UV sequencing team group and Fisabio

The genomic analysis has been carried out by the Joint Unit in Infection and Public Health of the University of Valencia and the Foundation for the Promotion of Health and Biomedical Research of the Valencian Community Fisabio, the Molecular Epidemiology Research Group, both led by Fernando González Candelas, professor of Genetics and researcher at the Institute of Integrative Systems Biology (I2SysBio) of the Universitat de València and the CSIC, and the Fisabio Sequencing and Bioinformatics Service coordinated by Giuseppe d’Auria and Llúcia Martínez.

The Valencian research teams have managed to sequence the complete genome of three samples of patients infected with COVID-19 from the Microbiology laboratory of the University Clinical Hospital of Valencia, the first sequences of the SARS-CoV2 virus obtained in Spain. This sequencing of complete genomes adds to the effort being made worldwide in all laboratories to find out what the transmission routes have been and how the different lineages of the virus spread.

“The primary objective is to more reliably identify the foci and transmission chains of the coronavirus. The main conclusion from the analysis of the first samples is that the strains come from different transmission routes,” explains researcher Fernando González Candelas.

The sequences are now accessible in the database of the GISAID Initiative, a public consortium dedicated to the study of the influenza virus (www.gisaid.org); the Nextstrain platform, which allows you to visualize the spatial and temporal progression of the pandemic based on the more than 500 genomes deposited since last December by 40 countries (https://nextstrain.org); and the Genbank database of genetic sequences of the NIH (National Institutes of Health of the United States) (https://www.ncbi.nlm.nih.gov/genbank/).

The groups formed by research personnel specialized in virology, epidemiology and bioinformatics have determined that one of the strains analyzed is related to other European strains (from Italy, Germany, Luxembourg, France, Scotland, the Netherlands, etc.). “The next step will be to analyze sequences from more patient samples from hospitals in the Valencian Community to be able to verify the links between them and with the transmission chains established by specialist epidemiology personnel,” explains Fernando González.

The analysis of viral genomes allows us to know the routes by which the virus has entered our community and how it is currently transmitted, which will help health authorities to control the spread of the virus in our community much better. Furthermore, the sequencing of the virus genome allows us to know the mutations that the virus has suffered since the epidemic began and the conclusion reached after the analysis carried out is that, until now, no mutation has been found associated with greater virulence, lethality, or any interesting property from a clinical point of view.

The samples have been sequenced using MinIOn, a third-generation sequencer from Oxford Nanopore Technologies. The infrastructure used in the research has been possible thanks to the co-financing of the European Union through the Operational Program of the European Regional Development Fund (ERDF) of the Valencian Community 2014-2020.

More information:

www.uv.es/i2sysBio

http://fisabio.san.gva.es/ca/inicio

http://www.fisabio-ngs.com/

Photograph captions:

1. Sequencing Team Group

2. Image of a fragment of the sequences of the analyzed SARS-CoV-2 virus. In blue a mutation of the virus is observed with respect to the reference genome.

3. Phylogeny of the SARS-CoV-2 coronavirus. The arrows indicate the lineages of the viruses isolated in Valencia.