Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting

Jutte J.C. de Vries; Julianne R. Brown; Natacha Couto; Martin Beer; Philippe Le Mercier; Igor Sidorov; Anna Papa; Nicole Fischer; Bas B. Oude Munnink; Christophe Rodriquez; Maryam Zaheri; Arzu Sayiner; Mario Hönemann; Alba Perez Cataluna; Ellen C. Carbo; Claudia Bachofen; Jakub Kubacki; Dennis Schmitz; Katerina Tsioka; Sébastien Matamoros; Dirk Höper; Marta Hernandez; Elisabeth Puchhammer-Stöckl; Aitana Lebrand; Michael Huber; Peter Simmonds; Eric C.J. Claas; F. Xavier López-Labrador

doi:10.1016/j.jcv.2021.104812

Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting

Jutte J.C. de Vries^*, Julianne R. Brown, Natacha Couto, Martin Beer, Philippe Le Mercier, Igor Sidorov, Anna Papa, Nicole Fischer, Bas B. Oude Munnink, Christophe Rodriquez, Maryam Zaheri, Arzu Sayiner, Mario Hönemann, Alba Perez Cataluna, Ellen C. Carbo, Claudia Bachofen, Jakub Kubacki, Dennis Schmitz, Katerina Tsioka, Sébastien MatamorosDirk Höper, Marta Hernandez, Elisabeth Puchhammer-Stöckl, Aitana Lebrand, Michael Huber, Peter Simmonds, Eric C.J. Claas, F. Xavier López-Labrador

^*Corresponding author for this work

Virology

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Abstract

Metagenomic next-generation sequencing (mNGS) is an untargeted technique for determination of microbial DNA/RNA sequences in a variety of sample types from patients with infectious syndromes. mNGS is still in its early stages of broader translation into clinical applications. To further support the development, implementation, optimization and standardization of mNGS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mNGS for viral diagnostics to share methodologies and experiences, and to develop application guidelines. Following the ENNGS publication Recommendations for the introduction of mNGS in clinical virology, part I: wet lab procedure in this journal, the current manuscript aims to provide practical recommendations for the bioinformatic analysis of mNGS data and reporting of results to clinicians.

Original language	English
Article number	104812
Journal	Journal of Clinical Virology
Volume	138
Early online date	2 Apr 2021
DOIs	https://doi.org/10.1016/j.jcv.2021.104812
Publication status	Published - May 2021

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Publisher Copyright:
© 2021

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Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part IIFinal published version, 707 KBLicence: CC BY

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de Vries, J. J. C., Brown, J. R., Couto, N., Beer, M., Le Mercier, P., Sidorov, I., Papa, A., Fischer, N., Oude Munnink, B. B., Rodriquez, C., Zaheri, M., Sayiner, A., Hönemann, M., Cataluna, A. P., Carbo, E. C., Bachofen, C., Kubacki, J., Schmitz, D., Tsioka, K., ... López-Labrador, F. X. (2021). Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting. Journal of Clinical Virology, 138, [104812]. https://doi.org/10.1016/j.jcv.2021.104812

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title = "Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting",

abstract = "Metagenomic next-generation sequencing (mNGS) is an untargeted technique for determination of microbial DNA/RNA sequences in a variety of sample types from patients with infectious syndromes. mNGS is still in its early stages of broader translation into clinical applications. To further support the development, implementation, optimization and standardization of mNGS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mNGS for viral diagnostics to share methodologies and experiences, and to develop application guidelines. Following the ENNGS publication Recommendations for the introduction of mNGS in clinical virology, part I: wet lab procedure in this journal, the current manuscript aims to provide practical recommendations for the bioinformatic analysis of mNGS data and reporting of results to clinicians.",

