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Haemagglutinin and neuraminidase sequencing delineate nosocomial influenza outbreaks with accuracy equivalent to whole genome sequencing

Haemagglutinin and neuraminidase sequencing delineate nosocomial influenza outbreaks with accuracy equivalent to whole genome sequencing
Haemagglutinin and neuraminidase sequencing delineate nosocomial influenza outbreaks with accuracy equivalent to whole genome sequencing

OBJECTIVES: We describe haemagglutinin (HA) and neuraminidase (NA) sequencing in an apparent cross-site influenza A(H1N1) outbreak in renal transplant and haemodialysis patients, confirmed with whole genome sequencing (WGS).

METHODS: Isolates were sequenced from influenza positive individuals. Phylogenetic trees were constructed using HA and NA sequencing and subsequently WGS. Sequence data was analysed to determine genetic relatedness of viruses obtained from inpatient and outpatient cohorts and compared with epidemiological outbreak information.

RESULTS: There were 6 patient cases of influenza in the inpatient renal ward cohort (associated with 3 deaths) and 9 patient cases in the outpatient haemodialysis unit cohort (no deaths). WGS confirmed clustered transmission of two genetically different influenza A(H1N1)pdm09 strains initially identified by analysis of HA and NA genes. WGS took longer, and in this case was not required to determine whether or not the two seemingly linked outbreaks were related.

CONCLUSION: Rapid sequencing of HA and NA genes may be sufficient to aid early influenza outbreak investigation making it appealing for future outbreak investigation. However, as next generation sequencing becomes cheaper and more widely available and bioinformatics software is now freely accessible next generation whole genome analysis may increasingly become a valuable tool for real-time Influenza outbreak investigation.

Journal Article
0163-4453
377-384
Houghton, Rebecca
5ec00f0e-49b1-4b6d-930e-9603370c3cc4
Ellis, Joanna
60f685f9-10b8-43b5-ae55-1d4c240b52c8
Galiano, Monica
1f03920e-81de-4715-922f-ee82a72249aa
Clark, Tristan W.
712ec18e-613c-45df-a013-c8a22834e14f
Wyllie, Sarah
1625ce23-0143-4114-919f-9721d9878e5d
Houghton, Rebecca
5ec00f0e-49b1-4b6d-930e-9603370c3cc4
Ellis, Joanna
60f685f9-10b8-43b5-ae55-1d4c240b52c8
Galiano, Monica
1f03920e-81de-4715-922f-ee82a72249aa
Clark, Tristan W.
712ec18e-613c-45df-a013-c8a22834e14f
Wyllie, Sarah
1625ce23-0143-4114-919f-9721d9878e5d

Houghton, Rebecca, Ellis, Joanna, Galiano, Monica, Clark, Tristan W. and Wyllie, Sarah (2017) Haemagglutinin and neuraminidase sequencing delineate nosocomial influenza outbreaks with accuracy equivalent to whole genome sequencing. Journal of Infection, 74 (4), 377-384. (doi:10.1016/j.jinf.2016.12.015).

Record type: Article

Abstract

OBJECTIVES: We describe haemagglutinin (HA) and neuraminidase (NA) sequencing in an apparent cross-site influenza A(H1N1) outbreak in renal transplant and haemodialysis patients, confirmed with whole genome sequencing (WGS).

METHODS: Isolates were sequenced from influenza positive individuals. Phylogenetic trees were constructed using HA and NA sequencing and subsequently WGS. Sequence data was analysed to determine genetic relatedness of viruses obtained from inpatient and outpatient cohorts and compared with epidemiological outbreak information.

RESULTS: There were 6 patient cases of influenza in the inpatient renal ward cohort (associated with 3 deaths) and 9 patient cases in the outpatient haemodialysis unit cohort (no deaths). WGS confirmed clustered transmission of two genetically different influenza A(H1N1)pdm09 strains initially identified by analysis of HA and NA genes. WGS took longer, and in this case was not required to determine whether or not the two seemingly linked outbreaks were related.

CONCLUSION: Rapid sequencing of HA and NA genes may be sufficient to aid early influenza outbreak investigation making it appealing for future outbreak investigation. However, as next generation sequencing becomes cheaper and more widely available and bioinformatics software is now freely accessible next generation whole genome analysis may increasingly become a valuable tool for real-time Influenza outbreak investigation.

Full text not available from this repository.

More information

Accepted/In Press date: 19 December 2016
e-pub ahead of print date: 16 January 2017
Published date: April 2017
Additional Information: Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.
Keywords: Journal Article

Identifiers

Local EPrints ID: 413561
URI: https://eprints.soton.ac.uk/id/eprint/413561
ISSN: 0163-4453
PURE UUID: ea096ef6-837b-4518-bb37-9bb3c653456a
ORCID for Tristan W. Clark: ORCID iD orcid.org/0000-0001-6026-5295

Catalogue record

Date deposited: 25 Aug 2017 16:31
Last modified: 03 Dec 2019 01:35

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