Ricardo Valverde (Fiocruz News Agency)
This Thursday (17/2) the Fiocruz Genomic Network released new figures on the lineages and variants of the Sars-CoV-2 virus in Brazil. The data are computed every week on the Network’s platform, using data obtained from the EpiCoV platform, from GISAID (Global Initiative on Sharing All Influenza Data), an international platform used to share the genomic data of influenza and Sars-CoV-2 viruses.
The Fiocruz Genomic Network site gathers data about lineages and variants of the Sars-CoV-2 virus in Brazil (Image: Josué Damacena - IOC/Fiocruz)
As previously observed, the Omicron variant is still widely predominant in the country, and up to the wrapping up of this latest batch of data, three of its lineages had already been identified in Brazil: BA.1 (9,821 genomes), BA.1.1 (1,269 genomes) and BA.2 (8 genomes). Another highlight released together with the new data is the fact that the Laboratory of Measles and Respiratory Viruses of the Oswaldo Cruz Institute (IOC/Fiocruz) has now made available a biorepository with reference lineages of Sars-CoV-2, isolated, to be used in additional studies. This will make it possible to share these data with other groups of researchers, for comparison, neutralization assays, and other research purposes.
The researchers of the Fiocruz Genomic Network have also given a warning: the time between collecting the sample and the entering of the genome in the GISAID platform must be reduced so that Brazil can actually have real-time genomic surveillance. The Network’s publication shows that the median of this interval between collection and delivery to GISAID was 59 days, with an average of 82 days and with significant differences between states. Things change very fast in the field of genomics, which requires that processes be quicker.
In the period encompassed by the new data, Fiocruz units deposited a total of 6,539 genomes into the GISAID’s EpiCoV platform. The sampling used by the Fiocruz Genomic Network to support the national network of respiratory virus surveillance is based on representative samples of cases that tested positive for Sars-CoV-2 through RT-PCR, carried out in each of the country’s states, and soon samples of unusual events identified by local surveillance agencies.
The researchers of the Fiocruz Genomic Network emphasize that the entire surveillance monitoring has only been possible thanks to the GISAID platform, and mainly to the partnership and collaboration of the State Public Health Laboratories (LACENs in the Portuguese acronym) and the General Coordination of Laboratories of the Ministry of Health. It also relies on the collaborators of the GISAID platform in Brazil, who contribute with deposits.
According to the Network, researchers of the Leonidas and Maria Deane Institute (ILMD/Fiocruz Amazônia) detected a loss of information in the genome of a few of the samples circulating in Brazil as a consequence of drop-out, the inability to amplify certain regions of the genome to identify the variant. To solve this problem, two solutions have been tested and improved and resulted in a significant reduction of this loss in four regions of the genome of samples belonging to the Gamma, Delta, and Omicron variants.
The Fiocruz Genomic Network consists of researchers from different Brazilian states. Among them are the Oswaldo Cruz Institute, the Aggeu Magalhães Institute (IAM/Fiocruz Pernambuco), the Leônidas and Maria Deane Institute (ILMD/Fiocruz Amazônia), the Gonçalo Moniz Institute (IGM/Fiocruz Bahia), Fiocruz Ceará, Fiocruz Mato Grosso do Sul, Fiocruz Rondônia, Fiocruz Paraná, and Fiocruz Piauí.
The data of the new report can be found on the website of the Genomic Network. In addition to texts, infographics, tables and visual aids, the site also has a glossary section and a FAQ.