New method allows faster and cheaper assessment of the variants that are circulating in a given population
Published this April, an article co-authored by Instituto D’Or de Pesquisa e Ensino (IDOR) and the Federal University of Minas Gerais (UFMG) discusses a new variant of SARS-CoV-2, the COVID-19 virus that has been identified.
The increased number of severe cases across Brazil has led to higher concern about the emergence of new and more dangerous variants of the new coronavirus. Dr. Renato Santana, researcher with IDOR and UFMG and author of said study, has explained that in the state of Minas Gerais, 13 identified variants are circulating, being the two most worrying variants the B.1.1.7, identified in the United Kingdom, and the P.1, which emerged in Manaus. Dr. Santana’s team collaborated in the identification of the latter variant.
He adds that the possible new variant may have traits of P.1 and also of P.2, strands that are not associated with high mortality rate but which are more contagious. Therefore, the new variant may not be claimed to be more dangerous. “We cannot really say it is a new variant, to be able to claim that we need to investigate more genomes and more cases”, he adds. Dr. Santana was responsible for the discovery after collecting clinical samples in the metropolitan area of Belo Horizonte, which led to sequencing 85 genomes of SARS-CoV-2 between October 2020 and March 2021.
Investigating the genetics of the virus does not yield only alarming news, though. Through collaboration with Brazil’s Genome Surveillance Network, Dr. Santana has developed a new methodology to identify new variants in a faster and less costly manner.
Identifying a new variant requires Next Generation Sequencing (NGS), a process that may take days or even weeks. The major challenge has been having to assess hundreds of samples to then reducing them to the number of ideal samples that may lead to identifying which variants are circulating where.
As the process did not meet the urgency and the meager resources available, the researchers managed to change it by using NGS only to assess samples that had been previously mapped out and a possible new variant had been diagnosed by PCR testing. This change reduced the assessment from weeks to around 4 hours, thus significantly increasing the number of assessed samples to thousands and being able to assess the variants circulating in a given geography much more accurately.
During a meeting held with the World Health Organization (OMS) on April 16, Dr. Santana was requested to share his methodology with genome surveillance teams around the world to support speeding up the assessment of variants in other countries. ”The idea was to keep the methodology open-access and available to everyone. This methodology will also be exported in addition to being used across Brazil by Rede Vírus, an initiative undertaken by the Brazilian Department of Technology that aims at diagnosis and research conducted in laboratories across the country”, he adds. This new methodology is currently being used by IDOR in Rio Janeiro through a partnership with Richet Laboratory, which provides the samples for the study. “We shall soon have the history of variants circulating in Rio too!”, predicts Dr. Santana.