Evidence map›Paper›PMID 31790967›Full record

ArticleJournal of clinical virology : the official publication of the Pan American Society for Clinical Virology2020

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

Sacha Stelzer-Braid, Matthew Wynn, Richard Chatoor, Matthew Scotch, Vidiya Ramachandran, Hooi-Ling Teoh, Michelle A Farrar, Hugo Sampaio, Peter Ian Andrews, Maria E Craig and 6 more

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.6field-weighted citation impact, top 27% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed, 7 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

16 authors at 7 institutions in 2 countries.

Sacha Stelzer-BraidVirology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia. Electronic address: s.stelzer-braid@unsw.edu.au.
Matthew WynnVirology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia.
Richard ChatoorVirology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia.
Matthew ScotchCollege of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Public Health and Community Medicine, University of New South Wales, Sydney, NSW 2033, Australia.
Vidiya RamachandranSerology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Sydney, NSW 2031, Australia.
Hooi-Ling TeohDepartment of Neurology, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia.
Michelle A FarrarDepartment of Neurology, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia.
Hugo SampaioDepartment of Neurology, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia.
Peter Ian AndrewsDepartment of Neurology, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia.
Maria E CraigVirology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia.
C Raina MacIntyreCollege of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; Biosecurity Program, Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia; Watts College of Public Service and Community Solutions, Arizona State University, Phoenix, AZ 85004, USA.
Hemalatha VaradhanNSW Health Pathology, John Hunter Hospital, Newcastle, Australia.
Alison KessonDepartment of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, Australia.
Philip N BrittonDepartment of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, Australia; Marie Bashir Institute, University of Sydney, Australia.
James NewcombePathology North, Royal North Shore Hospital, St Leonards, Sydney, Australia.
William D RawlinsonVirology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia; Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Sydney, NSW 2031, Australia; School of Women's and Children's Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia.
New South Wales Department of Health · AUUNSW Sydney · AUCenter for Environmental Health · USChildren's Hospital at Westmead · AUJohn Hunter Hospital · AURoyal North Shore Hospital · AUThe University of Sydney · AU

Funding

Merging Viral Genetics with Climate and Population Data for Zoonotic SurveillanceR01LM012080 · NLM · ARIZONA STATE UNIVERSITY-TEMPE CAMPUS · PI SCOTCH, MATTHEW · 2015 to 2017
$1.1M
NLM NIH HHS R01 LM012080
6 · The paper itself

Abstract

backgroundThe 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.

objectivesTo 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

designWe 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.

resultsWe 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.

conclusionsThis 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.

Indexed as

Disease OutbreaksGenome, ViralHigh-Throughput Nucleotide SequencingPhylogenyAustraliaChildChild, PreschoolChinaCitiesEnterovirus A, HumanEnterovirus InfectionsFemaleGenetic VariationGenotypeHumansInfantAustraliaEnterovirusEV-A71Hand, foot and mouth diseasePhylogenyWhole genome sequencing

Identifiers

PMID31790967
PMCPMC7384352
OpenAlexW2983382968

What OpenQuestion holds

Textmetadata
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.