‘Neither Alternative Was Good News’: A Brazilian Immunologist Traces the Spread of the P.1 COVID Variant
Above, in a scene from the documentary “The Virus That Shook the World,” people carry a coffin in Brazil. Most of that country’s recent deaths have been due to the COVID variant known as P.1.
There are currently more than 1,200 variant lineages of the COVID-19 coronavirus identified in the world. Viruses are constantly mutating, so any mutation from the original strain identified in Wuhan, China, is considered a variant. The more times COVID-19 is transmitted from person to person, the higher the risk of mutations.
But not all variants are of equal concern to public health experts, who focus on the ones that could make COVID-19 more transmissible, more severe or that could interfere with vaccine efficacy or testing accuracy.
Of those 1,200 lineages, the CDC reports five variants of concern circulating in the United States. B.1.1.7 — the most prevalent in the U.S., at 53,819 cases — was first reported in Kent, in southeastern England, in December 2020. It spread rapidly across the UK and then on to more than 100 countries. P.1, the second most common variant in the U.S. at 2,598 cases, was first reported on Jan. 10, 2021, in Japanese travelers returning to Tokyo from Manaus, Brazil.
Home to 2 million people, Manaus’ makeshift cemeteries appear in the new FRONTLINE documentary The Virus That Shook the World. Brazil is second only to the U.S. in total number of COVID-19 deaths, with P.1 — first identified in the U.S. on Jan. 26, when a Minnesota patient fell ill after a trip to Brazil — causing most of Brazil’s new infections in March and April. P.1 has also been responsible for roughly 30% of the country’s nearly 400,000 deaths to date, according to Brasil.io, a collaborative dashboard.
To understand how P.1 rose and spread to 40 countries and counting, FRONTLINE spoke in Portuguese with Ester Sabino, an immunologist and professor at the Institute of Tropical Medicine, University of Sao Paulo, and the local coordinator of a virus-research initiative between Brazil and the United Kingdom. Her team was the first to sequence the COVID-19 genome in Brazil and was one of the first to detect the P.1 variant.
When was the P.1 variant first identified in Brazil?
The week of Jan. 4, 2021, we received the samples from a Manaus laboratory. We presented the results to the Manaus health secretary on Jan. 10, the same day the report from Japan happened.
When we saw the first sequence, we were alarmed, because it was very different. There were several mutations in the sequence, including those associated with higher transmission in B.1.1.7, the UK variant. We had a meeting with other teams and informed them of what we found. Fiocruz [another Brazilian public health institute] also found it.
We had published a paper saying that many people [up to 76% of Manaus’ population, as of October 2020] had been exposed to the virus. So, anything that could start a new epidemic in Manaus would require a different understanding.
A variant would explain the problem: Either people lost their immunity to the virus too fast, or something very different was going on. Neither alternative was good news.
Where does a variant come from?
This is something that we still don’t understand, even for the variant detected in Kent. It has many mutations, has appeared suddenly and has spread rapidly. P.1 is also like that. The calculation we did is that it started at some point in November in Manaus, or in a place in the Amazon close to Manaus. There is a hypothesis that variants with a lot of mutations at the same time come from immunocompromised patients, but it’s still a hypothesis.
Talk us through the timeline, as P.1 spread.
In November and December, the variant started spreading in Manaus. So, all the flights leaving Manaus were possibly carrying infected passengers to many places in Brazil and the world. Even after the scientists detected the problem, Brazil’s government didn’t cancel flights. Many patients and family members were transferred to other cities in Brazil for treatment, and flights continued. The variant was spreading, bit by bit, and taking over.
We had an increase of gatherings at the end of the year. By January and February, P.1 had spread all over Brazil. In March, [the variant spread] in a synchronized way: All [Brazilian] states had high transmission rates at the same time. P.1 is up to 2.4 times more transmissible, in comparison to the first wave of infections. It’s not possible yet to compare P.1 and the other two variants [from Kent and South Africa].
Has P.1 morphed into further variants?
Not yet. We have to keep sequencing P.1 to understand how it will evolve. First, we had to understand how much it had spread throughout Brazil and how fast. This week, data from Rio de Janeiro state shows that almost 100% of new infections there are attributed to P.1.
How many other variants are currently circulating in Brazil?
We have detected three variants in Brazil, mostly recently the South African variant. There are thousands of lineages, but what really matters is the variants of concern: when a variant starts taking over or there’s any type of change to its behavior.
What did Brazil do to contain the variant?
It’s very hard in Brazil, because we have a president telling people to go outside all the time. [President Jair Bolsonaro has called complaints from critics plots against him.]
Brazil’s health ministry is very disorganized. [Brazil has had four different health ministers since the pandemic began, and the Bolsonaro administration stopped making COVID data publicly available online from June 5 to June 9, 2020, when a supreme court judge ordered it to resume.]
It’s very hard for individuals, groups or even states to act without federal coordination.
What’s been done here won’t solve the problem. … You need a plan, clear communication that people can understand, and that if we want to protect the population, everyone will have to work hard. Social distancing, wearing a mask: There’s no other choice.
Are there lessons for other countries?
The good news is that P.1 seems to be sensitive to the vaccine.
Variants will appear in many different places in the world, so it’s very important that the whole world gets vaccinated. If the U.S. population is vaccinated, of course, the U.S. will be safer. But it will never be totally safe, if variants keep appearing all over the world.