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; C Raina MacIntyre; Hemalatha Varadhan; Alison Kesson; Philip N Britton; James Newcombe; William D Rawlinson

doi:10.1016/j.jcv.2019.104216

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

J Clin Virol. 2020 Jan:122:104216. doi: 10.1016/j.jcv.2019.104216. Epub 2019 Nov 17.

Authors

Sacha Stelzer-Braid¹, Matthew Wynn², Richard Chatoor², Matthew Scotch³, Vidiya Ramachandran⁴, Hooi-Ling Teoh⁵, Michelle A Farrar⁵, Hugo Sampaio⁵, Peter Ian Andrews⁵, Maria E Craig⁶, C Raina MacIntyre⁷, Hemalatha Varadhan⁸, Alison Kesson⁹, Philip N Britton¹⁰, James Newcombe¹¹, William D Rawlinson¹²

Affiliations

¹ Virology 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.
² Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia.
³ College 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.
⁴ Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Sydney, NSW 2031, Australia.
⁵ Department 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.
⁶ Virology 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.
⁷ College 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.
⁸ NSW Health Pathology, John Hunter Hospital, Newcastle, Australia.
⁹ Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, Australia.
¹⁰ Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, Australia; Marie Bashir Institute, University of Sydney, Australia.
¹¹ Pathology North, Royal North Shore Hospital, St Leonards, Sydney, Australia.
¹² Virology 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.

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.

Keywords: Australia; EV-A71; Enterovirus; Hand, foot and mouth disease; Phylogeny; Whole genome sequencing.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Australia / epidemiology
Child
Child, Preschool
China / epidemiology
Cities / epidemiology
Disease Outbreaks*
Enterovirus A, Human / classification
Enterovirus A, Human / genetics*
Enterovirus A, Human / pathogenicity
Enterovirus Infections / epidemiology*
Enterovirus Infections / virology
Female
Genetic Variation
Genome, Viral*
Genotype
High-Throughput Nucleotide Sequencing*
Humans
Infant
Infant, Newborn
Male
Phylogeny*
Phylogeography
Vietnam / epidemiology

Grants and funding

R01 LM012080/LM/NLM NIH HHS/United States