Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23.
J Infect
; 88(6): 106164, 2024 Jun.
Article
in En
| MEDLINE
| ID: mdl-38692359
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.Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Influenza B virus
/
Influenza, Human
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Nanopore Sequencing
Limits:
Adolescent
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Adult
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Aged
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Child
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Female
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Humans
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Male
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Middle aged
Country/Region as subject:
Europa
Language:
En
Journal:
J Infect
/
J. infect
/
Journal of infection
Year:
2024
Document type:
Article
Affiliation country:
Country of publication: