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Wang DS, Phu A, McKee K, Strasser SI, Sheils S, Weltman M, Sellar S, Davis JS, Young M, Braund A, Farrell GC, Blunn A, Harding D, Ralton L, Muller K, Davison SA, Shaw D, Wood M, Hajkowicz K, Skolen R, Davies J, Tate-Baker J, Doyle A, Tuma R, Hazeldine S, Lam W, Edmiston N, Zohrab K, Pratt W, Watson B, Zekry A, Stephens C, Clark PJ, Day M, Park G, Kim H, Wilson M, McGarity B, Menzies N, Russell D, Lam T, Boyd P, Kok J, George J, Douglas MW. Hepatitis C Virus Antiviral Drug Resistance and Salvage Therapy Outcomes Across Australia. Open Forum Infect Dis 2024; 11:ofae155. [PMID: 38651137 PMCID: PMC11034952 DOI: 10.1093/ofid/ofae155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/15/2024] [Indexed: 04/25/2024] Open
Abstract
Background Hepatitis C virus (HCV) infection can now be cured with well-tolerated direct-acting antiviral (DAA) therapy. However, a potential barrier to HCV elimination is the emergence of resistance-associated substitutions (RASs) that reduce the efficacy of antiviral drugs, but real-world studies assessing the clinical impact of RASs are limited. Here, an analysis of the impact of RASs on retreatment outcomes for different salvage regimens in patients nationally who failed first-line DAA therapy is reported. Methods We collected data from 363 Australian patients who failed first-line DAA therapy, including: age, sex, fibrosis stage, HCV genotype, NS3/NS5A/NS5B RASs, details of failed first-line regimen, subsequent salvage regimens, and treatment outcome. Results Of 240 patients who were initially retreated as per protocol, 210 (87.5%) achieved sustained virologic response (SVR) and 30 (12.5%) relapsed or did not respond. The SVR rate for salvage regimens that included sofosbuvir/velpatasvir/voxilaprevir was 94.3% (n = 140), sofosbuvir/velpatasvir 75.0% (n = 52), elbasvir/grazoprevir 81.6% (n = 38), and glecaprevir/pibrentasvir 84.6% (n = 13). NS5A RASs were present in 71.0% (n = 210) of patients who achieved SVR and in 66.7% (n = 30) of patients who subsequently relapsed. NS3 RASs were detected in 20 patients (20%) in the SVR group and 1 patient in the relapse group. NS5B RASs were observed in only 3 patients. Cirrhosis was a predictor of relapse after retreatment, as was previous treatment with sofosbuvir/velpatasvir. Conclusions In our cohort, the SVR rate for sofosbuvir/velpatasvir/voxilaprevir was higher than with other salvage regimens. The presence of NS5A, NS5B, or NS3 RASs did not appear to negatively influence retreatment outcomes.
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Affiliation(s)
- Dao Sen Wang
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, NSW, Australia
| | - Amy Phu
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, NSW, Australia
| | - Kristen McKee
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, NSW, Australia
| | - Simone I Strasser
- AW Morrow Gastroenterology and Liver Centre, The University of Sydney and Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Sinead Sheils
- AW Morrow Gastroenterology and Liver Centre, The University of Sydney and Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Martin Weltman
- Department of Gastroenterology and Hepatology, Nepean Hospital, Kingswood, NSW, Australia
| | - Sue Sellar
- Department of Gastroenterology and Hepatology, Nepean Hospital, Kingswood, NSW, Australia
| | - Joshua S Davis
- Department of Infectious Diseases, University of Newcastle and John Hunter Hospital, Newcastle, NSW, Australia
| | - Mel Young
- Department of Infectious Diseases, University of Newcastle and John Hunter Hospital, Newcastle, NSW, Australia
| | - Alicia Braund
- Department of Gastroenterology and Hepatology, Gold Coast University Hospital, Southport, QLD, Australia
| | - Geoffrey C Farrell
- Department of Gastroenterology and Hepatology, Australian National University and The Canberra Hospital, Canberra, ACT, Australia
| | - Anne Blunn
- Department of Gastroenterology and Hepatology, Australian National University and The Canberra Hospital, Canberra, ACT, Australia
| | - Damian Harding
- Department of Gastroenterology and Hepatology, Lyell McEwin Hospital, Elizabeth Vale, SA, Australia
| | - Lucy Ralton
- Department of Gastroenterology and Hepatology, Lyell McEwin Hospital, Elizabeth Vale, SA, Australia
| | - Kate Muller
- Department of Gastroenterology and Hepatology, Flinders Medical Centreand Flinders University, Adelaide, SA, Australia
| | - Scott A Davison
- Department of Gastroenterology and Hepatology, University of New South Wales and Liverpool Hospital, Liverpool, NSW, Australia
| | - David Shaw
- Department of Infectious Diseases, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - Marnie Wood
- Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Krispin Hajkowicz
- Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Richard Skolen
- Infectious Diseases Unit, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Jane Davies
- Menzies School of Health Research and Royal Darwin Hospital, Darwin, NT, Australia
| | - Jaclyn Tate-Baker
- Menzies School of Health Research and Royal Darwin Hospital, Darwin, NT, Australia
| | - Adam Doyle
- Department of Gastroenterology and Hepatology, Royal Perth Hospital, Perth, WA, Australia
| | - Rhoda Tuma
- Department of Gastroenterology and Hepatology, Royal Perth Hospital, Perth, WA, Australia
| | - Simon Hazeldine
- Department of Gastroenterology and Hepatology, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Wendy Lam
- Department of Gastroenterology and Hepatology, Fiona Stanley Hospital, Murdoch, WA, Australia
| | - Natalie Edmiston
- Department of Gastroenterology and Hepatology, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - Krista Zohrab
- Department of Gastroenterology and Hepatology, School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | - William Pratt
- Department of Medicine, Shoalhaven Hospital, Nowra, NSW, Australia
| | - Belinda Watson
- Department of Medicine, Shoalhaven Hospital, Nowra, NSW, Australia
| | - Amany Zekry
- Department of Gastroenterology and Hepatology, St George Hospital, Kogarah, NSW, Australia
| | - Carlie Stephens
- Department of Gastroenterology and Hepatology, St George Hospital, Kogarah, NSW, Australia
| | - Paul J Clark
- Rockhampton Blood Borne Virus & Sexual Health Service and School of Medicine, University of Brisbane, Brisbane, QLD, Australia
| | - Melany Day
- Rockhampton Blood Borne Virus & Sexual Health Service and School of Medicine, University of Brisbane, Brisbane, QLD, Australia
| | - Gordon Park
- Department of Gastroenterology and Hepatology, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Hami Kim
- Department of Gastroenterology and Hepatology, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Mark Wilson
- Department of Gastroenterology and Hepatology, Royal Hobart Hospital, Hobart, TAS, Australia
| | | | | | - Darren Russell
- Cairns Sexual Health Service and James Cook University Cairns, St Cairns City, QLD, Australia
| | - Thao Lam
- Department of Drug Health, Western Sydney Local Health District, Westmead, NSW, Australia
| | - Peter Boyd
- Department of Medicine, Cairns Hospital, Cairns, QLD, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - Jacob George
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, NSW, Australia
| | - Mark W Douglas
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology, Sydney Infectious Diseases Institute, The University of Sydney at Westmead Hospital, Sydney, NSW, Australia
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Winkler NE, Koirala A, Kaur G, Prasad S, Hirani R, Baker J, Hoad V, Gosbell IB, Irving DO, Hueston L, O'Sullivan MV, Kok J, Dwyer DE, Macartney K. Seroprevalence of Japanese encephalitis virus-specific antibodies in Australia following novel epidemic spread: protocol for a national cross-sectional study. BMJ Open 2024; 14:e075569. [PMID: 38326269 PMCID: PMC10860057 DOI: 10.1136/bmjopen-2023-075569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 11/08/2023] [Indexed: 02/09/2024] Open
Abstract
INTRODUCTION Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus that causes encephalitis and other morbidity in Southeast Asia. Since February 2022, geographically dispersed JEV human, animal and vector detections occurred on the Australian mainland for the first time. This study will determine the prevalence of JEV-specific antibodies in human blood with a focus on populations at high risk of JEV exposure and determine risk factors associated with JEV seropositivity by location, age, occupation and other factors. METHOD Samples are collected using two approaches: from routine blood donors (4153 samples), and active collections targeting high-risk populations (convenience sampling). Consent-based sampling for the latter includes a participant questionnaire on demographic, vaccination and exposure data. Samples are tested for JEV-specific total antibody using a defined epitope-blocking ELISA, and total antibody to Australian endemic flaviviruses Murray Valley encephalitis and Kunjin viruses. ANALYSIS Two analytic approaches will occur: descriptive estimates of seroprevalence and multivariable logistic regression using Bayesian hierarchical models. Descriptive analyses will include unadjusted analysis of raw data with exclusions for JEV-endemic country of birth, travel to JEV-endemic countries, prior JEV-vaccination, and sex-standardised and age-standardised analyses. Multivariable logistic regression will determine which risk factors are associated with JEV seropositivity likely due to recent transmission within Australia and the relative contribution of each factor when accounting for effects within the model. ETHICS National Mutual Acceptance ethical approval was obtained from the Sydney Children's Hospitals Network Human Research Ethics Committee (HREC). Local approvals were sought in each jurisdiction. Ethical approval was also obtained from the Australian Red Cross Lifeblood HREC. DISSEMINATION Findings will be communicated to participants and their communities, and human and animal health stakeholders and policy-makers iteratively and after final analyses. Understanding human infection rates will inform procurement and targeted allocation of limited JEV vaccine, and public health strategies and communication campaigns, to at-risk populations.
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Affiliation(s)
- Noni Ella Winkler
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases, Westmead, New South Wales, Australia
| | - Archana Koirala
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Guddu Kaur
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases, Westmead, New South Wales, Australia
- National Centre for Epidemiology and Population Health, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Shayal Prasad
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases, Westmead, New South Wales, Australia
| | - Rena Hirani
- Australian Red Cross Lifeblood, Sydney, New South Wales, Australia
- Faculty of Science and Engineering, Macquarie University, Macquarie Park, New South Wales, Australia
| | - Jannah Baker
- The University of Sydney, Sydney, New South Wales, Australia
| | - Veronica Hoad
- Australian Red Cross Lifeblood, Perth, Western Australia, Australia
| | - Iain B Gosbell
- Australian Red Cross Lifeblood, Sydney, New South Wales, Australia
- School of Medicine, Western Sydney University, Penrith South DC, New South Wales, Australia
| | - David O Irving
- Australian Red Cross Lifeblood, Sydney, New South Wales, Australia
- Faculty of Health, University of Technology Sydney, Broadway, New South Wales, Australia
| | - Linda Hueston
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
- Griffith University Menzies Health Institute Queensland, Brisbane, Queensland, Australia
| | - Matthew Vn O'Sullivan
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Jen Kok
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Dominic E Dwyer
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Kristine Macartney
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases, Westmead, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
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3
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Hurley S, Kim KW, Domazetovska A, Yau C, Yeang M, Donovan L, Kok J, Rawlinson W. Mpox detection in clinical specimens by three commercial real-time PCR assays demonstrates comparable results. Pathology 2024:S0031-3025(24)00051-5. [PMID: 38395680 DOI: 10.1016/j.pathol.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/26/2023] [Accepted: 11/12/2023] [Indexed: 02/25/2024]
Affiliation(s)
- Siobhan Hurley
- Department of Microbiology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Ki Wook Kim
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New Souh Wales, Sydney, NSW, Australia; Serology and Virology Division, Microbiology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Ana Domazetovska
- Serology and Virology Division, Microbiology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Cynthia Yau
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New Souh Wales, Sydney, NSW, Australia; Serology and Virology Division, Microbiology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Malinna Yeang
- Serology and Virology Division, Microbiology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Linda Donovan
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - William Rawlinson
- Serology and Virology Division, Microbiology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia; Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, UNSW, Kensington, NSW, Australia.
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4
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Asquith W, Hueston L, Dwyer D, Kok J, Ko D, Fennel M, Rockett R, Rai NJ, Li Y, Sriramoju S, Sutor A, O'Sullivan M. Characterizing the acute antibody response of monkeypox and MVA-BN vaccine following an Australian outbreak. J Med Virol 2024; 96:e29407. [PMID: 38240403 DOI: 10.1002/jmv.29407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024]
Abstract
In response to the emergence of the monkeypox virus (MPXV) in Australia in May 2022, we developed and evaluated indirect immunofluorescence assays (IFA) for MPXV and Vaccinia virus (VACV) IgG and IgM antibodies using serum samples from patients with nucleic acid amplification test (NAAT)-confirmed mpox and uninfected unvaccinated controls. Additionally, 47 healthcare workers receiving two doses of the third-generation smallpox vaccine Modified Vaccinia Ankara-Bavarian Nordic (MVA-BN) undertook serial serum collection to describe the serological response to vaccination. MPXV antibodies were detected in 16/18 individuals with NAAT-confirmed mpox (sensitivity 0.89, specificity 1.00), and VACV antibodies were detected in 28/29 individuals who received two doses of MVA-BN vaccine (sensitivity 0.97, specificity 1.00). Detectable antibody in subjects historically vaccinated with early-generation vaccines against smallpox was found in 7/7 subjects, at a median of 48 years following vaccination. MPXV NAAT-positive patients with serum samples collected within the first 14 days after rash onset had detectable IgG and IgM in 9/12 and 5/12 of patients, respectively, with maintenance of IgG and disappearance of IgM titers after 60 days. While specificity was high when testing unvaccinated and uninfected subjects, significant cross-reactivity between MPXV and VACV antibodies was observed.
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Affiliation(s)
- Will Asquith
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
| | - Linda Hueston
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
| | - Dominic Dwyer
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Camperdown, New South Wales, Australia
| | - Jen Kok
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Camperdown, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, New South Wales, Australia
| | - Danny Ko
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
| | - Michael Fennel
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
| | - Rebecca Rockett
- Sydney Infectious Disease Institute, The University of Sydney, Camperdown, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, New South Wales, Australia
| | - Neela Joshi Rai
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, New South Wales, Australia
| | - Ying Li
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, New South Wales, Australia
| | - Shirisha Sriramoju
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, New South Wales, Australia
| | - Allison Sutor
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, New South Wales, Australia
| | - Matthew O'Sullivan
- Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, New South Wales, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Camperdown, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, New South Wales, Australia
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5
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Lam C, Johnson-Mackinnon J, Basile K, Fong W, Suster CJ, Gall M, Agius J, Chandra S, Draper J, Martinez E, Drew A, Wang Q, Chen SC, Kok J, Dwyer DE, Sintchenko V, Rockett RJ. A laboratory framework for ongoing optimization of amplification-based genomic surveillance programs. Microbiol Spectr 2023; 11:e0220223. [PMID: 37966271 PMCID: PMC10715188 DOI: 10.1128/spectrum.02202-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/13/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE This study provides a laboratory framework to ensure ongoing relevance and performance of amplification-based whole genome sequencing to strengthen public health surveillance during extended outbreaks or pandemics. The framework integrates regular reviews of the performance of a genomic surveillance system and highlights the importance of ongoing monitoring and the identification and implementation of improvements to whole genome sequencing methods to enhance public health responses to pathogen outbreaks.
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Affiliation(s)
- Connie Lam
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Jessica Johnson-Mackinnon
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Kerri Basile
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
| | - Winkie Fong
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Carl J.E. Suster
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Mailie Gall
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Jessica Agius
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Shona Chandra
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Jenny Draper
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Alexander Drew
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Sharon C. Chen
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Dominic E. Dwyer
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Rebecca J. Rockett
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
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6
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Hurley S, Eden JS, Bingham J, Rodriguez M, Neave MJ, Johnson A, Howard-Jones AR, Kok J, Anazodo A, McMullan B, Williams DT, Watson J, Solinas A, Kim KW, Rawlinson W. Fatal Human Neurologic Infection Caused by Pigeon Avian Paramyxovirus-1, Australia. Emerg Infect Dis 2023; 29:2482-2487. [PMID: 37987582 PMCID: PMC10683822 DOI: 10.3201/eid2912.230250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023] Open
Abstract
Avian paramyxovirus type 1 (APMV-1) is a virus of birds that results in a range of outcomes, from asymptomatic infections to outbreaks of systemic respiratory and neurologic disease, depending on the virus strain and the avian species affected. Humans are rarely affected; those who are predominantly experience mild conjunctivitis. We report a fatal case of neurologic disease in a 2-year-old immunocompromised child in Australia. Metagenomic sequencing and histopathology identified the causative agent as the pigeon variant of APMV-1. This diagnosis should be considered in neurologic conditions of undefined etiologies. Agnostic metagenomic sequencing methods are useful in such settings to direct diagnostic and therapeutic efforts.
