1
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Minney‐Smith CA, Foley DA, Sikazwe CT, Levy A, Smith DW. The seasonality of respiratory syncytial virus in Western Australia prior to implementation of SARS‐CoV‐2 non‐pharmaceutical interventions. Influenza Other Respir Viruses 2023; 17:e13117. [PMID: 36970572 PMCID: PMC10035409 DOI: 10.1111/irv.13117] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/27/2023] [Accepted: 02/14/2023] [Indexed: 03/11/2023] Open
Abstract
Background Respiratory syncytial virus (RSV) seasonality is dependent on the local climate. We assessed the stability of RSV seasonality prior to the SARS-CoV-2 pandemic in Western Australia (WA), a state spanning temperate and tropical regions. Method RSV laboratory testing data were collected from January 2012 to December 2019. WA was divided into three regions determined by population density and climate: Metropolitan, Northern and Southern. Season threshold was calculated per region at 1.2% annual cases, with onset the first of ≥2 weeks above this threshold and offset as the last week before ≥2 weeks below. Results The detection rate of RSV in WA was 6.3/10,000. The Northern region had the highest detection rate (15/10,000), more than 2.5 times the Metropolitan region (detection rate ratio 2.7; 95% CI, 2.6-2.9). Test percentage positive was similar in the Metropolitan (8.6%) and Southern (8.7%) regions, with the lowest in the Northern region (8.1%). RSV seasons in the Metropolitan and Southern regions occurred annually, with a single peak and had consistent timing and intensity. The Northern tropical region did not experience a distinct season. Proportion of RSV A to RSV B in the Northern region differed from the Metropolitan region in 5 of the 8 years studied. Conclusions Detection rate of RSV in WA is high, especially in the Northern region, where climate, an expanded at-risk population and increased testing may have contributed to greater numbers. Before the SARS-CoV-2 pandemic, RSV seasonality in WA was consistent in timing and intensity for the Metropolitan and Southern regions.
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Affiliation(s)
- Cara A. Minney‐Smith
- Department of Microbiology PathWest Laboratory Medicine WA Nedlands Western Australia Australia
| | - David A. Foley
- Department of Microbiology PathWest Laboratory Medicine WA Nedlands Western Australia Australia
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute University of Western Australia Perth Western Australia Australia
- School of Medicine University of Western Australia Perth Western Australia Australia
| | - Chisha T. Sikazwe
- Department of Microbiology PathWest Laboratory Medicine WA Nedlands Western Australia Australia
- Infection, and Immunity, Biomedical Sciences University of Western Australia Perth Western Australia Australia
| | - Avram Levy
- Department of Microbiology PathWest Laboratory Medicine WA Nedlands Western Australia Australia
- Infection, and Immunity, Biomedical Sciences University of Western Australia Perth Western Australia Australia
| | - David W. Smith
- Department of Microbiology PathWest Laboratory Medicine WA Nedlands Western Australia Australia
- School of Medicine University of Western Australia Perth Western Australia Australia
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2
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Foley DA, Sikazwe CT, Minney-Smith CA, Ernst T, Moore HC, Nicol MP, Smith DW, Levy A, Blyth CC. An Unusual Resurgence of Human Metapneumovirus in Western Australia Following the Reduction of Non-Pharmaceutical Interventions to Prevent SARS-CoV-2 Transmission. Viruses 2022; 14:2135. [PMID: 36298690 PMCID: PMC9612024 DOI: 10.3390/v14102135] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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] [Received: 08/30/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 09/25/2023] Open
Abstract
Non-pharmaceutical interventions (NPIs) to reduce SARS-CoV-2 transmission disrupted respiratory virus seasonality. We examined the unusual return of human metapneumovirus (hMPV) in Western Australia following a period of absence in 2020. We analysed hMPV laboratory testing data from 1 January 2017 to 31 December 2021. Whole-genome sequencing of selected hMPV-positive samples was performed using a tiled-amplicon approach. Following an absence in spring 2020, an unusual hMPV surge was observed during the wet summer season in the tropical Northern region in late 2020. Following a six-month delay, an intense winter season occurred in the subtropical/temperate Southern and Metropolitan regions. Compared to 2017-2019, hMPV incidence in 2021 increased by 3-fold, with a greater than 4-fold increase in children aged 1-4 years. There was a collapse in hMPV diversity in 2020, with the emergence of a single subtype. NPIs contributed to an absent 2020 season and a clonal hMPV resurgence. The summer surge and delayed winter season suggest that prevailing temperature and humidity are keys determinant of hMPV transmission. The increased incidence in 2021 was linked to an expanded cohort of hMPV-naïve 1-4-year-old children and waning population immunity. Further intense and unusual respiratory virus seasons are expected as COVID-19 associated NPIs are removed.
