Next generation sequencing of human enterovirus strains from an outbreak of enterovirus A71 shows applicability to outbreak investigations.

Stelzer-Braid, S; Wynn, M; Chatoor, R; Scotch, M; Ramachandran, V; Teoh, H-L; Farrar, MA; Sampaio, H; Andrews, PI; Craig, ME; MacIntyre, CR; Varadhan, H; Kesson, A; Britton, PN; Newcombe, J; Rawlinson, WD

Next generation sequencing of human enterovirus strains from an outbreak of enterovirus A71 shows applicability to outbreak investigations.

Wynn, M Chatoor, R Scotch, M Ramachandran, V Teoh, H-L Farrar, MA Sampaio, H Andrews, PI Craig, ME MacIntyre, CR Varadhan, H Kesson, A Britton, PN Newcombe, J Rawlinson, WD

Permalink

Publisher:: ELSEVIER
Publication Type:: Journal Article
Citation:: Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, 2020, 122, pp. 104216
Issue Date:: 2020-01

Closed Access

	Filename	Description	Size
	1-s2.0-S138665321930246X-main.pdf	Published version	3.91 MB		View/Open

Copyright Clearance Process

Recently Added
In Progress
Closed Access

This item is closed access and not available.

Full metadata record

Field	Value	Language
dc.contributor.author	Stelzer-Braid, S https://orcid.org/0000-0001-6037-9305
dc.contributor.author	Wynn, M
dc.contributor.author	Chatoor, R
dc.contributor.author	Scotch, M
dc.contributor.author	Ramachandran, V
dc.contributor.author	Teoh, H-L
dc.contributor.author	Farrar, MA
dc.contributor.author	Sampaio, H
dc.contributor.author	Andrews, PI
dc.contributor.author	Craig, ME
dc.contributor.author	MacIntyre, CR
dc.contributor.author	Varadhan, H
dc.contributor.author	Kesson, A
dc.contributor.author	Britton, PN
dc.contributor.author	Newcombe, J
dc.contributor.author	Rawlinson, WD
dc.date.accessioned	2021-04-10T01:26:10Z
dc.date.available	2019-11-11
dc.date.available	2021-04-10T01:26:10Z
dc.date.issued	2020-01
dc.identifier.citation	Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, 2020, 122, pp. 104216
dc.identifier.issn	1386-6532
dc.identifier.issn	1873-5967
dc.identifier.uri	http://hdl.handle.net/10453/147977
dc.description.abstract	<h4>Background</h4>The most recent documented Australian outbreak of enterovirus A71 (EV-A71) occurred in Sydney from 2012 to 2013. Over a four-month period more than 100 children presented to four paediatric hospitals with encephalitic presentations including fever and myoclonic jerks. The heterogeneous presentations included typical encephalomyelitis, and cardiopulmonary complications.<h4>Objectives</h4>To characterise the genomes of enterovirus strains circulating during the 2013 Sydney EV-A71 outbreak and determine their phylogeny, phylogeography and association between genome and clinical phenotype.<h4>Study design</h4>We performed an analysis of enterovirus (EV) positive specimens from children presenting to hospitals in the greater Sydney region of Australia during the 2013 outbreak. We amplified near full-length genomes of EV, and used next generation sequencing technology to sequence the virus. We used phylogenetic/phylogeographic analysis to characterize the outbreak viruses.<h4>Results</h4>We amplified and sequenced 23/63 (37 %) genomes, and identified the majority (61 %) as EV-A71. The EV-A71 sequences showed high level sequence homology to C4a genogroups of EV-A71 circulating in China and Vietnam during 2012-13. Phylogenetic analysis showed EV-A71 strains associated with more severe symptoms, including encephalitis or cardiopulmonary failure, grouped together more closely than those from patients with hand, foot and mouth disease. Amongst the non-EV-A71 sequences were five other EV subtypes (representing enterovirus subtypes A and B), reflecting the diversity of EV co-circulation within the community.<h4>Conclusions</h4>This is the first Australian study investigating the near full-length genome of EV strains identified during a known outbreak of EV-A71. EV-A71 sequences were very similar to strains circulating in Asia during the same time period. Whole genome sequencing offers additional information over routine diagnostic testing such as characterisation of emerging recombinant strains and inform vaccine design.
dc.format	Print-Electronic
dc.language	eng
dc.publisher	ELSEVIER
dc.relation.ispartof	Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology
dc.relation.isbasedon	10.1016/j.jcv.2019.104216
dc.rights	info:eu-repo/semantics/closedAccess
dc.subject	0605 Microbiology, 1103 Clinical Sciences, 1108 Medical Microbiology
dc.subject.classification	Virology
dc.subject.mesh	Humans
dc.subject.mesh	Enterovirus A, Human
dc.subject.mesh	Enterovirus Infections
dc.subject.mesh	Cities
dc.subject.mesh	Disease Outbreaks
dc.subject.mesh	Phylogeny
dc.subject.mesh	Genotype
dc.subject.mesh	Genome, Viral
dc.subject.mesh	Child
dc.subject.mesh	Child, Preschool
dc.subject.mesh	Infant
dc.subject.mesh	Infant, Newborn
dc.subject.mesh	Vietnam
dc.subject.mesh	China
dc.subject.mesh	Australia
dc.subject.mesh	Female
dc.subject.mesh	Male
dc.subject.mesh	Genetic Variation
dc.subject.mesh	Phylogeography
dc.subject.mesh	High-Throughput Nucleotide Sequencing
dc.subject.mesh	Australia
dc.subject.mesh	Child
dc.subject.mesh	Child, Preschool
dc.subject.mesh	China
dc.subject.mesh	Cities
dc.subject.mesh	Disease Outbreaks
dc.subject.mesh	Enterovirus A, Human
dc.subject.mesh	Enterovirus Infections
dc.subject.mesh	Female
dc.subject.mesh	Genetic Variation
dc.subject.mesh	Genome, Viral
dc.subject.mesh	Genotype
dc.subject.mesh	High-Throughput Nucleotide Sequencing
dc.subject.mesh	Humans
dc.subject.mesh	Infant
dc.subject.mesh	Infant, Newborn
dc.subject.mesh	Male
dc.subject.mesh	Phylogeny
dc.subject.mesh	Phylogeography
dc.subject.mesh	Vietnam
dc.title	Next generation sequencing of human enterovirus strains from an outbreak of enterovirus A71 shows applicability to outbreak investigations.
dc.type	Journal Article
utslib.citation.volume	122
utslib.location.activity	Netherlands
utslib.for	0605 Microbiology
utslib.for	1108 Medical Microbiology
utslib.for	0605 Microbiology
utslib.for	1103 Clinical Sciences
utslib.for	1108 Medical Microbiology
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Life Sciences
utslib.copyright.status	closed_access	*
dc.date.updated	2021-04-10T01:26:05Z
pubs.publication-status	Published
pubs.volume	122

