If there were any positive points in the coronavirus epidemic, the reason would be that we are facing signs of a revolution in the field of genetic sequencing. The agility in unraveling the epidemic indicates that there is a new milestone in science, capable of bringing answers to the population in record time.
“When we started, it took almost four years, a doctoral thesis, to sequence a gene of around three thousand pairs. Today, the entire human genome, four billion pairs, can be sequenced in one day, just to get an idea of how the technology has evolved”, says professor at the Unicamp Biology Institute, Paulo Arruda. The professor was one of the members of the team that analyzed the Xylella fastidiosa, the first living being to be genetically sequenced in Brazil, in 2000, and the first phytopathogen to be sequenced in the world. At that time, even using the most modern technologies, it took three years to complete the research. Two decades later, improved methodologies and equipment allowed the coronavirus sequencing in Brazil, by the team from the Institute of Tropical Medicine (IMT) at the University of São Paulo (USP), Adolfo Lutz and Oxford, was carried out in two days.
Paulo, who also worksm in the Central Laboratory of High Performance Technologies (LaCTAD) from Unicamp, explains that technology improvements were only possible thanks to multidisciplinary work. “The evolution of technologies happened and accelerated due to the challenge of sequencing the human genome, back in the early 1980s.” Physicists, chemists and biologists joined in and, in 2000, the first human DNA sequence was released, the result of 10 years of research. The work, which involves discovering the order of the nitrogenous bases that make up DNA, cost billions of dollars. Today, machines that work in sequencing, in addition to being fast, are increasingly accessible.
The device Nanopore, used by the Brazilian team in the coronavirus, for example, costs from a thousand dollars. The technology was developed by a startup created by Chemistry students at the University of Oxford, Nanopore Oxford. Slightly larger than a pen drive, the equipment has a membrane covered in pores the size of a few nanometers, a measurement that is equivalent to one centimeter divided by 10 million. These pores are so small that only a DNA, or RNA, molecule can pass through. With an electrical voltage on the membrane, each time the bases pass, the current changes. The difference in signals determines which type of base passed through.
“As they pass, they cause these differences in current interruption. Each nitrogenous base gives a different electrical signal that says 'now an adenine has passed, now a guanine, and so on'. This is being recorded”, points out Paulo. Therefore, the researcher says that the longest part of the process is obtaining the sample that will be placed in the device. After the machine translates the genomic composition, bioinformatics tools are used, which allow comparisons to be made with materials made available by scientists from other countries. Thus, the puzzle of the trajectory of the virus, or another being analyzed, is assembled, as well as the changes it presents in each region where it is disseminated can be observed.
“No one imagined that it would be possible to do something like this, on this scale and with such great resolving power. It can be loaded to carry out real-time analysis, for example, of isolated groups, allowing you to go to different locations, in distant regions, take samples and carry out sequencing on site. It revolutionized sequencing technology, quickly and easily”, says the researcher.
The same technology has already been used in Brazil recently in the Zika virus epidemic. However, the first complete sequencing of Zika occurred in 2016, almost a year after the virus was discovered in the country. Therefore, Paulo believes that the speed in understanding the coronavirus epidemic is a new milestone. “We can consider, yes, that science has reached a point that can be considered a great milestone in terms of the speed with which it is able to unveil the genome of this virus.”
Why is sequencing important?
For the professor, the importance of sequencing is broad and the applications will be increasingly explored. In the case of the coronavirus, he mentions the possibility of knowing whether there are changes in the genetic code of the virus strains. “Will the strain of the virus that came here have a change in the genetic code and make it more aggressive? How will we know? With genome sequencing, it is possible to say whether it is identical to the strain found in China, Italy, and so on.”
In relation to the work in progress by the USP team and Adolfo Lutz, it has already been pointed out by scientists that the genome of the virus of the first person infected in Brazil has more similarities with the one found in Germany than with the one found in China. “The importance of knowledge is this: knowing whether the strain that is infecting and causing illness in individuals here is the same. If it is different, it is necessary to understand whether it has become more or less aggressive”, says Paulo.
Sequencing, moreover, is important in the development of possible treatments and vaccines. Due to changes in the virus, the researcher emphasizes that it is not yet possible to know whether vaccines developed in Brazil, China or elsewhere in the world will be effective only in the country of origin or more broadly.
“In biology you have to test to know. A change in one base in the virus's genome sequence does not necessarily mean that it will behave differently and will not react. Everything will depend on tests. It is necessary to compare the viruses in the database, with viruses that have already been sequenced, see where the difference is, what type of protein it affects. It’s a matter of accumulating knowledge that you end up discovering and correlating”, he ponders.
The researcher also indicates that, currently, scientists are working on developing a vaccine based on the virus's own RNA. This type of vaccine would coordinate the production of proteins that are antigens and, thus, stimulate the immune system against the virus. “In China alone there are dozens of groups working on this. The speed with which knowledge is generated is extraordinary. Never before has a viral epidemic been scrutinized from a scientific point of view like this and with resources mobilized around the world to make this possible. But there is no way to predict yet whether it will be efficient or not, you need to test it on individuals and see if it controls it or not. Will the Brazilian strain behave differently? We don’t know, we have to test and see.”
As bets for a recent future, Paulo believes that scientists will soon begin researching the types of mutations that allowed the coronavirus to pass from an animal to humans, becoming infectious there. “This virus probably came from a pangolin, a type of armadillo, but in this animal it is not infectious. When he managed to overcome the species barrier and infect man, he became infectious. Something that will stimulate the scientific community will be sequencing viruses from wild animals, especially those that are eventually used as food,” he notes.
On a broader level, Paulo Arruda highlights that the prospects are even more challenging. He participates in the project Earth BioGenome Project, which aims to sequence the different microorganisms that are on planet Earth. The idea is to map two million species. “But it’s not a virus, it’s infinitely more complex. It's like sequencing billions or trillions of viruses like this. Is this doable? AND. Because of these technologies”, he highlights. Today, it is estimated that only 14% of eukaryotic beings are known genetically. The world-class project aims to enable advances in the conservation of species and the development of the bioeconomy.
The teacher, who coordinates the Center for Research in Genomics Applied to Climate Change at Fapesp, also highlights the potential of genetic sequencing in the context of agriculture. At the moment, one of the strands of research focuses on the analysis of plants that live in environments considered stressful, with poor soils and little rainfall. The idea is to know how they manage to survive in these regions so that it is possible to study how to produce food capable of withstanding the challenges of climate change.
Uncovering what is currently unknown is the potential of the area of biotechnology, for the professor. “Humanity’s challenge is to produce food, produce new medicines and produce energy in a sustainable way, without destroying the environment. It’s not much and we’re making our contribution.”