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Affiliation(s)
| | | | - John Bingham
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - Michael Rodriguez
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - Matthew J. Neave
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - Alexandra Johnson
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - Annaleise R. Howard-Jones
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - Jen Kok
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - Antoinette Anazodo
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - Brendan McMullan
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - David T. Williams
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - James Watson
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
| | - Annalisa Solinas
- Prince of Wales Hospital, Randwick, New South Wales, Australia (S. Hurley, K.W. Kim)
- Westmead Institute for Medical Research Centre for Virus Research, Westmead, New South Wales, Australia (J.S. Eden)
- Sydney Institute for Infectious Diseases, University of Sydney Faculty of Medicine and Health, Sydney, New South Wales, Australia (J.S. Eden, A.R. Howard-Jones)
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia (J. Bingham, M.J. Neave, D.T. Williams, J. Watson)
- Prince of Wales and Sydney Children’s Hospital, Randwick (M. Rodriguez, A. Solinas)
- Sydney Children’s Hospital, Randwick (A. Johnson, B. McMullan)
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology–Institute of Clinical Pathology and Medical Research, Westmead (A.R. Howard-Jones, J. Kok)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick (A. Anazodo)
- University of New South Wales Faculty of Medicine and Health, School of Clinical Medicine, Sydney (B. McMullan, K. Kim)
- Prince of Wales Hospital and Community Health Services, Sydney (W. Rawlinson)
- University of New South Wales Schools of Clinical Medicine, Biotechnology and Biomolecular Sciences, Sydney (W. Rawlinson)
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7
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O’Neill GK, Taylor J, Kok J, Dwyer DE, Dilcher M, Hua H, Levy A, Smith D, Minney-Smith CA, Wood T, Jelley L, Huang QS, Trenholme A, McAuliffe G, Barr I, Sullivan SG. Circulation of influenza and other respiratory viruses during the COVID-19 pandemic in Australia and New Zealand, 2020-2021. Western Pac Surveill Response J 2023; 14:1-9. [PMID: 37946717 PMCID: PMC10630701 DOI: 10.5365/wpsar.2023,14.3.948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
Objective Circulation patterns of influenza and other respiratory viruses have been globally disrupted since the emergence of coronavirus disease (COVID-19) and the introduction of public health and social measures (PHSMs) aimed at reducing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. Methods We reviewed respiratory virus laboratory data, Google mobility data and PHSMs in five geographically diverse regions in Australia and New Zealand. We also described respiratory virus activity from January 2017 to August 2021. Results We observed a change in the prevalence of circulating respiratory viruses following the emergence of SARS-CoV-2 in early 2020. Influenza activity levels were very low in all regions, lower than those recorded in 2017-2019, with less than 1% of laboratory samples testing positive for influenza virus. In contrast, rates of human rhinovirus infection were increased. Respiratory syncytial virus (RSV) activity was delayed; however, once it returned, most regions experienced activity levels well above those seen in 2017-2019. The timing of the resurgence in the circulation of both rhinovirus and RSV differed within and between the two countries. Discussion The findings of this study suggest that as domestic and international borders are opened up and other COVID-19 PHSMs are lifted, clinicians and public health professionals should be prepared for resurgences in influenza and other respiratory viruses. Recent patterns in RSV activity suggest that these resurgences in non-COVID-19 viruses have the potential to occur out of season and with increased impact.
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Affiliation(s)
- Genevieve K O’Neill
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Janette Taylor
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Dominic E Dwyer
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Meik Dilcher
- Canterbury Health Laboratories, Christchurch, New Zealand
| | - Harry Hua
- Canterbury Health Laboratories, Christchurch, New Zealand
| | - Avram Levy
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - David Smith
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
| | | | - Timothy Wood
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Lauren Jelley
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Q Sue Huang
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
- Institute of Environmental Science and Research, Wellington, New Zealand
| | | | - Gary McAuliffe
- Virology and Immunology Department, LabPLUS, Auckland City Hospital, Auckland District Health Board, Auckland, New Zealand
| | - Ian Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sheena G Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Infectious Diseases and Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, Victoria, Australia
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8
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Stewart AG, Chen SCA, Hamilton K, Harris-Brown T, Korman TM, Figtree M, Worth LJ, Kok J, Van der Poorten D, Byth K, Slavin MA, Paterson DL. Clostridioides difficile Infection: Clinical Practice and Health Outcomes in 6 Large Tertiary Hospitals in Eastern Australia. Open Forum Infect Dis 2023; 10:ofad232. [PMID: 37274181 PMCID: PMC10237225 DOI: 10.1093/ofid/ofad232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 04/26/2023] [Indexed: 06/06/2023] Open
Abstract
Background Clostridioides difficile infection (CDI) is associated with significant morbidity and mortality in both healthcare and community settings. We aimed to define the predisposing factors, risks for severe disease, and mortality determinants of CDI in eastern Australia over a 1-year period. Methods This is an observational retrospective study of CDI in hospitalized patients aged ≥18 years in 6 tertiary institutions from 1 January 2016 to 31 December 2016. Patients were identified through laboratory databases and medical records of participating institutions. Clinical, imaging, and laboratory data were input into an electronic database hosted at a central site. Results A total of 578 patients (578 CDI episodes) were included. Median age was 65 (range, 18-99) years and 48.2% were male. Hospital-onset CDI occurred in 64.0%. Recent antimicrobial use (41.9%) and proton pump inhibitor use (35.8%) were common. Significant risk factors for severe CDI were age <65 years (P < .001), malignancy within the last 5 years (P < .001), and surgery within the previous 30 days (P < .001). Significant risk factors for first recurrence included severe CDI (P = .03) and inflammatory bowel disease (P = .04). Metronidazole was the most common regimen for first episodes of CDI with 65.2% being concordant with Australian treatment guidelines overall. Determinants for death at 60 days included age ≥65 years (P = .01), severe CDI (P < .001), and antibiotic use within the prior 30 days (P = .02). Of those who received metronidazole as first-line therapy, 10.1% died in the 60-day follow-up period, compared to 9.8% of those who received vancomycin (P = .86). Conclusions Patients who experience CDI are vulnerable and require early diagnosis, clinical surveillance, and effective therapy to prevent complications and improve outcomes.
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Affiliation(s)
- Adam G Stewart
- Correspondence: Adam Stewart, BBiomedSci, MBBS(Hons), MPHTM, Centre for Clinical Research, University of Queensland, Bldg 71/918 RBWH Herston, Brisbane, QLD 4029, Australia (); David Paterson, Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, #10-01, Singapore 117549 ()
| | - Sharon C A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Sydney, Australia
- Department of Infectious Diseases, Westmead Hospital, University of Sydney, Sydney, Australia
| | - Kate Hamilton
- Department of Infectious Diseases, Westmead Hospital, University of Sydney, Sydney, Australia
| | - Tiffany Harris-Brown
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
| | - Tony M Korman
- Monash Infectious Diseases, Monash University and Monash Health, Melbourne, Australia
| | - Melanie Figtree
- Department of Infectious Diseases, Royal North Shore Hospital, Sydney, Australia
| | - Leon J Worth
- Department of Infectious Diseases, Peter MacCallum Centre, Melbourne, Australia
- National Centre for Infections in Cancer, Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Sydney, Australia
| | | | - Karen Byth
- Research and Education Network, Western Sydney Local Health District, Sydney, Australia
- National Health and Medical Research Council Clinical Trials Centre, Sydney University, Sydney, Australia
| | - Monica A Slavin
- Department of Infectious Diseases, Peter MacCallum Centre, Melbourne, Australia
- Department of Infectious Diseases, Royal Melbourne Hospital, Melbourne, Australia
| | - David L Paterson
- Correspondence: Adam Stewart, BBiomedSci, MBBS(Hons), MPHTM, Centre for Clinical Research, University of Queensland, Bldg 71/918 RBWH Herston, Brisbane, QLD 4029, Australia (); David Paterson, Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, #10-01, Singapore 117549 ()
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9
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Fong W, Rockett RJ, Agius JE, Chandra S, Johnson-Mckinnon J, Sim E, Lam C, Arnott A, Gall M, Draper J, Maddocks S, Chen S, Kok J, Dwyer D, O'Sullivan M, Sintchenko V. SABRes: in silico detection of drug resistance conferring mutations in subpopulations of SARS-CoV-2 genomes. BMC Infect Dis 2023; 23:303. [PMID: 37158832 PMCID: PMC10165565 DOI: 10.1186/s12879-023-08236-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 04/08/2023] [Indexed: 05/10/2023] Open
Abstract
The emergence of resistance to antiviral drugs increasingly used to treat SARS-CoV-2 infections has been recognised as a significant threat to COVID-19 control. In addition, some SARS-CoV-2 variants of concern appear to be intrinsically resistant to several classes of these antiviral agents. Therefore, there is a critical need for rapid recognition of clinically relevant polymorphisms in SARS-CoV-2 genomes associated with significant reduction of drug activity in virus neutralisation experiments. Here we present SABRes, a bioinformatic tool, which leverages on expanding public datasets of SARS-CoV-2 genomes and allows detection of drug resistance mutations in consensus genomes as well as in viral subpopulations. We have applied SABRes to detect resistance-conferring mutations in 25,197 genomes generated over the course of the SARS-CoV-2 pandemic in Australia and identified 299 genomes containing resistance conferring mutations to the five antiviral therapeutics that retain effectiveness against currently circulating strains of SARS-CoV-2 - Sotrovimab, Bebtelovimab, Remdesivir, Nirmatrelvir and Molnupiravir. These genomes accounted for a 1.18% prevalence of resistant isolates discovered by SABRes, including 80 genomes with resistance conferring mutations found in viral subpopulations. Timely recognition of these mutations within subpopulations is critical as these mutations can provide an advantage under selective pressure and presents an important step forward in our ability to monitor SARS-CoV-2 drug resistance.
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Affiliation(s)
- Winkie Fong
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia.
| | - Rebecca J Rockett
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Jessica E Agius
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Shona Chandra
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia
| | - Jessica Johnson-Mckinnon
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Eby Sim
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
| | - Connie Lam
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Alicia Arnott
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Mailie Gall
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Jenny Draper
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Susan Maddocks
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Sharon Chen
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Jen Kok
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Dominic Dwyer
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Matthew O'Sullivan
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, NSW, Westmead, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
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10
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Tulloch RL, Kim K, Sikazwe C, Michie A, Burrell R, Holmes EC, Dwyer DE, Britton PN, Kok J, Eden JS. RAPID prep: A Simple, Fast Protocol for RNA Metagenomic Sequencing of Clinical Samples. Viruses 2023; 15:v15041006. [PMID: 37112986 PMCID: PMC10146689 DOI: 10.3390/v15041006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Emerging infectious disease threats require rapid response tools to inform diagnostics, treatment, and outbreak control. RNA-based metagenomics offers this; however, most approaches are time-consuming and laborious. Here, we present a simple and fast protocol, the RAPIDprep assay, with the aim of providing a cause-agnostic laboratory diagnosis of infection within 24 h of sample collection by sequencing ribosomal RNA-depleted total RNA. The method is based on the synthesis and amplification of double-stranded cDNA followed by short-read sequencing, with minimal handling and clean-up steps to improve processing time. The approach was optimized and applied to a range of clinical respiratory samples to demonstrate diagnostic and quantitative performance. Our results showed robust depletion of both human and microbial rRNA, and library amplification across different sample types, qualities, and extraction kits using a single workflow without input nucleic-acid quantification or quality assessment. Furthermore, we demonstrated the genomic yield of both known and undiagnosed pathogens with complete genomes recovered in most cases to inform molecular epidemiological investigations and vaccine design. The RAPIDprep assay is a simple and effective tool, and representative of an important shift toward the integration of modern genomic techniques with infectious disease investigations.
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Affiliation(s)
- Rachel L Tulloch
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Karan Kim
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Chisha Sikazwe
- PathWest Laboratory Medicine WA, Department of Microbiology, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Alice Michie
- PathWest Laboratory Medicine WA, Department of Microbiology, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Rebecca Burrell
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Departments of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Dominic E Dwyer
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- NSW Health Pathology Institute for Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Philip N Britton
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Departments of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Jen Kok
- NSW Health Pathology Institute for Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
| | - John-Sebastian Eden
- Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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11
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Maamary J, Maddocks S, Barnett Y, Wong S, Rodriguez M, Hueston L, Jeoffreys N, Eden JS, Dwyer DE, Floyd T, Plit M, Kok J, Brew B. New Detection of Locally Acquired Japanese Encephalitis Virus Using Clinical Metagenomics, New South Wales, Australia. Emerg Infect Dis 2023; 29:627-630. [PMID: 36823673 PMCID: PMC9973708 DOI: 10.3201/eid2903.220632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
In the context of an emerging Japanese encephalitis outbreak within Australia, we describe a novel locally acquired case in New South Wales. A man in his 70s had rapidly progressive, fatal meningoencephalitis, diagnosed as caused by Japanese encephalitis virus by RNA-based metagenomic next-generation sequencing performed on postmortem brain tissue.
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Tang JW, Dilcher M, Bird PW, Kok J, Lee CK, Nishimura H, Oon L, Alston G, Dwyer DE, Holmes CW, Jennings LC. Practical problems and responses for SARS-CoV-2 laboratory testing during the COVID-19 pandemic. Clin Microbiol Infect 2023; 29:560-562. [PMID: 36773772 PMCID: PMC9911976 DOI: 10.1016/j.cmi.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/23/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Affiliation(s)
- Julian W. Tang
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom,Respiratory Sciences, University of Leicester, Leicester, United Kingdom,Corresponding author. Julian W. Tang, Clinical Microbiology, 5/F Sandringham Building, Leicester Royal Infirmary, Infirmary Square, Leicester, LE1 5WW, United Kingdom
| | - Meik Dilcher
- Canterbury Health Laboratories, Christchurch, New Zealand
| | - Paul W. Bird
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom,Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Chun Kiat Lee
- Department of Laboratory Medicine, National University Hospital, Singapore
| | | | - Lynette Oon
- Department of Molecular Pathology, Singapore General Hospital, Singapore
| | - Ginna Alston
- Canterbury Health Laboratories, Christchurch, New Zealand
| | - Dominic E. Dwyer
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Christopher W. Holmes
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom,Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Lance C. Jennings
- Canterbury Health Laboratories, Christchurch, New Zealand,Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
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13
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Suster CJE, Arnott A, Blackwell G, Gall M, Draper J, Martinez E, Drew AP, Rockett RJ, Chen SCA, Kok J, Dwyer DE, Sintchenko V. Guiding the design of SARS-CoV-2 genomic surveillance by estimating the resolution of outbreak detection. Front Public Health 2022; 10:1004201. [PMID: 36276383 PMCID: PMC9581317 DOI: 10.3389/fpubh.2022.1004201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/16/2022] [Indexed: 01/27/2023] Open
Abstract
Genomic surveillance of SARS-CoV-2 has been essential to inform public health response to outbreaks. The high incidence of infection has resulted in a smaller proportion of cases undergoing whole genome sequencing due to finite resources. We present a framework for estimating the impact of reduced depths of genomic surveillance on the resolution of outbreaks, based on a clustering approach using pairwise genetic and temporal distances. We apply the framework to simulated outbreak data to show that outbreaks are detected less frequently when fewer cases are subjected to whole genome sequencing. The impact of sequencing fewer cases depends on the size of the outbreaks, and on the genetic and temporal similarity of the index cases of the outbreaks. We also apply the framework to an outbreak of the SARS-CoV-2 Delta variant in New South Wales, Australia. We find that the detection of clusters in the outbreak would have been delayed if fewer cases had been sequenced. Existing recommendations for genomic surveillance estimate the minimum number of cases to sequence in order to detect and monitor new virus variants, assuming representative sampling of cases. Our method instead measures the resolution of clustering, which is important for genomic epidemiology, and accommodates sampling biases.
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Affiliation(s)
- Carl J. E. Suster
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
| | - Alicia Arnott
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Grace Blackwell
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Mailie Gall
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Jenny Draper
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Elena Martinez
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Alexander P. Drew
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Rebecca J. Rockett
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Dominic E. Dwyer
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead, NSW, Australia
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14
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Escarate E, Jones CG, Clarke E, Clark P, Norton S, Bag S, Kok J, Dwyer DE, Lindley RI, Booy R. Rapid on-site molecular Point of Care Testing during influenza outbreaks in aged care facilities improves antiviral use and reduces hospitalisation. Aust N Z J Public Health 2022; 46:884-888. [PMID: 36190193 DOI: 10.1111/1753-6405.13307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/01/2022] [Accepted: 08/01/2022] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVE Western Sydney Local Health District (WSLHD) measured the utility and validity of rapid molecular point-of-care testing (POCT) in aged care facilities (ACFs) experiencing influenza-like illness (ILI) outbreaks against routine laboratory testing. METHODS A descriptive epidemiological study into 82 respiratory outbreaks reported across 63 ACFs within WSLHD supporting approximately 6,500 residents aged ≥65 years and staffed by ∼6,500 employees, from 1 August 2018 to 31 December 2019. RESULTS WSLHD Public Health Unit performed on-site testing at 27 ACF outbreaks (34%), while 53(66%) ACFs conducted only routine laboratory testing. The Xpert®Xpress Flu/RSV molecular PCR provided a sensitivity and specificity of 100%. Those with on-site testing, antiviral prophylaxis was prescribed at 75% of facilities within 24 hours of testing, as opposed to 32% of those using laboratory testing (p<0.01). There were 24 of 181 ACF residents hospitalised in the POCT group compared to 76 of 357 in the laboratory-only group (OR=0.57; p=0.02). CONCLUSIONS On-site ACF testing is reliable and practical for early identification of influenza, enabling timely use of antiviral treatment and prophylaxis, and was associated with decreased hospitalisation. PUBLIC HEALTH IMPLICATIONS Enhanced respiratory surveillance and on-site testing should be strongly considered as part of routine management of respiratory outbreaks in ACFs and may reduce outbreak severity.
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Affiliation(s)
- Elizabeth Escarate
- Centre for Population Health, Western Sydney Public Health Unit, New South Wales
| | - Christian G Jones
- Centre for Population Health, Western Sydney Public Health Unit, New South Wales.,Sydney Medical School, The University of Sydney, New South Wales
| | - Elizabeth Clarke
- Centre for Population Health, Western Sydney Public Health Unit, New South Wales
| | - Penelope Clark
- Centre for Population Health, Western Sydney Public Health Unit, New South Wales
| | - Sophie Norton
- Centre for Population Health, Western Sydney Public Health Unit, New South Wales
| | - Shopna Bag
- Centre for Population Health, Western Sydney Public Health Unit, New South Wales.,Sydney Medical School, The University of Sydney, New South Wales
| | - Jen Kok
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, The University of Sydney, New South Wales.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research Westmead Hospital, New South Wales
| | - Dominic E Dwyer
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, The University of Sydney, New South Wales.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research Westmead Hospital, New South Wales
| | - Richard I Lindley
- Sydney Medical School, The University of Sydney, New South Wales.,The George Institute for Global Health, Sydney, New South Wales
| | - Robert Booy
- Sydney Medical School, The University of Sydney, New South Wales.,Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, The University of Sydney, New South Wales
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15
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Basile K, Rockett RJ, McPhie K, Fennell M, Johnson-Mackinnon J, Agius JE, Fong W, Rahman H, Ko D, Donavan L, Hueston L, Lam C, Arnott A, Chen SCA, Maddocks S, O’Sullivan MV, Dwyer DE, Sintchenko V, Kok J. Improved Neutralisation of the SARS-CoV-2 Omicron Variant following a Booster Dose of Pfizer-BioNTech (BNT162b2) COVID-19 Vaccine. Viruses 2022; 14:v14092023. [PMID: 36146829 PMCID: PMC9501619 DOI: 10.3390/v14092023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/02/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
In late November 2021, the World Health Organization declared the SARS-CoV-2 lineage B.1.1.529 the fifth variant of concern, Omicron. This variant has acquired over 30 mutations in the spike protein (with 15 in the receptor-binding domain), raising concerns that Omicron could evade naturally acquired and vaccine-derived immunity. We utilized an authentic virus, multicycle neutralisation assay to demonstrate that sera collected one, three, and six months post-two doses of Pfizer-BioNTech BNT162b2 had a limited ability to neutralise SARS-CoV-2. However, four weeks after a third dose, neutralising antibody titres were boosted. Despite this increase, neutralising antibody titres were reduced fourfold for Omicron compared to lineage A.2.2 SARS-CoV-2.
