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Pollak NM, Rawle DJ, Yan K, Buckley C, Le TT, Wang CYT, Ertl NG, van Huyssteen K, Crkvencic N, Hashmi M, Lyons RE, Whiley DM, Suhrbier A, Macdonald J. Rapid inactivation and sample preparation for SARS-CoV-2 PCR-based diagnostics using TNA-Cifer Reagent E. Front Microbiol 2023; 14:1238542. [PMID: 37869655 PMCID: PMC10590215 DOI: 10.3389/fmicb.2023.1238542] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/07/2023] [Indexed: 10/24/2023] Open
Abstract
RT-qPCR remains a key diagnostic methodology for COVID-19/SARS-CoV-2. Typically, nasal or saliva swabs from patients are placed in virus transport media (VTM), RNA is extracted at the pathology laboratory, and viral RNA is measured using RT-qPCR. In this study, we describe the use of TNA-Cifer Reagent E in a pre-clinical evaluation study to inactivate SARS-CoV-2 as well as prepare samples for RT-qPCR. Adding 1 part TNA-Cifer Reagent E to 5 parts medium containing SARS-CoV-2 for 10 min at room temperature inactivated the virus and permitted RT-qPCR detection. TNA-Cifer Reagent E was compared with established column-based RNA extraction and purification methodology using a panel of human clinical nasal swab samples (n = 61), with TNA-Cifer Reagent E showing high specificity (100%) and sensitivity (97.37%). Mixtures of SARS-CoV-2 virus and TNA-Cifer Reagent E could be stored for 3 days at room temperature or for 2 weeks at 4°C without the loss of RT-qPCR detection sensitivity. The detection sensitivity was preserved when TNA-Cifer Reagent E was used in conjunction with a range of VTM for saliva samples but only PBS (Gibco) and Amies Orange for nasal samples. Thus, TNA-Cifer Reagent E improves safety by rapidly inactivating the virus during sample processing, potentially providing a safe means for molecular SARS-CoV-2 testing outside traditional laboratory settings. The reagent also eliminates the need for column-based and/or automated viral RNA extraction/purification processes, thereby providing cost savings for equipment and reagents, as well as reducing processing and handling times.
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Affiliation(s)
- Nina M. Pollak
- Center for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- DMTC Limited, Kew, VIC, Australia
| | - Daniel J. Rawle
- Inflammation Biology Group, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Kexin Yan
- Inflammation Biology Group, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Cameron Buckley
- Faculty of Medicine, UQ Centre for Clinical Research, The University of Queensland, Herston, QLD, Australia
| | - Thuy T. Le
- Inflammation Biology Group, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Claire Y. T. Wang
- Queensland Paediatric Infectious Diseases Laboratory, Centre for Children's Health Research, Brisbane, QLD, Australia
| | - Nicole G. Ertl
- Faculty of Medicine, UQ Centre for Clinical Research, The University of Queensland, Herston, QLD, Australia
| | | | | | - Misha Hashmi
- Bio Molecular Systems, Potts Point, NSW, Australia
| | | | - David M. Whiley
- Faculty of Medicine, UQ Centre for Clinical Research, The University of Queensland, Herston, QLD, Australia
- Microbiology Department, Pathology Queensland, Herston, QLD, Australia
| | - Andreas Suhrbier
- Inflammation Biology Group, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- GVN Center of Excellence, Australian Infectious Disease Research Centre, Herston, QLD, Australia
| | - Joanne Macdonald
- Center for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- BioCifer Pty Ltd., Auchenflower, QLD, Australia
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2
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Ertl NG, Irwin AD, Macdonald J, Bauer MJ, Wang CYT, Harris PNA, Heney C, Zowawi HM, Whiley DM. Rapid molecular detection of CMY-2, and CTX-M group 1 and 9 variants via recombinase polymerase amplification. JAC Antimicrob Resist 2023; 5:dlad023. [PMID: 36936189 PMCID: PMC10020033 DOI: 10.1093/jacamr/dlad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 02/19/2023] [Indexed: 03/18/2023] Open
Abstract
Background Due to their prevalence worldwide, the β-lactamases CTX-M and plasmid-mediated CMY-2 are important antimicrobial resistance enzymes in a clinical setting. While culture- and PCR-based detection methods exist for these targets, they are time consuming and require specialist equipment and trained personnel to carry out. Methods In this study, three rapid diagnostic single-plex and a prototype triplex assay were developed, using recombinase polymerase amplification with lateral flow detection (RPA-LF), and tested for their sensitivity and specificity using two isolate DNA panels (n = 90 and n = 120 isolates). In addition, the RPA-LF assays were also tested with a small number of faecal extract samples (n = 18). Results The RPA-LF assays were able to detect bla CXT-M-group-1, bla CTX-M-group-9 and bla CMY-2-type variants with high sensitivity (82.1%-100%) and specificity (100%) within a short turnaround time (15-20 min for amplification and detection). Conclusions RPA-LF assays developed in this study have the potential to be used at or close to the point of care, as well as in low-resource settings, producing rapid results to support healthcare professionals in their treatment decisions.