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Affiliation(s)
- David Anthony Foley
- Department of Microbiology, PathWest Laboratory Medicine, Perth 6009, Australia
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth 6009, Australia
- School of Medicine, University of Western Australia, Perth 6009, Australia
| | - Chisha T. Sikazwe
- Department of Microbiology, PathWest Laboratory Medicine, Perth 6009, Australia
- Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth 6009, Australia
| | | | - Timo Ernst
- Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth 6009, Australia
| | - Hannah C. Moore
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth 6009, Australia
- Faculty of Health Sciences, School of Population Health, Curtin University, Perth 6102, Australia
| | - Mark P. Nicol
- Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth 6009, Australia
| | - David W. Smith
- Department of Microbiology, PathWest Laboratory Medicine, Perth 6009, Australia
- School of Medicine, University of Western Australia, Perth 6009, Australia
| | - Avram Levy
- Department of Microbiology, PathWest Laboratory Medicine, Perth 6009, Australia
- Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth 6009, Australia
| | - Christopher C. Blyth
- Department of Microbiology, PathWest Laboratory Medicine, Perth 6009, Australia
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth 6009, Australia
- School of Medicine, University of Western Australia, Perth 6009, Australia
- Department of Infectious Diseases, Perth Children’s Hospital, Perth 6009, Australia
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3
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Ngeh S, Vogt F, Sikazwe CT, Levy A, Pingault NM, Smith DW, Effler PV. Travel-associated SARS-CoV-2 transmission documented with whole genome sequencing following a long-haul international flight. J Travel Med 2022; 29:6582210. [PMID: 35532195 PMCID: PMC9129214 DOI: 10.1093/jtm/taac057] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/29/2022] [Indexed: 11/14/2022]
Abstract
BACKGROUND Multiple instances of flight-associated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission during long-haul flights have been reported during the COVID-19 pandemic. However, comprehensive investigations of passenger risk behaviours, before, during and after the flight, are scarce. METHODS To investigate suspected SARS-CoV-2 transmission during a flight from United Arab Emirates to Australia in July 2020, systematic, repeated polymerase chain reaction (PCR) testing of passengers in hotel quarantine was linked to whole genome sequencing. Epidemiological analyses of in-depth interviews covering behaviours during the flight and activities pre- and post-boarding were used to identify risk factors for infection. RESULTS Seventeen of the 95 passengers from four different travel origins had PCR-confirmed infection yielding indistinguishable genomic sequences. Two of the 17 passengers were symptomatic within 2 days of the flight, and classified as co-primary cases. Seven secondary cases were seated within two rows of the co-primary cases, but five economy passengers seated further away and three business class passengers were also infected (attack rate = 16% [15/93]). In multivariable analysis, being seated within two rows of a primary case [odds ratio (OR) 7.16; 95% confidence interval (CI) 1.66-30.85] and spending more than an hour in the arrival airport (OR 4.96; 95% CI 1.04-23.60) were independent predictors of secondary infection, suggesting travel-associated SARS-CoV-2 transmission likely occurred both during and after the flight. Self-reported increased hand hygiene, frequent aisle walking and using the bathroom on the plane did not independently affect the risk of SARS-CoV-2 acquisition. CONCLUSIONS This investigation identified substantial in-flight transmission among passengers seated both within and beyond two rows of the primary cases. Infection of passengers in separate cabin classes also suggests transmission occurred outside the cabin environment, likely at the arrival airport. Recognizing that transmission may occur pre- and post-boarding may inform contact tracing advice and improve efforts to prevent future travel-associated outbreaks.