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Affiliation(s)
- Kerri Basile
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
- Correspondence: (K.B.); (J.K.)
| | - Rebecca J. Rockett
- Centre for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Sydney, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW 2006, Australia
| | - Kenneth McPhie
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
- The Westmead Institute for Medical Research, Westmead, Sydney, NSW 2145, Australia
| | - Michael Fennell
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
| | - Jessica Johnson-Mackinnon
- Centre for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Sydney, NSW 2145, Australia
| | - Jessica E. Agius
- Centre for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Sydney, NSW 2145, Australia
| | - Winkie Fong
- Centre for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Sydney, NSW 2145, Australia
| | - Hossinur Rahman
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
| | - Danny Ko
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
| | - Linda Donavan
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
| | - Linda Hueston
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
- Menzies Health Institute Queensland, Griffith University, Brisbane, QLD 4222, Australia
| | - Connie Lam
- Centre for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Sydney, NSW 2145, Australia
| | - Alicia Arnott
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
| | - Sharon C.-A. Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
- Centre for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Sydney, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW 2006, Australia
| | - Susan Maddocks
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
| | - Matthew V. O’Sullivan
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
- Centre for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Sydney, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW 2006, Australia
| | - Dominic E. Dwyer
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
- Centre for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Sydney, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW 2006, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
- Centre for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Sydney, NSW 2145, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
- Centre for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Sydney, NSW 2145, Australia
- Correspondence: (K.B.); (J.K.)
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16
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Jones CG, Escarate E, Clarke E, Clark P, Norton S, Bag S, Kok J, Dwyer D, Lindley RI, Booy R. Outbreaks of Human Metapneumovirus in Western Sydney Aged-Care Facilities in 2018. Commun Dis Intell (2018) 2022; 46. [DOI: 10.33321/cdi.2022.46.54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background Human metapneumovirus (hMPV), first described in 2001, is a cause of acute respiratory tract infection in the elderly, with symptoms ranging from mild to severe, including pneumonia, but outbreaks are rarely described. Methods Between 1 July and 31 December 2018, there were three outbreaks of Influenza-like Illness (ILI) where hMPV was the primary pathogen observed, among 64 aged-care facilities (ACFs) in Western Sydney. These outbreaks were investigated by the Western Sydney Local Health District (WSLHD) Public Health Unit (PHU); multiplex polymerase chain reaction (PCR) testing was performed on nasopharyngeal swabs collected by the ACF. Results hMPV was the main causative pathogen in three outbreaks (27, 28, and 15 symptomatic cases, respectively) in late winter and early spring. Fifty-five residents and 15 staff cases (70 total cases) were identified; hMPV was detected in 12 of 63 specimens submitted. Of the cases in residents, eight were hospitalised (8/63; 15%), including five with confirmed hMPV and a further one epidemiologically linked to a positive case. Six residents died (6/63; 11%) during the hMPV outbreaks; four of these had laboratory-confirmed hMPV, with a further case epidemiologically linked to a hMPV case, with a primary diagnosis of pneumonia/viral pneumonia. The sixth death was not epidemiologically linked, nor did this case exhibit any respiratory symptoms during the outbreak; however, it was reported in line with public health guidelines. Conclusion A major challenge in 2018 was the incompleteness of testing for, and awareness of, hMPV as a viral cause of ILI by facilities, laboratories, and emergency departments, which generally opted for rapid testing for influenza and RSV only. There is no licensed vaccine or approved treatment for hMPV, so efficient infection control measures are most important.
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Pham D, Maddocks S, Dwyer DE, Sintchenko V, Kok J, Rockett RJ. Development and Validation of an In-House Real-Time Reverse-Transcriptase Polymerase Chain Reaction Assay for SARS-CoV-2 Omicron Lineage Subtyping between BA.1 and BA.2. Viruses 2022; 14:v14081760. [PMID: 36016382 PMCID: PMC9416591 DOI: 10.3390/v14081760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 11/18/2022] Open
Abstract
In order to rapidly differentiate sublineages BA.1 and BA.2 of the SARS-CoV-2 variant of concern Omicron, we developed a real-time reverse-transcriptase polymerase chain reaction to target the discriminatory spike protein deletion at amino acid position 69–70 (S:del69–70). Compared to the gold standard of whole genome sequencing, the candidate assay was 100% sensitive and 99.4% specific. Sublineage typing by RT-PCR can provide a rapid, high throughput and cost-effective method to enhance surveillance as well as potentially guiding treatment and infection control decisions.
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Affiliation(s)
- David Pham
- Centre for Infectious Diseases & Microbiology Laboratory Services, New South Wales Health, Pathology—Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
- Correspondence:
| | - Susan Maddocks
- Centre for Infectious Diseases & Microbiology Laboratory Services, New South Wales Health, Pathology—Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Dominic E. Dwyer
- Centre for Infectious Diseases & Microbiology Laboratory Services, New South Wales Health, Pathology—Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW 2145, Australia
- Centre for Infectious Diseases & Microbiology—Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases & Microbiology Laboratory Services, New South Wales Health, Pathology—Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW 2145, Australia
- Centre for Infectious Diseases & Microbiology—Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Jen Kok
- Centre for Infectious Diseases & Microbiology Laboratory Services, New South Wales Health, Pathology—Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW 2145, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW 2145, Australia
- Centre for Infectious Diseases & Microbiology—Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Rebecca J. Rockett
- Sydney Infectious Diseases Institute, The University of Sydney, Westmead, NSW 2145, Australia
- Centre for Infectious Diseases & Microbiology—Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
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18
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Pham D, Howard-Jones AR, Hueston L, Jeoffreys N, Doggett S, Rockett R, Eden JS, Sintchenko V, Chen SCA, O’Sullivan MV, Maddocks S, Dwyer DE, Kok J. Emergence of Japanese encephalitis in Australia: a diagnostic perspective. Pathology 2022; 54:669-677. [DOI: 10.1016/j.pathol.2022.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/05/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022]
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Kouli O, Murray V, Bhatia S, Cambridge WA, Kawka M, Shafi S, Knight SR, Kamarajah SK, McLean KA, Glasbey JC, Khaw RA, Ahmed W, Akhbari M, Baker D, Borakati A, Mills E, Thavayogan R, Yasin I, Raubenheimer K, Ridley W, Sarrami M, Zhang G, Egoroff N, Pockney P, Richards T, Bhangu A, Creagh-Brown B, Edwards M, Harrison EM, Lee M, Nepogodiev D, Pinkney T, Pearse R, Smart N, Vohra R, Sohrabi C, Jamieson A, Nguyen M, Rahman A, English C, Tincknell L, Kakodkar P, Kwek I, Punjabi N, Burns J, Varghese S, Erotocritou M, McGuckin S, Vayalapra S, Dominguez E, Moneim J, Salehi M, Tan HL, Yoong A, Zhu L, Seale B, Nowinka Z, Patel N, Chrisp B, Harris J, Maleyko I, Muneeb F, Gough M, James CE, Skan O, Chowdhury A, Rebuffa N, Khan H, Down B, Fatimah Hussain Q, Adams M, Bailey A, Cullen G, Fu YXJ, McClement B, Taylor A, Aitken S, Bachelet B, Brousse de Gersigny J, Chang C, Khehra B, Lahoud N, Lee Solano M, Louca M, Rozenbroek P, Rozitis E, Agbinya N, Anderson E, Arwi G, Barry I, Batchelor C, Chong T, Choo LY, Clark L, Daniels M, Goh J, Handa A, Hanna J, Huynh L, Jeon A, Kanbour A, Lee A, Lee J, Lee T, Leigh J, Ly D, McGregor F, Moss J, Nejatian M, O'Loughlin E, Ramos I, Sanchez B, Shrivathsa A, Sincari A, Sobhi S, Swart R, Trimboli J, Wignall P, Bourke E, Chong A, Clayton S, Dawson A, Hardy E, Iqbal R, Le L, Mao S, Marinelli I, Metcalfe H, Panicker D, R HH, Ridgway S, Tan HH, Thong S, Van M, Woon S, Woon-Shoo-Tong XS, Yu S, Ali K, Chee J, Chiu C, Chow YW, Duller A, Nagappan P, Ng S, Selvanathan M, Sheridan C, Temple M, Do JE, Dudi-Venkata NN, Humphries E, Li L, Mansour LT, Massy-Westropp C, Fang B, Farbood K, Hong H, Huang Y, Joan M, Koh C, Liu YHA, Mahajan T, Muller E, Park R, Tanudisastro M, Wu JJG, Chopra P, Giang S, Radcliffe S, Thach P, Wallace D, Wilkes A, Chinta SH, Li J, Phan J, Rahman F, Segaran A, Shannon J, Zhang M, Adams N, Bonte A, Choudhry A, Colterjohn N, Croyle JA, Donohue J, Feighery A, Keane A, McNamara D, Munir K, Roche D, Sabnani R, Seligman D, Sharma S, Stickney Z, Suchy H, Tan R, Yordi S, Ahmed I, Aranha M, El Sabawy D, Garwood P, Harnett M, Holohan R, Howard R, Kayyal Y, Krakoski N, Lupo M, McGilberry W, Nepon H, Scoleri Y, Urbina C, Ahmad Fuad MF, Ahmed O, Jaswantlal D, Kelly E, Khan MHT, Naidu D, Neo WX, O'Neill R, Sugrue M, Abbas JD, Abdul-Fattah S, Azlan A, Barry K, Idris NS, Kaka N, Mc Dermott D, Mohammad Nasir MN, Mozo M, Rehal A, Shaikh Yousef M, Wong RH, Curran E, Gardner M, Hogan A, Julka R, Lasser G, Ní Chorráin N, Ting J, Browne R, George S, Janjua Z, Leung Shing V, Megally M, Murphy S, Ravenscroft L, Vedadi A, Vyas V, Bryan A, Sheikh A, Ubhi J, Vannelli K, Vawda A, Adeusi L, Doherty C, Fitzgerald C, Gallagher H, Gill P, Hamza H, Hogan M, Kelly S, Larry J, Lynch P, Mazeni NA, O'Connell R, O'Loghlin R, Singh K, Abbas Syed R, Ali A, Alkandari B, Arnold A, Arora E, Azam R, Breathnach C, Cheema J, Compton M, Curran S, Elliott JA, Jayasamraj O, Mohammed N, Noone A, Pal A, Pandey S, Quinn P, Sheridan R, Siew L, Tan EP, Tio SW, 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Carroll L, Goede A, Harbourne A, Lakhani A, Lami M, Larwood J, Martin J, Merchant J, Pattenden S, Pradhan A, Raafat N, Rothwell E, Shammoon Y, Sudarshan R, Vickers E, Wingfield L, Ashworth I, Azizi S, Bhate R, Chowdhury T, Christou A, Davies L, Dwaraknath M, Farah Y, Garner J, Gureviciute E, Hart E, Jain A, Javid S, Kankam HK, Kaur Toor P, Kaz R, Kermali M, Khan I, Mattson A, McManus A, Murphy M, Nair K, Ngemoh D, Norton E, Olabiran A, Parry L, Payne T, Pillai K, Price S, Punjabi K, Raghunathan A, Ramwell A, Raza M, Ritehnia J, Simpson G, Smith W, Sodeinde S, Studd L, Subramaniam M, Thomas J, Towey S, Tsang E, Tuteja D, Vasani J, Vio M, Badran A, Adams J, Anthony Wilkinson J, Asvandi S, Austin T, Bald A, Bix E, Carrick M, Chander B, Chowdhury S, Cooper Drake B, Crosbie S, D Portela S, Francis D, Gallagher C, Gillespie R, Gravett H, Gupta P, Ilyas C, James G, Johny J, Jones A, Kinder F, MacLeod C, Macrow C, Maqsood-Shah A, Mather J, McCann L, McMahon R, Mitham E, Mohamed M, Munton E, Nightingale K, O'Neill K, Onyemuchara I, Senior R, Shanahan A, Sherlock J, Spyridoulias A, Stavrou C, Stokes D, Tamang R, Taylor E, Trafford C, Uden C, Waddington C, Yassin D, Zaman M, Bangi S, Cheng T, Chew D, Hussain N, Imani-Masouleh S, Mahasivam G, McKnight G, Ng HL, Ota HC, Pasha T, Ravindran W, Shah K, Vishnu K S, Zaman S, Carr W, Cope S, Eagles EJ, Howarth-Maddison M, Li CY, Reed J, Ridge A, Stubbs T, Teasdaled D, Umar R, Worthington J, Dhebri A, Kalenderov R, Alattas A, Arain Z, Bhudia R, Chia D, Daniel S, Dar T, Garland H, Girish M, Hampson A, Kyriacou H, Lehovsky K, Mullins W, Omorphos N, Vasdev N, Venkatesh A, Waldock W, Bhandari A, Brown G, Choa G, Eichenauer CE, Ezennia K, Kidwai Z, Lloyd-Thomas A, Macaskill Stewart A, Massardi C, Sinclair E, Skajaa N, Smith M, Tan I, Afsheen N, Anuar A, Azam Z, Bhatia P, Davies-kelly N, Dickinson S, Elkawafi M, Ganapathy M, Gupta S, Khoury EG, Licudi D, Mehta V, Neequaye S, Nita G, Tay VL, Zhao S, Botsa E, Cuthbert H, Elliott J, Furlepa M, Lehmann J, Mangtani A, Narayan A, Nazarian S, Parmar C, Shah D, Shaw C, Zhao Z, Beck C, Caldwell S, Clements JM, French B, Kenny R, Kirk S, Lindsay J, McClung A, McLaughlin N, Watson S, Whiteside E, Alyacoubi S, Arumugam V, Beg R, Dawas K, Garg S, Lloyd ER, Mahfouz Y, Manobharath N, Moonesinghe R, Morka N, Patel K, Prashar J, Yip S, Adeeko ES, Ajekigbe F, Bhat A, Evans C, Farrugia A, Gurung C, Long T, Malik B, Manirajan S, Newport D, Rayer J, Ridha A, Ross E, Saran T, Sinker A, Waruingi D, Allen R, Al Sadek Y, Alves do Canto Brum H, Asharaf H, Ashman M, Balakumar V, Barrington J, Baskaran R, Berry A, Bhachoo H, Bilal A, Boaden L, Chia WL, Covell G, Crook D, Dadnam F, Davis L, De Berker H, Doyle C, Fox C, Gruffydd-Davies M, Hafouda Y, Hill A, Hubbard E, Hunter A, Inpadhas V, Jamshaid M, Jandu G, Jeyanthi M, Jones T, Kantor C, Kwak SY, Malik N, Matt R, McNulty P, Miles C, Mohomed A, Myat P, Niharika J, Nixon A, O'Reilly D, Parmar K, Pengelly S, Price L, Ramsden M, Turnor R, Wales E, Waring H, Wu M, Yang T, Ye TTS, Zander A, Zeicu C, Bellam S, Francombe J, Kawamoto N, Rahman MR, Sathyanarayana A, Tang HT, Cheung J, Hollingshead J, Page V, Sugarman J, Wong E, Chiong J, Fung E, Kan SY, Kiang J, Kok J, Krahelski O, Liew MY, Lyell B, Sharif Z, Speake D, Alim L, Amakye NY, Chandrasekaran J, Chandratreya N, Drake J, Owoso T, Thu YM, Abou El Ela Bourquin B, Alberts J, Chapman D, Rehnnuma N, Ainsworth K, Carpenter H, Emmanuel T, Fisher T, Gabrel M, Guan Z, Hollows S, Hotouras A, Ip Fung Chun N, Jaffer S, Kallikas G, Kennedy N, Lewinsohn B, Liu FY, Mohammed S, Rutherfurd A, Situ T, Stammer A, Taylor F, Thin N, Urgesi E, Zhang N, Ahmad MA, Bishop A, Bowes A, Dixit A, Glasson R, Hatta S, Hatt K, Larcombe S, Preece J, Riordan E, Fegredo D, Haq MZ, Li C, McCann G, Stewart D, Baraza W, Bhullar D, Burt G, Coyle J, Deans J, Devine A, Hird R, Ikotun O, Manchip G, Ross C, Storey L, Tan WWL, Tse C, Warner C, Whitehead M, Wu F, Court EL, Crisp E, Huttman M, Mayes F, Robertson H, Rosen H, Sandberg C, Smith H, Al Bakry M, Ashwell W, Bajaj S, Bandyopadhyay D, Browlee O, Burway S, Chand CP, Elsayeh K, Elsharkawi A, Evans E, Ferrin S, Fort-Schaale A, Iacob M, I K, Impelliziere Licastro G, Mankoo AS, Olaniyan T, Otun J, Pereira R, Reddy R, Saeed D, Simmonds O, Singhal G, Tron K, Wickstone C, Williams R, Bradshaw E, De Kock Jewell V, Houlden C, Knight C, Metezai H, Mirza-Davies A, Seymour Z, Spink D, Wischhusen S. Evaluation of prognostic risk models for postoperative pulmonary complications in adult patients undergoing major abdominal surgery: a systematic review and international external validation cohort study. Lancet Digit Health 2022; 4:e520-e531. [PMID: 35750401 DOI: 10.1016/s2589-7500(22)00069-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 01/07/2022] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Stratifying risk of postoperative pulmonary complications after major abdominal surgery allows clinicians to modify risk through targeted interventions and enhanced monitoring. In this study, we aimed to identify and validate prognostic models against a new consensus definition of postoperative pulmonary complications. METHODS We did a systematic review and international external validation cohort study. The systematic review was done in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched MEDLINE and Embase on March 1, 2020, for articles published in English that reported on risk prediction models for postoperative pulmonary complications following abdominal surgery. External validation of existing models was done within a prospective international cohort study of adult patients (≥18 years) undergoing major abdominal surgery. Data were collected between Jan 1, 2019, and April 30, 2019, in the UK, Ireland, and Australia. Discriminative ability and prognostic accuracy summary statistics were compared between models for the 30-day postoperative pulmonary complication rate as defined by the Standardised Endpoints in Perioperative Medicine Core Outcome Measures in Perioperative and Anaesthetic Care (StEP-COMPAC). Model performance was compared using the area under the receiver operating characteristic curve (AUROCC). FINDINGS In total, we identified 2903 records from our literature search; of which, 2514 (86·6%) unique records were screened, 121 (4·8%) of 2514 full texts were assessed for eligibility, and 29 unique prognostic models were identified. Nine (31·0%) of 29 models had score development reported only, 19 (65·5%) had undergone internal validation, and only four (13·8%) had been externally validated. Data to validate six eligible models were collected in the international external validation cohort study. Data from 11 591 patients were available, with an overall postoperative pulmonary complication rate of 7·8% (n=903). None of the six models showed good discrimination (defined as AUROCC ≥0·70) for identifying postoperative pulmonary complications, with the Assess Respiratory Risk in Surgical Patients in Catalonia score showing the best discrimination (AUROCC 0·700 [95% CI 0·683-0·717]). INTERPRETATION In the pre-COVID-19 pandemic data, variability in the risk of pulmonary complications (StEP-COMPAC definition) following major abdominal surgery was poorly described by existing prognostication tools. To improve surgical safety during the COVID-19 pandemic recovery and beyond, novel risk stratification tools are required. FUNDING British Journal of Surgery Society.