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Affiliation(s)
- Nicole G Ertl
- Corresponding author. E-mail: ; @padstamundo, @MolecularEngeer
| | - Adam D Irwin
- The University of Queensland, UQ Centre for Clinical Research, Faculty of Medicine, Brisbane, QLD, Australia
- Infection Management and Prevention Service, Children’s Health Queensland, Brisbane, QLD, Australia
| | - Joanne Macdonald
- Centre for Bioinnovation and School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Michelle J Bauer
- The University of Queensland, UQ Centre for Clinical Research, Faculty of Medicine, Brisbane, QLD, Australia
| | - Claire Y T Wang
- Infection Management and Prevention Service, Children’s Health Queensland, Brisbane, QLD, Australia
| | - Patrick N A Harris
- The University of Queensland, UQ Centre for Clinical Research, Faculty of Medicine, Brisbane, QLD, Australia
- Microbiology Department, Central Laboratory, Pathology Queensland, Brisbane, QLD, Australia
| | - Claire Heney
- Microbiology Department, Central Laboratory, Pathology Queensland, Brisbane, QLD, Australia
| | - Hosam M Zowawi
- The University of Queensland, UQ Centre for Clinical Research, Faculty of Medicine, Brisbane, QLD, Australia
- College of Medicine, King Saud bin Abdul-Aziz University for Health Science (KSAU-HS), Riyadh, Saudi Arabia
- King Abdullah International Medical Research Centre (KAIMRC), Riyadh, Saudi Arabia
| | - David M Whiley
- The University of Queensland, UQ Centre for Clinical Research, Faculty of Medicine, Brisbane, QLD, Australia
- Infection Management and Prevention Service, Children’s Health Queensland, Brisbane, QLD, Australia
- Microbiology Department, Central Laboratory, Pathology Queensland, Brisbane, QLD, Australia
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Bialasiewicz S, May M, Tozer S, Day R, Bernard A, Zaugg J, Gartrell K, Alexandersen S, Chamings A, Wang CYT, Clark J, Grimwood K, Heney C, Schlapbach LJ, Ware RS, Speers D, Andrews RM, Lambert S. Novel Human Parechovirus 3 Diversity, Recombination, and Clinical Impact Across 7 Years: An Australian Story. J Infect Dis 2022; 227:278-287. [PMID: 35867852 PMCID: PMC9833435 DOI: 10.1093/infdis/jiac311] [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: 12/23/2021] [Revised: 07/12/2022] [Accepted: 07/21/2022] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND A novel human parechovirus 3 Australian recombinant (HPeV3-AR) strain emerged in 2013 and coincided with biennial outbreaks of sepsis-like illnesses in infants. We evaluated the molecular evolution of the HPeV3-AR strain and its association with severe HPeV infections. METHODS HPeV3-positive samples collected from hospitalized infants aged 5-252 days in 2 Australian states (2013-2020) and from a community-based birth cohort (2010-2014) were sequenced. Coding regions were used to conduct phylogenetic and evolutionary analyses. A recombinant-specific polymerase chain reaction was designed and utilized to screen all clinical and community HPeV3-positive samples. RESULTS Complete coding regions of 54 cases were obtained, which showed the HPeV3-AR strain progressively evolving, particularly in the 3' end of the nonstructural genes. The HPeV3-AR strain was not detected in the community birth cohort until the initial outbreak in late 2013. High-throughput screening showed that most (>75%) hospitalized HPeV3 cases involved the AR strain in the first 3 clinical outbreaks, with declining prevalence in the 2019-2020 season. The AR strain was not statistically associated with increased clinical severity among hospitalized infants. CONCLUSIONS HPeV3-AR was the dominant strain during the study period. Increased hospital admissions may have been from a temporary fitness advantage and/or increased virulence.
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Affiliation(s)
- Seweryn Bialasiewicz
- Correspondence: Seweryn Bialasiewicz, MSc, PhD, Australian Centre for Ecogenomics, The University of Queensland, Level 5, Bldg 76, St Lucia, QLD 4072, Australia ()
| | | | - Sarah Tozer
- Children’s Health Queensland Hospital and Health Service, Centre for Children’s Health Research, South Brisbane, Australia
| | - Rebecca Day
- Children’s Health Queensland Hospital and Health Service, Centre for Children’s Health Research, South Brisbane, Australia
| | - Anne Bernard
- QCIF Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
| | - Julian Zaugg
- School of Chemistry and Molecular Biosciences, The University of Queensland, Australian Centre for Ecogenomics, St Lucia, Australia
| | - Kyana Gartrell
- Children’s Health Queensland Hospital and Health Service, Centre for Children’s Health Research, South Brisbane, Australia
| | - Soren Alexandersen
- School of Medicine, Deakin University, Geelong, Australia,Statens Serum Institut, Copenhagen, Denmark
| | | | - Claire Y T Wang
- Children’s Health Queensland Hospital and Health Service, Centre for Children’s Health Research, South Brisbane, Australia
| | - Julia Clark
- Children’s Health Queensland Hospital and Health Service, South Brisbane, Australia
| | - Keith Grimwood
- School of Medicine and Dentistry, Menzies Health Institute Queensland, Griffith University, Southport, Australia,Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Southport, Australia
| | - Claire Heney
- Department of Microbiology, Pathology Queensland, Herston, Australia
| | - Luregn J Schlapbach
- Children’s Health Queensland Hospital and Health Service, South Brisbane, Australia,Department of Intensive Care and Neonatology, Children’s Research Center, University Children’s Hospital Zürich, Zürich, Switzerland
| | - Robert S Ware
- School of Medicine and Dentistry, Menzies Health Institute Queensland, Griffith University, Southport, Australia
| | - David Speers
- Department of Microbiology, PathWest Laboratory Medicine Western Australia, Queen Elizabeth II Medical Centre, Nedlands, Australia,School of Medicine, University of Western Australia, Crawley, Australia
| | - Ross M Andrews
- National Centre for Epidemiology and Population Health, Australian National University, Canberra, Australia
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El-Heneidy A, Cheung C, Lambert SB, Wang CYT, Whiley DM, Sly PD, Ware RS, Grimwood K. Histo-blood group antigens and rotavirus vaccine virus shedding in Australian infants. Pathology 2022; 54:928-934. [PMID: 35817636 DOI: 10.1016/j.pathol.2022.04.006] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 03/27/2022] [Accepted: 04/13/2022] [Indexed: 11/18/2022]
Abstract
Rotavirus vaccine performance varies between high and low income countries. One possible explanation is inherited histo-blood group antigens (HBGAs) the expression of which differs between populations. HBGAs are polymorphic glycans on mucosal surfaces. Their presence indicates the secretor phenotype, while their absence identifies a non-secretor status. HBGAs can act as rotavirus receptors and might influence live-attenuated rotavirus vaccine virus replication and shedding. Studies in low and middle income countries of the human rotavirus vaccine Rotarix (RV1), suggest HBGA secretor phenotype is important for vaccine immunogenicity. We investigated in a high income country the association between HBGA phenotype (secretor and Lewis) and the bovine-human reassortment vaccine RotaTeq (RV5) vaccine shedding in the stools of infants following each vaccine dose. Eighty-two infants from an Australian birth cohort provided saliva and weekly stool samples after RV5 vaccination doses. Lewis and secretor HBGA phenotyping was identified from saliva samples and confirmed by genotyping. Vaccine virus strains were detected by real-time polymerase chain reaction assays. No significant association between secretor status and vaccine virus shedding was identified. The proportion of infants who shed rotavirus following the first RV5 dose for secretor and non-secretor infants was 57/64 (89%) and 17/18 (94%), respectively, decreasing to 24/64 (33%) and 9/18 (50%) after the second dose and 26/64 (42%) and 8/18 (44%) following the third vaccine dose, respectively. Similarly, no significant differences were observed in vaccine virus shedding by Lewis, or combined Lewis and secretor status, after each vaccine dose. We found HBGAs were not associated with RV5 vaccine virus shedding in Australian infants.
