TELE-Vir: Point-of-incidence toolbox for emerging virus threats
The Project #TELEVIR
The TELE-Vir project key aim is to develop a very fast point-of-incidence (poi) toolbox for identification and characterisation of emerging virus threats for humans and/or domestic and wildlife animals. Third-generation sequencing using the MinION device (Oxford Nanopore Technologies) has shown to be a promising fast diagnostic sequencing tool. We believe that when combined with a suitable field- deployable point-of-care approach, and a direct upload of genomic, phenotypic and epidemiological data into a user-friendly bioinformatics toolkit, a very fast identification and characterisation can be performed.
The poi toolbox will be built on already developed point-of-care virus inactivation and nucleic acid extraction methods and expanded to a standardised protocol for the MinION sequencing of both DNA and RNA virus in clinical specimens. The bioinformatics part will be built on an already existing bioinformatics platform like the INSaFLU and will enroll user-friendly graphical interfaces from the very beginning of the workflow (assessment of quality of sequencing reads) until the final outputs (e.g., phylogeography charts enriched with associated sample metadata and relevant viral genotypic and phenotypic features such as the available data on virulence, host (and, if applicable, vector) ranges, transmissibility, persistence in the host and in the environment, drug resistance, antigenicity, etc.).
In addition, a graphical output of results will be accessible to a non-expert audience. This poi toolbox allows for an easy, rapid and user friendly in situ identification with immediate characterisation and hence a very fast response and improved decision-making during an outbreak or a potential outbreak of an emerging or re-emerging virus threat, which will aid in the overall outbreak preparedness in Europe.
Fomsgaard, AS., Rosenstierne, MW. (2020). An alternative workflow for molecular detection of SARS-CoV-2 – escape from the NA extraction kit-shortage, Copenhagen, Denmark, March 2020. Eurosurveillance. 25(14), pp: 2000398. DOI: https://doi.org/10.2807/1560-7917.ES.2020.25.14.2000398