Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure

López‐Labrador, F. Xavier; Brown, Julianne R.; Fischer, Nicole; Harvala, Heli; Boheemen, Sander van; Cinek, Ondřej; Sayıner, Arzu; Madsen, Tina Vasehus; Auvinen, Eeva; Kufner, Verena; Huber, Michael; Rodriguez, Christophe; Jonges, Marcel; Hönemann, Mario; Susi, Petri; Sousa, Hugo; Klapper, Paul E.; Pérez-Cataluña, Alba; Hernández, Marta; Molenkamp, Richard; Hoek, Lia van der; Schuurman, Rob; Couto, Natacha; Leuzinger, Karoline; Simmonds, Peter; Beer, Martin; Höper, Dirk W.; Kamminga, Sergio; Feltkamp, Mariet C.W.; Rodrı́guez-Dı́az, Jesús; Keyaerts, Els; Nielsen, Xiaohui Chen; Puchhammer‐Stöckl, Elisabeth; Kroes, Aloys C.M.; Buesa, Javier; Breuer, Judith; Claas, Eric C. J.; Vries, Jutte J.C. de

doi:10.1016/j.jcv.2020.104691

Cited by 55 publications

(60 citation statements)

References 47 publications

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“…Given the multistep nature of the process and the generation of large amounts of detailed data generated, it is essential that, where possible, standardization and quality checks to support consistency and integrity of data outputs are considered and implemented. For other applications, including those relevant to bacteriology and molecular pathology, quality guidelines have already been developed [ 18 , 19 , 20 ]. However, these are still lacking for the HPV field.…”

Section: Introductionmentioning

confidence: 99%

Human Papillomavirus Detection by Whole-Genome Next-Generation Sequencing: Importance of Validation and Quality Assurance Procedures

Mühr

Guerendiain

Cuschieri

et al. 2021

Viruses

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Next-generation sequencing (NGS) yields powerful opportunities for studying human papillomavirus (HPV) genomics for applications in epidemiology, public health, and clinical diagnostics. HPV genotypes, variants, and point mutations can be investigated in clinical materials and described in previously unprecedented detail. However, both the NGS laboratory analysis and bioinformatical approach require numerous steps and checks to ensure robust interpretation of results. Here, we provide a step-by-step review of recommendations for validation and quality assurance procedures of each step in the typical NGS workflow, with a focus on whole-genome sequencing approaches. The use of directed pilots and protocols to ensure optimization of sequencing data yield, followed by curated bioinformatical procedures, is particularly emphasized. Finally, the storage and sharing of data sets are discussed. The development of international standards for quality assurance should be a goal for the HPV NGS community, similar to what has been developed for other areas of sequencing efforts including microbiology and molecular pathology. We thus propose that it is time for NGS to be included in the global efforts on quality assurance and improvement of HPV-based testing and diagnostics.

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Section: Introductionmentioning

confidence: 99%

Human Papillomavirus Detection by Whole-Genome Next-Generation Sequencing: Importance of Validation and Quality Assurance Procedures

Mühr

Guerendiain

Cuschieri

et al. 2021

Viruses

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“…CMg can potentially be applied to any type of samples, provided that a sufficient amount of nucleic acids can be extracted [11]. The first step, called pre-extraction step, consists of accessing the nucleic acids of the potentially present microorganisms by breaking their cell membranes and walls.…”

Section: Pre-extraction Stepmentioning

confidence: 99%

The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives

d’Humières

Salmona

Dellière

et al. 2021

Drugs

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Clinical metagenomics (CMg) is the process of sequencing nucleic acid of clinical samples to obtain clinically relevant information such as the identification of microorganisms and their susceptibility to antimicrobials. Over the last decades, sequencing and bioinformatic solutions supporting CMg have much evolved and an increasing number of case reports and series covering various infectious diseases have been published. Metagenomics is a new approach to infectious disease diagnosis that is currently being developed and is certainly one of the most promising for the coming years. However, most CMg studies are retrospective, and few address the potential impact CMg could have on patient management, including initiation, adaptation, or cessation of antimicrobials. In this narrative review, we have discussed the potential role of CMg in bacteriology, virology, mycology, and parasitology. Several reports and case-series confirm that CMg is an innovative tool with which one can (i) identify more microorganisms than with conventional methods in a single test, (ii) obtain results within hours, and (iii) tailor the antimicrobial regimen of patients. However, the cost-efficiency of CMg and its real impact on patient management are still to be determined.

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“…Since the amount of pathogen in a sample is relatively low and human background is high, several strategies have been applied to increase the sensitivity of mNGS based on physical or enzymatic pre-processing of samples for human DNA depletion (3) (4). Another strategy is hybridization enrichment, with the application of a virome probe panel that targets all known vertebrate viruses to increase the sensitivity of virus detection and characterization (5, 6).…”

Section: Introductionmentioning

confidence: 99%

Viral metagenomic sequencing in a cohort of international travellers returning with febrile illness

Reyes

Carbo

Slooten

et al. 2021

Preprint

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Background Diagnosis of infections in returning international travellers can be challenging because of the broad spectrum of potential infectious aetiologies potentially involved. Viral metagenomic next-generation sequencing (mNGS) has the potential to detect any virus present in a patient sample and is increasingly being used for difficult to diagnose cases. The aim of this study was to analyse the performance of mNGS for viral pathogen detection in the clinical setting of international travellers returning with febrile illness. Methods Thirty-eight serum samples from international travellers returning with febrile illness and presenting at the outpatient clinic of the Leiden University Medical Center in the Netherlands in the time period 2015-2016 were selected retrospectively. Samples were processed for viral metagenomic sequencing using a probe panel capturing all known vertebrate viruses. Bioinformatic analysis was performed using Genome Detective software for metagenomic virus detection. Metagenomic virus findings were compared with viral pathogen detection using conventional methods. Results In 8 out of the 38 patients (21%), a pathogenic virus was detected by mNGS. All viral pathogens detected by conventional assays were also detected by mNGS: dengue virus (n=4 patients), Epstein-Barr virus (n=2), hepatitis B virus (n=1). In addition, mNGS resulted in additional pathogenic findings in 2 patients (5%): dengue virus (n=1), and hepatitis C virus (n=1). Non-pathogenic viruses detected were: GB virus C (n=1) and torque teno viruses (n=3). High genome coverage and depth using capture probes enabled typing of the dengue viruses detected. Conclusions Viral metagenomics has the potential to assist the detection of viral pathogens and co-infections in one step in international travellers with a febrile syndrome. Furthermore, viral enrichment by probes resulted in high genome coverage and depth which enabled dengue virus typing.

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Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure

Cited by 55 publications

References 47 publications

Human Papillomavirus Detection by Whole-Genome Next-Generation Sequencing: Importance of Validation and Quality Assurance Procedures

Human Papillomavirus Detection by Whole-Genome Next-Generation Sequencing: Importance of Validation and Quality Assurance Procedures

The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives

Viral metagenomic sequencing in a cohort of international travellers returning with febrile illness

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