South African virus variant is identified for the 1st time in Brazil – unpublished report

RIO DE JANEIRO, BRAZIL –  The South African variant of coronavirus, known as B.1.351, was identified for the first time in Brazil, through genetic analysis, in a sample collected in the city of Sorocaba (interior of São Paulo).

The discovery was made by a group of researchers, members of a genomic surveillance network that monitors the dissemination of the Covid-19 virus in the state of São Paulo, coordinated by the Butantan Institute and with participation from USP and other research institutions.

The South African variant worries scientists because it is more transmissible and can evade infected people’s immune systems.

The discovery is described in an article published as a preprint on the medRxiv website on April 4. The work originated from establishing a genomic surveillance network of the SARS-CoV-2 virus in the state of São Paulo, integrating several laboratories, including some privately owned.

“The focus of the research is to sequence and obtain SARS-CoV-2 genomes in several locations in the state, to understand the dynamics of the virus dissemination in the population, as well as to find potential new variants,” explains researcher Rafael dos Santos Bezerra from the School of Medicine of Ribeirão Preto (FMRP) at USP, one of the authors of the work.

“This has already been proving effective with the finding of the South African strain found in the city of Sorocaba.”

In all, the researchers sequenced and generated 217 genomes of the virus, from an initial collection of samples in several cities in São Paulo’s interior, including Sorocaba, Araçatuba, Marília, Taubaté, Campinas, and Ribeirão Preto, as well as cities in the Greater São Paulo and Baixada Santista regions.

“We then classified each isolate of the virus, according to its respective lineage, and characterized the pattern of mutations,” describes Bezerra.

“To trace the evolutionary history of these sequences, we performed genetic analysis and, finally, reconstructed the temporal history of the B.1.351 isolate, thus being able to estimate a possible date of introduction of the lineage in the country.”

Of the 217 genomes analyzed, 64.05% belonged to the P.1 strain, which appeared in the state of Amazonas and was first identified in Japan, followed by the B.1.1.28 strains, which was the one with the largest distribution in Brazil and probably originated P.1, with 25.34% and B.1.1.7, known as the English variant of coronavirus, which appeared in 5.99% of the samples.

“The P.2 strain, also possibly originating from B.1.1.28, which is a variant of great scientific interest, was detected in only 0.92% of the cases. This shows a possible advance of P.1 over other lineages that were predominant in São Paulo, such as B.1.1.28,” reports the researcher.

“Although the South African variant was identified in only a single sample, this fact is worrisome because it behaves very similarly to P.1, with greater transmissibility and immune system escape.

According to the paper, Sorocaba’s strain shares 15 mutations with the isolate initially characterized in South Africa but lacks six of these defining mutations and has in its genome nine unique mutations.

“However, genetic analyses demonstrate the undeniable proximity of our isolate to the South African strain, and it clusters with other sequences of this same type, more precisely with isolates of the variant sequenced in Europe,” Bezerra points out.

“The origin of the most recent common ancestor of this genomic variant was inferred between mid-October and late December 2020. The analysis of the generated sequences demonstrated the predominance of the P.1 strain and allowed the early detection of the South African strain for the first time in Brazil.”

Source: UOL