76% of infections in Brazil originate from three coronavirus strains

The greater genetic mapping of coronavirus variants in circulation in Brazil suggests that 76% of infections in the country were caused by only three strains. By sequencing the genetic material from 427 virus samples in Latin America, the researchers concluded that more than 100 infected people crossed the country's border to start the epidemic, but only a few triggered local outbreaks.
The information, which is important to monitor the geographical spread of the virus and guide future vaccine projects, is described in a study published on Thursday (23) in the journal "Science", in one of the most comprehensive scientific papers on the presence of coronavirus in Brazil published so far.
In all, 15 Brazilian institutions participated in the project conducted by the University of Oxford, which leads the study of Imperial College London, in addition to other foreign research centers. USP, Unicamp and UFRJ coordinated genetic sequencing from samples collected in more than 80 municipalities in 20 states
A detailed epidemiological analysis of the work crossed data from Covid-19 case records, people mobility measured by cell phones and the relationships between sequenced genomes.
In the study, signed by 81 scientists, the message is clear: the epidemic is still out of control in the country and it is necessary to expand measures of social distancing, testing and tracking contacts (the latter a measure never adopted by the country on a larger scale).
"This study sheds light on epidemic transmission and the evolutionary trajectories of Sars-CoV-2 strains in Brazil and provides evidence that current interventions remain insufficient to keep virus transmission under control in the country," the scientists write.
The study provides an update of the estimate of the so-called "basic reproduction number" for Brazil, the variable *R0*, which indicates how many people each individual with the coronavirus usually infects
According to the study, the measures of social distancing managed to bring down the *R0* of Brazil from 3 or more to something between 1.0 and 1.6, a level that is still insufficient to contain the progress of Covid-19. (The epidemic only slows down *R0* below 1.0).
The crossing of genetic material data between one virus and another is a powerful tool in epidemiology, because it allows to investigate whether the virus found in one location is related to another, and reassemble the spreading trajectories.
Adopting this strategy, the researchers, led by Nuno Faria of the University of Oxford, identified that the epidemic had two distinct moments in Brazil. One of them was until about March 20, when most of the spread occurred within the states, and a second moment, after that date, in which there were many events of transport of viruses from southeastern states to others of the country.
"The dynamics of the epidemic that happened in the beginning, is that we had a lot of imports from different countries to Brazil, and we closed airports for international flights but had not yet closed for domestic flights," explains Renato Santana, a geneticist at UFMG who is one of the co-authors of the study in "Science". "Only then was there a movement to start closing state borders, but the virus had already spread between different states forming these three great lineages that we are talking about in the study."