The Valencian research teams have succeeded in sequencing the complete genome of three samples of COVID-19 infected patients from the Microbiology Laboratory of Clínico Universitary 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 genomic analysis has been carried out by teams formed by members of the Joint Unit for Infection and Public Health of the University of Valencia and the Foundation for the Promotion of Health and Biomedical Research of Valencia Region (Fisabio), led by Fernando González Candelas, Professor of Genetics at the University. Candelas is a researcher at the Institute of Integrative Systems Biology (I2SysBio) and also at the Sequencing and Bioinformatics Service at Fisabio, a service coordinated by Giuseppe d'Auria and Llúcia Martínez.
“The primary objective is to identify more reliably the focus and transmission chains of the coronavirus. The main conclusion of the analysis of the first samples is that the strains come from different transmission routes”, explains the researcher Fernando González Candelas.
Image of a fragment of the SARS-CoV-2 virus sequences analysed. Blue shows a mutation of the virus with respect to the reference genome. Font: Fernando González Candelas
The sequences are already accessible in the GISAID Initiative database, a public consortium dedicated to the study of the influenza virus (https://www.gisaid.org/); the Nextstrain platform, which allows visualising the spatial and temporal progression of the pandemic from the more than 500 genomes deposited since last December by 40 countries (https://nextstrain.org/); and the Genbank database of genetic sequences from the National Institutes of Health of the United States (https://www.ncbi.nlm.nih.gov/genbank).
The groups are formed by staff specialised in virology, epidemiology and bioinformatics and have determined that one of the strains analysed is related to other European ones (from Italy, Germany, Luxembourg, France, Scotland, the Netherlands, etc.). “The next step will be to analyse sequences of more samples of patients from the hospitals of the Valencia region in order to check the links between them and with the transmission chains established by the epidemiology specialist personnel”, explains Fernando González.
Phylogeny of the SARS-CoV-2 coronavirus. The arrows indicate the lineages of the viruses isolated in Valencia. Font: Fernando González Candelas
The analysis of viral genomes allows us to know the ways in which the virus has entered our region and how it is transmitted at this time, which will help health authorities to better control the spread of the virus in Comunitat Valenciana. In addition, the sequencing of the genome allows us to know the mutations that the virus has suffered since the epidemic bega. The conclusion is that, until now, no mutation has been associated with increased virulence, lethality or some 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.