Genome Coverage as a Better Diagnostic Parameter than Read Count for Metagenomic Identification of Viral Pathogens in Clinical Stool Samples
Refereed conference paper presented and published in conference proceedings


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AbstractBackground
Metagenomic next-generation sequencing (mNGS) is transforming infectious disease diagnostics and has been successfully used to diagnose unexplained acute viral infections previously tested negative by conventional diagnostic assays. However, most validation studies have focused on respiratory and cerebrospinal fluid samples. There is a lack of data on validating the robustness of mNGS-based diagnostics in other sample types.

Aim of Study
To investigate the robustness of mNGS-based virus identification in fecal material using common diagnostic parameters.

Materials & Methods
We investigated two candidate diagnostic parameters (mapped sequencing reads and virus genome coverage) by performing a pan-virus mNGS on a well-characterized panel of 181 norovirus-positive stool samples with low to high viral loads.

Results
We showed that percentage of virus genome coverage (%GC) had a much higher tolerance against decreasing input viral load compared to the commonly used percentage of on-target reads (%OTR). The virus detection rate at majority %OTRs threshold (≥50%) decreased from 82% among high viral load (Ct<10) samples to 0% among low viral load (Ct≥20) samples. In contrast, the virus detection rate at majority %GC threshold (≥50%) was 100% in high viral load samples and consistently above 30% in low viral load samples.

Conclusions
Our findings provide evidence that currently available diagnostic mNGS workflows utilizing virus genome coverage as a diagnostic parameter can also be applied to stool samples to enhance detection of intestinal viruses. Our study also highlights the need to validate existing mNGS workflows in pathogen detection and to benchmark different diagnostic parameters across clinical sample types.

Acknowledgements
The project team was supported in part by research grants from the commissioned Health and Medical Research Fund of Food and Health Bureau of the HKSAR Government (to M.C.W.C.; reference numbers CU-16-A14, CU-17-B6, CU-17-B7, and CU-17-B8).
All Author(s) ListMartin Chi-Wai Chan, Lin-Yao Zhang, Grace C.Y. Lui, Yun Kit Yeoh, Margaret Ip, Mamie Hui, Zigui Chen, Wai-Tat Wong, Ting F. Leung, Raymond W.M. Lai, David S.C. Hui, Paul K.S. Chan, Kirsty Kwok
Name of Conference66th Annual Meeting of the Japanese Society for Virology
Start Date of Conference28/10/2018
End Date of Conference30/10/2018
Place of ConferenceKyoto
Country/Region of ConferenceJapan
Year2018
Month10
LanguagesEnglish-United States

Last updated on 2018-19-12 at 09:42