The coronavirus genome (covid-19) isolated in the second Brazilian patient diagnosed with the disease on Saturday, February 29, is different from that found in the first case, confirmed on February 26.
“The first isolate proved to be genetically more similar to the virus sequenced in Germany. This second genome is more similar to that sequenced in England. And both are different from Chinese sequences. This fact suggests that the coronavirus epidemic is maturing in Europe, that is, internal transmission is already occurring in European countries. For a more accurate analysis, however, we need data from Italy, which has not yet been sequenced, ”said Ester Sabino, director of the Institute of Tropical Medicine (IMT) at the University of São Paulo (USP), to Agência Fapesp.
The complete sequencing of the second viral isolate was completed in just 24 hours by researchers from Instituto Adolfo Lutz and USP. The study data, supported by Fapesp, should be released soon.
After the publication of the first Brazilian sequence of covid-19 on the Virological.org website, on February 28, Italian researchers contacted the USP team to request the sharing of the protocols used.
The viral isolates of the two Brazilian patients diagnosed with covid-19 were sequenced by a group coordinated by Claudio Tavares Sacchi, responsible for the Strategic Laboratory of the Adolfo Lutz Institute (LEIAL), and Jaqueline Goes de Jesus, postdoctoral fellow at USP Medical School .
The work has been conducted with support from the Joint Brazil-UK Center for Discovery, Diagnosis, Genomics and Arbovirus Epidemiology (Cadde) – a network of researchers dedicated to responding and analyzing epidemic data in real time, coordinated by Sabino and Nuno Faria , from the University of Oxford, UK. The project, whose main focus is the study of arboviruses, such as dengue and zika, is supported by Fapesp, the Medical Research Council and the Newton Fund (the last two in the United Kingdom).
“Our initial objective was to train the Adolfo Lutz team and to implement the necessary technology for real-time monitoring of the dengue epidemic underway in Brazil. When the coronavirus cases in China were released in January, we started to prepare ourselves to also monitor this new disease in real time ”, said Sabino.
The group makes use of a portable device known as MinION, used for the first time in the country in 2016 to retrospectively trace the spread and evolution of the Zika virus in the Americas (read more at http://agencia.fapesp.br/25356/) .
“This agility is only possible now thanks to the continuous funding that our group at IMT-USP has received since 2016. The sequencing protocols were developed by a student during a research internship in Birmingham [Reino Unido]. We were able to lower the cost of the molecular test from $ 500 [R$ 2,2 mil] for $ 20 [R$ 89]. It is a huge technological gain for the country, ”said Sabino.
According to the researcher, the main advantage of real-time monitoring of an epidemic is the possibility of identifying where exactly the virus that arrived in the country came from. Such information can guide containment actions and help to reduce the spread of the disease.
“It is a new tool for epidemiological surveillance, which for the time being was only tested in Africa, during the Ebola epidemic,” said Sabino. “We want to release this second sequence soon to help people in Italy analyze their data. We share with the Italians the protocol used by our team and put them in contact with the Cadde group in England. ”
According to Sacchi, while only sporadic cases of covid-19 are confirmed in São Paulo, all genomes will be sequenced. If positive tests start to multiply on a large scale, the work will be guided by the Epidemiological Surveillance Center (CVE) of the State Department of Health, which is also part of the Cadde Project.
“In this case, the sequencing will be done by sampling and based on statistical methods, in order to guarantee that the sampled cases are representative of the total”, explained the researcher from Adolfo Lutz.
If it is possible to sequence a large number of viral isolates, several types of analysis may be performed in the future, such as the evolution of the virus and the identification of strains with the worst clinical evolution, for example.