Detection of a #Reassortant #H9N2 #Avian #Influenza Virus with #Intercontinental Gene Segments in a Resident #Australian Chestnut #Teal (Viruses, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Viruses. 2020 Jan 13;12(1). pii: E88. doi: 10.3390/v12010088.

Detection of a Reassortant H9N2 Avian Influenza Virus with Intercontinental Gene Segments in a Resident Australian Chestnut Teal.

Bhatta TR1,2, Chamings A1,2, Vibin J1,2, Klaassen M1,3, Alexandersen S1,2,4.

Author information: 1 Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia. 2 School of Medicine, Deakin University, Geelong, Victoria 3220, Australia. 3 Centre for Integrative Ecology, Deakin University, Victoria 3220, Australia. 4 Barwon Health, University Hospital Geelong, Geelong, Victoria 3220, Australia.



The present study reports the genetic characterization of a low-pathogenicity H9N2 avian influenza virus, initially from a pool and subsequently from individual faecal samples collected from Chestnut teals (Anas castanea) in southeastern Australia. Phylogenetic analyses of six full gene segments and two partial gene segments obtained from next-generation sequencing showed that this avian influenza virus, A/Chestnut teal/Australia/CT08.18/12952/2018 (H9N2), was a typical, low-pathogenicity, Eurasian aquatic bird lineage H9N2 virus, albeit containing the North American lineage nucleoprotein (NP) gene segment detected previously in Australian wild birds. This is the first report of a H9N2 avian influenza virus in resident wild birds in Australia, and although not in itself a cause of concern, is a clear indication of spillover and likely reassortment of influenza viruses between migratory and resident birds, and an indication that any lineage could potentially be introduced in this way.

KEYWORDS: Chestnut teal; Eurasian lineage; H9N2; avian influenza virus; low pathogenicity; phylogenetic analysis; reassortant

PMID: 31940999 DOI: 10.3390/v12010088

Keywords: Avian Influenza; H9N2; Wild Birds; Reassortant strain; Australia.


SCN1A #variants in #vaccine‐related febrile #seizures: a prospective study (Ann Neurol., abstract)

[Source: Annals of Neurology, full page: (LINK). Abstract, edited.]

SCN1A variants in vaccine‐related febrile seizures: a prospective study

JA Damiano,  L Deng,  WH Li,  R Burgess,  AL Schneider,  NW Crawford,  J Buttery, M Gold,  P Richmond,  KK Macartney,  MS Hildebrand,  IE Scheffer,  N Wood,  SF Berkovic

First published: 22 November 2019 / DOI:

This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1002/ana.25650.




Febrile seizures may follow vaccination. Common variants in the sodium channel gene, SCN1A, are associated with febrile seizures and rare pathogenic variants in SCN1A cause the severe developmental and epileptic encephalopathy Dravet Syndrome. Following vaccination, febrile seizures may raise the spectre of poor outcome and inappropriately implicate vaccination as the cause. We aimed to determine the prevalence of SCN1A variants in children having their first febrile seizure either proximal to vaccination, or unrelated to vaccination compared to controls.


We performed SCN1A sequencing, blind to clinical category, in a prospective cohort of children presenting with their first febrile seizure as vaccine proximate (n=69), or as non‐vaccine proximate (n=75), and children with no history of seizures (n=90) recruited in Australian paediatric hospitals.


We detected two pathogenic variants in vaccine proximate cases (p.R568X and p.W932R), both of whom developed Dravet syndrome, and one in a non‐vaccine proximate case (p.V947L) who had Febrile seizures plus from 9 months. All had generalised tonic‐clonic seizures lasting longer than 15 minutes. We also found enrichment of a reported risk allele, rs6432860‐T, in children with febrile seizures compared to controls (Odds Ratio 1.91 [95% CI 1.31‐ 2.81]).


Pathogenic SCN1A variants may be identified in infants with vaccine proximate febrile seizures. As early diagnosis of Dravet syndrome is essential for optimal management and outcome. SCN1A sequencing in infants with prolonged febrile seizures, proximate to vaccination, should become routine.

This article is protected by copyright. All rights reserved.