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Gulholm T, Yeang M, Nguyen I, Andrews PI, Balgahom R, Beresford R, Branley J, Briest R, Britton P, Burrell R, Gehrig N, Kesson A, Kok J, Maley M, Newcombe J, Samarasekara H, Van Hal S, Varadhan H, Thapa K, Jones S, Newton P, Naing Z, Stelzer-Braid S, Rawlinson W. Molecular typing of enteroviruses: comparing 5'UTR, VP1 and whole genome sequencing methods. Pathology 2022; 54:779-783. [PMID: 35738943 DOI: 10.1016/j.pathol.2022.03.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 03/03/2022] [Accepted: 03/21/2022] [Indexed: 12/15/2022]
Abstract
Enteroviruses (EV) commonly cause hand, foot and mouth disease (HFMD), and can also cause potentially fatal neurological and systemic complications. In our laboratory, sequencing 5' untranslated region (UTR) of the viral genome has been the routine method of genotyping EVs. During a recent localised outbreak of aseptic meningitis, sequencing the 5'UTR identified the causative virus as EV-A71, which did not fit with the clinical syndrome or illness severity. When genotyped using a different target gene, VP1, the result was different. This led us to evaluate the accuracy of the two different target genome regions and compare them against whole genome sequencing (WGS). We aimed to optimise the algorithm for detection and characterisation of EVs in the diagnostic laboratory. We hypothesised that VP1 and WGS genotyping would provide different results than 5'UTR in a subset of samples. Clinical samples from around New South Wales which were positive for EV by commercial polymerase chain reaction (PCR) assays were genotyped by targeting three different viral genome regions: the 5'UTR, VP1 and WGS. Sequencing was performed by Sanger and next generation sequencing. The subtyping results were compared. Of the 74/118 (63%) samples that were successfully typed using both the 5'UTR and the VP1 method, the EV typing result was identical for 46/74 (62%) samples compared to WGS as the gold standard. The same EV group but different EV types were found in 22/74 (30%) samples, and 6/74 (8%) samples belonged to different EV groups depending on typing method used. Genotyping with WGS and VP1 is more accurate than 5'UTR. Genotyping by the 5'UTR method is very sensitive, but less specific.
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Affiliation(s)
- T Gulholm
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia; Department of Infectious Diseases, Prince of Wales Hospital, Randwick, NSW, Australia; UNSW Clinical School, Faculty of Medicine UNSW, Kensington, NSW, Australia.
| | - M Yeang
- Virology Research Laboratory, Serology and Virology Division (SAViD), New South Wales Health Pathology East, Prince of Wales Hospital, Randwick, NSW, Australia
| | - I Nguyen
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - P I Andrews
- Department of Neurology, Sydney Children's Hospital, Randwick, NSW, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
| | - R Balgahom
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia
| | - R Beresford
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Liverpool, NSW, Australia
| | - J Branley
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia; Nepean Clinical School, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - R Briest
- Department of Neurology, Sydney Children's Hospital, Randwick, NSW, Australia
| | - P Britton
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, NSW, Australia; University of Sydney Children's Hospital Westmead Clinical School, NSW, Australia
| | - R Burrell
- Marie Bashir Institute of Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia
| | - N Gehrig
- NSW Health Pathology, John Hunter Hospital, Newcastle, NSW, Australia
| | - A Kesson
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Child and Adolescent Health, The University of Sydney, Sydney, NSW, Australia
| | - J Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW, Australia
| | - M Maley
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Liverpool, NSW, Australia
| | - J Newcombe
- Department of Microbiology, NSW Health Pathology, Royal North Shore Hospital, Sydney, NSW, Australia
| | - H Samarasekara
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia
| | - S Van Hal
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - H Varadhan
- NSW Health Pathology, John Hunter Hospital, Newcastle, NSW, Australia
| | - K Thapa
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - S Jones
- Department of Microbiology, NSW Health Pathology, The Wollongong Hospital, Wollongong, NSW, Australia
| | - P Newton
- Department of Microbiology, NSW Health Pathology, The Wollongong Hospital, Wollongong, NSW, Australia
| | - Z Naing
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - S Stelzer-Braid
- Virology Research Laboratory, Serology and Virology Division (SAViD), New South Wales Health Pathology East, Prince of Wales Hospital, Randwick, NSW, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - W Rawlinson
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia; Department of Infectious Diseases, Prince of Wales Hospital, Randwick, NSW, Australia; Virology Research Laboratory, Serology and Virology Division (SAViD), New South Wales Health Pathology East, Prince of Wales Hospital, Randwick, NSW, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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Agius JE, Johnson-Mackinnon JC, Fong W, Gall M, Lam C, Basile K, Kok J, Arnott A, Sintchenko V, Rockett RJ. SARS-CoV-2 Within-Host and in vitro Genomic Variability and Sub-Genomic RNA Levels Indicate Differences in Viral Expression Between Clinical Cohorts and in vitro Culture. Front Microbiol 2022; 13:824217. [PMID: 35663867 PMCID: PMC9161297 DOI: 10.3389/fmicb.2022.824217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/18/2022] [Indexed: 12/23/2022] Open
Abstract
Background Low frequency intrahost single nucleotide variants (iSNVs) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) have been increasingly recognised as predictive indicators of positive selection. Particularly as growing numbers of SARS-CoV-2 variants of interest (VOI) and concern (VOC) emerge. However, the dynamics of subgenomic RNA (sgRNA) expression and its impact on genomic diversity and infection outcome remain poorly understood. This study aims to investigate and quantify iSNVs and sgRNA expression in single and longitudinally sampled cohorts over the course of mild and severe SARS-CoV-2 infection, benchmarked against an in vitro infection model. Methods Two clinical cohorts of SARS-CoV-2 positive cases in New South Wales, Australia collected between March 2020 and August 2021 were sequenced. Longitudinal samples from cases hospitalised due to SARS-CoV-2 infection (severe) (n = 16) were analysed and compared with cases that presented with SARS-CoV-2 symptoms but were not hospitalised (mild) (n = 23). SARS-CoV-2 genomic diversity profiles were also examined from daily sampling of culture experiments for three SARS-CoV-2 variants (Lineage A, B.1.351, and B.1.617.2) cultured in VeroE6 C1008 cells (n = 33). Results Intrahost single nucleotide variants were detected in 83% (19/23) of the mild cohort cases and 100% (16/16) of the severe cohort cases. SNP profiles remained relatively fixed over time, with an average of 1.66 SNPs gained or lost, and an average of 4.2 and 5.9 low frequency variants per patient were detected in severe and mild infection, respectively. sgRNA was detected in 100% (25/25) of the mild genomes and 92% (24/26) of the severe genomes. Total sgRNA expressed across all genes in the mild cohort was significantly higher than that of the severe cohort. Significantly higher expression levels were detected in the spike and the nucleocapsid genes. There was significantly less sgRNA detected in the culture dilutions than the clinical cohorts. Discussion and Conclusion The positions and frequencies of iSNVs in the severe and mild infection cohorts were dynamic overtime, highlighting the importance of continual monitoring, particularly during community outbreaks where multiple SARS-CoV-2 variants may co-circulate. sgRNA levels can vary across patients and the overall level of sgRNA reads compared to genomic RNA can be less than 1%. The relative contribution of sgRNA to the severity of illness warrants further investigation given the level of variation between genomes. Further monitoring of sgRNAs will improve the understanding of SARS-CoV-2 evolution and the effectiveness of therapeutic and public health containment measures during the pandemic.
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Affiliation(s)
- Jessica E. Agius
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Jessica C. Johnson-Mackinnon
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, Westmead, NSW, Australia
- *Correspondence: Jessica C. Johnson-Mackinnon,
| | - Winkie Fong
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Mailie Gall
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology – Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Connie Lam
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Kerri Basile
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology – Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology – Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Alicia Arnott
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology – Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology – Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Rebecca J. Rockett
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, Westmead, NSW, Australia
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Rockett RJ, Draper J, Gall M, Sim EM, Arnott A, Agius JE, Johnson-Mackinnon J, Fong W, Martinez E, Drew AP, Lee C, Ngo C, Ramsperger M, Ginn AN, Wang Q, Fennell M, Ko D, Hueston L, Kairaitis L, Holmes EC, O'Sullivan MN, Chen SCA, Kok J, Dwyer DE, Sintchenko V. Co-infection with SARS-CoV-2 Omicron and Delta variants revealed by genomic surveillance. Nat Commun 2022; 13:2745. [PMID: 35585202 PMCID: PMC9117272 DOI: 10.1038/s41467-022-30518-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/21/2022] [Indexed: 12/02/2022] Open
Abstract
Co-infections with different variants of SARS-CoV-2 are a key precursor to recombination events that are likely to drive SARS-CoV-2 evolution. Rapid identification of such co-infections is required to determine their frequency in the community, particularly in populations at-risk of severe COVID-19, which have already been identified as incubators for punctuated evolutionary events. However, limited data and tools are currently available to detect and characterise the SARS-CoV-2 co-infections associated with recognised variants of concern. Here we describe co-infection with the SARS-CoV-2 variants of concern Omicron and Delta in two epidemiologically unrelated adult patients with chronic kidney disease requiring maintenance haemodialysis. Both variants were co-circulating in the community at the time of detection. Genomic surveillance based on amplicon- and probe-based sequencing using short- and long-read technologies identified and quantified subpopulations of Delta and Omicron viruses in respiratory samples. These findings highlight the importance of integrated genomic surveillance in vulnerable populations and provide diagnostic pathways to recognise SARS-CoV-2 co-infection using genomic data. Here, using genomic approaches, Rockett et al. identify Omicron and Delta SARS-CoV-2 co-infections in two adults, highlighting the usefulness of genomic surveillance for the timely recognition of co-infections in situations when different variants of the virus are circulating in the community.
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Affiliation(s)
- Rebecca J Rockett
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia
| | - Jenny Draper
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Mailie Gall
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Eby M Sim
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Alicia Arnott
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Jessica E Agius
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia
| | - Jessica Johnson-Mackinnon
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia
| | - Winkie Fong
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia
| | - Elena Martinez
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Alexander P Drew
- Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Clement Lee
- Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Christine Ngo
- Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Marc Ramsperger
- Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Andrew N Ginn
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Qinning Wang
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Michael Fennell
- Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Danny Ko
- Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Linda Hueston
- Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Lukas Kairaitis
- Renal Services Blacktown Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.,School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Matthew N O'Sullivan
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Sharon C-A Chen
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Jen Kok
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Dominic E Dwyer
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia.,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia
| | - Vitali Sintchenko
- Sydney Institute for Infectious Diseases, University of Sydney, Sydney, NSW, Australia. .,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia. .,Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead, NSW, Australia. .,School of Medical Sciences, University of Sydney, Sydney, NSW, Australia.
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Kovoor JG, Jacobsen JHW, Duncan J, Addo AA, Tivey DR, Babidge WJ, Penn D, Churchill J, Collinson TG, Kok J, Kelly S, Lu VH, Beavis VS, MacCormick AD, Kearney BJ, Gowans EJ, Hewett PJ, Hugh TJ, Woo HH, Padbury RT, Scott DA, Frydenberg M, Maddern GJ. Achieving safe surgery after COVID-19 vaccination. ANZ J Surg 2022; 92:946-949. [PMID: 35535005 PMCID: PMC9321689 DOI: 10.1111/ans.17654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/10/2022] [Accepted: 03/12/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Joshua G Kovoor
- University of Adelaide, Discipline of Surgery, The Queen Elizabeth Hospital, Adelaide, South Australia, Australia.,Research, Audit and Academic Surgery, Royal Australasian College of Surgeons, Adelaide, South Australia, Australia.,Basil Hetzel Institute for Translational Health Research, Adelaide, South Australia, Australia
| | - Jonathan Henry W Jacobsen
- Research, Audit and Academic Surgery, Royal Australasian College of Surgeons, Adelaide, South Australia, Australia
| | - Joanna Duncan
- Research, Audit and Academic Surgery, Royal Australasian College of Surgeons, Adelaide, South Australia, Australia
| | - Afua A Addo
- Research, Audit and Academic Surgery, Royal Australasian College of Surgeons, Adelaide, South Australia, Australia
| | - David R Tivey
- University of Adelaide, Discipline of Surgery, The Queen Elizabeth Hospital, Adelaide, South Australia, Australia.,Research, Audit and Academic Surgery, Royal Australasian College of Surgeons, Adelaide, South Australia, Australia
| | - Wendy J Babidge
- University of Adelaide, Discipline of Surgery, The Queen Elizabeth Hospital, Adelaide, South Australia, Australia.,Research, Audit and Academic Surgery, Royal Australasian College of Surgeons, Adelaide, South Australia, Australia
| | - David Penn
- Launceston General Hospital, Launceston, Tasmania, Australia
| | | | | | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Sydney, New South Wales, Australia
| | - Shane Kelly
- St John of God Healthcare, Perth, Western Australia, Australia
| | - Vicky H Lu
- St Vincent's Hospital, Sydney, New South Wales, Australia.,Retina and Vitreous Centre, Sydney, New South Wales, Australia
| | - Vanessa S Beavis
- Department of Anaesthesia and Perioperative Medicine, Auckland City Hospital, Auckland, New Zealand
| | - Andrew D MacCormick
- Department of Surgery, South Auckland Clinical School, University of Auckland, Auckland, New Zealand.,Department of Surgery, Counties Manukau District Health Board, Auckland, New Zealand
| | - Brendon J Kearney
- Department of Haematology, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Eric J Gowans
- University of Adelaide, Discipline of Surgery, The Queen Elizabeth Hospital, Adelaide, South Australia, Australia.,Basil Hetzel Institute for Translational Health Research, Adelaide, South Australia, Australia
| | - Peter J Hewett
- University of Adelaide, Discipline of Surgery, The Queen Elizabeth Hospital, Adelaide, South Australia, Australia
| | - Thomas J Hugh
- Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia.,Surgical Education, Research and Training Institute, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Henry H Woo
- Sydney Adventist Hospital, University of Sydney, Sydney, New South Wales, Australia
| | - Robert T Padbury
- Flinders University, Adelaide, South Australia, Australia.,Division of Surgery and Perioperative Medicine, Flinders Medical Centre, Adelaide, South Australia, Australia
| | - David A Scott
- Department of Anaesthesia and Acute Pain Medicine, St Vincent's Hospital, Melbourne, Victoria, Australia.,Department of Critical Care, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Mark Frydenberg
- Department of Urology, Cabrini Institute, Cabrini Health, Melbourne, Victoria, Australia.,Department of Surgery, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Guy J Maddern
- University of Adelaide, Discipline of Surgery, The Queen Elizabeth Hospital, Adelaide, South Australia, Australia.,Research, Audit and Academic Surgery, Royal Australasian College of Surgeons, Adelaide, South Australia, Australia.,Basil Hetzel Institute for Translational Health Research, Adelaide, South Australia, Australia
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24
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Borman P, Westerhoff J, Winchester N, Knox C, Kok J, Raaymakers B, Fast M. PO-1718 Visual biofeedback on the Unity MR-linac as driver for treatment efficiency. Radiother Oncol 2022. [DOI: 10.1016/s0167-8140(22)03682-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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25
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Rockett R, Basile K, Maddocks S, Fong W, Agius JE, Johnson-Mackinnon J, Arnott A, Chandra S, Gall M, Draper J, Martinez E, Sim EM, Lee C, Ngo C, Ramsperger M, Ginn AN, Wang Q, Fennell M, Ko D, Lim HL, Gilroy N, O'Sullivan MVN, Chen SCA, Kok J, Dwyer DE, Sintchenko V. Resistance Mutations in SARS-CoV-2 Delta Variant after Sotrovimab Use. N Engl J Med 2022; 386:1477-1479. [PMID: 35263515 PMCID: PMC8929376 DOI: 10.1056/nejmc2120219] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
| | | | - Susan Maddocks
- Western Sydney Local Health District, Westmead, NSW, Australia
| | - Winkie Fong
- Western Sydney Local Health District, Westmead, NSW, Australia
| | | | | | | | - Shona Chandra
- Western Sydney Local Health District, Westmead, NSW, Australia
| | - Mailie Gall
- NSW Health Pathology, Sydney, NSW, Australia
| | | | | | - Eby M Sim
- NSW Health Pathology, Sydney, NSW, Australia
| | - Clement Lee
- NSW Health Pathology, Sydney, NSW, Australia
| | | | | | | | | | | | - Danny Ko
- NSW Health Pathology, Sydney, NSW, Australia
| | - H Ling Lim
- Western Sydney Local Health District, Westmead, NSW, Australia
| | - Nicky Gilroy
- Western Sydney Local Health District, Westmead, NSW, Australia
| | | | | | - Jen Kok
- NSW Health Pathology, Sydney, NSW, Australia
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26
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Tang JW, Caniza MA, Dinn M, Dwyer DE, Heraud JM, Jennings LC, Kok J, Kwok KO, Li Y, Loh TP, Marr LC, Nara EM, Perera N, Saito R, Santillan-Salas C, Sullivan S, Warner M, Watanabe A, Zaidi SK. An exploration of the political, social, economic and cultural factors affecting how different global regions initially reacted to the COVID-19 pandemic. Interface Focus 2022; 12:20210079. [PMID: 35261734 PMCID: PMC8831085 DOI: 10.1098/rsfs.2021.0079] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/13/2022] [Indexed: 12/15/2022] Open
Abstract
Responses to the early (February–July 2020) COVID-19 pandemic varied widely, globally. Reasons for this are multiple but likely relate to the healthcare and financial resources then available, and the degree of trust in, and economic support provided by, national governments. Cultural factors also affected how different populations reacted to the various pandemic restrictions, like masking, social distancing and self-isolation or self-quarantine. The degree of compliance with these measures depended on how much individuals valued their needs and liberties over those of their society. Thus, several themes may be relevant when comparing pandemic responses across different regions. East and Southeast Asian populations tended to be more collectivist and self-sacrificing, responding quickly to early signs of the pandemic and readily complied with most restrictions to control its spread. Australasian, Eastern European, Scandinavian, some Middle Eastern, African and South American countries also responded promptly by imposing restrictions of varying severity, due to concerns for their wider society, including for some, the fragility of their healthcare systems. Western European and North American countries, with well-resourced healthcare systems, initially reacted more slowly, partly in an effort to maintain their economies but also to delay imposing pandemic restrictions that limited the personal freedoms of their citizens.
