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Uppsala, Uppsala län, Sweden

Daphne Jackson Road, Guildford, England, United Kingdom

Rua Rio Ave 1600, Carnide, Área Metropolitana de Lisboa, Portugal

Madrid, Comunidad de Madrid, Spain

Teramo, Abruzzo, Italy

Bettola-Zeloforomagno, Lombardy, Italy

Hudcova 296, Brno, Jihovýchod, Czech Republic

Aleja Partyzantów 57, Puławy, województwo lubelskie, Poland

14 Rue Pierre et Marie Curie, Maisons-Alfort, Île-de-France, France

Artillerivej 5, Copenhagen, Region Hovedstaden, Denmark

OHEJP Tele-vir project logo

The Project #TELE-VIR

Start: 1 January 2020
Duration: 2.5 Years
Domain: Emerging Threats
Keywords: Metagenomics, Point-of-incidence, Emerging virus, Diagnostic, Phenotypic characterisation
Contact: Katja Spiess (SSI)

TELE-Vir: Point-of-incidence toolbox for emerging virus threats

It is crucial to address new emerging virus threats and to better control virus outbreaks. The SARS-CoV-2 pandemic and the reoccurrence of emerging high virus pathogens, as for example Ebola- and West Nile virus, highlighted the importance of rapid diagnostics and improved methods to detect viruses, as early detection can assist interventive measures in order to avoid intensive outbreaks. Therefore, novel advanced virus detection methods are warranted to be prepared for future pandemics and next dangerous pathogen identification.

In the TELEVIR project, we developed a point of incidence (POI) toolbox, for metagenomic virus detection in the field that will contribute to the identification of known viruses as well as of emerging virus threats. Metagenomic next-generation sequencing (mNGS) has the ability to identify pathogens in as hypothesis-free manner compared to targeted strategies (Fomsgaard et al., J. Clin. Virol. Plus, 2(4), 100120 (2022)). This is of advantage to conventional diagnostic tests, since different pathogens can produce similar symptoms, which makes it difficult to choose for a specific (targeted) test. Moreover, out POI toolbox includes methods that can be transferred into a field setting to detect any kind of virus, in animals and humans, even in geographical areas without available laboratory infrastructure. In work package (WP) 3 we established a POI protocol that includes sample pre-treatment, nucleic acids extraction, isothermal random amplification followed by non-targeted sequencing using the Oxford Nanopore Technology (ONT) system. It requires a minimum of laboratory equipment to be field employable and is relatively fast. WP2 supported this approach by:

  1. improving and adapting the “surveillance oriented” INSaFLU-TELEVIR platform to handle sequence data (ONT, Illumina and Ion Torrent) of any virus (from reads to quality control, mutations detection, consensus generation, classification, alignments, genotype-phenotype” screening, phylogenetics, integrative phylogeographical and temporal analysis) and
  2. by developing, benchmarking and implementing a novel pathogen detection module, from reads and quality control for the identification of both RNA and DNA viruses.

The POI toolbox was successfully tested in proof-of-concept studies by the TELEVIR members (WP4), for example under different conditions in the field in Norway, South France and West Africa or by testing diverse sample material frozen and fresh material from in vivo laboratory studies to compare our POI protocol to well established detection methods. Sequencing data obtained from the partners performing the wet-lab activities were analysed with the INSaFLU-TELEVIR platform, as a complement to the multiple sample/virus tests performed during the tool development, benchmarking and final refinement.  We could detect a broad range of RNA as well as DNA viruses in different sample materials, proving a good symbiosis between the developed POI protocol and the INSaFLU- TELEVIR platform, towards the deployment of a “start-to-end” framework that can potentiate strengthened timely metagenomics virus detection and routine genomics surveillance.

In summary, the TELEVIR 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.

Project Outputs and Outcomes

  • To be able to react fast to new virus outbreaks the point of incidence (POI) protocol was established for unbiased detection of RNA and DNA viruses, that comprises sample pre-treatment, nucleic acids extraction, isothermal random amplification followed by library preparation for non-targeted sequencing using the Oxford Nanopore Technology (ONT) system. The POI protocol requires a minimum of laboratory equipment to be field employable.
  • We established an open and user-oriented “start-to-end” bioinformatics framework for metagenomics virus detection and routine genomic surveillance, the INSaFLU-TELEVIR platform. This web-based (also locally installable) platform handles read sequence data (ONT, Illumina and Ion Torrent) of “any” virus, enabling the identification of both RNA and DNA viruses, while providing multiple surveillance-oriented features towards mutations detection, consensus generation, lineage/genotype classification, alignments, “genotype-phenotype” screening, phylogenetics, and integrative phylogeographical and temporal analysis.
  • The POI toolbox consist of the INSaFLU-TELEVIR platform and the POI protocol and was successfully tested in proof of concept/field studies.
  • The recent virus pandemic made it clear that there is a strong need to identify new emerging virus threats. International stakeholders should recognize the potential of the POI toolbox to rapidly detect any virus in diseased humans and animals in the field. This tool can be especially relevant for regions with low laboratory infrastructure or with a high biodiversity.

Project Assets

Sghaier, S., Sailleau, C., Marcacci, M., Thabet, S., Curini, V., Hassine, T. B., Teodori, L., Portanti, O., Hammami, S., Jurisic, L., Spedicato, M., Postic, L., Gazani, I,, Osman, R. B., Zientara, S., Bréard, E., Calistri, P., Richt, J. A., Holmes, E. C., Savini, G., Di Giallonardo, F., Lorusso, A. (2023). Epizootic Haemorrhagic Disease Virus Serotype 8 in Tunisia, 2021. Viruses. 15(1), 16. DOI:

Fomsgaard, A., Rasmussen, M., Spiess, K., Fomsgaard, A., Graham, B., Fonager, J. (2022). Improvement of field deployable metagenomics virus detection by a simple pretreatment method. Journal of Clinical Virology Plus. 2(4), 100120. DOI:

Isidro, J., Borges, V., Pinto, M., Sobral, D., Santos, J. D., Nunes, A., Mixão, V., Ferreira, R., Santos, D., Duarte, S., Vieira, L., Borrego, M. J., Núncio, S., Lopes de Carvalho, I., Pelerito, A., Cordeiro, R., Gomes, J. P. (2022). Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus. Nature Medicine. 28, 1569–1572. DOI:

Fomsgaard, A. S., Rosenstierne, M.W. (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), 2000398. DOI:


Project Events

One Health EJP Project Kick-off meeting- 13th November 2019, Berlin, Germany

TELE-Vir Kick-off meeting- 21st-22nd January 2020, IZSAM, Italy

TELE-Vir Consortium meeting- 23th November 2020

Work package Leader meeting- 12th January 2021

1st Annual TELE-Vir Consortium meeting- 25th January 2021, online & organised by SSI, Denmark

TELE-Vir Consortium meeting- 9th March 2021

TELE-Vir Consortium meeting- 24th April 2021

TELE-Vir Consortium meeting- 18th June 2021

TELE-Vir Consortium meeting- 29th September 2021

Work package Leader meeting- 12th November 2021

TELE-Vir Consortium meeting- 10th February 2022

TELE-Vir Consortium meeting- 6th May 2022

2nd Annual TELE-Vir Consortium meeting- 23rd June 2022, SSI, Denmark

TELE-Vir Workshop on POI toolbox training- 23-24th June 2022, SSI, Denmark

TELE-Vir Consortium meeting- 12th July 2022

TELE-Vir Consortium meeting- 31st September 2022

Project leader meeting- 5th October 2022

TELE-Vir Consortium meeting- 18th November 2022



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