Keywords: Drugs Safety; Vaccines; Genetics; Pediatrics; Encephalopathy; Australia.


Next generation #sequencing of #human #enterovirus strains from an #outbreak of #EVA71 shows applicability to outbreak investigations (J Clin Invest., abstract)

[Source: Journal of Clinical Investigation, full page: (LINK). Abstract, edited.]

Journal of Clinical Virology / Available online 17 November 2019, 104216 / In Press, Journal Pre-proof

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

Sacha Stelzer-Braid a,b, Matthew Wynn a, Richard Chatoor a, Matthew Scotchc d,e, Vidiya Ramachandran f, Hooi-Ling Teoh g, h, Michelle A.Farrarg h, Hugo Sampaio g,h, Peter Ian Andrews g,h, Maria E.Craig a,h, C. Raina Mac Intyre c,i,j, Hemalatha Varadhan k, Alison Kesson l, Philip N.Britton l,m, James Newcomb e,n, William D.Rawlinson a,b,h

{a} Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia; {b} School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia; {c} College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA; {d} Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; {e} School of Public Health and Community Medicine, University of New South Wales, Sydney, NSW 2033, Australia; {f} Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Sydney, NSW 2031, Australia; {g} Department of Neurology, Sydney Children’s Hospital, Sydney, Australia; {h} School of Women’s and Children’s Health, University of New South Wales Medicine, Sydney, NSW 2052, Australia; {i} Biosecurity Program, Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia; {j} Watts College of Public Service and Community Solutions, Arizona State University, Phoenix, AZ 85004, USA; {k} NSW Health Pathology, John Hunter Hospital, Newcastle, United Kingdom; {l} Department of Infectious Diseases and Microbiology, The Children’s Hospital at Westmead, Australia; {m} Marie Bashir Institute, University of Sydney, Australia; {n} Pathology North, Royal North Shore Hospital, St Leonards, Australia

Received 24 April 2019, Revised 8 October 2019, Accepted 11 November 2019, Available online 17 November 2019.




  • Near full-length genome analysis using next generation sequencing identified EV-A71 and other enterovirus A and B subtypes circulating.
  • The Sydney EV-A71 2013 strain was very similar to EV-A71 circulating in China and Vietnam during the previous year.
  • Strains causing more severe clinical manifestations grouped together phylogenetically.




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.


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.


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.


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

© 2019 Published by Elsevier B.V.

Keywords: HFMD; Enterovirus; EV-A71; Australia.


Divergent #Barmah Forest Virus from #Papua New Guinea (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 25, Number 12—December 2019 / Dispatch

Divergent Barmah Forest Virus from Papua New Guinea

Leon Caly  , Paul F. Horwood, Dhanasekaran Vijaykrishna, Stacey Lynch, Andrew R. Greenhill, William Pomat, Glennis Rai, Debbie Kisa, Grace Bande, Julian Druce, and Mohammad Y. Abdad

Author affiliations: Victorian Infectious Diseases Reference Laboratory of Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia (L. Caly, J. Druce); James Cook University, Townsville, Queensland, Australia (P.F. Horwood); Monash University, Clayton, Victoria, Australia (D. Vijaykrishna); AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia (S. Lynch); Federation University Australia, Gippsland, Victoria, Australia (A.R. Greenhill); Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea (W. Pomat, G. Rai, D. Kisa):; Divine Word University, Madang, Papua New Guinea (G. Bande); National Centre for Infectious Diseases, Singapore (M.Y. Abdad)



We report a case of Barmah Forest virus infection in a child from Central Province, Papua New Guinea, who had no previous travel history. Genomic characterization of the virus showed divergent origin compared with viruses previously detected, supporting the hypothesis that the range of Barmah Forest virus extends beyond Australia.

Keywords: Barmah Forest Virus; Papua New Guinea.


Heterogeneity in #influenza seasonality and #vaccine #effectiveness in #Australia, #Chile, #NZ and #ZA: early #estimates of the 2019 influenza season (Euro Surveill., abstract)

[Source: Eurosurveillance, full page: (LINK). Abstract, edited.]

