Low sequencing of Covid-19 samples raises risks in Brazil

One year and nine months after the start of the pandemic, Brazil still has little monitoring of the variants of the new coronavirus that circulate throughout the country. Of the 22 million confirmed Covid-19 cases, only 0.35% have been laboratory sequenced.

The index is even lower than that of countries with a similar socioeconomic level, such as Chile (0.91%) and South Africa (0.82%). This type of test allows for the identification of mutations present in the sample and for indicating the advancement of new strains.

With Ômicron in the country, screening helps to understand where the variant arrives, how fast it spreads and whether it is associated with the severity of infections in certain locations.

Minimum mark

According to specialists, the ideal would be to reach the minimum mark of 0.5% of sequenced cases. The number of tests, moreover, would have to be expanded. The integration of the laboratory structure and a faster release of the collected virus samples are challenges to overcome the problem.

Fernando Spilki, virologist and professor at Feevale University, says that genomic sequencing has made considerable progress in the country since the beginning of the health crisis, but that it could improve.

“From February of last year until the beginning of this year, there were about 2,000 sequences registered in Gisaid (the platform that gathers the sequences). Since then, the number has gone to 75 thousand. Last year, we couldn’t even sequence 0.1% of the samples”, said Spilki.

The virologist explains that the confirmation of the first cases of Ômicron in Brazil, associated with greater preparation of laboratories since the beginning of the pandemic, has the potential to intensify testing and sequencing procedures in Brazilian territory.

He reinforces that genomic sequencing can be combined with genotyping, a strategy to identify differences in the genetic makeup of people, which can be performed using PCR tests.

Disparity

Virologist and scientific researcher at the Todos pela Saúde Institute (ITpS), Anderson Brito says that one of the main problems in the country at the beginning of the pandemic was the disparity between regions in the performance of genetic sequencing. “There were states with pretty big coverage, and others with practically nothing.”

According to him, the presence of institutions such as the Oswaldo Cruz Foundation (Fiocruz) in places such as Rio de Janeiro has enabled large-scale sequencing since the beginning of 2020, while states such as Maranhão, Piauí and Tocantins had “a huge gap in genomic surveillance” .

“If a new variant emerged in these regions, it could have circulated for a few weeks without us knowing,” said Brito.

He says that the improvement in surveillance only happened when there was an increase in the proportion of cases sequenced and in territorial coverage, with cooperation between states with different conditions.

More agility

The country needs to move forward to monitor the advancement of the Ômicron variant, not only in terms of the scope of sequencing, but also in terms of agility. Today, samples sequenced in Brazil take, according to the median available on the Gisaid platform, around 59 days to be published. In Peru, the index is 55 days, while in Chile it is 27.

For Brito, the reduction in the registration time of sequencing is essential to allow public managers to have the real dimension of the situation in the country. For that, he says, it would be necessary to have more teams working to quickly release the genomes in Brazil.

“If the Ômicron sample is collected today, but the sequencing comes out in two months, it ends up getting late.”

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