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Affiliation(s)
- Asmaa El-Heneidy
- School of Medicine and Dentistry, and Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, Southport, Qld, Australia.
| | - Catherine Cheung
- Children's Health Queensland Hospital and Health Service, South Brisbane, Qld, Australia; Child Heath Research Centre, The University of Queensland, South Brisbane, Qld, Australia
| | - Stephen B Lambert
- Child Heath Research Centre, The University of Queensland, South Brisbane, Qld, Australia
| | - Claire Y T Wang
- Children's Health Queensland Hospital and Health Service, South Brisbane, Qld, Australia; Child Heath Research Centre, The University of Queensland, South Brisbane, Qld, Australia
| | - David M Whiley
- The University of Queensland Centre for Clinical Research, and Pathology Queensland Central Laboratory, Herston, Qld, Australia
| | - Peter D Sly
- Children's Health and Environment Program, Child Health Research Centre, The University of Queensland, South Brisbane, Qld, Australia
| | - Robert S Ware
- School of Medicine and Dentistry, and Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, Southport, Qld, Australia
| | - Keith Grimwood
- School of Medicine and Dentistry, and Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, Southport, Qld, Australia; Departments of Paediatrics and Infectious Diseases, Gold Coast Health, Southport, Qld, Australia
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Ayfan AKS, Macdonald J, Harris PNA, Heney C, Paterson DL, Trembizki E, Wang CYT, Whiley DM, Zowawi HM, Irwin AD. Rapid detection of NDM and VIM carbapenemase encoding genes by recombinase polymerase amplification and lateral flow-based detection. Eur J Clin Microbiol Infect Dis 2021; 40:2447-2453. [PMID: 33974185 DOI: 10.1007/s10096-021-04267-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 10/28/2020] [Accepted: 04/29/2021] [Indexed: 12/26/2022]
Abstract
Carbapenemase-producing organisms (CPOs) pose a serious clinical threat and rapid detection tools are essential to aid in patient management. We developed rapid and simple molecular tests to detect blaNDM-type and blaVIM-type carbapenemase genes using recombinase polymerase amplification (RPA) combined with a lateral flow detection. The tests could provide results in approximately 15 min when using DNA extracts, with limits of detection of 9.2 copies/μl for the blaNDM-type assay and 7.5 copies/μl for blaVIM-type assay, and successfully detected all isolates harbouring the carbapenemase encoding genes in a panel of 57 isolates. These RPA tests may be suitable for use in low-resource settings to tailor rapid implementation of infection control precautions and antibiotic stewardship.
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Affiliation(s)
- Abdulrahman K S Ayfan
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
- Faculty of Science, Biochemistry Department, King Abdul-Aziz University (KAU), Jeddah, Saudi Arabia
| | - Joanne Macdonald
- School of Science and Engineering, Genecology Research Centre, University of Sunshine Coast (USC), Sunshine Coast, Australia
| | - Patrick N A Harris
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
- Department of Microbiology, Pathology Queensland, Brisbane, Australia
| | - Claire Heney
- Department of Microbiology, Pathology Queensland, Brisbane, Australia
| | - David L Paterson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
| | - Ella Trembizki
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
| | - Claire Y T Wang
- Infection Management and Prevention Service, Queensland Children's Hospital, Brisbane, Australia
| | - David M Whiley
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
- Department of Microbiology, Pathology Queensland, Brisbane, Australia
| | - Hosam M Zowawi
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
- College of Medicine, King Saud bin Abdul-Aziz University for Health Science (KSAU-HS), Riyadh, Saudi Arabia
- King Abdullah International Medical Research Centre (KAIMRC), Riyadh, Saudi Arabia
| | - Adam D Irwin
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia.
- Infection Management and Prevention Service, Queensland Children's Hospital, Brisbane, Australia.
