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タイトル: Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23

概要: ObjectivesWe evaluated Nanopore sequencing for influenza surveillance. MethodsInfluenza A and B PCR-positive samples from hospital patients in Oxfordshire, UK, and a UK-wide population survey from winter 2022-23 underwent Nanopore sequencing following targeted rt-PCR amplification. ResultsFrom 941 infections, successful sequencing was achieved in 292/388(75%) available Oxfordshire samples: 231(79%) A/H3N2, 53(18%) A/H1N1, and 8(3%) B/Victoria and in 53/113(47%) UK-wide samples. Sequencing was more successful at lower Ct values. Most same-sample replicate sequences had identical haemagglutinin segments (124/141;88%); a subset of samples also Illumina sequenced were very similar to Nanopore sequences. Comparison of Oxfordshire and UK-wide sequences showed frequent inter-regional transmission. Infections were closely-related to 2022-23 vaccine strains. Only one sample had a neuraminidase inhibitor resistance mutation. 849/941(90%) Oxfordshire infections were community-acquired. 63/88(72%) potentially healthcare-associated cases shared a hospital ward with [≥]1 known infectious case. 33 epidemiologically-plausible transmission links had sequencing data for both source and recipient: 8 were within [≤]5 SNPs, of these, 5(63%) involved potential sources that were also hospital-acquired. ConclusionsNanopore influenza sequencing was reproducible and antiviral resistance rare. Inter-regional transmission was common; most infections were genomically similar. Hospital-acquired infections are likely an important source of nosocomial transmission and should be prioritised for infection prevention and control. HighlightsO_LINanopore sequencing is a reproducible tool for influenza surveillance C_LIO_LIInter-regional transmission of influenza was common across the UK C_LIO_LIInfluenza anti-viral resistance was rare C_LIO_LIIn 1 year most infections were genetically similar, hindering transmission studies C_LIO_LIHospital-acquired infections are likely a key source of nosocomial transmission C_LI