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Affiliation(s)
- Julian W. Tang
- Respiratory Sciences, University of Leicester, Leicester, UK
| | | | - Mike Dinn
- British Antarctic Survey Medical Unit, Emergency Department, University Hospitals Plymouth NHS Trust, Plymouth, UK
| | - Dominic E. Dwyer
- NSW Health Pathology - Institute for Clinical Pathology and Medical Research, and University of Sydney, Westmead, New South Wales, Australia
| | | | - Lance C. Jennings
- Department of Pathology and Biomedical Science, University of Otago, and Canterbury Health Laboratories, Christchurch, New Zealand
| | - Jen Kok
- NSW Health Pathology - Institute for Clinical Pathology and Medical Research, and University of Sydney, Westmead, New South Wales, Australia
| | - Kin On Kwok
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
- Hong Kong Institute of Asia-Pacific Studies, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
- Shenzhen Research Institute of the Chinese University of Hong Kong, Shenzhen, People's Republic of China
| | - Yuguo Li
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Tze Ping Loh
- Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Linsey C. Marr
- Civil and Environmental Engineering, Virginia Tech, VA, USA
| | - Eva Megumi Nara
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Nelun Perera
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Reiko Saito
- Division of International Health, Niigata University, Niigata, Japan
| | | | - Sheena Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, Melbourne, Australia
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Matt Warner
- British Antarctic Survey Medical Unit, Emergency Department, University Hospitals Plymouth NHS Trust, Plymouth, UK
| | - Aripuanã Watanabe
- Department of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora, Juiz de Fora, Brazil
| | - Sabeen Khurshid Zaidi
- Karachi Institute of Medical Sciences affiliated with National University of Medical Sciences, Karachi, Pakistan
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27
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Howe AY, Rodrigo C, Cunningham E, Douglas MW, Dietz J, Grebely J, Popping S, Sfalcin JA, Parczewski M, Sarrazin C, de Salazar A, Fuentes A, Sayan M, Quer J, Kjellin M, Kileng H, Mor O, Lennerstrand J, Fourati S, di Maio VC, Chulanov V, Pawlotsky JM, Harrigan PR, Ceccherini-Silberstein F, Garcia F, Martinello M, Matthews G, Fernando FF, Esteban JI, Müllhaupt B, Wiesch JSZ, Buggisch P, Neumann-Haefelin C, Berg T, Berg CP, Schattenberg JM, Moreno C, Stauber R, Lloyd A, Dore G, Applegate T, Ignacio J, Garcia-Cehic D, Gregori J, Rodriguez-Frias F, Rando A, Angelico M, Andreoni M, Babudieri S, Bertoli A, Cento V, Coppola N, Craxì A, Paolucci S, Parruti G, Pasquazzi C, Perno CF, Teti E, Vironet C, Lannergård A, Duberg AS, Aleman S, Gutteberg T, Soulier A, Gourgeon A, Chevaliez S, Pol S, Carrat F, Salmon D, Kaiser R, Knopes E, Gomes P, de Kneght R, Rijnders B, Poljak M, Lunar M, Usubillaga R, Seguin C, Tay E, Wilson C, Wang DS, George J, Kok J, Pérez AB, Chueca N, García-Deltoro M, Martínez-Sapiña AM, Lara-Pérez MM, García-Bujalance S, Aldámiz-Echevarría T, Vera-Méndez FJ, Pineda JA, Casado M, Pascasio JM, Salmerón J, Alados-Arboledas JC, Poyato A, Téllez F, Rivero-Juárez A, Merino D, Vivancos-Gallego MJ, Rosales-Zábal JM, Ocete MD, Simón MÁ, Rincón P, Reus S, De la Iglesia A, García-Arata I, Jiménez M, Jiménez F, Hernández-Quero J, Galera C, Balghata MO, Primo J, Masiá M, Espinosa N, Delgado M, von-Wichmann MÁ, Collado A, Santos J, Mínguez C, Díaz-Flores F, Fernández E, Bernal E, De Juan J, Antón JJ, Vélez M, Aguilera A, Navarro D, Arenas JI, Fernández C, Espinosa MD, Ríos MJ, Alonso R, Hidalgo C, Hernández R, Téllez MJ, Rodríguez FJ, Antequera P, Delgado C, Martín P, Crespo J, Becerril B, Pérez O, García-Herola A, Montero J, Freyre C, Grau C, Cabezas J, Jimenez M, Rodriguez MAM, Quilez C, Pardo MR, Muñoz-Medina L, Figueruela B. Characteristics of hepatitis C virus resistance in an international cohort after a decade of direct-acting antivirals. JHEP Rep 2022; 4:100462. [PMID: 35434589 PMCID: PMC9010635 DOI: 10.1016/j.jhepr.2022.100462] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/05/2022] [Indexed: 10/24/2022] Open
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28
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Begum H, Dwyer DE, Holmes M, Irving LB, Simpson G, Senanayake S, Korman T, Friedman ND, Cooley L, Wark P, Bowler S, Kok J, Upham JW, Fatovich DM, Waterer GW, Macartney K, Blyth CC, Crawford N, Buttery J, Marshall HS, Clark JE, Francis JR, Kotsimbos T, Kelly PM, Cheng AC. Surveillance for severe influenza and COVID-19 in patients admitted to sentinel Australian hospitals in 2020: the Influenza Complications Alert Network (FluCAN). Commun Dis Intell (2018) 2022; 46. [DOI: 10.33321/cdi.2022.46.13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Introduction Influenza is a common cause of acute respiratory infection, and is a major cause of morbidity and mortality. Coronavirus disease 2019 (COVID-19) is an acute respiratory infection that emerged as a pandemic worldwide before the start of the 2020 Australian influenza season. This report summarises the epidemiology of hospitalisations with laboratory-confirmed influenza and COVID-19 during the 2020 influenza season in a sentinel surveillance system. Methods The Influenza Complications Alert Network (FluCAN) is a sentinel hospital-based surveillance program that operates at sites in all jurisdictions in Australia. Influenza and COVID-19 cases were defined as patients hospitalised at sentinel hospitals and confirmed by nucleic acid detection. Results There were 448 patients with COVID-19 admitted between 16 March and 31 December 2020, and only 20 patients with influenza admitted between 1 April and 30 November 2020, to one of 22 FluCAN hospitals. Of the COVID-19 cases, 173 (39%) were > 65 years of age, 36 (8%) were children (< 16 years), 6 (1%) were Aboriginal and Torres Strait Islander peoples, 4 (1%) were pregnant and 289 (65%) had chronic comorbidities. COVID-19 hospital admissions peaked between weeks 13 and 15 (first wave) nationally, and again between weeks 31 and 35 (Victoria), with most admissions represented by those above 40 years of age. Discussion There was an unusually low number of hospital admissions with laboratory-confirmed influenza in this season, compared to recent seasons. This is likely to be due to effective public health interventions and international border closures as a result of a rise in COVID-19 respiratory infections and associated hospitalisations.
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29
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Borsovszky M, Norton S, Bag SK, Kok J. Salmonella Paratyphi A infection: implications for public health management of extra-intestinal presentations – case study of a neck abscess. Commun Dis Intell (2018) 2021; 45. [DOI: 10.33321/cdi.2021.45.66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
This study explores the implications of unusual presentations of Salmonella enterica subsp. enterica ser. Paratyphi (S. Paratyphi) infection for public health management, through a literature review and case study. In 2016, a 36-year-old male presented with a five-day history of right sided painful neck swelling, coryza and a two-day history of fevers after arriving in Australia from India nine weeks earlier. S. Paratyphi A was isolated from a fine needle aspirate sample. A descriptive epidemiological review was performed of confirmed cases of S. Paratyphi notified in New South Wales between 2008 and 2017. S. Paratyphi was isolated in blood and/or faecal samples in 247 cases (98.4%). Only four specimens (1.6%) were from a focal site. A literature review of extraintestinal infections of S. Paratyphi A or B was performed. Of the 41 such cases reported, 16 (39%) had a clear history of a prior gastroenteritis and/or febrile illness, or information suggested this was highly likely. No preceding gastroenteritis or febrile illness occurred in 15 (37%) of the cases. Information was reviewed and presented with a public health lens, valuable for ‘evidence-informed’ public health risk assessment of contacts and exposures related to these types of S. Paratyphi infection. S. Paratyphi infection usually presents as an enteric fever illness. Our case illustrates the variable nature of infectious diseases and the importance of laboratory testing in obtaining a diagnosis. S. Paratyphi can have unusual presentations, which may require adjustment in the public health management of the case. Public health staff should keep an open mind when investigating possible sources and assessing risk. In Western Sydney, this disease is largely associated with residents travelling to high-incidence countries to visit family and friends, and receiving family visits from these countries. The increasing number of cases of S. Paratyphi (prior to COVID-19) in Western Sydney and the importance of awareness of the risk of enteric fever to travellers to endemic regions is highlighted.
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30
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Arnott A, Draper J, Rockett RJ, Lam C, Sadsad R, Gall M, Martinez E, Byun R, Musto J, Marais B, Chen SCA, Kok J, Dwyer DE, Sintchenko V. Documenting elimination of co-circulating COVID-19 clusters using genomics in New South Wales, Australia. BMC Res Notes 2021. [PMID: 34789337 DOI: 10.1186/s13104-021-05827-x4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
OBJECTIVE To adapt 'fishplots' to describe real-time evolution of SARS-CoV-2 genomic clusters. RESULTS This novel analysis adapted the fishplot to depict the size and duration of circulating genomic clusters over time in New South Wales, Australia. It illuminated the effectiveness of interventions on the emergence, spread and eventual elimination of clusters and distilled genomic data into clear information to inform public health action.
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Affiliation(s)
- Alicia Arnott
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Jenny Draper
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Rebecca J Rockett
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Connie Lam
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Rosemarie Sadsad
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia
- Sydney Informatics Hub, Core Research Facilities, The University of Sydney, Sydney, NSW, Australia
| | - Mailie Gall
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Roy Byun
- Health Protection New South Wales, NSW Ministry of Health, Sydney, NSW, Australia
| | - Jennie Musto
- Health Protection New South Wales, NSW Ministry of Health, Sydney, NSW, Australia
| | - Ben Marais
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
- Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Dominic E Dwyer
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia.
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia.
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia.
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31
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Arnott A, Draper J, Rockett RJ, Lam C, Sadsad R, Gall M, Martinez E, Byun R, Musto J, Marais B, Chen SCA, Kok J, Dwyer DE, Sintchenko V. Documenting elimination of co-circulating COVID-19 clusters using genomics in New South Wales, Australia. BMC Res Notes 2021; 14:415. [PMID: 34789337 PMCID: PMC8596089 DOI: 10.1186/s13104-021-05827-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
Objective To adapt ‘fishplots’ to describe real-time evolution of SARS-CoV-2 genomic clusters. Results This novel analysis adapted the fishplot to depict the size and duration of circulating genomic clusters over time in New South Wales, Australia. It illuminated the effectiveness of interventions on the emergence, spread and eventual elimination of clusters and distilled genomic data into clear information to inform public health action. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05827-x.
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Affiliation(s)
- Alicia Arnott
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia.,Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Jenny Draper
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Rebecca J Rockett
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Connie Lam
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Rosemarie Sadsad
- Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia.,Sydney Informatics Hub, Core Research Facilities, The University of Sydney, Sydney, NSW, Australia
| | - Mailie Gall
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Roy Byun
- Health Protection New South Wales, NSW Ministry of Health, Sydney, NSW, Australia
| | - Jennie Musto
- Health Protection New South Wales, NSW Ministry of Health, Sydney, NSW, Australia
| | - Ben Marais
- Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia.,Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia.,Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia.,Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Dominic E Dwyer
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia.,Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia. .,Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, NSW, Australia. .,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Sydney, NSW, Australia.
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32
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Kovoor JG, Scott DA, Beavis VS, Kok J, MacCormick AD, Padbury RT, Hugh TJ, Hewett PJ, Collinson TG, Frydenberg M. Proposed Delay for Safe Surgery after COVID-19. J Am Coll Surg 2021. [PMCID: PMC8531685 DOI: 10.1016/j.jamcollsurg.2021.07.209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Howard-Jones AR, Maddocks S, Basile K, Dwyer DE, Branley J, Kok J. Prolonged PCR positivity in elderly patients infected with SARS-CoV-2. Pathology 2021; 53:914-916. [PMID: 34635324 PMCID: PMC8457930 DOI: 10.1016/j.pathol.2021.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/12/2021] [Accepted: 08/20/2021] [Indexed: 11/23/2022]
Affiliation(s)
- Annaleise R Howard-Jones
- New South Wales Health Pathology - Nepean, Nepean Hospital, Kingswood, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia.
| | - Susan Maddocks
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - Kerri Basile
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - Dominic E Dwyer
- Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia; Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - James Branley
- New South Wales Health Pathology - Nepean, Nepean Hospital, Kingswood, NSW, Australia; Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Westmead Hospital, Westmead, NSW, Australia
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Robertson M, Eden JS, Levy A, Carter I, Tulloch RL, Cutmore EJ, Horsburgh BA, Sikazwe CT, Dwyer DE, Smith DW, Kok J. The spatial-temporal dynamics of respiratory syncytial virus infections across the east-west coasts of Australia during 2016-17. Virus Evol 2021; 7:veab068. [PMID: 34532066 PMCID: PMC8438877 DOI: 10.1093/ve/veab068] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 04/19/2021] [Accepted: 07/22/2021] [Indexed: 01/03/2023] Open
Abstract
Respiratory syncytial virus (RSV) is an important human respiratory pathogen. In temperate regions, a distinct seasonality is observed, where peaks of infections typically occur in early winter, often preceding the annual influenza season. Infections are associated with high rates of morbidity and mortality and in some populations exceed that of influenza. Two subtypes, RSV-A and RSV-B, have been described, and molecular epidemiological studies have shown that both viruses mostly co-circulate. This trend also appears to be the case for Australia; however, previous genomic studies have been limited to cases from one Eastern state—New South Wales. As such, the broader spatial patterns and viral traffic networks across the continent are not known. Here, we conducted a whole-genome study of RSV comparing strains across eastern and Western Australia during the period January 2016 to June 2017. In total, 96 new RSV genomes were sequenced, compiled with previously generated data, and examined using a phylodynamic approach. This analysis revealed that both RSV-A and RSV-B strains were circulating, and each subtype was dominated by a single genotype, RSV-A ON1-like and RSV-B BA10-like viruses. Some geographical clustering was evident in strains from both states with multiple distinct sub-lineages observed and relatively low mixing across jurisdictions, suggesting that endemic transmission was likely seeded from imported, unsampled locations. Overall, the RSV phylogenies reflected a complex pattern of interactions across multiple epidemiological scales from fluid virus traffic across global and regional networks to fine-scale local transmission events.