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Wang CYT, Ballard EL, Pava Z, Marquart L, Gaydon J, Murphy SC, Whiley D, O'Rourke P, McCarthy JS. Analytical validation of a real-time hydrolysis probe PCR assay for quantifying Plasmodium falciparum parasites in experimentally infected human adults. Malar J 2021; 20:181. [PMID: 33838672 PMCID: PMC8035755 DOI: 10.1186/s12936-021-03717-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 04/14/2020] [Accepted: 03/29/2021] [Indexed: 11/10/2022] Open
Abstract
Background Volunteer infection studies have become a standard model for evaluating drug efficacy against Plasmodium infections. Molecular techniques such as qPCR are used in these studies due to their ability to provide robust and accurate estimates of parasitaemia at increased sensitivity compared to microscopy. The validity and reliability of assays need to be ensured when used to evaluate the efficacy of candidate drugs in clinical trials. Methods A previously described 18S rRNA gene qPCR assay for quantifying Plasmodium falciparum in blood samples was evaluated. Assay performance characteristics including analytical sensitivity, reportable range, precision, accuracy and specificity were assessed using experimental data and data compiled from phase 1 volunteer infection studies conducted between 2013 and 2019. Guidelines for validation of laboratory-developed molecular assays were followed. Results The reportable range was 1.50 to 6.50 log10 parasites/mL with a limit of detection of 2.045 log10 parasites/mL of whole blood based on a parasite diluted standard series over this range. The assay was highly reproducible with minimal intra-assay (SD = 0.456 quantification cycle (Cq) units [0.137 log10 parasites/mL] over 21 replicates) and inter-assay (SD = 0.604 Cq units [0.182 log10 parasites/mL] over 786 qPCR runs) variability. Through an external quality assurance program, the QIMR assay was shown to generate accurate results (quantitative bias + 0.019 log10 parasites/mL against nominal values). Specificity was 100% after assessing 164 parasite-free human blood samples. Conclusions The 18S rRNA gene qPCR assay is specific and highly reproducible and can provide reliable and accurate parasite quantification. The assay is considered fit for use in evaluating drug efficacy in malaria clinical trials. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-03717-y.
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Affiliation(s)
- Claire Y T Wang
- Centre for Children's Health Research, Children's Health Queensland, Brisbane, Australia. .,Child Health Research Centre, The University of Queensland, Brisbane, Australia.
| | - Emma L Ballard
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Zuleima Pava
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Louise Marquart
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jane Gaydon
- Centre for Children's Health Research, Children's Health Queensland, Brisbane, Australia.,Child Health Research Centre, The University of Queensland, Brisbane, Australia
| | - Sean C Murphy
- Departments of Laboratory Medicine and Microbiology, University of Washington, Seattle, WA, USA.,Center for Emerging and Re-Emerging Infectious Diseases, University of Washington, Seattle, WA, USA
| | - David Whiley
- Centre for Children's Health Research, Children's Health Queensland, Brisbane, Australia.,UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Peter O'Rourke
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - James S McCarthy
- QIMR Berghofer Medical Research Institute, Brisbane, Australia.,School of Medicine, The University of Queensland, Brisbane, Australia
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7
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Wang CYT, Ware RS, Lambert SB, Mhango LP, Tozer S, Day R, Grimwood K, Bialasiewicz S. Parechovirus A Infections in Healthy Australian Children During the First 2 Years of Life: A Community-based Longitudinal Birth Cohort Study. Clin Infect Dis 2021; 71:116-127. [PMID: 31406985 PMCID: PMC7108192 DOI: 10.1093/cid/ciz761] [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: 04/14/2019] [Accepted: 08/07/2019] [Indexed: 12/13/2022] Open
Abstract
Background Hospital-based studies identify parechovirus (PeV), primarily PeV-A3, as an important cause of severe infections in young children. However, few community-based studies have been published and the true PeV infection burden is unknown. We investigated PeV epidemiology in healthy children participating in a community-based, longitudinal birth cohort study. Methods Australian children (n = 158) enrolled in the Observational Research in Childhood Infectious Diseases (ORChID) study were followed from birth until their second birthday. Weekly stool and nasal swabs and daily symptom diaries were collected. Swabs were tested for PeV by reverse-transcription polymerase chain reaction and genotypes determined by subgenomic sequencing. Incidence rate, infection characteristics, clinical associations, and virus codetections were investigated. Results PeV was detected in 1423 of 11 124 (12.8%) and 17 of 8100 (0.2%) stool and nasal swabs, respectively. Major genotypes among the 306 infection episodes identified were PeV-A1 (47.9%), PeV-A6 (20.1%), and PeV-A3 (18.3%). The incidence rate was 144 episodes (95% confidence interval, 128–160) per 100 child-years. First infections appeared at a median age of 8 (interquartile range, 6.0–11.7) months. Annual seasonal peaks changing from PeV-A1 to PeV-A3 were observed. Infection was positively associated with age ≥6 months, summer season, nonexclusive breastfeeding at age <3 months, and formal childcare attendance before age 12 months. Sole PeV infections were either asymptomatic (38.4%) or mild (32.7%), while codetection with other viruses in stool swabs was common (64.4%). Conclusions In contrast with hospital-based studies, this study showed that diverse and dynamically changing PeV genotypes circulate in the community causing mild or subclinical infections in children. Parechovirus can cause severe illnesses in children. However, studies focus mainly on hospitalized populations. True disease burden in the community remains largely unknown. From our community-based cohort, we found diverse parechovirus genotypes in the community, causing mild or subclinical infections in children.
