Brazil is the next country to conduct a nationwide study on the coronavirus within the platform created by the British government to help other countries expand their capacity for genomic sequencing of the virus, called NVAP (New Variant Assessment Platform).
The study, carried out in partnership with the Corona-Ômica Network of the MCTI (Ministry of Science, Technology and Innovation), will be the largest genomic surveillance initiative ever conducted in Brazil and should identify the variants and subtypes that circulate in the 27 Brazilian states to help understand the transmission of SARS-CoV-2 within the national territory.
The research is funded by the UKHSA (United Kingdom’s National Health Safety Agency) and has the support of researchers from different Brazilian federal universities and the Pardini Group, a diagnostic medicine network that will make the positive tests collected from more than 6 thousand own laboratories and partners.
The team’s goal is to sequence the complete SARS-CoV-2 genome from about 5,000 laboratory samples collected per month for approximately 6 months.
The virologist and professor at UFMG, Renato Santana, is one of the research coordinators and explains the importance of expanding genomic surveillance in Brazil.
“The goal set by the WHO is for countries to be able to sequence between 5% and 10% of positive cases. But while nations like the United Kingdom and Denmark managed to sequence almost 50% of cases, we did not reach 1%. In a country like Brazil , with continental dimensions, the virus was practically not sequenced”, he says.
In addition, Santana explains that the geographic expansion of sample collection will also provide an overview of Covid-19 in the interior of the country.
“The studies conducted so far have focused on large urban centers, mainly capitals, and only now will we fill the gap of other cities that were previously neglected.”
The objective is that greater sequencing will allow researchers to evaluate new variants in Brazilian territory, in addition to evaluating the transmission rate.
“If there is a variant that escapes the vaccines we have, for example, we will show the importance of booster doses focused on these variants. The study can guide public policies for immunization and protection measures. The idea is to generate quality information so that we can support public health measures”, highlights the virologist.
Sequencing step by step
The virus genome, unlike the human genome, is not DNA, but RNA, a type of nucleic acid. The molecule is also present in us humans, but it does not govern our genome.
In order to be able to sequence all the genes of the virus, the researchers collect the positive swab samples and send them so that the RNA can be extracted in the laboratory. Then they turn that RNA molecule into DNA.
“From there, we use a strategy that allows us to amplify the entire genome of the virus, which we put in automatic sequencers”, says Santana. Sequencers are machines linked to computers that calculate chemical reactions all the time.
According to the expert, the virus constantly makes small changes to its own genome, but an adaptive advantage is needed for it to be able to establish itself as a new variant.
“It would, for example, run away from vaccine protection or replicate much faster.”
Until reaching the final result, the whole process takes around two weeks. According to Professor Renato, the study samples have already been selected with random coverage of the entire national territory and the viral RNA has already been extracted from all samples. Now, the teams await the arrival of the reagents for the genomic analysis sent by England.
“The British government’s participation goes beyond funding. There is also training for scientists on how to perform bioinformatics analysis and deal with molecular epidemiology. The researchers will learn analysis methodologies so that knowledge stays in Brazil”, points out the virologist.
As a result, the integration of epidemiological data will be important for the association between Sars-CoV-2 strains and covid-19 transmission rates, in addition to helping to assess the effectiveness of the vaccination program in Brazil.
“Everything we learn from the genomics of Sars-Cov2 can be applied to other pandemics, other viruses. These are studies that generate expertise and analysis training, not only of covid-19, but prepare us for other viruses such as influenza, dengue, zika, chikingunya, etc.”, concludes the specialist.
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