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What do we know so far about the variants of COVID-19 first identified in Brazil?

This article was published on
March 11, 2021

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Major Brazilian cities are recording new daily highs in COVID-19 deaths as of March 2021, sparking concerns about the risks of a variant known as P.1 that was first identified in Brazil. P.1 is still being studied, but preliminary research suggests it could be associated with an increase in transmissibility and/or reinfection.

Major Brazilian cities are recording new daily highs in COVID-19 deaths as of March 2021, sparking concerns about the risks of a variant known as P.1 that was first identified in Brazil. P.1 is still being studied, but preliminary research suggests it could be associated with an increase in transmissibility and/or reinfection.

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What our experts say

The virus SARS-CoV-2 that causes COVID-19 has been mutating like other viruses, but most are not variants of concern (abbreviated as VOC) that would significantly impact the current COVID-19 pandemic. Recent variants that have concerned scientists include B.1.1.7 (also called VUI-202012/01) from the U.K., B.1.351 (also called 501.V2) from South Africa, and P.1 (also called 20J/501Y.V3) and P.2 from Brazil.

These variants of concern have multiple mutations, including in spike proteins that enable the virus to enter cells in the human body and cause infection. Scientists are monitoring whether these variants are more transmissible and more able to evade antibodies generated from previous infection or vaccination. This means the variants could potentially spread at higher rates between people, reinfect more individuals who have had COVID-19, and be harder to protect against using some of the current vaccines. 

P.1 is a variant descended from the B.1.1.28 lineage that was first reported in Japan among four travelers from Brazil during a routine screening at Haneda airport on January 6, 2021. The P.1 variant includes subvariants 28-AM-1 and 28-AM-2, which are thought to have developed independently of each other in the Brazilian Amazonas region.

Seventeen unique mutations have been identified in the P.1 variant. The P.1 variant is a growing concern in several major cities of Brazil, such as Manaus (the largest city in the Amazon region), and there are additional concerns about international spillover effects as this variant has already been detected in other countries like the United States. 

In Manaus, where a majority of the population is likely to have been infected with COVID-19 (up to 76% according to a study of blood donors from October 2020), the recent surge in COVID-19 hospitalizations has been concerning. A study in the Lancet suggests the P.1 variant could be among a few of the reasons why this Brazilian city is seeing a resurgence in COVID-19 cases, when it was hoped that there would be at least some level of population immunity by now. According to genomic sequencing work done in Manaus, the P.1 variant was identified in 42-52% of cases from December 2020 and 85% of cases in January 2021, without showing up in earlier samples from March to November 2020. For other lineages that were detected in 96% of cases from March to November 2020, the frequency declined to 8% by January 2021. 

P.2 is another variant that descended from the B.1.1.28 lineage from Brazil, thought to have originated in Rio de Janeiro. The P.2 variant’s mutations also include E484K, located in a spike protein receptor binding domain, which has been called an escape mutation and nicknamed “Eek.” In contrast to the P.1 variant, the P.2 variant has not been found to have the additional mutations of concern K417T and N501Y located in spike protein receptor binding domains. According to genomic sequencing work done in Manaus, the P.2 variant was detected in 25.4% of cases in December 2020 but this decreased in January 2021, suggesting it may have been outcompeted by the P.1 variant. Genomic sequencing work done in Rio de Janeiro suggests the P.2 variant was still restricted more to the Rio de Janeiro state capital as of October 2020, although it was found to be increasing in frequency in other areas. 

As of early 2021, while the P.1 and P.2 variants from Brazil are both being monitored, experts have been particularly concerned with the P.1 variant. According to two pre-print studies, the P.1 variant may be 1.4 to 2.2 times more transmissible than non-P.1 lineages. More research is needed to better understand the P.1. and P.2 variants and their potential impacts. 

Preliminary studies with the Oxford-AstraZeneca vaccine, Pfizer-BioNTech vaccine, and China’s Sinovac CoronaVac vaccine suggest these vaccine candidates offer at least some protection against severe illness from the P.1 variant. However, the team behind the study of the AstraZeneca vaccine warns there could be less protection against the P.1 variant and the team behind the New England Journal of Medicine study of the Pfizer-BioNTech vaccine was only able to do laboratory testing, as the Pfizer-BioNTech vaccine has not yet been rolled out in Brazil. 

Context and background

According to the Philippine Genome Center Executive Director Cynthia Saloma and Department of Health Undersecretary Maria Rosario Vergeire, the Brazilian variant P.1 has not yet been detected in the Philippines. This clarification was announced after Quezon City Mayor Joy Belmonte reported there were 13 cases of the B.1.1.7 variant from the U.K., 4 cases of the B.1.351 variant from South Africa, and 1 case of a Brazilian variant (reported to be a common variant of Brazilian origin descended from B.1.1.28 but not a variant of concern like P.1). 

Resources

  1. Science Brief: Emerging SARS-CoV-2 Variants (U.S. CDC)
  2. What are the Brazil, South Africa and UK variants and will vaccines work? (BBC)
  3. What we now know — and don’t know — about the coronavirus variants (STAT News)
  4. Brief report: New Variant Strain of SARS-CoV-2 Identified in Travelers from Brazil (Japan National Institute of Infectious Diseases)
  5. Virus Variant in Brazil Infected Many Who Had Already Recovered from COVID-19 (NYTimes)
  6. Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings (Virological)
  7. Phylogenetic relationship of SARS-CoV-2 sequences from Amazonas with emerging Brazilian variants harboring mutations E484K and N501Y in the Spike protein (Virological)
  8. Spike E484K mutation in the first SARS-CoV-2 reinfection case confirmed in Brazil, 2020 (Virological)
  9. SARS-CoV-2 reinfection by the new Variant of Concern (VOC) P.1 in Amazonas, Brazil (Virological)
  10. Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence (The Lancet)
  11. COVID-19 epidemic in the Brazilian state of Amazonas was driven by long-term persistence of endemic SARS-CoV-2 lineages and the recent emergence of the new Variant of Concern P.1 (Nature Portfolio Journal Pre-Print)
  12. Levels of SARS-CoV-2 Lineage P.1 Neutralization by Antibodies Elicited after Natural Infection and Vaccination (Pre-Prints with the Lancet)
  13. Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil (medRxiv)
  14. Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil (medRxiv)
  15. Circulating SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity (medRxiv)
  16. Covid-19: Brazil experts issue warning as hospitals 'close to collapse' (BBC)
  17. Brazil’s Covid Crisis Is a Warning to the Whole World, Scientists Say (New York Times)

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