A methodology that aims to make monitoring of the new coronavirus variants simpler and more agile, as well as cheaper, has just been developed at Fiocruz Pernambuco. It is based on a technique that is already widely used and available in Brazil and worldwide, the Sanger sequencing - also called sequencing by capillary electrophoresis. The paper with this finding has just been made available online as a preprint at the MedRxiv platform.

The test was prepared by the Fiocruz PE team, which monitors new SARS-CoV-2 variants in the state, using state-of-the-art infrastructure and technology available at the Biosafety Level 3 Laboratory (NB3) and at the Technology Platform Center (NPT) of the institution. The work is performed from samples provided by Lacen/PE, by order of the Health Department of the State of Pernambuco (SES/PE). The group is also part of the Covid-19 Genomic Monitoring Network of the Oswaldo Cruz Foundation.

This work takes on greater relevance when observing the emergence and spread of new variants and the pandemic resurgence in Brazil and worldwide.  The explosion of Covid-19 cases observed throughout Brazil in March, for example, is related to the P.1 variant, initially identified in the state of Amazonas, which has been spreading rapidly across the country.

“It is very important that P.1 variant, as well as all other new coronavirus variants, are continuously monitored. These data are essential for combating the disease, both from an epidemiological point of view, as well as in the adaptation of new vaccines and diagnostic tests”, emphasizes the Public Health technician at Fiocruz PE, Matheus Figueira Bezerra, lead author of the paper. The publication is co-authored by other professionals and a graduate student in Biosciences and Biotechnology in Health, all from the institution: researchers Gabriel Wallau (Entomology and Bioinformatics), Marcelo Paiva (Entomology), Cássia Docena (NPT), Sinval Brandão Filho (Immunology), Constância Ayres (Entomology), the technician Viviane Carvalho (NPT), and the doctoral candidate in BBH Laís Ceschini Machado. 

The study points out that the complete sequencing of the viral genome, considered today the gold standard for identifying these variants, has a complex execution, presenting some difficulties when applied in epidemiological surveillance of the pandemic. The cost per sample is high, especially at a time when the Brazilian currency is devalued. The number of laboratories in Brazil (and worldwide) that have a next-generation sequencer is not enough to meet the current demand. The procedure to perform the complete sequencing of the viral genome is time-consuming and the interpretation of the results is complex, requiring the work by professionals specialized in Bioinformatics and the use of computers with high data processing capacity, making the results take up to weeks to be ready. In addition to all this, some items required for sequencing are in short supply at suppliers due to high demand, which makes researchers' work difficult.