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Affiliation(s)
- Claire Y T Wang
- Centre for Children's Health Research, Queensland Children's Hospital Brisbane, Brisbane, Australia.,Child Health Research Centre, School of Medicine, The University of Queensland, Brisbane, Australia
| | - Robert S Ware
- Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
| | - Stephen B Lambert
- Centre for Children's Health Research, Queensland Children's Hospital Brisbane, Brisbane, Australia.,Child Health Research Centre, School of Medicine, The University of Queensland, Brisbane, Australia
| | - Lebogang P Mhango
- Centre for Children's Health Research, Queensland Children's Hospital Brisbane, Brisbane, Australia.,Child Health Research Centre, School of Medicine, The University of Queensland, Brisbane, Australia
| | - Sarah Tozer
- Centre for Children's Health Research, Queensland Children's Hospital Brisbane, Brisbane, Australia.,Child Health Research Centre, School of Medicine, The University of Queensland, Brisbane, Australia
| | - Rebecca Day
- Centre for Children's Health Research, Queensland Children's Hospital Brisbane, Brisbane, Australia.,Child Health Research Centre, School of Medicine, The University of Queensland, Brisbane, Australia
| | - Keith Grimwood
- School of Medicine and Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia.,Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Gold Coast, Australia
| | - Seweryn Bialasiewicz
- Centre for Children's Health Research, Queensland Children's Hospital Brisbane, Brisbane, Australia.,Child Health Research Centre, School of Medicine, The University of Queensland, Brisbane, Australia
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8
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Wang CYT, Buckley C, Bletchly C, Harris P, Whiley D. Contamination of SARS-CoV-2 RT-PCR probes at the oligonucleotide manufacturer. Pathology 2020; 52:814-816. [PMID: 32888705 PMCID: PMC7437487 DOI: 10.1016/j.pathol.2020.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 01/21/2023]
Affiliation(s)
- Claire Y T Wang
- Centre for Children's Health Research, Children's Health Queensland, Brisbane, Qld, Australia.
| | - Cameron Buckley
- The University of Queensland Centre for Clinical Research, The University of Queensland, Brisbane, Qld, Australia
| | - Cheryl Bletchly
- Pathology Queensland Central Laboratory, Brisbane, Qld, Australia
| | - Patrick Harris
- The University of Queensland Centre for Clinical Research, The University of Queensland, Brisbane, Qld, Australia; Pathology Queensland Central Laboratory, Brisbane, Qld, Australia
| | - David Whiley
- The University of Queensland Centre for Clinical Research, The University of Queensland, Brisbane, Qld, Australia; Pathology Queensland Central Laboratory, Brisbane, Qld, Australia
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9
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Wang CYT, Ballard E, Llewellyn S, Marquart L, Bousema T, McCarthy JS, Collins KA. Assays for quantification of male and female gametocytes in human blood by qRT-PCR in the absence of pure sex-specific gametocyte standards. Malar J 2020; 19:218. [PMID: 32576184 PMCID: PMC7310411 DOI: 10.1186/s12936-020-03291-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/17/2020] [Indexed: 12/25/2022] Open
Abstract
Background Malaria transmission from humans to Anopheles mosquitoes requires the presence of gametocytes in human peripheral circulation, and the dynamics of transmission are determined largely by the density and sex ratio of the gametocytes. Molecular methods are thus employed to measure gametocyte densities, particularly when assessing transmission epidemiology and the efficacy of transmission-blocking interventions. However, accurate quantification of male and female gametocytes with molecular methods requires pure male and female gametocytes as reference standards, which are not widely available. Methods qRT-PCR assays were used to quantify levels of sex-specific mRNA transcripts in Plasmodium falciparum female and male gametocytes (pfs25 and pfMGET, respectively) using synthetic complimentary RNA standards and in vitro cultured gametocytes. Assays were validated and assay performance was investigated in blood samples of clinical trial participants using these standards and compared to absolute quantification by droplet digital PCR (ddPCR). Results The number of transcript copies per gametocyte were determined to be 279.3 (95% CI 253.5–307.6) for the female-specific transcript pfs25, and 12.5 (95% CI 10.6–14.9) for the male-specific transcript pfMGET. These numbers can be used to convert from transcript copies/mL to gametocyte/mL. The reportable range was determined to be 5.71 × 106 to 5.71 female gametocytes/mL for pfs25, and 1.73 × 107 to 1.73 × 101 male gametocytes/mL for pfMGET. The limit of detection was 3.9 (95% CI 2.5–8.2) female gametocytes/mL for pfs25, and 26.9 (95% CI 19.3–51.7) male gametocytes/mL for PfMGET. Both assays showed minimal intra-assay and inter-assay variability with coefficient of variation < 3%. No cross-reactivity was observed in both assays in uninfected human blood samples. Comparison of results from ddPCR to qRT-PCR assays on clinical blood samples indicated a high-level agreement (ICC = 0.998 for pfs25 and 0.995 for pfMGET). Conclusions This study reports the validation of qRT-PCR assays that are able to accurately quantify female and male P. falciparum gametocytes at sub-microscopic densities. The assays showed excellent reproducibility, sensitivity, precision, specificity, and accuracy. The methodology will enable the estimation of gametocyte density in the absence of pure female and male gametocyte standards, and will facilitate clinical trials and epidemiological studies.
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Affiliation(s)
- Claire Y T Wang
- QPID Laboratory, Centre for Children's Health Research, Brisbane, QLD, Australia
| | - Emma Ballard
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Stacey Llewellyn
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Louise Marquart
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Teun Bousema
- Radboud Institute for Health Science, Radboud University Medical Center, Nijmegen, The Netherlands
| | - James S McCarthy
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Katharine A Collins
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia. .,Radboud Institute for Health Science, Radboud University Medical Center, Nijmegen, The Netherlands.