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Affiliation(s)
- Sera Ngeh
- Communicable Disease Control Directorate, Department of Health Western Australia, PO Box 6172, Perth Business Centre, Perth, WA 6849, Australia.,National Centre for Epidemiology and Population Health, Australian National University, 62 Mills Road, Acton, Canberra ACT 2601, Australia
| | - Florian Vogt
- Communicable Disease Control Directorate, Department of Health Western Australia, PO Box 6172, Perth Business Centre, Perth, WA 6849, Australia.,National Centre for Epidemiology and Population Health, Australian National University, 62 Mills Road, Acton, Canberra ACT 2601, Australia.,Global Health Program, The Kirby Institute, Level 6, Wallace Wurth Building, High Street, University of New South Wales, Sydney, Kensington NSW 2052, Australia
| | - Chisha T Sikazwe
- Department of Microbiology, PathWest Laboratory Medicine Western Australia, QE2 Medical Centre, Locked Bay 2009, Nedlands, WA, 6909, Australia.,School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Avram Levy
- Department of Microbiology, PathWest Laboratory Medicine Western Australia, QE2 Medical Centre, Locked Bay 2009, Nedlands, WA, 6909, Australia.,School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Nevada M Pingault
- Communicable Disease Control Directorate, Department of Health Western Australia, PO Box 6172, Perth Business Centre, Perth, WA 6849, Australia
| | - David W Smith
- Department of Microbiology, PathWest Laboratory Medicine Western Australia, QE2 Medical Centre, Locked Bay 2009, Nedlands, WA, 6909, Australia.,School of Medicine, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Paul V Effler
- Communicable Disease Control Directorate, Department of Health Western Australia, PO Box 6172, Perth Business Centre, Perth, WA 6849, Australia.,School of Medicine, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
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4
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Foley DA, Phuong LK, Peplinski J, Lim SMJ, Lee WH, Keane A, Wong JWS, Minney-Smith CA, Martin AC, Mace AO, Sikazwe CT, Le H, Levy A, Borland M, Hazelton B, Moore HC, Blyth C, Yeoh D, Bowen AC. Examining the entire delayed respiratory syncytial virus season in Western Australia. Arch Dis Child 2022; 107:517-519. [PMID: 34930725 DOI: 10.1136/archdischild-2021-323375] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/08/2021] [Indexed: 11/03/2022]
Affiliation(s)
- David Anthony Foley
- Microbiology, PathWest Laboratory Medicine Western Australia, Perth, Western Australia, Australia .,Wesfarmers Centre of Vaccines and Infecitous Diseases, University of Western Australia, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Linny Kimly Phuong
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Joseph Peplinski
- Department of General Paediatrics, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Selina Mei Jy Lim
- Infectious Diseases Department, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Wei Hao Lee
- Department of General Paediatrics, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Aoife Keane
- Department of General Paediatrics, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Jessica Win See Wong
- Department of General Paediatrics, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Cara A Minney-Smith
- Microbiology, PathWest Laboratory Medicine Western Australia, Perth, Western Australia, Australia
| | - Andrew C Martin
- Department of General Paediatrics, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Ariel O Mace
- Department of General Paediatrics, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Chisha T Sikazwe
- Microbiology, PathWest Laboratory Medicine Western Australia, Perth, Western Australia, Australia.,Infection and Immunity, Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
| | - Huong Le
- Wesfarmers Centre of Vaccines and Infecitous Diseases, University of Western Australia, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Avram Levy
- Microbiology, PathWest Laboratory Medicine Western Australia, Perth, Western Australia, Australia.,Infection and Immunity, Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
| | - Meredith Borland
- Emergency Medicine, Perth Children's Hospital, Nedlands, Western Australia, Australia.,Divisions of Paediatrics and Emergency Medicine, University of Western Australia, Crawley, Western Australia, Australia
| | - Briony Hazelton
- Microbiology, PathWest Laboratory Medicine Western Australia, Perth, Western Australia, Australia.,Infectious Diseases Department, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Hannah C Moore
- Wesfarmers Centre of Vaccines and Infecitous Diseases, University of Western Australia, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Christopher Blyth
- Microbiology, PathWest Laboratory Medicine Western Australia, Perth, Western Australia, Australia.,Wesfarmers Centre of Vaccines and Infecitous Diseases, University of Western Australia, Telethon Kids Institute, Perth, Western Australia, Australia.,Infectious Diseases Department, Perth Children's Hospital, Perth, Western Australia, Australia.,School of Paediatrics and Child Health, University of Western Australia, Subiaco, Western Australia, Australia