Heterogeneity in influenza seasonality and vaccine effectiveness in Australia, Chile, New Zealand and South Africa: early estimates of the 2019 influenza season

Sheena G Sullivan1, Carmen S Arriola2, Judy Bocacao3, Pamela Burgos4, Patricia Bustos5, Kylie S Carville6, Allen C Cheng7,8, Monique BM Chilver9, Cheryl Cohen10, Yi-Mo Deng11, Nathalie El Omeiri12, Rodrigo A Fasce13, Orienka Hellferscee10, Q Sue Huang3, Cecilia Gonzalez4, Lauren Jelley3, Vivian KY Leung1, Liza Lopez14, Johanna M McAnerney10, Andrea McNeill14, Maria F Olivares15, Heidi Peck11, Viviana Sotomayor15, Stefano Tempia2,10,16,17, Natalia Vergara15, Anne von Gottberg10, Sibongile Walaza10, Timothy Wood14

Affiliations: 1 World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, and Doherty Department, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia; 2 Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States; 3 National Influenza Centre, Institute of Environmental Science and Research, Wellington, New Zealand; 4 Programa Nacional de Inmunizaciones, Ministerio de Salud, Santiago, Chile; 5 Sección de Virus Respiratorios y Exantematicos, Instituto de Salud Publica de Chile, Santiago, Chile; 6 Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia; 7 School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia; 8 Department of Infectious Diseases, Alfred Health, and Central Clinical School, Monash University, Melbourne, Australia; 9 Discipline of General Practice, University of Adelaide, Adelaide, Australia; 10 National Institute for Communicable Diseases, Johannesburg, South Africa; 11 WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Reference and Research on Influenza, Melbourne, Australia; 12 Pan American Health Organization(PAHO)/WHO Regional Office for the Americas, Washington, United States; 13 Subdepartamento de Enfermedades Virales, Instituto de Salud Publica de Chile, Santiago, Chile; 14 Health Intelligence Team, Institute of Environmental Science and Research, Wellington, New Zealand; 15 Departamento de Epidemiologia, Ministerio de Salud, Santiago, Chile; 16 Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa; 17 MassGenics, Duluth, United States

Correspondence:  Sheena G Sullivan

Citation style for this article: Sullivan Sheena G, Arriola Carmen S, Bocacao Judy, Burgos Pamela, Bustos Patricia, Carville Kylie S, Cheng Allen C, Chilver Monique BM, Cohen Cheryl, Deng Yi-Mo, El Omeiri Nathalie, Fasce Rodrigo A, Hellferscee Orienka, Huang Q Sue, Gonzalez Cecilia, Jelley Lauren, Leung Vivian KY, Lopez Liza, McAnerney Johanna M, McNeill Andrea, Olivares Maria F, Peck Heidi, Sotomayor Viviana, Tempia Stefano, Vergara Natalia, von Gottberg Anne, Walaza Sibongile, Wood Timothy. Heterogeneity in influenza seasonality and vaccine effectiveness in Australia, Chile, New Zealand and South Africa: early estimates of the 2019 influenza season. Euro Surveill. 2019;24(45):pii=1900645.

Received: 23 Oct 2019;   Accepted: 06 Nov 2019



We compared 2019 influenza seasonality and vaccine effectiveness (VE) in four southern hemisphere countries: Australia, Chile, New Zealand and South Africa. Influenza seasons differed in timing, duration, intensity and predominant circulating viruses. VE estimates were also heterogeneous, with all-ages point estimates ranging from 7–70% (I2: 33%) for A(H1N1)pdm09, 4–57% (I2: 49%) for A(H3N2) and 29–66% (I2: 0%) for B. Caution should be applied when attempting to use southern hemisphere data to predict the northern hemisphere influenza season.

©  This work is licensed under a Creative Commons Attribution 4.0 International License.

Keywords: Seasonal Influenza; Vaccines; Australia; Chile; New Zealand; South Africa.


Early #signal #detection of #adverse events following #influenza #vaccination using proportional reporting ratio, Victoria, #Australia (PLOS One, abstract)

[Source: PLOS  One, full page: (LINK). Abstract, edited.]