Abstract:

Background

The most recent documented Australian outbreak of enterovirus A71 (EV-A71) occurred in Sydney from 2012 to 2013. Over a four-month period more than 100 children presented to four paediatric hospitals with encephalitic presentations including fever and myoclonic jerks. The heterogeneous presentations included typical encephalomyelitis, and cardiopulmonary complications.

Objectives

To characterise the genomes of enterovirus strains circulating during the 2013 Sydney EV-A71 outbreak and determine their phylogeny, phylogeography and association between genome and clinical phenotype.

Study design

We performed an analysis of enterovirus (EV) positive specimens from children presenting to hospitals in the greater Sydney region of Australia during the 2013 outbreak. We amplified near full-length genomes of EV, and used next generation sequencing technology to sequence the virus. We used phylogenetic/phylogeographic analysis to characterize the outbreak viruses.

Results

We amplified and sequenced 23/63 (37 %) genomes, and identified the majority (61 %) as EV-A71. The EV-A71 sequences showed high level sequence homology to C4a genogroups of EV-A71 circulating in China and Vietnam during 2012-13. Phylogenetic analysis showed EV-A71 strains associated with more severe symptoms, including encephalitis or cardiopulmonary failure, grouped together more closely than those from patients with hand, foot and mouth disease. Amongst the non-EV-A71 sequences were five other EV subtypes (representing enterovirus subtypes A and B), reflecting the diversity of EV co-circulation within the community.

Conclusions

This is the first Australian study investigating the near full-length genome of EV strains identified during a known outbreak of EV-A71. EV-A71 sequences were very similar to strains circulating in Asia during the same time period. Whole genome sequencing offers additional information over routine diagnostic testing such as characterisation of emerging recombinant strains and inform vaccine design.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/147977