| | - Daniel Yeoh
- Infectious Diseases Department, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Asha C Bowen
- Wesfarmers Centre of Vaccines and Infecitous Diseases, University of Western Australia, Telethon Kids Institute, Perth, Western Australia, Australia.,Infectious Diseases Department, Perth Children's Hospital, Perth, Western Australia, Australia
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5
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Foley DA, Phuong LK, Peplinski J, Lim SM, Lee WH, Farhat A, Minney-Smith CA, Martin AC, Mace AO, Sikazwe CT, Le H, Levy A, Hoeppner T, Borland ML, Hazelton B, Moore HC, Blyth C, Yeoh DK, Bowen AC. Examining the interseasonal resurgence of respiratory syncytial virus in Western Australia. Arch Dis Child 2022; 107:e7. [PMID: 34433552 PMCID: PMC8390145 DOI: 10.1136/archdischild-2021-322507] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/12/2021] [Indexed: 12/28/2022]
Abstract
BACKGROUND Following a relative absence in winter 2020, a large resurgence of respiratory syncytial virus (RSV) detections occurred during the 2020/2021 summer in Western Australia. This seasonal shift was linked to SARS-CoV-2 public health measures. We examine the epidemiology and RSV testing of respiratory-coded admissions, and compare clinical phenotype of RSV-positive admissions between 2019 and 2020. METHOD At a single tertiary paediatric centre, International Classification of Diseases, 10th edition Australian Modification-coded respiratory admissions longer than 12 hours were combined with laboratory data from 1 January 2019 to 31 December 2020. Data were grouped into bronchiolitis, other acute lower respiratory infection (OALRI) and wheeze, to assess RSV testing practices. For RSV-positive admissions, demographics and clinical features were compared between 2019 and 2020. RESULTS RSV-positive admissions peaked in early summer 2020, following an absent winter season. Testing was higher in 2020: bronchiolitis, 94.8% vs 89.2% (p=0.01); OALRI, 88.6% vs 82.6% (p=0.02); and wheeze, 62.8% vs 25.5% (p<0.001). The 2020 peak month, December, contributed almost 75% of RSV-positive admissions, 2.5 times the 2019 peak. The median age in 2020 was twice that observed in 2019 (16.4 vs 8.1 months, p<0.001). The proportion of RSV-positive OALRI admissions was greater in 2020 (32.6% vs 24.9%, p=0.01). There were no clinically meaningful differences in length of stay or disease severity. INTERPRETATION The 2020 RSV season was in summer, with a larger than expected peak. There was an increase in RSV-positive non-bronchiolitis admissions, consistent with infection in older RSV-naïve children. This resurgence raises concern for regions experiencing longer and more stringent SARS-CoV-2 public health measures.
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Affiliation(s)
- David Anthony Foley
- Microbiology, PathWest Laboratory Medicine, Perth, Western Australia, Australia
- Wesfarmers Centre for Vaccines and Infectious Diseases, University of Western Australia, Telethon Kids Institute, Nedlands, Western Australia, Australia
| | - Linny Kimly Phuong
- Murdoch Children's Research Institute, Infection and Immunity, Parkville, Victoria, Australia
| | - Joseph Peplinski
- Department of General Paediatrics, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Selina Mei Lim
- Infectious Diseases Department, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Wei Hao Lee
- Department of General Paediatrics, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Asifa Farhat
- Department of General Paediatrics, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Cara A Minney-Smith
- Microbiology, PathWest Laboratory Medicine, Perth, Western Australia, Australia
| | - Andrew C Martin
- Department of General Paediatrics, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Ariel O Mace
- Department of General Paediatrics, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Chisha T Sikazwe
- Microbiology, PathWest Laboratory Medicine, Perth, Western Australia, Australia
- Infection and Immunity, Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
| | - Huong Le
- Wesfarmers Centre for Vaccines and Infectious Diseases, University of Western Australia, Telethon Kids Institute, Nedlands, Western Australia, Australia
| | - Avram Levy
- Microbiology, PathWest Laboratory Medicine, Perth, Western Australia, Australia
- Infection and Immunity, Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
| | - Tobias Hoeppner
- Emergency Medicine, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Meredith L Borland
- Emergency Medicine, Perth Children's Hospital, Nedlands, Western Australia, Australia
- Divisions of Paediatrics and Emergency Medicine, University of Western Australia, Crawley, Western Australia, Australia
| | - Briony Hazelton
- Microbiology, PathWest Laboratory Medicine, Perth, Western Australia, Australia
- Infectious Diseases Department, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Hannah C Moore