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Affiliation(s)
- Mark Robertson
- NSW Health Pathology-Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Redbank Road, Westmead Hospital, Westmead, NSW 2145, Australia
| | - John-Sebastian Eden
- Centre for Virus Research, Westmead Institute for Medical Research, 176 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - Avram Levy
- Department of Microbiology, PathWest Laboratory Medicine WA, Hospital Ave, Nedlands, WA 6009, Australia
| | - Ian Carter
- NSW Health Pathology-Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Redbank Road, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Rachel L Tulloch
- Centre for Virus Research, Westmead Institute for Medical Research, 176 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - Elena J Cutmore
- Centre for Virus Research, Westmead Institute for Medical Research, 176 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - Bethany A Horsburgh
- Centre for Virus Research, Westmead Institute for Medical Research, 176 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - Chisha T Sikazwe
- Department of Microbiology, PathWest Laboratory Medicine WA, Hospital Ave, Nedlands, WA 6009, Australia
| | - Dominic E Dwyer
- NSW Health Pathology-Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Redbank Road, Westmead Hospital, Westmead, NSW 2145, Australia
| | - David W Smith
- Department of Microbiology, PathWest Laboratory Medicine WA, Hospital Ave, Nedlands, WA 6009, Australia
| | - Jen Kok
- NSW Health Pathology-Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Redbank Road, Westmead Hospital, Westmead, NSW 2145, Australia
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35
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Tang JW, Bialasiewicz S, Dwyer DE, Dilcher M, Tellier R, Taylor J, Hua H, Jennings L, Kok J, Levy A, Smith D, Barr IG, Sullivan SG. Where have all the viruses gone? Disappearance of seasonal respiratory viruses during the COVID-19 pandemic. J Med Virol 2021; 93:4099-4101. [PMID: 33760278 PMCID: PMC8250511 DOI: 10.1002/jmv.26964] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 01/06/2023]
Affiliation(s)
- Julian W. Tang
- Department of Respiratory SciencesUniversity of LeicesterLeicesterUK
| | - Seweryn Bialasiewicz
- The University of QueenslandAustralian Centre for EcogenomicsBrisbaneAustralia
- Children's Health QueenslandCentre for Children's Health ResearchBrisbaneAustralia
| | - Dominic E. Dwyer
- NSWHP‐Institute of Clinical Pathology and Medical ResearchWestmead HospitalWestmeadAustralia
| | - Meik Dilcher
- Canterbury Health LaboratoriesChristchurchNew Zealand
| | | | - Janette Taylor
- NSWHP‐Institute of Clinical Pathology and Medical ResearchWestmead HospitalWestmeadAustralia
| | - Harry Hua
- Canterbury Health LaboratoriesChristchurchNew Zealand
| | | | - Jen Kok
- NSWHP‐Institute of Clinical Pathology and Medical ResearchWestmead HospitalWestmeadAustralia
| | - Avram Levy
- Department of MicrobiologyPathwest Laboratory MedicineNedlandsAustralia
| | - David Smith
- Department of MicrobiologyPathwest Laboratory MedicineNedlandsAustralia
| | - Ian G. Barr
- World Health Organization Collaborating Centre for Reference and Research on InfluenzaMelbourneAustralia
| | - Sheena G. Sullivan
- World Health Organization Collaborating Centre for Reference and Research on InfluenzaMelbourneAustralia
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36
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Seth-Smith HMB, Bénard A, Bruisten SM, Versteeg B, Herrmann B, Kok J, Carter I, Peuchant O, Bébéar C, Lewis DA, Puerta T, Keše D, Balla E, Zákoucká H, Rob F, Morré SA, de Barbeyrac B, Galán JC, de Vries HJC, Thomson NR, Goldenberger D, Egli A. Ongoing evolution of Chlamydia trachomatis lymphogranuloma venereum: exploring the genomic diversity of circulating strains. Microb Genom 2021; 7. [PMID: 34184981 PMCID: PMC8461462 DOI: 10.1099/mgen.0.000599] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lymphogranuloma venereum (LGV), the invasive infection of the sexually transmissible infection (STI) Chlamydia trachomatis, is caused by strains from the LGV biovar, most commonly represented by ompA-genotypes L2b and L2. We investigated the diversity in LGV samples across an international collection over seven years using typing and genome sequencing. LGV-positive samples (n=321) from eight countries collected between 2011 and 2017 (Spain n=97, Netherlands n=67, Switzerland n=64, Australia n=53, Sweden n=37, Hungary n=31, Czechia n=30, Slovenia n=10) were genotyped for pmpH and ompA variants. All were found to contain the 9 bp insertion in the pmpH gene, previously associated with ompA-genotype L2b. However, analysis of the ompA gene shows ompA-genotype L2b (n=83), ompA-genotype L2 (n=180) and several variants of these (n=52; 12 variant types), as well as other/mixed ompA-genotypes (n=6). To elucidate the genomic diversity, whole genome sequencing (WGS) was performed from selected samples using SureSelect target enrichment, resulting in 42 genomes, covering a diversity of ompA-genotypes and representing most of the countries sampled. A phylogeny of these data clearly shows that these ompA-genotypes derive from an ompA-genotype L2b ancestor, carrying up to eight SNPs per isolate. SNPs within ompA are overrepresented among genomic changes in these samples, each of which results in an amino acid change in the variable domains of OmpA (major outer membrane protein, MOMP). A reversion to ompA-genotype L2 with the L2b genomic backbone is commonly seen. The wide diversity of ompA-genotypes found in these recent LGV samples indicates that this gene is under immunological selection. Our results suggest that the ompA-genotype L2b genomic backbone is the dominant strain circulating and evolving particularly in men who have sex with men (MSM) populations.
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Affiliation(s)
- Helena M B Seth-Smith
- Clinical Bacteriology & Mycology, University Hospital Basel, University of Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Angèle Bénard
- Present address: Healthcare Systems Research Group, VHIR, Universitat Autònoma de Barcelona, Passeig de la Vall d'Hebron 119-129, 08035 Barcelona, Spain.,Wellcome Trust Sanger Institute, Cambridge, UK
| | - Sylvia M Bruisten
- Department of Infectious Diseases, GGD Public Health Service of Amsterdam, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity (AII), Location Academic Medical Centre, Amsterdam, The Netherlands
| | - Bart Versteeg
- Department of Infectious Diseases, GGD Public Health Service of Amsterdam, Amsterdam, The Netherlands.,Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Björn Herrmann
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity & Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Ian Carter
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Olivia Peuchant
- CHU Bordeaux, Department of Bacteriology, French National Reference Center for bacterial STIs, Bordeaux, France
| | - Cécile Bébéar
- CHU Bordeaux, Department of Bacteriology, French National Reference Center for bacterial STIs, Bordeaux, France
| | - David A Lewis
- Western Sydney Sexual Health Centre, Western Sydney Local Health District, Parramatta, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity & Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Teresa Puerta
- Unidad de ITS/VIH, Centro Sanitario Sandoval, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Darja Keše
- University of Ljubljana, Faculty of Medicine, Institute of Microbiology and Immunology, Ljubljana, Slovenia
| | - Eszter Balla
- Bacterial STI Reference Laboratory, National Public Health Center (former National Center for Epidemiology), Budapest, Hungary
| | - Hana Zákoucká
- National Reference Laboratory for Diagnostics of Syphilis and Chlamydia Infections, National Institute of Public Health, Srobarova 48, 100 42, Prague 10, Czech Republic
| | - Filip Rob
- Department of Dermatovenereology, Second Faculty of Medicine, Charles University and Hospital Bulovka, Budinova 2, 180 81, Prague 8, Czech Republic
| | - Servaas A Morré
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center Amsterdam, Amsterdam, The Netherlands.,Institute for Public Health Genomics (IPHG), Department of Genetics and Cell Biology, Research Institute GROW, University of Maastricht, Maastricht, The Netherlands
| | - Bertille de Barbeyrac
- CHU Bordeaux, Department of Bacteriology, French National Reference Center for bacterial STIs, Bordeaux, France
| | - Juan Carlos Galán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal. Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain. CIBER en Epidemiología y Salud Pública (CIBERESP)
| | - Henry J C de Vries
- Department of Infectious Diseases, GGD Public Health Service of Amsterdam, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity (AII), Location Academic Medical Centre, Amsterdam, The Netherlands
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Cambridge, UK.,Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Daniel Goldenberger
- Clinical Bacteriology & Mycology, University Hospital Basel, University of Basel, Switzerland
| | - Adrian Egli
- Clinical Bacteriology & Mycology, University Hospital Basel, University of Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
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37
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Yong MK, Gottlieb D, Lindsay J, Kok J, Rawlinson W, Slavin M, Ritchie D, Bajel A, Grigg A. New advances in the management of cytomegalovirus in allogeneic haemopoietic stem cell transplantation. Intern Med J 2021; 50:277-284. [PMID: 31403736 DOI: 10.1111/imj.14462] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 08/06/2019] [Accepted: 08/06/2019] [Indexed: 12/11/2022]
Abstract
Cytomegalovirus (CMV) viraemia continues to be a frequent complication in the post-haemopoietic stem cell transplantation period despite a low incidence of CMV end-organ disease. Several significant advances in the understanding and management of CMV infection have occurred in the last few years including improved diagnostics, monitoring of CMV immunity, availability of novel anti-CMV drugs, and emerging use of immunotherapies including CMV-specific T-cell infusions. In addition to reviewing these advances we also explore some of the more practical prescribing issues of the older and newer CMV drugs including cost, toxicity and drug interactions to help clinicians navigate this new era of CMV management.
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Affiliation(s)
- Michelle K Yong
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia.,National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - David Gottlieb
- Department of Haematology and Bone Marrow Transplantation, Westmead Hospital, Sydney, New South Wales, Australia.,Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia.,Sydney Cellular Therapies Laboratory, Westmead Hospital, Sydney, New South Wales, Australia
| | - Julian Lindsay
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Pharmacy Department, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Sydney, New South Wales, Australia
| | - William Rawlinson
- NSW Health Pathology, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Monica Slavin
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia.,National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - David Ritchie
- Department of Clinical Haematology, Peter MacCallum Cancer Centre, Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Ashish Bajel
- Department of Clinical Haematology, Peter MacCallum Cancer Centre, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Andrew Grigg
- National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Clinical Haematology and Olivia Newton John Cancer Research Institute, Austin Hospital, Melbourne, Victoria, Australia
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38
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Kovoor JG, Scott NA, Tivey DR, Babidge WJ, Scott DA, Beavis VS, Kok J, MacCormick AD, Padbury RTA, Hugh TJ, Hewett PJ, Collinson TG, Maddern GJ, Frydenberg M. Proposed delay for safe surgery after COVID-19. ANZ J Surg 2021; 91:495-506. [PMID: 33656269 PMCID: PMC8014540 DOI: 10.1111/ans.16682] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND Long-term effects after COVID-19 may affect surgical safety. This study aimed to evaluate the literature and produce evidence-based guidance regarding the period of delay necessary for adequate recovery of patients following COVID-19 infection before undergoing surgery. METHODS A rapid review was combined with advice from a working group of 10 clinical experts across Australia and New Zealand. MEDLINE, medRxiv and grey literature were searched to 4 October 2020. The level of evidence was stratified according to the National Health and Medical Research Council evidence hierarchy. RESULTS A total of 1020 records were identified, from which 20 studies (12 peer-reviewed) were included. None were randomized trials. The studies comprised one case-control study (level III-2 evidence), one prospective cohort study (level III-2) and 18 case-series studies (level IV). Follow-up periods containing observable clinical characteristics ranged from 3 to 16 weeks. New or excessive fatigue and breathlessness were the most frequently reported symptoms. SARS-CoV-2 may impact the immune system for multiple months after laboratory confirmation of infection. For patients with past COVID-19 undergoing elective curative surgery for cancer, risks of pulmonary complications and mortality may be lowest at 4 weeks or later after a positive swab. CONCLUSION After laboratory confirmation of SARS-CoV-2 infection, minor surgery should be delayed for at least 4 weeks and major surgery for 8-12 weeks, if patient outcome is not compromised. Comprehensive preoperative and ongoing assessment must be carried out to ensure optimal clinical decision-making.
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Affiliation(s)
- Joshua G. Kovoor
- University of AdelaideAdelaideSouth AustraliaAustralia
- Australian Safety and Efficacy Register of New Interventional Procedures–SurgicalRoyal Australasian College of SurgeonsAdelaideSouth AustraliaAustralia
| | - N. Ann Scott
- Australian Safety and Efficacy Register of New Interventional Procedures–SurgicalRoyal Australasian College of SurgeonsAdelaideSouth AustraliaAustralia
| | - David R. Tivey
- Research Audit and Academic SurgeryRoyal Australasian College of SurgeonsAdelaideSouth AustraliaAustralia
- University of Adelaide, Discipline of SurgeryThe Queen Elizabeth HospitalAdelaideSouth AustraliaAustralia
| | - Wendy J. Babidge
- Research Audit and Academic SurgeryRoyal Australasian College of SurgeonsAdelaideSouth AustraliaAustralia
- University of Adelaide, Discipline of SurgeryThe Queen Elizabeth HospitalAdelaideSouth AustraliaAustralia
| | - David A. Scott
- Department of Anaesthesia and Acute Pain MedicineSt. Vincent's HospitalMelbourneVictoriaAustralia
- Anaesthesia Perioperative and Pain Medicine Unit, Melbourne Medical SchoolUniversity of MelbourneMelbourneVictoriaAustralia
| | - Vanessa S. Beavis
- Anaesthesia and Operating RoomsAuckland City HospitalAucklandNew Zealand
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory ServicesNSW Health Pathology – Institute of Clinical Pathology and Medical Research, Westmead HospitalWestmeadNew South WalesAustralia
| | - Andrew D. MacCormick
- Department of Surgery, South Auckland Clinical SchoolUniversity of AucklandAucklandNew Zealand
- Department of SurgeryCounties Manukau District Health BoardAucklandNew Zealand
| | - Robert T. A. Padbury
- Flinders UniversityAdelaideSouth AustraliaAustralia
- Division of Surgery and Perioperative MedicineFlinders Medical CentreAdelaideSouth AustraliaAustralia
| | - Thomas J. Hugh
- Northern Clinical SchoolUniversity of SydneySydneyNew South WalesAustralia
- Surgical EducationResearch and Training Institute, Royal North Shore HospitalSydneyNew South WalesAustralia
| | - Peter J. Hewett
- University of Adelaide, Discipline of SurgeryThe Queen Elizabeth HospitalAdelaideSouth AustraliaAustralia
| | | | - Guy J. Maddern
- Research Audit and Academic SurgeryRoyal Australasian College of SurgeonsAdelaideSouth AustraliaAustralia
- University of Adelaide, Discipline of SurgeryThe Queen Elizabeth HospitalAdelaideSouth AustraliaAustralia
| | - Mark Frydenberg
- Department of UrologyCabrini Institute, Cabrini HealthMelbourneVictoriaAustralia
- Department of Surgery, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
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39
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Shaban RZ, Li C, O'Sullivan MVN, Gerrard J, Stuart RL, Teh J, Gilroy N, Sorrell TC, White E, Bag S, Hackett K, Chen SCA, Kok J, Dwyer DE, Iredell JR, Maddocks S, Ferguson P, Varshney K, Carter I, Barratt R, Robertson M, Baskar SR, Friend C, Robosa RS, Sotomayor-Castillo C, Nahidi S, Macbeth DA, Alcorn KAD, Wattiaux A, Moore F, McMahon J, Naughton W, Korman TM, Catton M, Kanapathipillai R, Romanes F, Rowe E, Catford J, Kennedy B, Qiao M, Shaw D. COVID-19 in Australia: our national response to the first cases of SARS-CoV-2 infection during the early biocontainment phase. Intern Med J 2021; 51:42-51. [PMID: 33196128 PMCID: PMC7753759 DOI: 10.1111/imj.15105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND On 31 December 2019, the World Health Organization recognised clusters of pneumonia-like cases due to a novel coronavirus disease (COVID-19). COVID-19 became a pandemic 71 days later. AIM To report the clinical and epidemiological features, laboratory data and outcomes of the first group of 11 returned travellers with COVID-19 in Australia. METHODS This is a retrospective, multi-centre case series. All patients with confirmed COVID-19 infection were admitted to tertiary referral hospitals in New South Wales, Queensland, Victoria and South Australia. RESULTS The median age of the patient cohort was 42 years (interquartile range (IQR), 24-53 years) with six men and five women. Eight (72.7%) patients had returned from Wuhan, one from Shenzhen, one from Japan and one from Europe. Possible human-to-human transmission from close family contacts in gatherings overseas occurred in two cases. Symptoms on admission were fever, cough and sore throat (n = 9, 81.8%). Co-morbidities included hypertension (n = 3, 27.3%) and hypercholesterolaemia (n = 2, 18.2%). No patients developed severe acute respiratory distress nor required intensive care unit admission or mechanical ventilation. After a median hospital stay of 14.5 days (IQR, 6.75-21), all patients were discharged. CONCLUSIONS This is a historical record of the first COVID-19 cases in Australia during the early biocontainment phase of the national response. These findings were invaluable for establishing early inpatient and outpatient COVID-19 models of care and informing the management of COVID-19 over time as the outbreak evolved. Future research should extend this Australian case series to examine global epidemiological variation of this novel infection.