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10
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Arden KE, Greer RM, Wang CYT, Mackay IM. Genotypic diversity, circulation patterns and co-detections among rhinoviruses in Queensland, 2001. Access Microbiol 2019; 2:acmi000075. [PMID: 33062934 PMCID: PMC7525053 DOI: 10.1099/acmi.0.000075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 09/05/2019] [Accepted: 10/07/2019] [Indexed: 12/13/2022] Open
Abstract
Purpose Rhinoviruses (RVs) occur more frequently than other viruses and more often in people displaying symptoms than in those without. We sought to estimate the spectrum of RV diversity, RV species seasonality and to analyse RV involvement in respiratory virus co-detections. Methodology A convenience collection of 1179 airway sample extracts from patients with suspected respiratory infections, collected during 2001, was subjected to comprehensive molecular testing. Results RVs were the most common virus detected. We were able to genotype ~90 % of RV detections, identifying 70 distinct RVs, spanning all three species. RV-Bs were under-represented. We found RV species co-circulated at times, although one species usually dominated. Each species displayed a bimodal distribution. Conclusion Notably, RVs and influenza A viruses (IFAV) seldom co-occurred, supporting their roles as primary pathogens of the airway among acutely ill infants. Whether RV circulation has a moderating or controlling effect on the IFAV season or is controlled by it cannot be determined from these data. Despite the frequent perception that RVs commonly co-occur with another virus, our findings indicated this was not always the case. Nearly 80 % of RV detections occurred alone. Understanding more about population-level interference between viruses may allow us to harness aspects of it to generate a non-specific antiviral intervention that mimics a putative protective effect. For routine respiratory virus screening to best serve the patient, RV testing should be a principal component of any acute respiratory illness testing algorithm throughout the year.
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Affiliation(s)
- Katherine E Arden
- Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Ristan M Greer
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Claire Y T Wang
- Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,Centre for Children's Health Research, Children's Health Queensland South Brisbane, Queensland, 4101, Australia
| | - Ian M Mackay
- Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
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11
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Ballard E, Wang CYT, Hien TT, Tong NT, Marquart L, Pava Z, Tarning J, O'Rourke P, McCarthy JS. A validation study of microscopy versus quantitative PCR for measuring Plasmodium falciparum parasitemia. Trop Med Health 2019; 47:49. [PMID: 31485189 PMCID: PMC6712708 DOI: 10.1186/s41182-019-0176-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 06/16/2019] [Accepted: 08/12/2019] [Indexed: 12/02/2022] Open
Abstract
Microscopy and 18S qPCR are the most common and field-friendly methods for quantifying malaria parasite density, and it is important that these methods can be interpreted as giving equivalent results. We compared results of quantitative measurement of Plasmodium falciparum parasitemia by microscopy and by 18S qPCR in a phase 2a study. Microscopy positive samples (n = 355; median 810 parasites/μL [IQR 40–10,471]) showed close agreement with 18S qPCR in mean log10/mL transformed parasitemia values by paired t test (difference 0.04, 95%CI − 0.01–0.10, p = 0.088). Excellent intraclass correlation (0.97) and no evidence of systematic or proportional differences by Passing–Bablok regression were observed. 18S qPCR appears to give equivalent parasitemia values to microscopy, which indicates 18S qPCR is an appropriate alternative method to quantify parasitemia in clinical trials.
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Affiliation(s)
- Emma Ballard
- 1QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Claire Y T Wang
- Queensland Paediatric Infectious Diseases Laboratory, Centre for Children's Health Research, Brisbane, Australia
| | - Tran Tinh Hien
- 3Oxford University Clinical Research Unit-Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Nguyen Thanh Tong
- 3Oxford University Clinical Research Unit-Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Louise Marquart
- 1QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Zuleima Pava
- 1QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Joel Tarning
- 4Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,5Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Oxford University, Oxford, UK
| | - Peter O'Rourke
- 1QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - James S McCarthy
- 1QIMR Berghofer Medical Research Institute, Brisbane, Australia.,6The University of Queensland, Brisbane, Australia
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12
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Teoh L, Mackay IM, Van Asperen PP, Acworth JP, Hurwitz M, Upham JW, Siew WH, Wang CYT, Sloots TP, Neeman T, Chang AB. Presence of atopy increases the risk of asthma relapse. Arch Dis Child 2018; 103:346-351. [PMID: 29021189 DOI: 10.1136/archdischild-2017-312982] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 03/07/2017] [Revised: 08/16/2017] [Accepted: 09/11/2017] [Indexed: 01/31/2023]
Abstract
OBJECTIVES To describe the point prevalence of respiratory viruses/atypical bacteria using PCR and evaluate the impact of respiratory viruses/atypical bacteria and atopy on acute severity and clinical recovery in children with hospitalised and non-hospitalised asthma exacerbations. DESIGN This was a prospective study performed during 2009-2011. SETTING The study was performed in the emergency departments of two hospitals. PATIENTS 244 children aged 2-16 years presenting with acute asthma to the emergency departments were recruited. A nasopharyngeal aspirate and allergen skin prick test were performed. MAIN OUTCOME MEASURES The outcomes were divided into (1) acute severity outcomes (Australian National Asthma Council assessment, hospitalisation, Functional Severity Scale, Acute Asthma Score, asthma quality of life questionnaires for parents (PACQLQ) on presentation, asthma diary scores (ADS) on presentation and length of hospitalisation) and (2) recovery outcomes (PACQLQ for 21 days, ADS for 14 days and representation for asthma for 21 days). RESULTS PCR for viruses/atypical bacteria was positive in 81.7% of children (75.1% human rhinovirus, codetection in 14.2%). Mycoplasma pneumoniae and Chlamydophila pneumoniae were rarely detected. The presence of micro-organisms had little impact on acute asthma or recovery outcomes. Children with atopy were significantly more likely to relapse and represent for medical care by day 14 (OR 1.11, 95% CI 1.00 to 1.23). CONCLUSIONS The presence of any viruses is associated with asthma exacerbations but does not appear to influence asthma recovery. In contrast, atopy is associated with asthma relapse. M. pneumoniae and C. pneumoniae are rare triggers of acute asthma in young children.
