More than 120 complete arbovirus genomes are sequenced

An unprecedented achievement in world science. In just 15 days, a rotating genetic sequencing project led by the Oswaldo Cruz Foundation (Fiocruz) generated 126 complete virus genomes responsible for large outbreaks in the country, including 69 of dengue, 34 of chikungunya and 23 of zika. The samples came from infected patients in the Central-West region of the country. The team also collected more than 2,700 mosquitos from 19 species, mostly, Aedes aegypti, Aedes albopictus and Culex quinquefasciatus. The insects are being analyzed. The specialists are part of the project, Zibra 2: genetic mapping of zika and other arboviruses in Brazil, which is funded by the Department of Science and Technology (Decit) and the Department of Sanitary Surveillance and Health (SVS) of the Ministry of Health, the Pan American Health Organization (PAHO/WHO), the National Council for Scientific and Technological Development (CNPq) and the Coordination Office for the Development of Personnel with Higher Education (CAPES). The data were recently released at a meeting at the PAHO office in Brasilia.

Equipped with innovative genetic sequencing technology that fits in the palm of the hand, the group, composed of national and international researchers, has traveled more than 12,000 kilometers between the states of Mato Grosso, Mato Grosso do Sul, Goiás and the Federal District. In partnership with the General Coordination Office of Public Health Laboratories of the Ministry of Health (CGLAB/SVS/MS) and with the Central Public Health Laboratories, (Lacens) from the four states, the initiative had access to about 360 samples. The final numbers with all the details generated from the sequencing will be announced shortly in a scientific paper.

With the decoding of genomes, it will be possible to answer relevant questions to the Unified Health System (SUS), such as the origin of the virus, probable date of entry into the national territory, route and speed of expansion, and to calculate the possibility of new outbreaks. The process also allows the reconstruction of phylogenetic trees - a type of analysis that groups in the same branch the viruses that share a common ancestor, contributing towards explaining their trajectories and evolution. 

According to Luiz Alcântara, a researcher at the Oswaldo Cruz Institute's Flavivirus Laboratory (IOC/Fiocruz) and research leader, the benefits of the project will have an impact on studies conducted in Brazil and abroad. "This record is providing science with a wealth of raw material, which is the mapping of these three viruses to date. No project has managed to generate all these genomes in fifteen days”, he said. The team were also interested in the yellow fever virus and other lesser known ones such as mayaro, oropouche, São Luis encephalitis and West Nile fever.

Using the technique known as metagenomics, experts also intend to sequence samples that were negative for the eight viruses prioritized in the initiative. "To date, 28 samples have been tested for metagenomics. Of the five that presented positive results for chikungunya, four already had their full genomes generated”, said Marta Giovanetti, a visiting researcher from the same laboratory and a member of the team. For the analysis of patient samples - both negative and positive - the epidemiological week with the highest number of cases recorded in the last four years was considered.

The general coordinator of Public Health Laboratories of the Department of Sanitary Surveillance and Health of the Ministry of Health, André Luiz de Abreu, stressed the importance of the project. "With the incorporation of genomic surveillance into other areas of laboratory surveillance we can provide a much more substantive laboratory response with much more content for the actions that health surveillance, epidemiological surveillance, immunization, and entomology needed. This changes the level of laboratory surveillance”, he emphasized.

Initiative

The project included 13 experts, including researchers from IOC/Fiocruz, Evandro Chagas Institute (IEC), the Federal University of Minas Gerais (UFMG), University of São Paulo (USP), University of Birmingham and Oxford University, University of KwaZulu-Natal, South Africa, Lacen of Minas Gerais, Institute Leônidas and Maria Deane (Fiocruz Amazônia) and Hemocentro of Ribeirão Preto.

Zibra began in 2016, following the decree of the sanitary emergency caused by the zika virus. After working in the North (Amazonas and Roraima), Northeast (Rio Grande do Norte, Paraíba, Alagoas, Pernambuco and Bahia) and Southeast regions (São Paulo, Rio de Janeiro and Minas Gerais), besides the activities in Paraguay and Angola, the scientists successfully sequenced 203 genomes of zika virus, 260 yellow fever, 154 chikungunya and 129 dengue genomes.