TY - JOUR
T1 - Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples
AU - de Vries, Jutte J.C.
AU - Brown, Julianne R.
AU - Fischer, Nicole
AU - Sidorov, Igor A.
AU - Morfopoulou, Sofia
AU - Huang, Jiabin
AU - Munnink, Bas B.Oude
AU - Sayiner, Arzu
AU - Bulgurcu, Alihan
AU - Rodriguez, Christophe
AU - Gricourt, Guillaume
AU - Keyaerts, Els
AU - Beller, Leen
AU - Bachofen, Claudia
AU - Kubacki, Jakub
AU - Samuel, Cordey
AU - Florian, Laubscher
AU - Dennis, Schmitz
AU - Beer, Martin
AU - Hoeper, Dirk
AU - Huber, Michael
AU - Kufner, Verena
AU - Zaheri, Maryam
AU - Lebrand, Aitana
AU - Papa, Anna
AU - van Boheemen, Sander
AU - Kroes, Aloys C.M.
AU - Breuer, Judith
AU - Lopez-Labrador, F. Xavier
AU - Claas, Eric C.J.
N1 - Funding Information:
MH was supported by the Clinical Research Priority Program 'Comprehensive Genomic Pathogen Detection' of the University of Zurich. FXL received funding from Instituto de Salud Carlos III, Spain (Grant numbers PI18/01824 and PI18/01759 and CIBEResp ).
Funding Information:
We thank the COMPARE study group (https://www.compare-europe.eu/) and the EMBL-EBI (https://www.ebi.ac.uk/) for the availability of the Data Hubs. MH was supported by the Clinical Research Priority Program 'Comprehensive Genomic Pathogen Detection' of the University of Zurich. FXL received funding from Instituto de Salud Carlos III, Spain (Grant numbers PI18/01824 and PI18/01759 and CIBEResp).
Publisher Copyright:
© 2021
PY - 2021/8/1
Y1 - 2021/8/1
N2 - Introduction: Metagenomic sequencing is increasingly being used in clinical settings for difficult to diagnose cases. The performance of viral metagenomic protocols relies to a large extent on the bioinformatic analysis. In this study, the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS) initiated a benchmark of metagenomic pipelines currently used in clinical virological laboratories. Methods: Metagenomic datasets from 13 clinical samples from patients with encephalitis or viral respiratory infections characterized by PCR were selected. The datasets were analyzed with 13 different pipelines currently used in virological diagnostic laboratories of participating ENNGS members. The pipelines and classification tools were: Centrifuge, DAMIAN, DIAMOND, DNASTAR, FEVIR, Genome Detective, Jovian, MetaMIC, MetaMix, One Codex, RIEMS, VirMet, and Taxonomer. Performance, characteristics, clinical use, and user-friendliness of these pipelines were analyzed. Results: Overall, viral pathogens with high loads were detected by all the evaluated metagenomic pipelines. In contrast, lower abundance pathogens and mixed infections were only detected by 3/13 pipelines, namely DNASTAR, FEVIR, and MetaMix. Overall sensitivity ranged from 80% (10/13) to 100% (13/13 datasets). Overall positive predictive value ranged from 71-100%. The majority of the pipelines classified sequences based on nucleotide similarity (8/13), only a minority used amino acid similarity, and 6 of the 13 pipelines assembled sequences de novo. No clear differences in performance were detected that correlated with these classification approaches. Read counts of target viruses varied between the pipelines over a range of 2-3 log, indicating differences in limit of detection. Conclusion: A wide variety of viral metagenomic pipelines is currently used in the participating clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implicating the need for standardization and validation of metagenomic analysis for clinical diagnostic use. Future studies should address the selective effects due to the choice of different reference viral databases.
AB - Introduction: Metagenomic sequencing is increasingly being used in clinical settings for difficult to diagnose cases. The performance of viral metagenomic protocols relies to a large extent on the bioinformatic analysis. In this study, the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS) initiated a benchmark of metagenomic pipelines currently used in clinical virological laboratories. Methods: Metagenomic datasets from 13 clinical samples from patients with encephalitis or viral respiratory infections characterized by PCR were selected. The datasets were analyzed with 13 different pipelines currently used in virological diagnostic laboratories of participating ENNGS members. The pipelines and classification tools were: Centrifuge, DAMIAN, DIAMOND, DNASTAR, FEVIR, Genome Detective, Jovian, MetaMIC, MetaMix, One Codex, RIEMS, VirMet, and Taxonomer. Performance, characteristics, clinical use, and user-friendliness of these pipelines were analyzed. Results: Overall, viral pathogens with high loads were detected by all the evaluated metagenomic pipelines. In contrast, lower abundance pathogens and mixed infections were only detected by 3/13 pipelines, namely DNASTAR, FEVIR, and MetaMix. Overall sensitivity ranged from 80% (10/13) to 100% (13/13 datasets). Overall positive predictive value ranged from 71-100%. The majority of the pipelines classified sequences based on nucleotide similarity (8/13), only a minority used amino acid similarity, and 6 of the 13 pipelines assembled sequences de novo. No clear differences in performance were detected that correlated with these classification approaches. Read counts of target viruses varied between the pipelines over a range of 2-3 log, indicating differences in limit of detection. Conclusion: A wide variety of viral metagenomic pipelines is currently used in the participating clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implicating the need for standardization and validation of metagenomic analysis for clinical diagnostic use. Future studies should address the selective effects due to the choice of different reference viral databases.
UR - http://www.scopus.com/inward/record.url?scp=85109864987&partnerID=8YFLogxK
U2 - 10.1016/j.jcv.2021.104908
DO - 10.1016/j.jcv.2021.104908
M3 - Article
AN - SCOPUS:85109864987
SN - 1386-6532
VL - 141
JO - Journal of Clinical Virology
JF - Journal of Clinical Virology
M1 - 104908
ER -
