Researchers at the Institute of Tropical Medicine at the University of São Paulo (IMT-USP) and the Adolfo Lutz Institute (IAL), in partnership with British scientists at the University of Oxford, sequenced the genome of the new coronavirus found in Brazil in record time.
The process, which normally takes 15 days to complete, was carried out in 48 hours for the first patient identified with the disease in Brazil, and the information was released on Friday (28). The virus genome found in the country’s second confirmed case was also sequenced by the same team and published on Monday (2). They are the only two proven cases of the disease in Brazil.
Two Brazilian scientists stood out in the achievement. One of them is Ester Sabino, director of USP’s Institute of Tropical Medicine and coordinator of the Joint Brazil-UK Center for Discovery, Diagnosis, Genomics and Epidemiology of Arbovirus (Cadde), specialized in arbovirus epidemics, such as dengue and Zika.
The other is Jaqueline Goes de Jesus, who coordinated the sequencing, a postdoctoral fellow at USP’s Faculty of Medicine and a fellow at the funding agency Fapesp. Researcher Claudio Tavares Sacchi, from the Adolfo Lutz Institute, worked alongside her.
“On average, countries are managing to do the sequencing in 15 days. We wanted to do it in 24 hours, break the record, but it didn’t work (in the process). We did it in 48 hours, like the Pasteur Institute (in France) ”, Sabino told BBC News Brasil.
In Brazil, the number of suspected infection with the new coronavirus rose to 433 after the Ministry of Health changed the accounting methodology. There is still no evidence of transmission of the virus within the country.
The new coronavirus has killed more than 3,000 people worldwide, with more than 90,000 cases of infection. Initially called 2019-nCoV, it was later named Sars-CoV-2. The disease caused by him was named covid-19 by the WHO (World Health Organization).
What is sequencing for
Among the main uses of mapping the genome of a virus is to help understand the path of transmission and the time it is present in a given region or country. By unraveling the history of the coronavirus, authorities and researchers can take appropriate measures to try to contain its spread. The sequencing of diseases such as Ebola and Zika was fundamental in the development of strategies to combat them.
Several online databases provide information on sequenced Covid-19 genomes. Each country that publishes a sequencing contributes to building a volume of shared information that helps scientists and researchers around the world.
One of the main databases is from the National Genomic Data Center, China. As of Monday (2), 255 complete genomes of the new coronavirus, from 23 different countries, were listed on the institution’s website. Each of these genomes has its own genetic sequence. In Brazil, the federal government created the MCTIC Virus Network, linked to the Ministry of Science and Technology, in partnership with the Ministry of Health, to exchange information.
The first sample of the new coronavirus sequenced in Brazil, at the Adolfo Lutz Institute, showed greater correspondence with a virus sequenced in Germany. This indicates that he infected patients in that country before going to Italy, where the first Brazilian detected with the disease passed. The second Brazilian case, of a man who also returned contaminated from Italy, resembles a sequence found in England.
The diversity of sequences indicates that the virus is already well established in Europe, as there was time for it to develop more mutations. “This fact suggests that the coronavirus epidemic is maturing in Europe, that is, internal transmission is already occurring in European countries,” said Sabino to the Fapesp agency website.
In the United States, the sequencing of the genome of two victims helped to understand the behavior of the virus in Washington, the state where all six fatal victims registered in the USA have resided so far. Comparing coronavirus genomes found in people who did not know each other, researchers found that they were of the same strain. This suggested that the virus had been circulating in the region for about six weeks and that the victims were not infected by someone from outside the country.
Sequencing information can be accessed by laboratories and biotechnology companies. Based on the data, it is possible to perform diagnostic tests on patients with suspected viruses, as well as recreate stretches of the coronavirus genome for research aimed at making vaccines against the Sars-CoV-2.
“Having the genome sequence allows you to design vaccines that are likely to work, based on what we know about other coronaviruses. Genome sequencing is absolutely crucial, ”said Rachel Roper, a Canadian researcher who coordinates a SARS vaccine program, to The Scientist website.
Currently, researchers in several countries are rushing to develop a vaccine for covid-19. The work started in January, when the first genetic sequencing of SARS-CoV-2 was made available.
An American biotechnology company, Moderna, announced an experimental vaccine against the new coronavirus on February 24. The development took 42 days, considered a record time. In China, Clover Biopharmaceuticals, in partnership with Britain’s GlaxoSmithKline, said it could test a vaccine in April.
How to sequence a genome
Chinese scientists released the first sequencing of a genome of the new coronavirus on January 10. It was about a month after the first recorded case in the city of Wuhan, on December 8, when it was still an unknown virus. It was an extremely quick result. In the epidemic of another coronavirus, Sars-2, the first case was registered in November 2002, and the first genomic sequencing was only completed in April 2003.
The genome is the set of DNA or RNA (in the case of the coronavirus) contained in an organism. It includes all the information about that organism, from physical characteristics to behaviors. Sequencing a genome literally means writing a kilometer sequence of letters A, C, G and T (or G, C, U and A in the case of RNA). Each letter refers to one of the four types of base, or nucleotides present in DNA – the substances adenine, cytosine, guanine and thymine (in the case of RNA, uracil), respectively.
In each genomic sequence, the letters will be in different order. The human genome is made up of 3 billion of those letters. The SARS-CoV-2 genome has approximately 30,000 genetic “characters”.
Currently, the “reading” of the sequence is performed by high-tech equipment, small in size – only slightly larger than a pendrive. It is a much easier and cheaper procedure than at the time of the first SARS epidemic. The cost has been reduced by up to 100 times.