Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022–23 - 17/05/24
Summary |
Objectives |
We evaluated Nanopore sequencing for influenza surveillance.
Methods |
Influenza 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.
Results |
From 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.
Conclusions |
Nanopore 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.
Le texte complet de cet article est disponible en PDF.Highlights |
• | Nanopore sequencing is a reproducible tool for influenza surveillance. |
• | Inter-regional transmission of influenza was common across the UK. |
• | Influenza anti-viral resistance was rare. |
• | In 1 year most infections were genetically similar, hindering transmission studies. |
• | Hospital-acquired infections are likely a key source of nosocomial transmission. |
Keywords : Influenza, Respiratory virus, Sequencing, Epidemiology
Plan
Vol 88 - N° 6
Article 106164- juin 2024 Retour au numéro
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