The genetic sequencing of the new coronavirus in just 48 hours yielded a group of Brazilian scientists much more than the feeling of achievement. After the discovery, the researchers now juggle to report the results, give interviews and organize future plans. “We didn’t imagine it would have such repercussions”, he told an interview to Tilt the doctor Ester Sabino.
“I have already participated in other research, with stronger results [dentro da ciência] and it was never like that. It’s been a lot of news. But I think it is an opportunity to popularize science in Brazil, “said she, who is director of IMT (Institute of Tropical Medicine at the University of São Paulo) at USP (University of São Paulo) and coordinates CADDE (Centro Conjunto Brasil- United Kingdom for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology), network of researchers working with epidemics, responsible for the genetic analysis of the new coronavirus, officially classified as SARS-CoV-2.
To give you an idea, they were able to sequence in 48 hours what researchers from other countries are taking on average 15 days to do – with the exception of France, which also achieved in two days. This agility is a major step forward to help understand how the virus works and think about future strategies to contain the epidemic, as it shows the path taken by the virus and the mutations it suffers. In Brazil, four confirmed cases and 531 suspected.
Dr. Sabino explains that being able to do this in real time, while the epidemic is happening, is much better. Imagine that the virus can now be genetically traced much faster here in Brazil. It is easier to identify its origin. For example, it will be possible to know if a person was infected during a trip or if the contamination has already happened from a virus that has evolved and spread in the city / state / country itself.
In addition to being surprised by the repercussions, the doctor says that none of this would be possible without the work of a large team, with a lot of experience in the national epidemics of dengue, zika and chikungunya, and a much cheaper methodology than that used in others. study centers abroad.
Genome sequencing was carried out by biomedical practitioners Jaqueline Goes de Jesus, Ingra Morales and Flávia Sales and by pharmacist Erika Manuli, researchers from the USP Medical School, under the supervision of Sabino, within IMT-USP, in partnership with the Adolfo Lutz Institute (IAL) and the University of Oxford, through Professor Nuno Faria.
“We knew since January that the coronavirus would arrive in Brazil in an hour. We were just waiting [ter uma amostra]. When it arrived, we already had everything we needed to sequence “, explained Sabino.
As soon as the first Brazilian case was confirmed, released on February 26, the team received nasopharyngeal samples from the infected 61-year-old man, sent by the department of biomedical Claudio Tavares Sacchi, coordinator of the strategic laboratory of the Adolfo Lutz Institute. “It is the secretion that is between the nose and the trachea, because it is a virus that reaches the lung. But in other viruses we can collect samples of blood, urine,” explained researcher Ingra Morales.
Low-cost system revolutionized research
Then a process began in the laboratory for the extraction of RNA of the new virus. The first step was to break the cell in half to gain access to the genetic material, which was used for sequencing. A big difference here was using advanced technology, developed in the United Kingdom, but adapted by Brazilians. It is a portable device known as MinION, which is smaller than a cell phone and reads the genetic material of viruses of various types.
“MiniION does the nanopore sequencing [material poroso]. The RNA sample passes through it and generates a base genetics different in the end. The computer receives these results, performs a bioinformatics analysis and assembles the genome with the data it has “, detailed Morales.
Imagine that DNA is a 30,000-letter strand in a specific order. The sequencing done with the help of MiniION was able to identify the order in which they are organized in the virus of the collected sample, in a process that reached 96% of the genome in 48 hours.
This result was compared with 127 complete genomes of the new coronavirus, which had already been sequenced in 17 different countries – that was how it was discovered that the two Brazilian cases had different genomes (read more here).
“Me, Jaqueline and Flávia were together at the time [em que o processamento dos dados do sequenciamento terminou]. With Jaque doing the analysis, we contacted the Oxford people to see if it was working. When we saw that it had worked, we were very happy. It was very good, to show that we have a lot of good Brazilian scientists, who can do this kind of work at the same time at the cut of scholarships [de pesquisa] and little investment “, he said.
Thanks to Ingra Morales, a Fapesp fellow (São Paulo Research Foundation) at the time, it was possible to do the entire process at a low cost.
Developed in England, the original device cost $ 500 and required expensive protocols (ways of handling genetic material). During a period of study in the United Kingdom, the scientist developed an efficient way to sequence several samples at the same time (which optimizes the work) and reuse the chip of the electronic device more times, which still results in good savings. This caused the cost of testing to drop to $ 20 to $ 30 – the team did not have to buy new MinION, as it had the device in its laboratory.
“This sequencer model was first used with the ebola virus [em 2015]. Then, in 2016, researchers from the United Kingdom came to Brazil to work with the Zika virus, in partnership with us. I had the opportunity to study there for six months and we were able to create this cheaper way to sequence viruses “, explained Morales.
“Before, we did the studies, gathered the samples and sent them for analysis [fora do Brasil]. The results came after the epidemic was over, not while it was happening. We wanted to do it at a lower cost. With this value, the device can be used to help public health, “said Sabino.
The next steps
If it depends on Sabino, the laboratory should resume research on the dengue virus as soon as possible. In parallel, the team will assist in the sequencing of new samples of the coronavirus.
“Who is going to do and continue the virus surveillance is the Adolfo Lutz Institute. Here, we will have other things to do. The university must always be looking for the new thing. And not only to publish scientific articles, but to help the sector public or technological part of the industry in cases like these [de epidemia]”, he stressed.