#Indigenous #Australians at increased #risk of #COVID19 due to existing #health and socioeconomic #inequities (Lancet Reg Health W Pacif., summary)

[Source: Lancet Regional Health Western Pacific, full page: (LINK). Summary, edited.]

Indigenous Australians at increased risk of COVID-19 due to existing health and socioeconomic inequities

Aryati Yashadhana, Nellie Pollard-Wharton, Anthony B. Zwi, Brett Biles

Open Access | Published: July 24, 2020 | DOI: https://doi.org/10.1016/j.lanwpc.2020.100007


The rapid spread of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the associated coronavirus disease (COVID-19) has placed extreme pressure on health systems, governments, and economies. Heightened risk of COVID-19 severity and mortality among Indigenous and ethnic minority communities in the United States (U.S), the United Kingdom, and Brazil, emphasises existing and pervasive global health inequities. Aboriginal and Torres Strait Islander (hereafter Indigenous) Australians experience some of the worst health outcomes worldwide. Due to a range of existing health and socioeconomic inequities that increase vulnerabilities, Indigenous Australians are at heightened risk of mortality if infected with SARS-CoV-2, when compared to non-Indigenous Australians. The subsequent impact of the pandemic on mental health, and exposure to racism, among Indigenous Australians must also be carefully considered.


Keywords: SARS-CoV-2; COVID-19; Society; Poverty; Australia.


#COVID19 is rapidly #changing: Examining #public #perceptions and #behaviors in response to this evolving pandemic (PLOS One, abstract)

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


COVID-19 is rapidly changing: Examining public perceptions and behaviors in response to this evolving pandemic

Holly Seale , Anita E. Heywood, Julie Leask, Meru Sheel, Susan Thomas, David N.  Durrheim, Katarzyna Bolsewicz, Rajneesh Kaur

Published: June 23, 2020 | DOI: https://doi.org/10.1371/journal.pone.0235112




Since the emergence of SARS-CoV-2, the virus that causes coronavirus disease (COVID-19) in late 2019, communities have been required to rapidly adopt community mitigation strategies rarely used before, or only in limited settings. This study aimed to examine the attitudes and beliefs of Australian adults towards the COVID-19 pandemic, and willingness and capacity to engage with these mitigation measures. In addition, we aimed to explore the psychosocial and demographic factors that are associated with adoption of recommended hygiene-related and avoidance-related behaviors.


A national cross-sectional online survey of 1420 Australian adults (18 years and older) was undertaken between the 18 and 24 March 2020. The statistical analysis of the data included univariate and multivariate logistic regression analysis.


The survey of 1420 respondents found 50% (710) of respondents felt COVID-19 would ‘somewhat’ affect their health if infected and 19% perceived their level of risk as high or very high. 84·9% had performed ≥1 of the three recommended hygiene-related behaviors and 93·4% performed ≥1 of six avoidance-related behaviors over the last one month. Adopting avoidance behaviors was associated with trust in government/authorities (aOR: 6.0, 95% CI 2.6–11·0), higher perceived rating of effectiveness of behaviors (aOR: 4·0, 95% CI: 1·8–8·7), higher levels of perceived ability to adopt social distancing strategies (aOR: 5.0, 95% CI: 1·5–9.3), higher trust in government (aOR: 6.0, 95% CI: 2.6–11.0) and higher level of concern if self-isolated (aOR: 1.8, 95% CI: 1.1–3.0).


In the last two months, members of the public have been inundated with messages about hygiene and social (physical) distancing. However, our results indicate that a continued focus on supporting community understanding of the rationale for these strategies, as well as instilling community confidence in their ability to adopt or sustain the recommendations is needed.


Citation: Seale H, Heywood AE, Leask J, Sheel M, Thomas S, Durrheim DN, et al. (2020) COVID-19 is rapidly changing: Examining public perceptions and behaviors in response to this evolving pandemic. PLoS ONE 15(6): e0235112. https://doi.org/10.1371/journal.pone.0235112

Editor: Wen-Jun Tu, Chinese Academy of Medical Sciences and Peking Union Medical College, CHINA

Received: April 6, 2020; Accepted: June 2, 2020; Published: June 23, 2020

Copyright: © 2020 Seale 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: The data is available at https://figshare.com/articles/COVID-19_AustSurvey_xlsx/12298844.

Funding: No funding was received for this specific study. MS is supported by a fellowship from the Westpac Scholars Trust.

Competing interests: The authors have read the journal’s policy and the authors of this paper have the following competing interests: HS has previously received funding from drug companies for investigator driven research and consulting fees to present at conferences/workshops and develop resources (bio-CSL/Sequiris, GSK and Sanofi Pasteur). She has also participated in advisory board meeting for Sanofi Pasteur. This does not alter our adherence to PLOS ONE policies on sharing data and materials. There are no patents, products in development or marketed products associated with this research to declare.

Keywords: SARS-CoV-2; COVID-19; Society; Australia.