Early signal detection of adverse events following influenza vaccination using proportional reporting ratio, Victoria, Australia

Hazel J. Clothier , Jock Lawrie, Melissa A. Russell, Heath Kelly, Jim P. Buttery


Published: November 1, 2019 / DOI:




Timely adverse event following immunisation (AEFI) signal event detection is essential to minimise further vaccinees receiving unsafe vaccines. We explored the proportional reporting ratio (PRR) ability to detect two known signal events with influenza vaccines with the aim of providing a model for prospective routine signal detection and improving vaccine safety surveillance in Australia.


Passive AEFI surveillance reports from 2008–2017 relating to influenza vaccines were accessed from the Australian SAEFVIC (Victoria) database. Proportional reporting ratios were calculated for two vaccine-event categories; fever and allergic AEFI. Signal detection sensitivity for two known signal events were determined using weekly data; cumulative data by individual year and; cumulative for all previous years. Signal event thresholds of PRR ≥2 and Chi-square ≥4 were applied.


PRR provided sensitive signal detection when calculated cumulatively by individual year or by all previous years. Known signal events were detected 15 and 11 days earlier than traditional methods used at the time of the actual events.


Utilising a single jurisdiction’s data, PRR improved vaccine pharmacovigilance and showed the potential to detect important safety signals much earlier than previously. It has potential to maximise immunisation safety in Australia. This study progresses the necessary work to establish national cohesion for passive surveillance signal detection and strengthen routine Australian vaccine pharmacovigilance.


Citation: Clothier HJ, Lawrie J, Russell MA, Kelly H, Buttery JP (2019) Early signal detection of adverse events following influenza vaccination using proportional reporting ratio, Victoria, Australia. PLoS ONE 14(11): e0224702.

Editor: Eric HY Lau, The University of Hong Kong, CHINA

Received: May 30, 2019; Accepted: October 19, 2019; Published: November 1, 2019

Copyright: © 2019 Clothier et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: Data cannot be shared publicly because of confidentiality and data privacy regulations. Data are available from the SAEFVIC Murdoch Childrens Research Institute Data Access Coordinator (contact via 1300 882 924) for researchers who meet the criteria for access to confidential data.

Funding: SAEFVIC is funded by the Department of Health and Human Services, Victoria. Hazel Clothier receives an Australian Government Research Training Program Scholarship. Authors HC, JL and JB are employees of SAEFVIC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Keywords: Seasonal Influenza; Vaccines; Drugs Safety; Australia.


Locally Acquired #Human #Infection with #Swine-Origin #Influenza A(#H3N2) Variant Virus, #Australia, 2018 (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 26, Number 1—January 2020 / Dispatch

Locally Acquired Human Infection with Swine-Origin Influenza A(H3N2) Variant Virus, Australia, 2018

Yi-Mo Deng  , Frank Y.K. Wong, Natalie Spirason, Matthew Kaye, Rebecca Beazley, Miguel Grau, Songhua Shan, Vittoria Stevens, Kanta Subbarao, Sheena Sullivan, Ian G. Barr, and Vijaykrishna Dhanasekaran

Author affiliations: World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (Y.M. Deng, N. Spirason, M. Kaye, K. Subbarao, S. Sullivan, I.G. Barr, V. Dhanasekaran); CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (F.Y.K. Wong, S. Shan, V. Stevens); South Australian Department of Health and Wellbeing, Adelaide, South Australia, Australia (R. Beazley); Monash University, Melbourne (M. Grau, V. Dhanasekaran); University of Melbourne, Melbourne (S. Sullivan, I.G. Barr)



In 2018, a 15-year-old female adolescent in Australia was infected with swine influenza A(H3N2) variant virus. The virus contained hemagglutinin and neuraminidase genes derived from 1990s-like human seasonal viruses and internal protein genes from influenza A(H1N1)pdm09 virus, highlighting the potential risk that swine influenza A virus poses to human health in Australia.

Keywords: Swine Influenza; Influenza A; Seasonal Influenza; Reassortant strain; H3N2; H1N1pdm09; Human; Australia.