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Affiliation(s)
- Laurel Teoh
- Department of Paediatrics and Child Health, Centenary Hospital for Women and Children, Canberra, Australian Capital Territory, Australia.,Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Ian M Mackay
- Queensland Paediatric Infectious Diseases Laboratory, The University of Queensland, Brisbane, Queensland, Australia.,Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Peter P Van Asperen
- Department of Respiratory Medicine, The Children's Hospital at Westmead, Sydney Children's Hospitals Network, Westmead, New South Wales, Australia.,Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Jason P Acworth
- Emergency Medicine Department, Lady Cilento Children's Hospital, Brisbane, Queensland, Australia
| | - Mark Hurwitz
- Department of Respiratory and Sleep Medicine, The Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - John W Upham
- School of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Weng Hou Siew
- Queensland Paediatric Infectious Diseases Laboratory, The University of Queensland, Brisbane, Queensland, Australia
| | - Claire Y T Wang
- Queensland Paediatric Infectious Diseases Laboratory, The University of Queensland, Brisbane, Queensland, Australia.,Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Theo P Sloots
- Queensland Paediatric Infectious Diseases Laboratory, The University of Queensland, Brisbane, Queensland, Australia.,Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Teresa Neeman
- Statistical Consulting Unit, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Anne B Chang
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.,Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia.,Respiratory and Sleep Medicine Department, Lady Cilento Children's Hospital, Brisbane, Queensland, Australia
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13
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Pasay CJ, Rockett R, Sekuloski S, Griffin P, Marquart L, Peatey C, Wang CYT, O'Rourke P, Elliott S, Baker M, Möhrle JJ, McCarthy JS. Piperaquine Monotherapy of Drug-Susceptible Plasmodium falciparum Infection Results in Rapid Clearance of Parasitemia but Is Followed by the Appearance of Gametocytemia. J Infect Dis 2016; 214:105-13. [PMID: 27056954 PMCID: PMC4907420 DOI: 10.1093/infdis/jiw128] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [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: 12/23/2015] [Accepted: 03/24/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Piperaquine, coformulated with dihydroartemisinin, is a component of a widely used artemisinin combination therapy. There is a paucity of data on its antimalarial activity as a single agent. Such data, if available, would inform selection of new coformulations. METHODS We undertook a study in healthy subjects, using the induced blood stage malaria (IBSM) model to test the antimalarial activity of single doses of piperaquine (960, 640, and 480 mg) in 3 cohorts. In a pilot study in the third cohort, gametocyte clearance following administration of 15 mg, or 45 mg or no primaquine was investigated. RESULTS Parasite clearance over the 48-hour period after piperaquine administration was more rapid in the 960 mg cohort, compared with the 640 mg cohort (parasite reduction ratio, 2951 [95% confidence interval {CI}, 1520-5728] vs 586 [95% CI, 351-978]; P < .001). All 24 subjects developed gametocytemia as determined by pfs25 transcripts. Clearance of pfs25 was significantly faster in those receiving primaquine than in those not receiving primaquine (P < .001). CONCLUSIONS Piperaquine possesses rapid parasite-clearing activity, but monotherapy is followed by the appearance of gametocytemia, which could facilitate the spread of malaria. This new information should be taken into account when developing future antimalarial coformulations. CLINICAL TRIALS REGISTRATION ACTRN12613000565741.
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Affiliation(s)
| | - Rebecca Rockett
- School of Chemistry and Molecular Biosciences Queensland Pediatric Infectious Diseases Laboratory
| | | | - Paul Griffin
- QIMR Berghofer Medical Research Institute School of Medicine, University of Queensland Q-Pharm Department of Infectious Diseases, Mater Health Services and Mater Research Institute
| | | | | | | | | | | | | | | | - James S McCarthy
- QIMR Berghofer Medical Research Institute School of Medicine, University of Queensland Q-Pharm
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14
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Wurzel DF, Mackay IM, Marchant JM, Wang CYT, Yerkovich ST, Upham JW, Smith-Vaughan HC, Petsky HL, Chang AB. Adenovirus species C is associated with chronic suppurative lung diseases in children. Clin Infect Dis 2014; 59:34-40. [PMID: 24748519 PMCID: PMC4305137 DOI: 10.1093/cid/ciu225] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [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: 01/10/2023] Open
Abstract
Background. The role of human adenoviruses (HAdVs) in chronic respiratory disease pathogenesis is recognized. However, no studies have performed molecular sequencing of HAdVs from the lower airways of children with chronic endobronchial suppuration. We thus examined the major HAdV genotypes/species, and relationships to bacterial coinfection, in children with protracted bacterial bronchitis (PBB) and mild bronchiectasis (BE). Methods. Bronchoalveolar lavage (BAL) samples of 245 children with PBB or mild (cylindrical) BE were included in this prospective cohort study. HAdVs were genotyped (when possible) in those whose BAL had HAdV detected (HAdV+). Presence of bacterial infection (defined as ≥104 colony-forming units/mL) was compared between BAL HAdV+ and HAdV negative (HAdV−) groups. Immune function tests were performed including blood lymphocyte subsets in a random subgroup. Results. Species C HAdVs were identified in 23 of 24 (96%) HAdV+ children; 13 (57%) were HAdV-1 and 10 (43%) were HAdV-2. An HAdV+ BAL was significantly associated with bacterial coinfection with Haemophilus influenzae, Moraxella catarrhalis, or Streptococcus pneumoniae (odds ratio [OR], 3.27; 95% confidence interval, 1.38–7.75; P = .007) and negatively associated with Staphylococcus aureus infection (P = .03). Young age was related to increased rates of HAdV+. Blood CD16 and CD56 natural killer cells were significantly more likely to be elevated in those with HAdV (80%) compared with those without (56.1%) (P = .027). Conclusions. HAdV-C is the major HAdV species detected in the lower airways of children with PBB and BE. Younger age appears to be an important risk factor for HAdV+ of the lower airways and influences the likelihood of bacterial coinfection.