author = "{de Vries}, {Jutte J.C.} and Brown, {Julianne R.} and Natacha Couto and Martin Beer and {Le Mercier}, Philippe and Igor Sidorov and Anna Papa and Nicole Fischer and {Oude Munnink}, {Bas B.} and Christophe Rodriquez and Maryam Zaheri and Arzu Sayiner and Mario H{\"o}nemann and Cataluna, {Alba Perez} and Carbo, {Ellen C.} and Claudia Bachofen and Jakub Kubacki and Dennis Schmitz and Katerina Tsioka and S{\'e}bastien Matamoros and Dirk H{\"o}per and Marta Hernandez and Elisabeth Puchhammer-St{\"o}ckl and Aitana Lebrand and Michael Huber and Peter Simmonds and Claas, {Eric C.J.} and L{\'o}pez-Labrador, {F. Xavier}",

note = "Publisher Copyright: {\textcopyright} 2021",

year = "2021",

month = may,

doi = "10.1016/j.jcv.2021.104812",

language = "English",

volume = "138",

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de Vries, JJC, Brown, JR, Couto, N, Beer, M, Le Mercier, P, Sidorov, I, Papa, A, Fischer, N, Oude Munnink, BB, Rodriquez, C, Zaheri, M, Sayiner, A, Hönemann, M, Cataluna, AP, Carbo, EC, Bachofen, C, Kubacki, J, Schmitz, D, Tsioka, K, Matamoros, S, Höper, D, Hernandez, M, Puchhammer-Stöckl, E, Lebrand, A, Huber, M, Simmonds, P, Claas, ECJ & López-Labrador, FX 2021, 'Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting', Journal of Clinical Virology, vol. 138, 104812. https://doi.org/10.1016/j.jcv.2021.104812

TY - JOUR

T1 - Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II

T2 - bioinformatic analysis and reporting

AU - de Vries, Jutte J.C.

AU - Brown, Julianne R.

AU - Couto, Natacha

AU - Beer, Martin

AU - Le Mercier, Philippe

AU - Sidorov, Igor

AU - Papa, Anna

AU - Fischer, Nicole

AU - Oude Munnink, Bas B.

AU - Rodriquez, Christophe

AU - Zaheri, Maryam

AU - Sayiner, Arzu

AU - Hönemann, Mario

AU - Cataluna, Alba Perez

AU - Carbo, Ellen C.

AU - Bachofen, Claudia

AU - Kubacki, Jakub

AU - Schmitz, Dennis

AU - Tsioka, Katerina

AU - Matamoros, Sébastien

AU - Höper, Dirk

AU - Hernandez, Marta

AU - Puchhammer-Stöckl, Elisabeth

AU - Lebrand, Aitana

AU - Huber, Michael

AU - Simmonds, Peter

AU - Claas, Eric C.J.

AU - López-Labrador, F. Xavier

PY - 2021/5

Y1 - 2021/5

N2 - Metagenomic next-generation sequencing (mNGS) is an untargeted technique for determination of microbial DNA/RNA sequences in a variety of sample types from patients with infectious syndromes. mNGS is still in its early stages of broader translation into clinical applications. To further support the development, implementation, optimization and standardization of mNGS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mNGS for viral diagnostics to share methodologies and experiences, and to develop application guidelines. Following the ENNGS publication Recommendations for the introduction of mNGS in clinical virology, part I: wet lab procedure in this journal, the current manuscript aims to provide practical recommendations for the bioinformatic analysis of mNGS data and reporting of results to clinicians.

AB - Metagenomic next-generation sequencing (mNGS) is an untargeted technique for determination of microbial DNA/RNA sequences in a variety of sample types from patients with infectious syndromes. mNGS is still in its early stages of broader translation into clinical applications. To further support the development, implementation, optimization and standardization of mNGS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mNGS for viral diagnostics to share methodologies and experiences, and to develop application guidelines. Following the ENNGS publication Recommendations for the introduction of mNGS in clinical virology, part I: wet lab procedure in this journal, the current manuscript aims to provide practical recommendations for the bioinformatic analysis of mNGS data and reporting of results to clinicians.

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DO - 10.1016/j.jcv.2021.104812

M3 - Article

C2 - 33819811

AN - SCOPUS:85103629761

VL - 138

JO - Journal of Clinical Virology

JF - Journal of Clinical Virology

SN - 1386-6532

M1 - 104812

ER -

Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting

Abstract

Bibliographical note

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