters, birds, other animal names like red squirrel or aardvark, and local monsters. Áine O’Toole, a doctoral student at the University of Edinburgh who is part of the Pango team, suggested colors to indicate how different constellations of mutations were related. “You could end up with dusty pink or magenta or fuchsia,” she said. Sometimes, identifying a new variant by its characteristic mutation can be enough, especially when the mutations gain whimsical names. Last spring, O’Toole and her collaborators began calling D614G, one of the earliest known mutations, “Doug.” “We’d sort of not had a huge amount of human interaction,” she said. “This was our idea of humor in lockdown No. 1.” Other nicknames followed: “Nelly” for N501Y, a common thread in many new variants of concern, and “Eeek” for E484K, a mutation thought to make the virus less susceptible to vaccines. But Eeek has emerged in multiple variants worldwide simultaneously, underscoring the need for variants to have distinct names. The numbering system the WHO is considering is straightforward. But any new names will have to overcome the ease and simplicity of geographic labels for the general public. And scientists will need to strike a balance between labeling a variant quickly enough to forestall geographical names and cautiously enough that they do not wind up giving names to insignificant variants. “What I don’t want is a system where we have this long list of variants that all have WHO names, but really only three of them are important and the other 17 are not important,” Bedford said. Whatever the final system is, it also will need to be accepted by different groups of scientists as well as the general public. “Unless one really does become the kind of lingua franca, that will make things more confusing,” Hodcroft said. “If you don’t come up with something that people can say and type easily, and remember easily, they will just go back to using the geographic name.” This article originally appeared in The New York Times. © 2021 The New York Times Company
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