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. 2021 Jul;26(27):2000004.
doi: 10.2807/1560-7917.ES.2021.26.27.2000004.

Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season

Yifei Xu  1   2 , Kuiama Lewandowski  3 , Louise O Downs  4   5 , James Kavanagh  1   2 , Thomas Hender  3 , Sheila Lumley  4   5 , Katie Jeffery  4 , Dona Foster  1   2 , Nicholas D Sanderson  1   2 , Ali Vaughan  1   2 , Marcus Morgan  4 , Richard Vipond  3 , Miles Carroll  3 , Timothy Peto  1   2   4 , Derrick Crook  1   2   4 , A Sarah Walker  1   2 , Philippa C Matthews  2   4   5 , Steven T Pullan  3
Affiliations

Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season

Yifei Xu et al. Euro Surveill. 2021 Jul.

Abstract

BackgroundInfluenza virus presents a considerable challenge to public health by causing seasonal epidemics and occasional pandemics. Nanopore metagenomic sequencing has the potential to be deployed for near-patient testing, providing rapid infection diagnosis, rationalising antimicrobial therapy, and supporting infection-control interventions.AimTo evaluate the applicability of this sequencing approach as a routine laboratory test for influenza in clinical settings.MethodsWe conducted Oxford Nanopore Technologies (Oxford, United Kingdom (UK)) metagenomic sequencing for 180 respiratory samples from a UK hospital during the 2018/19 influenza season, and compared results to routine molecular diagnostic standards (Xpert Xpress Flu/RSV assay; BioFire FilmArray Respiratory Panel 2 assay). We investigated drug resistance, genetic diversity, and nosocomial transmission using influenza sequence data.ResultsCompared to standard testing, Nanopore metagenomic sequencing was 83% (75/90) sensitive and 93% (84/90) specific for detecting influenza A viruses. Of 59 samples with haemagglutinin subtype determined, 40 were H1 and 19 H3. We identified an influenza A(H3N2) genome encoding the oseltamivir resistance S331R mutation in neuraminidase, potentially associated with an emerging distinct intra-subtype reassortant. Whole genome phylogeny refuted suspicions of a transmission cluster in a ward, but identified two other clusters that likely reflected nosocomial transmission, associated with a predominant community-circulating strain. We also detected other potentially pathogenic viruses and bacteria from the metagenome.ConclusionNanopore metagenomic sequencing can detect the emergence of novel variants and drug resistance, providing timely insights into antimicrobial stewardship and vaccine design. Full genome generation can help investigate and manage nosocomial outbreaks.

Keywords: Nanopore; antiviral drug resistance; diagnosis; genetic diversity; influenza; metagenomics; nosocomial transmission; respiratory viruses.

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Conflict of interest statement

Conflict of interest: None declared.

Figures

Figure 1
Figure 1
Nanopore metagenomic sequencing of respiratory samples submitted to the clinical diagnostic laboratory at the Oxford University Hospitals NHS Foundation Trust, United Kingdom, 2018/19 influenza season (n = 90 influenza-positive samples)
Figure 2
Figure 2
Identification, subtyping, and recovery of influenza A virus genomes by Nanopore metagenomic sequencing of respiratory samples that tested influenza-positive in a clinical diagnostic laboratory, United Kingdom, 2018/19 influenza season (n = 90 respiratory samples)
Figure 3
Figure 3
Maximum likelihood phylogenies of H3N2 influenza A virus sequences recovered from respiratory samples collected from a hospital cohort, United Kingdom, 2018/19 influenza season (n = 11 H3 sequences and 13 N2 sequences)
Figure 4
Figure 4
Investigation of nosocomial transmission of influenza A(H3N2) virus in a hospital, United Kingdom, 2018/19 influenza season (n = 14 patients)
See this image and copyright information in PMC

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