Just two days after the first case of coronavirus in Latin America was confirmed in the city of São Paulo, researchers from the Adolfo Lutz Institute and from the universities of São Paulo (USP) and Oxford (United Kingdom) published the complete viral genome sequence, which received the name of SARS-CoV-2.
The data was released on Friday (28/02) on Virological.org, a forum for discussion and data sharing among virologists, epidemiologists and public health specialists. In addition to helping to understand how the virus is spreading around the world, this type of information is useful for the development of vaccines and diagnostic tests.
“By sequencing the virus genome, we are closer to knowing the origin of the epidemic. We know that the only confirmed case in Brazil came from Italy, however, Italians still do not know the origin of the outbreak in the Lombardy region, as they have not yet sequenced their samples. They have no idea who the zero patient is and they do not know if he came directly from China or went to another country before, ”said Ester Sabino, director of USP's Institute of Tropical Medicine (IMT).
According to Sabino, the Brazilian sequence is very similar to that of samples sequenced in Germany on January 28 and presents differences in relation to the genome observed in Wuhan, the epicenter of the epidemic in China. “This is a virus that undergoes few mutations, on average one per month. For this reason, there is no point in sequencing small sections of the genome. To understand how the spread is occurring and how the virus is evolving, it is necessary to map the complete genome ”, he explained.
This monitoring, according to Sabino, allows identifying the regions of the viral genome that suffer the least mutations - something essential for the development of vaccines and diagnostic tests. "If the test targets a region that changes frequently, the chance of loss of sensitivity is great," he said.
Together with Nuno Faria, from the University of Oxford, Sabino coordinates the Joint Brazil-UK Center for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE). The project, supported by FAPESP, the Medical Research Council and the Newton Fund (the last two in the United Kingdom), aims to study in real time epidemics of arboviruses, such as dengue and zika.
“Through this project, a network of researchers was created dedicated to responding and analyzing epidemic data in real time. The proposal is really to help health services and not just publish the information months after the problem occurred, ”said Sabino to Agência FAPESP.
According to the researcher, as soon as the first outbreak of COVID-19 was confirmed in China in January, the project team mobilized to obtain the necessary resources to sequence the virus as soon as it arrived in Brazil.
“We started working in partnership with the team at the Adolfo Lutz Institute and training researchers to use a sequencing technology known as MinION, which is portable and inexpensive. We used this methodology to monitor the evolution of the Zika virus in the Americas, but in this case, we were only able to trace the origin of the virus and the route of dissemination one year after the epidemic ended. This time, the team went into action as soon as the first case was confirmed, ”said Sabino (read more at: agencia.fapesp.br/25356/).
The first case of COVID-19 in Brazil (BR1) had a molecular diagnosis confirmed on February 26 by the Adolfo Lutz team. This is an infected patient in Italy, possibly between the 9th and 21st of this month. The sequencing of the viral genome was conducted by a team coordinated by Claudio Tavares Sacchi, responsible for the Strategic Laboratory of the Adolfo Lutz Institute (LEIAL), and Jaqueline Goes de Jesus, postdoctoral fellow at the Faculty of Medicine at USP and FAPESP scholarship holder.
“We were already predicting the arrival of the virus in the State of São Paulo and, as soon as we had confirmation, I contacted the partners of USP's Institute of Tropical Medicine. We had already been working together for a few months on the use of MinION technology to monitor dengue, ”Saccchi told Agência FAPESP.
“We were able to break some barriers with this work. The university trained teams and transferred technology so that sequencing could be done in the right place, which is the center responsible for epidemiological surveillance. That's how it has to be, ”said Sabino.
In addition to Lutz and USP, members of the Superintendency for Endemic Control (Sucen) and the Epidemiological Surveillance Center (CVE) also participate in the CADDE Project, both linked to the State Department of Health.
The infectologist and professor at FM-USP Esper Kallás has been assisting the State Department of Health, since mid-January, to develop a strategy to care for patients eventually infected with SARS-CoV-2. The Emilio Ribas Institute of Infectious Diseases and the Hospital das Clínicas of USP were chosen as reference institutions to deal with serious cases in the State.
“HC follows a protocol for containment of catastrophe called HICS [sistema de comando de incidentes hospitalares, na sigla em inglês], which has already been activated to assist victims of the school massacre in Suzano [ataque que deixou dez mortos em 2019] and during the yellow fever epidemic of 2018. Now, knowing that there is possibly a coronavirus epidemic on the way, we have already established all service flows, ”he said.
Also according to Kallás, a working group was created to discuss protocols for clinical studies that will be carried out with patients diagnosed and treated in the state public network.
"This strategic planning and the rapid publication of the viral genome are indicators of the capacity that the State of São Paulo has to respond with high quality science and to contribute to the understanding of threats to the health of the population," he said.
By Karina Toledo | FAPESP Agency