A New Strain of COVID-19 Is Being Blamed for a Surge in Cases in Brazil. Here's What to Know

Ciara Nugent
·7 min read
Coronavirus - Brazil
Coronavirus - Brazil

Cemetery workers in protective suits carry the coffin of a person who died of Covid-19 at Nossa Senhora Aparecida Cemetery in Manaus on Jan.15 Credit - Lucas Silva – Picture Alliance/Getty Images

Many hoped the Brazilian city of Manaus had seen the worst of the pandemic, after a first wave of COVID-19 tore through it in spring 2020, forcing authorities to dig mass graves and causing the mayor to break down during television interviews.

Yet a new wave of infections has once again driven the city’s health services to a state of collapse this month. On Jan. 14, Manaus reported 2,516 new cases of COVID-19 and 254 hospitalizations after a diagnosis, the highest daily numbers since the pandemic began. The city’s hospitals have run out of ICU beds and oxygen supplies, forcing doctors to perform manual ventilation and leading to patients being airlifted out of Amazonas state, of which Manaus is the capital. Dozens are dying in the city every day – 22% more on average than during the peak of the first wave.

On Jan. 16, in a letter sent to Brazil’s supreme court, the state government blamed the surge in cases on “an unfortunate and absolutely unforeseeable coincidence”: the emergence of a new strain of COVID-19 in the region in late 2020. It was first reported on Jan. 11 by Japanese researchers in from four people who had traveled from the state to Tokyo.

Based on the mutations that the variant has acquired, scientists say it’s likely to be more infectious, like strains identified in the U.K. and South Africa have proven to be. There’s also a risk it may potentially evade immune responses to COVID-19 — with a large percentage of Manaus residents thought to have already had COVID-19, scientists had hoped their antibodies would slow the virus down, but that does not appear to have happened. Some epidemiologists in Brazil say those characteristics mean new strain is the “most plausible explanation” for the new wave of cases in Manaus.

After news of the variant emerged, Italy and the U.K. announced bans on flights from Brazil and South America respectively in an attempt to keep it out of their countries (non-U.S. citizens are already barred from travelling to the U.S. after spending time in Brazil, a restriction President Joe Biden has pledged to extend.)

But it’s too early to say with certainty if the variant is driving greater transmission or reinfection in Manaus, according to Felipe Naveca, a researcher in the Amazonas branch of Fiocruz, Brazil’s national medical research body, who led a study of the new variant. He says a lack of social distancing and a change in the season have helped to spread COVID-19 in recent weeks. “We still can’t confirm what is the role of this new variant in the recent explosion of cases, we need to do more work to confirm how common it is,” Naveca says in recordings sent to TIME by Fiocruz. “But I think it’s one of the factors.”

Here’s what to know about the new Brazilian variant and the situation in Manaus.

What is driving the second wave in Manaus?

The new variant is likely playing a role, but it’s not the only cause of the heavy caseload in Manaus. Doctors have been harshly critical of the state government’s failure to introduce tight enough measures to stop the spread of COVID-19.

Amazonas began to relax social distancing restrictions over summer after the region’s first wave subsided, reopening schools and encouraging people to go back to work, while asking them to avoid gatherings and maintain hygiene measures. Eventually bars and entertainment venues were closed again, but restaurants stayed open. As infections began to rise again in the fall, epidemiologists—and the mayor of Manaus—called for a stricter lockdown.

But on Sept. 29, Brazilian President Jair Bolsonaro called the idea “absurd” and his supporters rallied against the plan. Shortly after, state governor Wilson Lima ruled out a full lockdown. In December, the state government tried to close all non-essential businesses for two weeks, but backed down after backlash from Bolsonaro supporters.

Lima said on Jan. 11 that Amazonas was “paying the price for a lot of clandestine events and gatherings during festivities at the end of the year.”

Naveca, the Fiocruz researcher, points out that the current wave of COVID-19 cases also follows the expected start of “respiratory virus season” in Manaus in mid-November, when local weather conditions favor the spread of similar diseases.

What is different about the Brazilian variant?

Like strains of COVID-19 that were first reported in the U.K. and South Africa in late 2020, the variant of COVID-19 that originated in Amazonas, dubbed P.1, has acquired a range of mutations, including on the spike protein it uses to interact with human cells. (Another Brazilian variant, P.2, reported in Rio de Janeiro state, is not yet of particular concern to scientists.)

Scientists studying mutations in the COVID-19 virus are watching out for three characteristics in particular, says Sharon Peacock, a Cambridge University public health and microbiology professor leading the COVID-19 Genomics U.K. Consortium. “Is it more lethal? Is it more transmissible? Does it find a chink in the immunology armour? That’s my list of the three things you really wouldn’t want to see come together in one place,” Peacock says.

The variant from Amazonas carries the same mutation that makes the U.K. variant easier to transmit, Peacock says. But it also carries two other mutations that have been identified in lab tests as “potentially escaping antibodies,” she adds. The South African variant also carries mutations linked to both transmissibility and ability to evade human immune response. There is no evidence that any of these three variants cause more serious illness.

Is the Amazonas variant re-infecting people who have already had COVID-19?

Evidence is sparse. While other cases of re-infection with the new variant are being studied, according to Fiocruz, the only confirmed case was of a 29 year-old woman first infected in March 2020, and re-infected in December 2020.

There are fears that the wave of infections in Manaus, where many people ought to have some antibodies to protect against COVID-19, is the result of the new variant evading those antibodies. In December, researchers who tested residents’ blood for antibodies, examined the number of excess deaths over time, and adjusted for demographic factors and asymptomatic cases, estimated that up to 76% of people in the city had been infected with COVID-19 by October — approaching the point at which “herd immunity” might be expected to kick in. Other epidemiologists have put the proportion already infected at “at least 30 to 40%.”

But Peacock says other factors could be at play. “The alternative explanations are that either people who were not infected in the first surge [are being infected], or people have got dwindling immunity and are getting re-infected,” she says. Scientists have long warned that COVID-19 antibodies do not last forever after infection, and start to become less and less effective after several months.

Will the variant that emerged in Amazonas evade vaccines?

Peacock says there is “no evidence” yet that the vaccines currently being rolled out will fail to protect against the variant of COVID-19 that emerged in Amazonas.

Scientists testing the efficacy of vaccines on the variants of COVID-19 that emerged in the U.K. and South Africa are so far confident that the vaccines do protect against them. On Jan. 20, Pfizer and BioNTech published a study, yet to be peer-reviewed, that finds their vaccine is equally effective against the U.K. strain as against previous forms of COVID-19. “It’s too soon to have done similar experiments with our variant, though, since it only emerged very recently,” Naveca says.

It’s possible a variant will one day emerge that renders the vaccines less effective, Peacock says. “But I think it will be kind of like a drip-drip, an incremental [reduction in] efficacy, because a single mutation on its own is very unlikely to lead to complete vaccine failure.”

Vaccine manufacturers are watching closely for the emergence of new mutations that would affect the vaccines, and considering how they might re-engineer them. “No vaccine against a coronavirus is likely to be effective forever—it would have been possible to predict some time ago that people may need to have repeated vaccinations over time,” Peacock says. “But we’re certainly not there yet. For now it’s a matter of rolling out the current vaccines as fast as possible, and then watching for new mutations as they arise. It can be quite difficult to predict exactly what’s coming, but we have got the tools to spot them.”