- Wesfarmers Centre for Vaccines and Infectious Diseases, University of Western Australia, Telethon Kids Institute, Nedlands, Western Australia, Australia
| | - Christopher Blyth
- Microbiology, PathWest Laboratory Medicine, Perth, Western Australia, Australia
- Wesfarmers Centre for Vaccines and Infectious Diseases, University of Western Australia, Telethon Kids Institute, Nedlands, Western Australia, Australia
- School of Paediatrics and Child Health, University of Western Australia, Subiaco, Western Australia, Australia
| | - Daniel K Yeoh
- Infectious Diseases Department, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Asha C Bowen
- Wesfarmers Centre for Vaccines and Infectious Diseases, University of Western Australia, Telethon Kids Institute, Nedlands, Western Australia, Australia
- Infectious Diseases Department, Perth Children's Hospital, Perth, Western Australia, Australia
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6
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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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7
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Yeoh DK, Foley DA, Minney-Smith CA, Martin AC, Mace AO, Sikazwe CT, Le H, Levy A, Blyth CC, Moore HC. Impact of Coronavirus Disease 2019 Public Health Measures on Detections of Influenza and Respiratory Syncytial Virus in Children During the 2020 Australian Winter. Clin Infect Dis 2021; 72:2199-2202. [PMID: 32986804 PMCID: PMC7543326 DOI: 10.1093/cid/ciaa1475] [Citation(s) in RCA: 267] [Impact Index Per Article: 89.0] [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: 09/06/2020] [Indexed: 11/14/2022] Open
Abstract
Public health measures targeting coronavirus disease 2019 have potential to impact transmission of other respiratory viruses. We found 98.0% and 99.4% reductions in respiratory syncytial virus and influenza detections, respectively, in Western Australian children through winter 2020 despite schools reopening. Border closures have likely been important in limiting external introductions.
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Affiliation(s)
- Daniel K Yeoh
- Infectious Diseases Department, Perth Children's Hospital, Perth, Australia.,National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - David A Foley
- Infectious Diseases Department, Perth Children's Hospital, Perth, Australia
| | - Cara A Minney-Smith
- Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Australia
| | - Andrew C Martin
- Department of General Paediatrics, Perth Children's Hospital, Perth, Australia
| | - Ariel O Mace
- Department of General Paediatrics, Perth Children's Hospital, Perth, Australia.,Department of General Paediatrics, Fiona Stanley Hospital, Perth, Australia.,Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Chisha T Sikazwe
- Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Australia.,Department of General Paediatrics, Fiona Stanley Hospital, Perth, Australia
| | - Huong Le
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Avram Levy
- Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Australia.,Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
| | - Christopher C Blyth
- Infectious Diseases Department, Perth Children's Hospital, Perth, Australia.,Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Australia.,Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia.,School of Medicine, University of Western Australia, Perth, Australia
| | - Hannah C Moore
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
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8
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Foley DA, Yeoh DK, Minney-Smith CA, Martin AC, Mace AO, Sikazwe CT, Le H, Levy A, Moore HC, Blyth CC. The Interseasonal Resurgence of Respiratory Syncytial Virus in Australian Children Following the Reduction of Coronavirus Disease 2019-Related Public Health Measures. Clin Infect Dis 2021; 73:e2829-e2830. [PMID: 33594407 PMCID: PMC7929151 DOI: 10.1093/cid/ciaa1906] [Citation(s) in RCA: 200] [Impact Index Per Article: 66.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- David A Foley
- Infectious Diseases Department, Perth Children's Hospital, Perth, Australia
| | - Daniel K Yeoh
- Infectious Diseases Department, Perth Children's Hospital, Perth, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria
| | - Cara A Minney-Smith
- Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Australia
| | - Andrew C Martin
- Department of General Paediatrics, Perth Children's Hospital, Perth, Australia
| | - Ariel O Mace
- Department of General Paediatrics, Perth Children's Hospital, Perth, Australia.,Department of General Paediatrics, Fiona Stanley Hospital, Perth, Australia.,Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Chisha T Sikazwe
- Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Australia.,Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
| | - Huong Le
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Avram Levy
- Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Australia.,Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