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Affiliation(s)
- Ramon Z Shaban
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Infectious Diseases and Sexual Health Services, Westmead Hospital, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia.,Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
| | - Cecilia Li
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Matthew V N O'Sullivan
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, New South Wales, Australia
| | - John Gerrard
- Department of Infectious Diseases and Immunology, Gold Coast University Hospital, Gold Coast, Queensland, Australia
| | - Rhonda L Stuart
- Monash Infectious Diseases, Monash Health, Melbourne, Victoria, Australia.,Centre for Inflammatory Diseases, Department of Medicine, Monash University, Melbourne, Victoria, Australia
| | - Joanne Teh
- Infectious Diseases Unit, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Nicole Gilroy
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, New South Wales, Australia
| | - Tania C Sorrell
- Infectious Diseases and Sexual Health Services, Westmead Hospital, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia
| | - Elizabeth White
- Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
| | - Shopna Bag
- Centre for Population Health, Western Sydney Public Health Unit, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, Westmead Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Kate Hackett
- Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
| | - Sharon C A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia
| | - Dominic E Dwyer
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia
| | - Jonathan R Iredell
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Susan Maddocks
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, New South Wales, Australia
| | - Patricia Ferguson
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, New South Wales, Australia
| | - Kavita Varshney
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Emergency Department Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
| | - Ian Carter
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, New South Wales, Australia
| | - Ruth Barratt
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Infectious Diseases and Sexual Health Services, Westmead Hospital, Sydney, New South Wales, Australia
| | - Mark Robertson
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, New South Wales, Australia.,Department of Microbiology and Infectious Diseases, NSW Health Pathology, Gosford Hospital, Central Coast, New South Wales, Australia
| | - Sai R Baskar
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, New South Wales, Australia.,Department of Microbiology and Infectious Diseases, NSW Health Pathology, Concord Repatriation General Hospital, Sydney, New South Wales, Australia
| | - Caren Friend
- Counter Disaster Unit, Western Sydney Local Health District, Sydney, New South Wales, Australia
| | - Roselle S Robosa
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, New South Wales Health Pathology, Westmead Hospital, Sydney, New South Wales, Australia
| | | | - Shizar Nahidi
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Deborough A Macbeth
- Department of Infectious Diseases and Immunology, Gold Coast University Hospital, Gold Coast, Queensland, Australia
| | - Kylie A D Alcorn
- Department of Infectious Diseases and Immunology, Gold Coast University Hospital, Gold Coast, Queensland, Australia
| | - Andre Wattiaux
- Gold Coast Public Health Unit, Gold Coast, Queensland, Australia
| | - Frederick Moore
- Public Health Virology Laboratory, Forensic and Scientific Services, Brisbane, Queensland, Australia
| | - Jamie McMahon
- Public Health Virology Laboratory, Forensic and Scientific Services, Brisbane, Queensland, Australia.,Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - William Naughton
- Monash Infectious Diseases, Monash Health, Melbourne, Victoria, Australia
| | - Tony M Korman
- Monash Infectious Diseases, Monash Health, Melbourne, Victoria, Australia.,Centre for Inflammatory Diseases, Department of Medicine, Monash University, Melbourne, Victoria, Australia
| | - Mike Catton
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, Peter Doherty Institute for Infections and Immunity, Melbourne, Victoria, Australia
| | | | - Finn Romanes
- Department of Health and Human Services, State Government Victoria, Melbourne, Victoria, Australia
| | - Emily Rowe
- Infectious Diseases Unit, Royal Adelaide Hospital, Adelaide, South Australia, Australia.,Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Jennifer Catford
- Infectious Diseases Unit, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Brendan Kennedy
- Infectious Diseases Unit, Royal Adelaide Hospital, Adelaide, South Australia, Australia.,Communicable Disease Control Branch, SA Health, Adelaide, South Australia, Australia
| | - Ming Qiao
- Directorate of Microbiology and Infectious Diseases, South Australia Pathology, Adelaide, South Australia, Australia
| | - David Shaw
- Infectious Diseases Unit, Royal Adelaide Hospital, Adelaide, South Australia, Australia
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Shaban RZ, Li C, O'Sullivan MVN, Kok J, Dempsey K, Ramsperger M, Brown M, Nahidi S, Sotomayor-Castillo C. Outbreak of community-acquired Staphylococcus aureus skin infections in an Australian professional football team. J Sci Med Sport 2020; 24:520-525. [PMID: 33303369 DOI: 10.1016/j.jsams.2020.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/14/2020] [Accepted: 11/08/2020] [Indexed: 10/23/2022]
Abstract
OBJECTIVES Skin and soft tissue infections commonly affect athletes and can lead to cluster outbreaks if not managed appropriately. We report the findings of an investigation into an outbreak of community-acquired Staphylococcus aureus infection in an Australian professional football team. DESIGN Retrospective cross-sectional study. METHODS Nose, axilla, groin and throat swab were collected from 47 participants. MRSA and MSSA isolates underwent antibiotic susceptibility testing, binary typing and whole genome sequencing. Infection control practitioners (ICPs) investigated the training grounds for risk factors in the transmission of S. aureus. RESULTS Almost half of the participants (n=23, 48.9%) were found to be colonised with MSSA. An outbreak cluster of MRSA ST5 closely related to the fusidic acid-resistant New Zealand NZAK3 clone was identified in a group of four players. MSSA ST15 and MSSA ST291 strains were found to have colonised and spread between two and five players, respectively. All participants were advised to undergo decolonisation treatment consisting of 4% chlorhexidine body wash and mupirocin nasal ointment for ten days. The ICP team identified several unhygienic practices within the club's shared facilities that may have played a role in the transmission of S. aureus. CONCLUSIONS We report for the first time a community-associated S. aureus outbreak involving the highly successful fusidic acid-resistant MRSA ST5 clone in a professional football club associated with inadequate hygiene procedures. Management and prevention of S. aureus relies heavily on hygiene education and adherence to personal and environmental hygiene practices and policies.
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Affiliation(s)
- Ramon Z Shaban
- Susan Wakil School of Nursing and Midwifery, Faculty of Medicine and Health, The University of Sydney, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Australia; New South Wales Biocontainment Centre and the Department of Infection Prevention and Control, Division of Infectious Diseases and Biosecurity, Westmead Hospital and Western Sydney Local Health District, Australia.
| | - Cecilia Li
- Susan Wakil School of Nursing and Midwifery, Faculty of Medicine and Health, The University of Sydney, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Australia
| | - Matthew V N O'Sullivan
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Australia; Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Australia
| | - Kathy Dempsey
- Clinical Excellence Commission, NSW Health, Australia
| | - Marc Ramsperger
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Australia
| | - Mitchell Brown
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Australia
| | - Shizar Nahidi
- Susan Wakil School of Nursing and Midwifery, Faculty of Medicine and Health, The University of Sydney, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Australia
| | - Cristina Sotomayor-Castillo
- Susan Wakil School of Nursing and Midwifery, Faculty of Medicine and Health, The University of Sydney, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Australia
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Sullivan SG, Carlson S, Cheng AC, Chilver MB, Dwyer DE, Irwin M, Kok J, Macartney K, MacLachlan J, Minney-Smith C, Smith D, Stocks N, Taylor J, Barr IG. Where has all the influenza gone? The impact of COVID-19 on the circulation of influenza and other respiratory viruses, Australia, March to September 2020. Euro Surveill 2020; 25:2001847. [PMID: 33243355 PMCID: PMC7693168 DOI: 10.2807/1560-7917.es.2020.25.47.2001847] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
The coronavirus disease pandemic was declared in March 2020, as the southern hemisphere's winter approached. Australia expected co-circulation of severe acute respiratory syndrome coronavirus 2, influenza and other seasonal respiratory viruses. However, influenza notifications were 7,029 (March-September) compared with an average 149,832 for the same period in 2015-2019 [corrected], despite substantial testing. Restrictions on movement within and into Australia may have temporarily eliminated influenza. Other respiratory pathogens also showed remarkably changed activity in 2020.
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Affiliation(s)
- Sheena G Sullivan
- 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
| | - Sandra Carlson
- FluTracking, Hunter New England Population Health, Newcastle, Australia
| | - Allen C Cheng
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
- Department of Infectious Diseases, Alfred Health, and Central Clinical School, Monash University, Melbourne, Australia
| | - Monique Bn Chilver
- Discipline of General Practice, University of Adelaide, Adelaide, Australia
| | - Dominic E Dwyer
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Australia
| | - Melissa Irwin
- Rapid Surveillance, Centre for Epidemiology and Evidence, NSW Ministry of Health, Sydney, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Australia
| | - Kristine Macartney
- National Centre for Immunisation Research and Surveillance and The Children's Hospital Westmead, Sydney, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Jennifer MacLachlan
- WHO Collaborating Centre for Viral Hepatitis, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | | | - David Smith
- PathWest Laboratory Medicine WA, Nedlands, Australia
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, Australia
| | - Nigel Stocks
- Discipline of General Practice, University of Adelaide, Adelaide, Australia
| | - Janette Taylor
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, and Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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42
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Basile K, McPhie K, Carter I, Alderson S, Rahman H, Donovan L, Kumar S, Tran T, Ko D, Sivaruban T, Ngo C, Toi C, O'Sullivan MV, Sintchenko V, Chen SCA, Maddocks S, Dwyer DE, Kok J. Cell-based culture of SARS-CoV-2 informs infectivity and safe de-isolation assessments during COVID-19. Clin Infect Dis 2020; 73:e2952-e2959. [PMID: 33098412 PMCID: PMC7665383 DOI: 10.1093/cid/ciaa1579] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Indexed: 12/23/2022] Open
Abstract
Background The detection of SARS-CoV-2 RNA by real-time polymerase chain reaction (PCR) in respiratory samples collected from persons recovered from COVID-19 does not necessarily indicate shedding of infective virions. By contrast, the isolation of SARS-CoV-2 using cell-based culture likely indicates infectivity, but there are limited data on the correlation between SARS-CoV-2 culture and PCR. Methods One hundred and ninety-five patients with varying severity of COVID-19 were tested (outpatients [n=178]), inpatients [n=12] and critically unwell patients admitted to the intensive care unit [ICU; n=5]). SARS-CoV-2 PCR positive samples were cultured in Vero C1008 cells and inspected daily for cytopathic effect (CPE). SARS-CoV-2-induced CPE was confirmed by PCR of culture supernatant. Where no CPE was observed, PCR was performed on day four to confirm absence of virus replication. Cycle threshold (Ct) of the day four PCR (Ctculture) and the PCR of the original clinical sample (Ctsample) were compared, and positive cultures were defined where Ctsample - Ctculture was ≥3. Findings Of 234 samples collected, 228 (97%) were from the upper respiratory tract. SARS-CoV-2 was only successfully isolated from samples with Ctsample ≤32, including in 28/181 (15%), 19/42 (45%) and 9/11 samples (82%) collected from outpatients, inpatients, and ICU patients, respectively. The mean duration from symptom onset to culture positivity was 4.5 days (range 0-18). SARS-CoV-2 was significantly more likely to be isolated from samples collected from inpatients (p<0∙001) and ICU patients (p<0∙0001) compared with outpatients respectively, and in samples with lower Ctsample. Conclusion SARS-CoV-2 culture may be used as a surrogate marker for infectivity and inform de-isolation protocols.
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Affiliation(s)
- Kerri Basile
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead NSW, Australia
| | - Kenneth McPhie
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead NSW, Australia.,Westmead Institute for Medical Research, Westmead NSW, Australia
| | - Ian Carter
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead NSW, Australia
| | - Susan Alderson
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead NSW, Australia
| | - Hossinur Rahman
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead NSW, Australia
| | - Linda Donovan
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead NSW, Australia
| | - Shanil Kumar
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead NSW, Australia
| | - Tyna Tran
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead NSW, Australia
| | - Danny Ko
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead NSW, Australia
| | - Tharshini Sivaruban
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead NSW, Australia
| | - Christine Ngo
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead NSW, Australia
| | - Cheryl Toi
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead NSW, Australia
| | - Matthew V O'Sullivan
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead NSW, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead NSW, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney NSW, Australia
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead NSW, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney NSW, Australia
| | - Susan Maddocks
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead NSW, Australia
| | - Dominic E Dwyer
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead NSW, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney NSW, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead NSW, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney NSW, Australia
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Alfelali M, Haworth EA, Barasheed O, Badahdah AM, Bokhary H, Tashani M, Azeem MI, Kok J, Taylor J, Barnes EH, El Bashir H, Khandaker G, Holmes EC, Dwyer DE, Heron LG, Wilson GJ, Booy R, Rashid H. Facemask against viral respiratory infections among Hajj pilgrims: A challenging cluster-randomized trial. PLoS One 2020; 15:e0240287. [PMID: 33048964 PMCID: PMC7553311 DOI: 10.1371/journal.pone.0240287] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/24/2020] [Indexed: 12/24/2022] Open
Abstract
Background In this large-scale cluster-randomized controlled trial (cRCT) we sought to assess the effectiveness of facemasks against viral respiratory infections. Methods and results Over three consecutive Hajj seasons (2013, 2014, 2015) pilgrims’ tents in Makkah were allocated to ‘facemask’ or ‘no facemask’ group. Fifty facemasks were offered to participants in intervention tents, to be worn over four days, and none were offered to participants in control tents. All participants recorded facemask use and respiratory symptoms in health diaries. Nasal swabs were collected from the symptomatic for virus detection by reverse transcription polymerase chain reaction. Clinical symptoms and laboratory results were analyzed by ‘intention- to-treat’ and ‘per-protocol’. A total of 7687 adult participants from 318 tents were randomized: 3864 from 149 tents to the intervention group, and 3823 from 169 tents to the control group. Participants were aged 18 to 95 (median 34, mean 37) years, with a male to female ratio of 1:1.2. Overall, respiratory viruses were detected in 277 of 650 (43%) nasal/pharyngeal swabs collected from symptomatic pilgrims. Common viruses were rhinovirus (35.1%), influenza (4.5%) and parainfluenza (1.7%). In the intervention arm, respectively 954 (24.7%) and 1842 (47.7%) participants used facemasks daily and intermittently, while in the control arm, respectively 546 (14.3%) and 1334 (34.9%) used facemasks daily and intermittently. By intention-to-treat analysis, facemask use did not seem to be effective against laboratory-confirmed viral respiratory infections (odds ratio [OR], 1.4; 95% confidence interval [CI], 0.9 to 2.1, p = 0.18) nor against clinical respiratory infection (OR, 1.1; 95% CI, 0.9 to 1.4, p = 0.40). Similarly, in a per-protocol analysis, facemask use did not seem to be effective against laboratory-confirmed viral respiratory infections (OR 1.2, 95% CI 0.9–1.7, p = 0.26) nor against clinical respiratory infection (OR 1.3, 95% CI 1.0–1.8, p = 0.06). Conclusion This trial was unable to provide conclusive evidence on facemask efficacy against viral respiratory infections most likely due to poor adherence to protocol.
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Affiliation(s)
- Mohammad Alfelali
- National Centre for Immunisation Research and Surveillance, The Children’s Hospital at Westmead and The University of Sydney, Sydney, New South Wales, Australia
- Department of Family and Community Medicine, Faculty of Medicine in Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Osamah Barasheed
- National Centre for Immunisation Research and Surveillance, The Children’s Hospital at Westmead and The University of Sydney, Sydney, New South Wales, Australia
- Research Center, King Abdullah Medical City, Mecca, Saudi Arabia
| | - Al-Mamoon Badahdah
- National Centre for Immunisation Research and Surveillance, The Children’s Hospital at Westmead and The University of Sydney, Sydney, New South Wales, Australia
- Department of Family and Community Medicine, Faculty of Medicine in Rabigh, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hamid Bokhary
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Umm Al-Qura University, Mecca, Saudi Arabia
| | - Mohamed Tashani
- Discipline of Child and Adolescent Health, The Children’s Hospital at Westmead Clinical School, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine, The University of Tripoli, Ain Zara, Tripoli, Libya
| | - Mohammad I. Azeem
- National Centre for Immunisation Research and Surveillance, The Children’s Hospital at Westmead and The University of Sydney, Sydney, New South Wales, Australia
| | - Jen Kok
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
- NSW Health Pathology - Institute for Clinical Pathology and Medical Research, Westmead Hospital and The University of Sydney, Sydney, New South Wales, Australia
| | - Janette Taylor
- NSW Health Pathology - Institute for Clinical Pathology and Medical Research, Westmead Hospital and The University of Sydney, Sydney, New South Wales, Australia
| | - Elizabeth H. Barnes
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Haitham El Bashir
- Rehabilitation Department, Al Jalila Children Specialty Hospital, Dubai, United Arab Emirates
| | - Gulam Khandaker
- Discipline of Child and Adolescent Health, The Children’s Hospital at Westmead Clinical School, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Central Queensland Public Health Unit, Central Queensland Hospital and Health Service, Rockhampton, Queensland, Australia
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Dominic E. Dwyer
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
- NSW Health Pathology - Institute for Clinical Pathology and Medical Research, Westmead Hospital and The University of Sydney, Sydney, New South Wales, Australia
| | - Leon G. Heron
- National Centre for Immunisation Research and Surveillance, The Children’s Hospital at Westmead and The University of Sydney, Sydney, New South Wales, Australia
| | - Godwin J. Wilson
- Department of Laboratory Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Robert Booy
- National Centre for Immunisation Research and Surveillance, The Children’s Hospital at Westmead and The University of Sydney, Sydney, New South Wales, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Harunor Rashid
- National Centre for Immunisation Research and Surveillance, The Children’s Hospital at Westmead and The University of Sydney, Sydney, New South Wales, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
- * E-mail:
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Gulholm T, Basile K, Kok J, Chen SCA, Rawlinson W. Laboratory diagnosis of severe acute respiratory syndrome coronavirus 2. Pathology 2020; 52:745-753. [PMID: 33131799 PMCID: PMC7543760 DOI: 10.1016/j.pathol.2020.09.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 12/20/2022]
Abstract
The first laboratory confirmed case of Coronavirus disease 2019 (COVID-19) in Australia was in Victoria on 25 January 2020 in a man returning from Wuhan city, Hubei province, the People's Republic of China. This was followed by three cases in New South Wales the following day. The Australian Government activated the Australian Health Sector Emergency Response Plan for Novel Coronavirus on 27 February 2020 in anticipation of a pandemic. Subsequently, the World Health Organization declared COVID-19 to be a Public Health Emergency of International Concern followed by a pandemic on 30 January 2020 and 11 March 2020, respectively. Laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, is key in identifying infected persons to guide timely public health actions of contact tracing and patient isolation to limit transmission of infection. This article aims to provide a comprehensive overview of current laboratory diagnostic methods for SARS-CoV-2, including nucleic acid testing, serology, rapid antigen detection and antibody tests, virus isolation and whole genome sequencing. The relative advantages and disadvantages of the different diagnostic tests are presented, as well as their value in different clinical, infection control and public health contexts. We also describe the challenges in the provision of SARS-CoV-2 diagnostics in Australia, a country with a relatively low COVID-19 incidence in the first pandemic wave but in which prevalence could rapidly change.
