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Unbiased Deep Sequencing of RNA Viruses from Clinical Samples
Published on: July 2, 2016
Multiplex MinION sequencing suggests enteric adenovirus F41 genetic diversity comparable to pre-COVID-19 era
Mailis Maes1, Fahad Khokhar2, Sam A J Wilkinson3
1Clinical Microbiology and Public Health Laboratory, UK Health Security Agency, Addenbrooke's Hospital, Cambridge, UK.
Insights
Human adenovirus F41 causes gastroenteritis and has been linked to pediatric hepatitis. This study developed a sequencing method to analyze F41 genetic diversity in UK children, finding lineages present before the COVID-19 pandemic.
Area of Science:
- Virology
- Genomics
- Pediatric Infectious Diseases
Background:
- Human adenovirus F41 (HAdV-F41) is a known cause of acute gastroenteritis in children.
- An increase in pediatric hepatitis of unknown origin has been reported globally, with HAdV-F41 implicated.
- Limited data exists on HAdV-F41 genetic diversity in the UK and the pandemic's impact.
Purpose of the Study:
- To evaluate an overlapping-amplicon sequencing method using Oxford Nanopore technology for HAdV-F41 genome analysis from clinical samples.
- To investigate the genetic diversity of HAdV-F41 in UK children.
- To assess the potential impact of the COVID-19 pandemic on HAdV-F41 diversity.
Main Methods:
- An overlapping-amplicon sequencing approach was applied to HAdV-F41 positive clinical samples from East of England (Jan-May 2022).
- Oxford Nanopore technology was utilized for genome sequencing.
- Sequencing data was analyzed to determine genome coverage and identify viral lineages.
Main Results:
- The method achieved >75% genome coverage in 13/22 samples and >50% in 19/22 samples.
- Two distinct HAdV-F41 lineages were identified in pediatric patients in the East of England in 2022.
- HAdV-F41 genomes from hepatitis cases were consistent with pre-pandemic diversity in the UK and Europe.
Conclusions:
- Overlapping amplicon sequencing is suitable for generating HAdV-F41 genomic data from clinical samples with high viral loads.
- The identified HAdV-F41 lineages in the UK were circulating prior to the COVID-19 pandemic.
- Further genomic surveillance is needed to monitor HAdV-F41 diversity and its association with pediatric hepatitis.
Abstract:
Human adenovirus F41 causes acute gastroenteritis in children, and has recently been associated with an apparent increase in paediatric hepatitis of unknown aetiology in the UK, with further cases reported in multiple countries. Relatively little is known about the genetic diversity of adenovirus F41 in UK children; and it is unclear what, if any, impact the COVID-19 pandemic has had on viral diversity in the UK. Methods that allow F41 to be sequenced from clinical samples without the need for viral culture are required to provide the genomic data to address these questions. Therefore, we evaluated an overlapping-amplicon method of sequencing adenovirus genomes from clinical samples using Oxford Nanopore technology. We applied this method to a small sample of adenovirus-species-F-positive extracts collected as part of standard care in the East of England region in January-May 2022. This method produced genomes with >75 % coverage in 13/22 samples and >50 % coverage in 19/22 samples. We identified two F41 lineages present in paediatric patients in the East of England in 2022. Where F41 genomes from paediatric hepatitis cases were available (n=2), these genomes fell within the diversity of F41 from the UK and continental Europe sequenced before and after the 2020-2021 phase of the COVID-19 pandemic. Our analyses suggest that overlapping amplicon sequencing is an appropriate method for generating F41 genomic data from high-virus-load clinical samples, and currently circulating F41 viral lineages were present in the UK and Europe before the COVID-19 pandemic.
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