Author:
Cane Jennifer,Sanderson Nicholas,Barnett Sophie,Vaughan Ali,Pott Megan,Kapel Natalia,Morgan Marcus,Jesuthasan Gerald,Samuel Reggie,Ehsaan Muhammad,Boothe Hugh,Haduli Eric,Studley Ruth,Rourke Emma,Diamond Ian,Fowler Tom,Watson Conall,Stoesser Nicole,Walker Ann Sarah,Street Teresa,Eyre David
Abstract
AbstractObjectivesWe 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.HighlightsNanopore sequencing is a reproducible tool for influenza surveillanceInter-regional transmission of influenza was common across the UKInfluenza anti-viral resistance was rareIn 1 year most infections were genetically similar, hindering transmission studiesHospital-acquired infections are likely a key source of nosocomial transmission
Publisher
Cold Spring Harbor Laboratory
Reference21 articles.
1. UK Health Security Agency. Surveillance of influenza and other seasonal respiratory viruses in the UK, winter 2022 to 2023. 2023; published online July 3. https://www.gov.uk/government/statistics/annual-flu-reports/surveillance-of-influenza-and-other-seasonal-respiratory-viruses-in-the-uk-winter-2022-to-2023 (accessed Oct 31, 2023).
2. UK Health Security Agency. Guidance on use of antiviral agents for the treatment and prophylaxis of seasonal influenza. 2021; published online Dec 1. https://www.gov.uk/government/publications/influenza-treatment-and-prophylaxis-using-anti-viral-agents (accessed Oct 31, 2023).
3. Failure to Detect Influenza A H1N1 Highlights the Need for Multiple Gene Targets in Influenza Molecular Tests;J Clin Microbiol,2023
4. Single-Reaction Genomic Amplification Accelerates Sequencing and Vaccine Production for Classical and Swine Origin Human Influenza A Viruses
5. Rapid multiplex MinION nanopore sequencing workflow for Influenza A viruses;BMC Infect Dis,2020