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Affiliation(s)
- T Gulholm
- Department of Infectious Diseases, Prince of Wales Hospital, Randwick, NSW, Australia.
| | - K Basile
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - J Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW, Australia
| | - S C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney Westmead Hospital, Westmead, NSW, Australia
| | - W Rawlinson
- NSW Health Pathology, Serology and Virology Division, Prince of Wales Hospital, Randwick, NSW, Australia; Virology Research Laboratory, Prince of Wales Hospital, University of New South Wales, Randwick, NSW, Australia; School of Medical Sciences and School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Kensington, NSW, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Kensington, NSW, Australia
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45
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Basile K, Maddocks S, Kok J, Dwyer DE. Accuracy amidst ambiguity: false positive SARS-CoV-2 nucleic acid tests when COVID-19 prevalence is low. Pathology 2020; 52:809-811. [PMID: 33087255 PMCID: PMC7524665 DOI: 10.1016/j.pathol.2020.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 01/03/2023]
Affiliation(s)
- K Basile
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia.
| | - S Maddocks
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - J Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - D E Dwyer
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
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Kovoor JG, Tivey DR, Williamson P, Tan L, Kopunic HS, Babidge WJ, Collinson TG, Hewett PJ, Hugh TJ, Padbury RTA, Frydenberg M, Douglas RG, Kok J, Maddern GJ. Screening and testing for COVID-19 before surgery. ANZ J Surg 2020; 90:1845-1856. [PMID: 32770653 PMCID: PMC7436563 DOI: 10.1111/ans.16260] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 07/29/2020] [Accepted: 08/04/2020] [Indexed: 02/06/2023]
Abstract
Background Preoperative screening for coronavirus disease 2019 (COVID‐19) aims to preserve surgical safety for both patients and surgical teams. This rapid review provides an evaluation of current evidence with input from clinical experts to produce guidance for screening for active COVID‐19 in a low prevalence setting. Methods An initial search of PubMed (until 6 May 2020) was combined with targeted searches of both PubMed and Google Scholar until 1 July 2020. Findings were streamlined for clinical relevance through the advice of an expert working group that included seven senior surgeons and a senior medical virologist. Results Patient history should be examined for potential exposure to severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). Hyposmia and hypogeusia may present as early symptoms of COVID‐19, and can potentially discriminate from other influenza‐like illnesses. Reverse transcription‐polymerase chain reaction is the gold standard diagnostic test to confirm SARS‐CoV‐2 infection, and although sensitivity can be improved with repeated testing, the decision to retest should incorporate clinical history and the local supply of diagnostic resources. At present, routine serological testing has little utility for diagnosing acute infection. To appropriately conduct preoperative testing, the temporal dynamics of SARS‐CoV‐2 must be considered. Relative to other thoracic imaging modalities, computed tomography has the greatest utility for characterizing pulmonary involvement in COVID‐19 patients who have been diagnosed by reverse transcription‐polymerase chain reaction. Conclusion Through a rapid review of the literature and advice from a clinical expert working group, evidence‐based recommendations have been produced for the preoperative screening of surgical patients with suspected COVID‐19.
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Affiliation(s)
- Joshua G Kovoor
- University of Adelaide, Adelaide, South Australia, Australia
| | - David R Tivey
- Research Audit and Academic Surgery, Royal Australasian College of Surgeons, Adelaide, South Australia, Australia.,University of Adelaide Discipline of Surgery, The Queen Elizabeth Hospital, Adelaide, South Australia, Australia
| | - Penny Williamson
- Research Audit and Academic Surgery, Royal Australasian College of Surgeons, Adelaide, South Australia, Australia
| | - Lorwai Tan
- Research Audit and Academic Surgery, Royal Australasian College of Surgeons, Adelaide, South Australia, Australia
| | - Helena S Kopunic
- Research Audit and Academic Surgery, Royal Australasian College of Surgeons, Adelaide, South Australia, Australia
| | - Wendy J Babidge
- Research Audit and Academic Surgery, Royal Australasian College of Surgeons, Adelaide, South Australia, Australia.,University of Adelaide Discipline of Surgery, The Queen Elizabeth Hospital, Adelaide, South Australia, Australia
| | | | - Peter J Hewett
- University of Adelaide Discipline of Surgery, The Queen Elizabeth Hospital, Adelaide, South Australia, Australia
| | - Thomas J Hugh
- Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia.,Surgical Education, Research and Training Institute, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Robert T A Padbury
- Flinders University, Adelaide, South Australia, Australia.,Division of Surgery and Perioperative Medicine, Flinders Medical Centre, Adelaide, South Australia, Australia
| | - Mark Frydenberg
- Department of Urology, Cabrini Institute, Cabrini Health, Melbourne, Victoria, Australia.,Department of Surgery, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Richard G Douglas
- Department of Surgery, The University of Auckland, Auckland, New Zealand
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Guy J Maddern
- Research Audit and Academic Surgery, Royal Australasian College of Surgeons, Adelaide, South Australia, Australia.,University of Adelaide Discipline of Surgery, The Queen Elizabeth Hospital, Adelaide, South Australia, Australia
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47
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Garnham K, Halliday CL, Joshi Rai N, Jayawadena M, Hasan T, Kok J, Nayyar V, Gottlieb DJ, Gilroy NM, Chen SCA. Introducing 1,3-Beta-D-glucan for screening and diagnosis of invasive fungal diseases in Australian high risk haematology patients: is there a clinical benefit? Intern Med J 2020; 52:426-435. [PMID: 32896984 DOI: 10.1111/imj.15046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/25/2020] [Accepted: 08/25/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Katherine Garnham
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales, Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - Catriona L Halliday
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales, Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - Neela Joshi Rai
- Clinical Trials Unit, Centre for Infectious Diseases and Microbiology, Westmead Hospital, Sydney, Australia
| | - Menuk Jayawadena
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales, Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Australia
| | - Tasnim Hasan
- Clinical Trials Unit, Centre for Infectious Diseases and Microbiology, Westmead Hospital, Sydney, Australia.,Department of Infectious Diseases, Westmead Hospital, Sydney, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales, Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.,Clinical Trials Unit, Centre for Infectious Diseases and Microbiology, Westmead Hospital, Sydney, Australia.,Department of Infectious Diseases, Westmead Hospital, Sydney, Australia
| | - Vineet Nayyar
- Department of Intensive Care Medicine, Westmead Hospital, Sydney, Australia
| | - David J Gottlieb
- Department of Haematology Medicine, Westmead Hospital, Sydney, Australia
| | - Nicole M Gilroy
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.,Clinical Trials Unit, Centre for Infectious Diseases and Microbiology, Westmead Hospital, Sydney, Australia.,Department of Infectious Diseases, Westmead Hospital, Sydney, Australia
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales, Health Pathology-Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.,Clinical Trials Unit, Centre for Infectious Diseases and Microbiology, Westmead Hospital, Sydney, Australia.,Department of Infectious Diseases, Westmead Hospital, Sydney, Australia
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48
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Hueston L, Kok J, Guibone A, McDonald D, Hone G, Goodwin J, Carter I, Basile K, Sandaradura I, Maddocks S, Sintchenko V, Gilroy N, Chen S, Dwyer DE, O’Sullivan MVN. The Antibody Response to SARS-CoV-2 Infection. Open Forum Infect Dis 2020; 7:ofaa387. [PMID: 32989419 PMCID: PMC7499696 DOI: 10.1093/ofid/ofaa387] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/22/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific antibodies has become an important tool, complementing nucleic acid tests (NATs) for diagnosis and for determining the prevalence of coronavirus disease 2019 (COVID-19) in population serosurveys. The magnitude and persistence of antibody responses are critical for assessing the duration of immunity. METHODS A SARS-CoV-2-specific immunofluorescent antibody (IFA) assay for immunoglobulin G (IgG), immunoglobulin A (IgA), and immunoglobulin M (IgM) was developed and prospectively evaluated by comparison to the reference standard of NAT on respiratory tract samples from individuals with suspected COVID-19. Neutralizing antibody responses were measured in a subset of samples using a standard microneutralization assay. RESULTS A total of 2753 individuals were eligible for the study (126 NAT-positive; prevalence, 4.6%). The median "window period" from illness onset to appearance of antibodies (range) was 10.2 (5.8-14.4) days. The sensitivity and specificity of either SARS-CoV-2 IgG, IgA, or IgM when collected ≥14 days after symptom onset were 91.3% (95% CI, 84.9%-95.6%) and 98.9% (95% CI, 98.4%-99.3%), respectively. The negative predictive value was 99.6% (95% CI, 99.3%-99.8%). The positive predictive value of detecting any antibody class was 79.9% (95% CI, 73.3%-85.1%); this increased to 96.8% (95% CI, 90.7%-99.0%) for the combination of IgG and IgA. CONCLUSIONS Measurement of SARS-CoV-2-specific antibody by IFA is an accurate method to diagnose COVID-19. Serological testing should be incorporated into diagnostic algorithms for SARS-CoV-2 infection to identify additional cases where NAT was not performed and resolve cases where false-negative and false-positive NATs are suspected. The majority of individuals develop robust antibody responses following infection, but the duration of these responses and implications for immunity remain to be established.
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Affiliation(s)
- Linda Hueston
- New South Wales Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, Australia
| | - Jen Kok
- New South Wales Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, Australia
| | - Ayla Guibone
- New South Wales Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, Australia
| | - Damien McDonald
- New South Wales Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, Australia
| | - George Hone
- New South Wales Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, Australia
| | - James Goodwin
- New South Wales Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, Australia
| | - Ian Carter
- New South Wales Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, Australia
| | - Kerri Basile
- New South Wales Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, Australia
| | - Indy Sandaradura
- New South Wales Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, Australia
- Department of Infectious Diseases, Westmead Hospital, Westmead, Australia
- Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Susan Maddocks
- New South Wales Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, Australia
- Department of Infectious Diseases, Westmead Hospital, Westmead, Australia
| | - Vitali Sintchenko
- New South Wales Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, Australia
- Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Nicole Gilroy
- Department of Infectious Diseases, Westmead Hospital, Westmead, Australia
| | - Sharon Chen
- New South Wales Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, Australia
- Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Dominic E Dwyer
- New South Wales Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, Australia
- Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Matthew V N O’Sullivan
- New South Wales Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, Australia
- Department of Infectious Diseases, Westmead Hospital, Westmead, Australia
- Sydney Medical School, The University of Sydney, Sydney, Australia
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49
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Lord H, Kok J, Fletcher-Lartey S, Alexander K. Is it or is it not? Lessons learned from a case of suspected vaccine strain measles. Eur J Public Health 2020. [DOI: 10.1093/eurpub/ckaa166.829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Measles continues to be a threat to Australia. While post eradication risks are low, imported measles cases from overseas travellers who are non-immune can cause small outbreaks. This case report discusses the challenge of identifying wild-type measles in an individual who was recently vaccinated with measles - containing vaccine (MCV).
Methods
A positive polymerase chain reaction (PCR) result for measles for an adult who had recently received a measles -containing vaccine was notified. Investigation revealed no known epidemiological link, recent overseas travel or contact with recent measles cases during the incubation period.
Results
The results of the initial sequencing to distinguish between wild-type and vaccine-strain measles were inconclusive. A decision was made to re-run the genotyping, collect additional specimens, and quarantine the case until a definitive result was obtained. Sequencing and genotyping revealed that this indeed was a wild-type measles strain.
Conclusions
Changing epidemiology of measles means distinguishing between wild-type and vaccine-strain measles has become a new challenge. The reflection of the public health management of this case has provided is a valuable teaching tool for public health professionals globally, particularly in low incidence measles countries.
Key messages
The lack of an epidemiological link can create confusion for public health staff when investigating possible measles cases. Changes in the epidemiology of measles means distinguishing between wild type and vaccine strain measles is a challenge.
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Affiliation(s)
- H Lord
- Centre for Research in Nursing and Health, South Eastern Sydney Local Health District, Kogarah, Australia
- School of Nursing, University of Wollongong, Wollongong, Australia
- Centre for Evidence based Initiatives in health Care, A Joanna Briggs Institute Centre for Excellence, Wollongong, Australia
| | - J Kok
- Centre for Infectious Diseases and Microbiology Laboratory S, NSW Health Pathology, Westmead, Australia
| | - S Fletcher-Lartey
- Public Health Unit, South Western Sydney Local Health District, Liverpool, Australia
| | - K Alexander
- Public Health Unit, South Western Sydney Local Health District, Liverpool, Australia
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50
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Badahdah AM, Bakarman MA, Khatami A, Tashani M, Barasheed O, Alfelali M, Azeem MI, Bokhary H, Soltan O, Lahra MM, Jeoffreys N, Kok J, Dwyer DE, Booy R, Rashid H. Meningococcal and pneumococcal carriage in Hajj pilgrims: findings of a randomized controlled trial. J Travel Med 2020; 27:5775502. [PMID: 32125434 DOI: 10.1093/jtm/taaa032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/12/2020] [Accepted: 02/26/2020] [Indexed: 11/13/2022]
Abstract
BACKGROUND Intense congestion during the Hajj pilgrimage amplifies the risk of meningococcal carriage and disease, and there have been many meningococcal outbreaks reported amongst pilgrims. Thus, a strict vaccination policy is enforced by the host country and either polysaccharide or conjugate quadrivalent meningococcal vaccines are mandatory. However, unlike conjugate vaccines, the polysaccharide vaccine is not thought to reduce pharyngeal carriage of meningococci. METHODS A single-blinded, randomized, controlled trial amongst pilgrims from Saudi Arabia and Australia during the Hajj seasons of 2016-2017 was conducted to compare MenACWY-Conjugate vaccine with MenACWY-Polysaccharide vaccine, to determine if the conjugate vaccine is more effective in reducing asymptomatic carriage of meningococci, and whether the effect may be long-standing. Oropharyngeal swabs were obtained pre-, immediately post- and 6-11 months following completion of Hajj and tested for the presence of meningococci. RESULTS Amongst 2000 individuals approached, only 1146 participants aged 18-91 (mean 37.6) years agreed to participate and were randomized to receive either the polysaccharide (n = 561) or the conjugate (n = 561) vaccine, 60.8% were male, and 93.5% were from Saudi Arabia. Amongst oropharyngeal swabs obtained before Hajj, only two (0.2%) tested positive for Neisseria meningitidis. Similarly, meningococci were identified in only one sample at each of the post-Hajj and late follow-up visits. None of the carriage isolates were amongst the serogroups covered by the vaccines. A post hoc analysis of the third swabs revealed that 22.4% of all participants (50/223) were positive for Streptococcus pneumoniae nucleic acid. CONCLUSION The low overall carriage rate of meningococci found amongst Hajj pilgrims in 2016 and 2017 demonstrates a successful vaccination policy, but neither supports nor refutes the superiority of meningococcal conjugate ACWY vaccine over the polysaccharide vaccine against carriage. Although an association could not be established in this study, molecular epidemiology would help to establish the role of Hajj in facilitating transmission of pneumococci and inform vaccination policy.
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Affiliation(s)
- Al-Mamoon Badahdah
- Department of Family and Community Medicine, Faculty of Medicine in Rabigh, King Abdulaziz University, Jeddah 22252, Saudi Arabia.,National Centre for Immunisation Research and Surveillance (NCIRS), The Children's Hospital at Westmead, NSW 2145, Australia.,The Discipline of Child and Adolescent Health, The Children's Hospital Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Marwan A Bakarman
- Department of Family and Community Medicine, Faculty of Medicine in Rabigh, King Abdulaziz University, Jeddah 22252, Saudi Arabia
| | - Ameneh Khatami
- The Discipline of Child and Adolescent Health, The Children's Hospital Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia.,Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Mohamed Tashani
- The Discipline of Child and Adolescent Health, The Children's Hospital Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia.,Faculty of Medicine, University of Tripoli, Ain Zara, Tripoli, Libya
| | - Osamah Barasheed
- The Executive Administration of Research and Innovation, King Abdullah Medical City in Holy Capital (KAMC-HC), Makkah 24246, Saudi Arabia
| | - Mohammad Alfelali
- Department of Family and Community Medicine, Faculty of Medicine in Rabigh, King Abdulaziz University, Jeddah 22252, Saudi Arabia.,National Centre for Immunisation Research and Surveillance (NCIRS), The Children's Hospital at Westmead, NSW 2145, Australia.,The Discipline of Child and Adolescent Health, The Children's Hospital Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Mohammad I Azeem
- National Centre for Immunisation Research and Surveillance (NCIRS), The Children's Hospital at Westmead, NSW 2145, Australia
| | - Hamid Bokhary
- Umm Al-Qura University, Makkah, Saudi Arabia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, University of Sydney, Westmead, NSW 2145, Australia
| | - Osama Soltan
- Microbiology department, Al Borg Medical Laboratories, Jeddah 21573, Saudi Arabia
| | - Monica M Lahra
- The World Health Organisation Collaborating Centre for STI and AMR, and Neisseria Reference Laboratory, New South Wales Health Pathology, Microbiology, Prince of Wales Hospital, Randwick, NSW, 2031, Australia.,Faculty of Medicine, The University of New South Wales, Randwick, NSW 2052, Australia
| | - Neisha Jeoffreys
- New South Wales Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead Hospital and University of Sydney, Westmead NSW 2145, Australia
| | - Jen Kok
- New South Wales Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead Hospital and University of Sydney, Westmead NSW 2145, Australia
| | - Dominic E Dwyer
- New South Wales Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead Hospital and University of Sydney, Westmead NSW 2145, Australia
| | - Robert Booy
- National Centre for Immunisation Research and Surveillance (NCIRS), The Children's Hospital at Westmead, NSW 2145, Australia.,The Discipline of Child and Adolescent Health, The Children's Hospital Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, University of Sydney, Westmead, NSW 2145, Australia
| | - Harunor Rashid
- National Centre for Immunisation Research and Surveillance (NCIRS), The Children's Hospital at Westmead, NSW 2145, Australia.,The Discipline of Child and Adolescent Health, The Children's Hospital Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, University of Sydney, Westmead, NSW 2145, Australia
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