ArticleThe Journal of infection2024
Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23.
Article in The Journal of infection, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Update and optimization of a multiplex RT-qPCR assay to overcome diagnostic failure in emerging influenza A(H3N2) subclades J.2 and K (Peru, 2024-2026).IJID regions · 2026Article
- Rapid detection of human and animal respiratory viruses using Microbe Finder (MiFiFrontiers in microbiology · 2026Article
- Review
- Patterns of the Circulation of Influenza in a Targeted Jordanian Subpopulation from November 2021 to April 2023.Pathogens (Basel, Switzerland) · 2025Article
- Analysis of the Monophyletic Lineage of Avian Influenza H5N1 Which Circulated in Venezuelan Birds During the 2022-2023 Outbreak.Microorganisms · 2024Article
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Authors and funding
21 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 %); 36/39 (92 %) Illumina vs. Nanopore comparisons were identical, and 3 (8 %) differed by 1 variant. 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.
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