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Affiliation(s)
- Danielle F Wurzel
- Queensland Children's Medical Research Institute, The University of Queensland Queensland Children's Respiratory Centre, Royal Children's Hospital
| | - Ian M Mackay
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Medical Research Institute, Sir Albert Sakzewski Virus Research Centre, Children's Health Queensland Hospital and Health Service, The University of Queensland, Herston
| | - Julie M Marchant
- Queensland Children's Medical Research Institute, The University of Queensland Queensland Children's Respiratory Centre, Royal Children's Hospital
| | - Claire Y T Wang
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Medical Research Institute, Sir Albert Sakzewski Virus Research Centre, Children's Health Queensland Hospital and Health Service, The University of Queensland, Herston
| | | | - John W Upham
- School of Medicine, The University of Queensland, Brisbane
| | - Heidi C Smith-Vaughan
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Helen L Petsky
- Queensland Children's Respiratory Centre, Royal Children's Hospital Queensland Children's Medical Research Institute, Queensland University of Technology, Brisbane
| | - Anne B Chang
- Queensland Children's Respiratory Centre, Royal Children's Hospital Queensland Children's Medical Research Institute, Queensland University of Technology, Brisbane Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
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15
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Wurzel DF, Marchant JM, Clark JE, Mackay IM, Wang CYT, Sloots TP, Upham JW, Yerkovich ST, Masters IB, Baker PJ, Anderson-James S, Chang AB. Respiratory virus detection in nasopharyngeal aspirate versus bronchoalveolar lavage is dependent on virus type in children with chronic respiratory symptoms. J Clin Virol 2013; 58:683-8. [PMID: 24125830 PMCID: PMC7173340 DOI: 10.1016/j.jcv.2013.09.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [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: 07/02/2013] [Revised: 09/12/2013] [Accepted: 09/13/2013] [Indexed: 12/14/2022]
Abstract
Background The comparative yield of respiratory virus detection from nasopharyngeal aspirate (NPA) versus bronchoalveolar lavage (BAL) is uncertain. Furthermore, the significance of virus detection and its relationship to lower airway neutrophilic inflammation is poorly studied. Objectives To evaluate the sensitivity, specificity and predictive values of NPA for detecting respiratory viruses in BAL; and to determine the relationship between viruses and lower airway neutrophilia in children with non-acute respiratory illness. Study design 150 paired NPA and BAL samples were obtained from 75 children aged <18 years undergoing flexible bronchoscopy for investigation of chronic respiratory symptoms. Viral studies were performed using polymerase chain reaction (PCR). Cellularity studies were performed on BALs. Diagnostic parameters of NPA compared to BAL and associations between viruses and lower airway %neutrophils were evaluated. Results NPA had a higher yield than BAL for detection of any respiratory virus (52 versus 38, respectively). NPA had a high sensitivity (92%) and low specificity (57%) for detecting HRV in BAL with poor kappa agreement value of 0.398 (95% CI 0.218–0.578, p < 0.001). NPA had a fair sensitivity (69%) and good specificity (90.3%) for detecting HAdV on BAL, kappa agreement was 0.561 (95% CI 0.321–0.801, p < 0.001). HAdV positivity on NPA, compared to negativity, was independently associated with heightened airway neutrophilia [mean difference (95% CI): 18 (1,35); p = 0.042]. Conclusions NPA has a higher yield for respiratory virus detection than BAL, however its diagnostic accuracy is dependent on viral species. Adenovirus positivity is associated with significantly heightened lower airway neutrophilia in children with chronic respiratory symptoms.
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Affiliation(s)
- Danielle F Wurzel
- Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, Australia; Queensland Children's Respiratory Centre, Royal Children's Hospital, Brisbane, Australia.
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16
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Wang CYT, Greer RM, Delwart E, Sloots TP, Mackay IM. A newly designed real-time RT-PCR for SAFV detects SAFV-2 and SAFV-3 in the respiratory tracts of ill children during 2011. J Clin Virol 2012; 55:173-6. [PMID: 22832058 PMCID: PMC7108345 DOI: 10.1016/j.jcv.2012.06.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [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: 04/13/2012] [Revised: 06/28/2012] [Accepted: 06/29/2012] [Indexed: 01/06/2023]
Affiliation(s)
- C Y T Wang
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Medical Research Institute, Sir Albert Sakzewski Virus Research Centre, Children's Health Services, The University of Queensland, Australia
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17
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Wang CYT, Arden KE, Greer R, Sloots TP, Mackay IM. A novel duplex real-time PCR for HPIV-4 detects co-circulation of both viral subtypes among ill children during 2008. J Clin Virol 2012; 54:83-5. [PMID: 22361219 DOI: 10.1016/j.jcv.2012.01.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 01/23/2012] [Indexed: 11/16/2022]
Abstract
The two subtypes of the human parainfluenzavirus type 4 (HPIV-4) are rarely sought in testing for acute respiratory illness (ARI) and this may be confounding our understanding of its role. This study presents a novel duplex real-time RT-PCR assay targeting the P gene that can detect and differentiate the two subtypes in a single reaction. Subtype-specific synthetic RNA positive controls were prepared and used to determine an analytical sensitivity of 10 copies per reaction with an 8log(10) dynamic range. The assays were validated using 1140 clinical specimens mostly nasopharyngeal aspirates collected from children during 2008. These included specimens previously determined to be positive for all commonly considered respiratory viruses. The novel assay did not cross-reaction with any other virus. Fourteen HPIV-4 positives, ten detected in the absence of any co-detections (four with rhinovirus), were identified in 2008 and their subtype confirmed by conventional RT-PCR and sequencing of P gene fragments. Most detections were in children two years of age or younger. Our assay proved suitably sensitive and specific for inclusion in future studies seeking to better understand the role HPIV-4 and other respiratory viruses in children with ARI.
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Affiliation(s)
- C Y T Wang
- Queensland paediatric infectious diseases Laboratory, Queensland Children's Medical Research Institute, Sir Albert Sakzewski Virus Research Centre, Children's Health Services District, University of Queensland, Australia
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