| | - Hannah C Moore
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Christopher C Blyth
- Infectious Diseases Department, Perth Children's Hospital, Perth, Australia.,Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Australia.,Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia.,School of Medicine, University of Western Australia, Perth, Australia
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Townsi N, Simpson SJ, Sikazwe CT, Chidlow GR, Hall GL, Pillow JJ, Wilson AC, Smith DW, Laing IA. Environmental exposure and parental collection does not affect detection or semi-quantitative load assessment of bacteria in nasal swab specimens from children. Infect Dis (Lond) 2017; 50:468-471. [PMID: 29237312 DOI: 10.1080/23744235.2017.1411607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Nada Townsi
- a Children's Lung Health, Telethon Kids Institute , Perth , Australia.,b Division Paediatrics, University of Western Australia , Perth , Australia.,c Ministry of Education , Riyadh , Saudi Arabia
| | - Shannon J Simpson
- a Children's Lung Health, Telethon Kids Institute , Perth , Australia.,d School of Physiotherapy and Exercise Science , Curtin University , Perth , Australia
| | - Chisha T Sikazwe
- e Department of Microbiology , Path West Laboratory Medicine , Perth , Australia.,f School of Biomedical Sciences , University of Western Australia , Perth , Australia
| | - Glenys R Chidlow
- e Department of Microbiology , Path West Laboratory Medicine , Perth , Australia
| | - Graham L Hall
- a Children's Lung Health, Telethon Kids Institute , Perth , Australia.,d School of Physiotherapy and Exercise Science , Curtin University , Perth , Australia.,g Centre of Child Health Research, University of Western Australia , Perth , Australia
| | - J Jane Pillow
- h School of Human Sciences , University of Western Australia , Perth , Australia.,i Centre of Neonatal Research and Education, University of Western Australia , Perth , Australia
| | - Andrew C Wilson
- a Children's Lung Health, Telethon Kids Institute , Perth , Australia.,d School of Physiotherapy and Exercise Science , Curtin University , Perth , Australia.,g Centre of Child Health Research, University of Western Australia , Perth , Australia.,j Department of Respiratory and Sleep Medicine , Princess Margaret Hospital for Children , Perth , Australia
| | - David W Smith
- e Department of Microbiology , Path West Laboratory Medicine , Perth , Australia.,f School of Biomedical Sciences , University of Western Australia , Perth , Australia
| | - Ingrid A Laing
- a Children's Lung Health, Telethon Kids Institute , Perth , Australia.,f School of Biomedical Sciences , University of Western Australia , Perth , Australia
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Sikazwe CT, Chidlow GR, Imrie A, Smith DW. Reliable quantification of rhinovirus species C using real-time PCR. J Virol Methods 2016; 235:65-72. [PMID: 27216896 PMCID: PMC7172306 DOI: 10.1016/j.jviromet.2016.05.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 02/03/2016] [Revised: 05/11/2016] [Accepted: 05/19/2016] [Indexed: 11/30/2022]
Abstract
BACKGROUND Rhinovirus C (RV-C) is an important respiratory pathogen of children, but little is known about its contribution to disease severity, though viral load appears to be important. Difficulty in RV-C cultivation and target sequence variation has precluded the development of a PCR based quantification method. OBJECTIVE The aim of this study was to develop and validate reverse transcription quantitative PCR (RT-qPCR) assays for a broad range of circulating RV-C genotypes in nasopharyngeal aspirates (NPAs). STUDY DESIGN Four assays were designed to quantify a 296bp region located within the 5' untranslated region (UTR) of RV-C types. These assays were based on in silico analysis of available RV-C sequences. Probes were designed to provide 100% homology to the corresponding RV-C genotypes. RESULTS The linear dynamic range of each of the four assays spanned eight orders of magnitude (10(4)-10(11) copies/mL). The limit of detection for assays 1-4 was estimated to be 1147 copies/mL, 765 copies/mL, 1138 copies/mL and 1470 copies/mL respectively. Each assay demonstrated a strong linear relationship (r(2)=>0.995) and amplification efficiency greater than 95%. Repeatability and reproducibility of the method were shown to be high, with coefficients of variations lower than 8% and 15% respectively.
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Affiliation(s)
- Chisha T Sikazwe
- School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia; Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Australia.
| | - Glenys R Chidlow
- Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Australia
| | - Allison Imrie
- School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia; Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Australia
| | - David W Smith
- School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia; Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Australia
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