The viral family grows
Viruses such as SARS-CoV-2 are classified into strains on the basis of small differences in their genetic material. Since Dec. 26, 2020, in addition to the British and South African variants, it appears the Carioca lineage also is a player.
In a preprint article, researchers analyzed the evolution of the epidemic in Rio de Janeiro from April 2020 until just before the new increase in incidence in December. They compared the complete sequences of the viral genome of 180 patients from different municipalities. The study, which is being jointly conducted by members of the Federal University of Rio de Janeiro and the National Laboratory for Scientific Computing, identified a new variant of SARS-CoV-2 that has five unique mutations (from one of the predominant strains). Concern arose because, in addition to those five genetic changes, many of the samples had a sixth – the well-known E484K mutation.
“The three lines – the U.K., South Africa, and Brazil – were almost synchronous publications, but there is no clear evidence that they have any kind of common ancestry,” Carolina M. Voloch, PhD, the article’s first author and a biologist and researcher at the Molecular Virology Laboratory and associate professor in the department of genetics at the Federal University of Rio de Janeiro, said in an interview.
Dr. Voloch’s research focuses on the use of bioinformatics tools to study the molecular, phylogenetic, and genomic evolution of viruses.
“The emergence of new strains is common for viruses,” she said. “It can be happening anywhere in the world at any time.”
She stressed that identifying when mutations emerge will help to define the new Brazilian lineage. Researchers are working to determine whether the neutralizing antibodies of patients who have been infected with other strains respond to this Rio de Janeiro strain.
“We hope to soon be sharing these results,” Dr. Voloch said.
The article’s authors estimated that the new strain likely appeared in early July. They say more analysis is needed to predict whether the changes have a major effect on viral infectivity, the host’s immune response, or the severity of the disease. Asked about the lineage that caused the reinfection in Bahia, Dr. Voloch said she hadn’t yet contacted the authors to conduct a joint analysis but added that the data disclosed in the preprint would not represent the same variant.
“There are only two of the five mutations that characterize the Rio de Janeiro lineage. However, it has the E484K mutation that is present in more than 94% of the samples of the new variant of Rio,” she said.
She added that there’s a possibility of reinfection by the lineage that’s circulating in Rio de Janeiro and in other states, as well as countries such as the United States, the United Kingdom, and Japan.
“The Carioca virus is being exported to the rest of the world,” Dr. Voloch said.
Virus’ diversity still unknown
Researchers now know that SARS-CoV-2 probably circulated silently in Brazil as early as February 2020 and reached all the nation’s regions before air travel was restricted. Since the first half of 2020, there have been two predominant strains.
“More than a dozen strains have been identified in Brazil, but more important than counting strains to identify the speed with which they arise – which is directly associated with the rate of infection, which is very high in the country,” said Dr. Motta.
The so-called variant of Rio de Janeiro, he said, has also been detected in other states in four regions of Brazil. The key to documenting variants is to get a more representative sample with genomes from other parts of the country.
As of Jan. 10, a total of 347,000 complete genome sequences had been shared globally through open databases since SARS-CoV-2 was first identified, but the contribution of countries is uneven. Although the cost and complexity of genetic sequencing has dropped significantly over time, effective sequencing programs still require substantial investments in personnel, equipment, reagents, and bioinformatics infrastructure.
According to Dr. Voloch, it will only be possible to combat the new coronavirus by knowing its diversity and understanding how it evolves. The Fiocruz Genomic Network has made an infographic available so researchers can track the strains circulating in Brazil. It›s the result of collaboration between researchers from Fiocruz and the GISAID Initiative, an international partnership that promotes rapid data sharing.
As of Jan. 5, researchers in Brazil had studied 1,897 genomes – not nearly enough.
“In Brazil, there is little testing and even less sequencing,” lamented Dr. Souza.
“In the U.K., 1 in 600 cases is sequenced. In Brazil it is less than 1 in 10 million cases,” Dr. Voloch added.
So far, no decisive factors for public health, such as greater virulence or greater transmissibility, have been identified in any of the strains established in Brazil. The million-dollar question is whether the emergence of new strains could have an impact on the effectiveness of vaccines being administered today.
“In one way or another, the vaccine is our best bet ever, even if in the future we identify escapist mutants and have to modify it,” Dr. Motta said. “It is what we do annually with influenza.”
Dr. Voloch, Dr. Motta, and Dr. Souza disclosed no relevant financial relationships.
A version of this article first appeared on the Portuguese edition of Medscape.com.