Evaluation of whole genome sequencing protocols and target-capture panels for detection of respiratory viruses in clinical specimens
- 1Virus Reference Department, UKHSA
- 2South London Specialist Virology Centre, King’s College Hospital NHS Foundation Trust
Abstract
Respiratory viruses are major contributors to global morbidity and mortality. When viral mutations compromise detection by conventional diagnostic assays, identifying cases and tracing transmission becomes challenging. Whole genome sequencing (WGS) improves on conventional diagnostics as it can detect viruses with novel mutations. This study evaluated the performance of the ePlex, a rapid multiplex polymerase chain reaction (PCR) assay (RMPA), an in-house real-time reverse transcription PCR assay (RT-qPCR) and WGS for detecting respiratory virus infections in clinical specimens. Sixty-one sequence libraries were prepared, and bait enriched from nasopharyngeal swabs, collected in 2021, which were negative for SARS-CoV-2 but positive for co-infections of respiratory viruses detected by the ePlex. An in-house bioinformatics pipeline enabled a metagenomic analysis approach to be compared with the ePlex and RT-qPCR. In most swabs, respiratory viruses were detected by WGS (average genome recovery: 85.9%) or RT-qPCR which concurred with the ePlex result, but as single viruses rather than co-infections. WGS recovered respiratory syncytial viruses (80%) and metapneumoviruses (70%) most often. This study demonstrates the power of WGS and bait capture in resolving the genomes of respiratory pathogens from limited clinical material. Detection of a single virus, rather than co-infections, in this instance could highlight the targeted nature of bait capture technology or competition between viruses during bait hybridization. The number of respiratory syncytial viruses detected (16/20) could be due to a spike in activity detected after the alleviation of non-pharmaceutical interventions in the COVID-19 pandemic.
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BibTeX
@article{kelly2026evaluation,
title = {{Evaluation of whole genome sequencing protocols and target-capture panels for detection of respiratory viruses in clinical specimens}},
author = {Daniel Kelly and Ketharani Yogananthan and Priya Subramaniam and Tiina Talts and Carmen F. Manso and Beatrix Kele and David F. Bibby and Mark Zuckerman and Jean L. Mbisa},
journal = {Frontiers in Microbiology},
year = {2026},
month = oct,
doi = {10.3389/fmicb.2026.1964559},
url = {https://www.frontiersin.org/articles/10.3389/fmicb.2026.1964559/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Evaluation of whole genome sequencing protocols and target-capture panels for detection of respiratory viruses in clinical specimens
AU - Daniel Kelly
AU - Ketharani Yogananthan
AU - Priya Subramaniam
AU - Tiina Talts
AU - Carmen F. Manso
AU - Beatrix Kele
AU - David F. Bibby
AU - Mark Zuckerman
AU - Jean L. Mbisa
PY - 2026
DA - 2026/10/23
JO - Frontiers in Microbiology
DO - 10.3389/fmicb.2026.1964559
UR - https://www.frontiersin.org/articles/10.3389/fmicb.2026.1964559/full
AB - Respiratory viruses are major contributors to global morbidity and mortality. When viral mutations compromise detection by conventional diagnostic assays, identifying cases and tracing transmission becomes challenging. Whole genome sequencing (WGS) improves on conventional diagnostics as it can detect viruses with novel mutations. This study evaluated the performance of the ePlex, a rapid multiplex polymerase chain reaction (PCR) assay (RMPA), an in-house real-time reverse transcription PCR assay (RT-qPCR) and WGS for detecting respiratory virus infections in clinical specimens. Sixty-one sequence libraries were prepared, and bait enriched from nasopharyngeal swabs, collected in 2021, which were negative for SARS-CoV-2 but positive for co-infections of respiratory viruses detected by the ePlex. An in-house bioinformatics pipeline enabled a metagenomic analysis approach to be compared with the ePlex and RT-qPCR. In most swabs, respiratory viruses were detected by WGS (average genome recovery: 85.9%) or RT-qPCR which concurred with the ePlex result, but as single viruses rather than co-infections. WGS recovered respiratory syncytial viruses (80%) and metapneumoviruses (70%) most often. This study demonstrates the power of WGS and bait capture in resolving the genomes of respiratory pathogens from limited clinical material. Detection of a single virus, rather than co-infections, in this instance could highlight the targeted nature of bait capture technology or competition between viruses during bait hybridization. The number of respiratory syncytial viruses detected (16/20) could be due to a spike in activity detected after the alleviation of non-pharmaceutical interventions in the COVID-19 pandemic.
SN - 1664-302X
ER -