An interlaboratory proficiency test using metagenomic sequencing as a diagnostic tool for the detection of RNA viruses in swine fecal material
Metagenomic shotgun sequencing (mNGS) is a generic molecular diagnostic method, involving laboratory preparation of samples, sequencing, bioinformatic analysis of millions of short sequences, and interpretation of the results. In this paper, we investigated the performance of mNGS on the detection of porcine astroviruses, a model for RNA viruses in a pig fecal material, among six European veterinary and public health laboratories. We showed that different methods for data generation affect mNGS performance among participants and that the selection of reference genomes is crucial for read classification. Follow-up investigation remains a critical factor for the diagnostic interpretation of mNGS results. The paper contributes to potential improvements of mNGS as a diagnostic tool in clinical settings.
Authors
- Per Wallgren (ORCID: https://orcid.org/0000-0002-3958-9620)
- Marcel Hulst (ORCID: https://orcid.org/0000-0001-8020-8853)
- Alex Bossers (ORCID: https://orcid.org/0000-0002-6586-717X)
- Mikhayil Hakhverdyan (ORCID: https://orcid.org/0000-0002-9481-2709)
- Sander van Boheemen (ORCID: https://orcid.org/0000-0003-3702-3313)
- Pierrick Lucas (ORCID: https://orcid.org/0000-0002-2844-6157)
- Steven Van Borm (ORCID: https://orcid.org/0000-0002-3464-2306)
- Yannick Blanchard (ORCID: https://orcid.org/0000-0002-4711-6671)
- Bas B. Oude Munnink (ORCID: https://orcid.org/0000-0002-9394-1189)
- Qiang Fu (ORCID: https://orcid.org/0000-0002-5957-2236)
- Miranda de Graaf (ORCID: https://orcid.org/0000-0002-7831-0098)
- Kevin Vanneste (ORCID: https://orcid.org/0009-0000-4051-0628)
- Lihong Liu (ORCID: https://orcid.org/0000-0002-5921-6805)
Institutions
- Erasmus MC (NL)
- Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail (FR)
- Sciensano (Belgium) (BE)
- Wageningen University & Research (NL)
Publication Details
- Journal
- Microbiology Spectrum
- Published
- 2024-08-20
- DOI
- https://doi.org/10.1128/spectrum.04208-23
- Citations
- 3
- Primary Topic
- Viral gastroenteritis research and epidemiology
- Type
- article
- Field-Weighted Citation Impact
- 1.17
Funders
- European Commission
- Uppsala Multidisciplinary Center for Advanced Computational Science