The #impact of #climate and #antigenic #evolution on seasonal #influenza virus #epidemics in #Australia (Nat Commun., abstract)

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

The impact of climate and antigenic evolution on seasonal influenza virus epidemics in Australia

Edward K. S. Lam, Dylan H. Morris, Aeron C. Hurt, Ian G. Barr & Colin A. Russell

Nature Communications volume 11, Article number: 2741 (2020)



Although seasonal influenza viruses circulate globally, prevention and treatment occur at the level of regions, cities, and communities. At these scales, the timing, duration and magnitude of epidemics vary substantially, but the underlying causes of this variation are poorly understood. Here, based on analyses of a 15-year city-level dataset of 18,250 laboratory-confirmed and antigenically-characterised influenza virus infections from Australia, we investigate the effects of previously hypothesised environmental and virological drivers of influenza epidemics. We find that anomalous fluctuations in temperature and humidity do not predict local epidemic onset timings. We also find that virus antigenic change has no consistent effect on epidemic size. In contrast, epidemic onset time and heterosubtypic competition have substantial effects on epidemic size and composition. Our findings suggest that the relationship between influenza population immunity and epidemiology is more complex than previously supposed and that the strong influence of short-term processes may hinder long-term epidemiological forecasts.

Keywords: Seasonal Influenza; Evolution; Australia.


#Suppressing the #Epidemic in #NSW (N Engl J Med., summary)

[Source: The New England Journal of Medicine, full page: (LINK). Summary, edited.]

Suppressing the Epidemic in New South Wales


To rapidly communicate short reports of innovative responses to Covid-19 around the world, along with a range of current thinking on policy and strategy relevant to the pandemic, the Journal has initiated the Covid-19 Notes series.


Facing the coronavirus pandemic, Australia has achieved national consensus on policies that were unprecedented for the past century. New South Wales (which has 8 million residents) and other jurisdictions appear to have successfully suppressed Covid-19 transmission after a rapid escalation of cases in March 2020.


Keywords: SARS-CoV-2; COVID-19; Australia; NSW.


An emergent #clade of #SARS-CoV-2 linked to returned #travellers from #Iran (Virus Evol., abstract)

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

An emergent clade of SARS-CoV-2 linked to returned travellers from Iran

John-Sebastian Eden, Rebecca Rockett, Ian Carter, Hossinur Rahman, Joep de Ligt, James Hadfield, Matthew Storey, Xiaoyun Ren, Rachel Tulloch, Kerri Basile, Jessica Wells, Roy Byun, Nicky Gilroy, Matthew V O’Sullivan, Vitali Sintchenko, Sharon C Chen, Susan Maddocks, Tania C Sorrell, Edward C Holmes, Dominic E Dwyer, Jen Kok, for the 2019-nCoV Study Group

Virus Evolution, Volume 6, Issue 1, January 2020, veaa027, https://doi.org/10.1093/ve/veaa027

Published: 10 April 2020



The SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea, and Iran. Phylogenetic analyses of whole-genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases.

COVID-19, SARS-CoV-2, genome sequencing, phylogenetics


Keywords: SARS-CoV-2; COVID-19; Iran; Australia; New Zealand; Evolution.


The Current #State of #COVID19 in #Australia: #Importation and #Spread (SSRN, abstract)

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

The Current State of COVID-19 in Australia: Importation and Spread

8 Pages Posted: 30 Mar 2020

Jessica Liebig, Government of the Commonwealth of Australia – Data61; Raja Jurdak, Government of the Commonwealth of Australia – Data61; Ahmad El Shoghri, Government of the Commonwealth of Australia – Data61; Dean Paini, Government of the Commonwealth of Australia – Health and Biosecurity




The rapid global spread of coronavirus disease (COVID-19) is unprecedented. The outbreak has quickly spread to more than 100 countries reporting over 100,000 confirmed cases. Australia reported its first case of COVID-19 on 25th January 2020 and has since implemented travel restrictions to stop further introduction of the virus.


We analysed daily global COVID-19 data published by the World Health Organisation to investigate the spread of the virus thus far. To assess the current risk of COVID-19 importation and local spread in Australia we predict international passenger flows into Australia during 2020.


Our analysis of global data shows that Australia can expect a similar growth rate of reported cases as observed in France and the United States. We identify travel patterns of Australian citizens/residents and foreign travellers that can inform the implementation of new and the alteration of existing travel restrictions related to COVID-19.


Our findings identify the risk reduction potential of current travel bans, based on the proportion of returning travellers to Australia that are residents or visitors. The similarity of the exponential growth in the epidemic curve in Australia to other countries guides forecasts of COVID-19 growth in Australia, and opportunities for drawing lessons from other countries with more advanced outbreaks.


Funding Statement: None.

Declaration of Interests: The authors declare no competing interests.

Ethics Approval Statement: Data is publicly available.

Keywords: COVID-19; Australia; Air travel; Infectious disease spread

Suggested Citation: Liebig, Jessica and Jurdak, Raja and El Shoghri, Ahmad and Paini, Dean, The Current State of COVID-19 in Australia: Importation and Spread (3/20/2020). Available at SSRN: https://ssrn.com/abstract=3559568 or http://dx.doi.org/10.2139/ssrn.3559568

Keywords: SARS-CoV-2; COVID-19; Australia.


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:  https://doi.org/10.1002/ana.25650

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.

DOI: https://doi.org/10.1016/j.jcv.2019.104216



  • 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.