Cane, Jennifer;
Sanderson, Nicholas;
Barnett, Sophie;
Vaughan, Ali;
Pott, Megan;
Kapel, Natalia;
Morgan, Marcus;
... Eyre, David W; + view all
(2024)
Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022–23.
Journal of Infection
, 88
(6)
, Article 106164. 10.1016/j.jinf.2024.106164.
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Abstract
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.
| Type: | Article |
|---|---|
| Title: | Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022–23 |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1016/j.jinf.2024.106164 |
| Publisher version: | http://dx.doi.org/10.1016/j.jinf.2024.106164 |
| Language: | English |
| Additional information: | © 2024 The Author(s). Published by Elsevier Ltd on behalf of The British Infection Association. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
| Keywords: | Influenza, Respiratory virus, Sequencing, Epidemiology |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Inst of Clinical Trials and Methodology UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > Inst of Clinical Trials and Methodology > MRC Clinical Trials Unit at UCL |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/10192248 |
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