Even though more and more coronavirus vaccines are being administered around the world, many countries are still struggling with epidemics and are struggling to provide help to those in need.
One of those countries is Brazil. Here they face a second wave of massive epidemics, numerous daily deaths and cases of collapsing health systems. In the city of Manaus, things looked unusually gloomy from December to early spring.
The city was hit so hard by the first wave of 2020 that it was in fact considered one of the few places in the world to have achieved collective immunity. About 75% of the city’s population had been infected. But then the second wave hit in November and December.
Now a new study published in Science with collaborators from Brazil, the United Kingdom and the University of Copenhagen shed light on the reasons why Manaus is again facing these difficulties.
“Our main explanation is that there is an aggressive variant of the coronavirus called P.1 which appears to be the cause of their problems. Our epidemiological model indicates that P.1 is likely to be more transmissible than previous strains of coronavirus and probably be able to escape the immunity acquired by infection with other strains, ”explains the corresponding author of the new study, Samir Bhatt, researcher at the Department of Public Health at the University of Copenhagen. .
Appeared in November
The researchers used many forms of Manaus data to characterize P.1 and its properties, including 184 DNA sequencing data samples. They find that P.1 genetically speaking is different from previous strains of coronavirus. He acquired 17 mutations including an important trio of mutations in the spike protein (K417T, E484K and N501Y).
“Our analysis shows that P.1 appeared in Manaus around November 2020. It went from undetectable in our genetic samples to 87% of positive samples in just seven weeks. as well as many other countries in the world, ”says Samir Bhatt.
Modeling Using Machine Learning
The researchers then used an epidemiological model to estimate the degree of transmissibility of P.1. In addition to estimating the signs of P.1 escaping the immunity acquired during a previous infection.
“Roughly speaking, our model integrates many data sources such as mortality counts and genetic sequences and compares two different virus strains to see which best explains the scenario that unfolded in Manaus. One was the ‘normal coronavirus’ and the other has been dynamically adjusted using machine learning to better adapt to actual events in Brazil, ”says Samir Bhatt.
This modeling allowed the researchers to conclude that P.1 is likely to be between 1.7 and 2.4 times more transmissible than non-P1 lines of the coronavirus.
They also conclude that P.1 is likely to be able to escape between 10 and 46% of the immunity acquired by infection with a non-P.1 coronavirus.
“As researchers, we must caution in extrapolating these results so that they are applicable everywhere else in the world. However, our results highlight the fact that increased surveillance of infections and different strains of the virus is necessary in many countries in order to fully control the pandemic, ”concludes Samir Bhatt.