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Tang HT, Nörz D, Grunwald M, Giersch K, Pfefferle S, Fischer N, Aepfelbacher M, Rohde H, Lütgehetmann M. Analytical and clinical validation of a novel, laboratory-developed, modular multiplex-PCR panel for fully automated high-throughput detection of 16 respiratory viruses. J Clin Virol 2024; 173:105693. [PMID: 38820916 DOI: 10.1016/j.jcv.2024.105693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/02/2024]
Abstract
BACKGROUND Viral respiratory Infections pose a health risk, especially to vulnerable patient populations. Effective testing programs can detect and differentiate these infections at an early stage, which is particularly important for high-risk clinical departments. The objective of this study was to develop and validate a multiplex PCR-panel for 16 different respiratory viruses on a fully-automated high-throughput platform. METHODS Three multiplex-PCR assays were designed to run on the cobas5800/6800/8800 systems, consolidating 16 viral targets: RESP1: SARS-CoV-2, influenza-A/B, RSV; RESP2: hMPV, hBoV, hAdV, rhino-/ENV; RESP3: HPIV-1-4, hCoV-229E, hCoV-NL63, hCoV-OC43, hCoV-HKU1. Analytic performance was evaluated using digital-PCR based standards and international reference material. Clinical performance was determined by comparing results from clinical samples with reference assays. RESULTS Analytical sensitivity (i.e. lower limit of detection (LoD), 95 % probability of detection) was determined as follows: SARS-CoV-2: 29.3 IU/ml, influenza-A: 179.9 cp/ml, influenza-B: 333.9 cp/ml and RSV: 283.1 cp/ml. LoDs of other pathogens ranged between 9.4 cp/ml (hCoV-NL63) and 21,419 cp/ml (HPIV-2). Linearity was verified over 4-7 log-steps with pooled standard differentials (SD) ranging between 0.18-0.70ct. Inter-/intra-run variability (precision) was assessed for all targets over 3 days. SDs ranged between 0.13-0.74ct. Positive agreement in clinical samples was 99.4 % and 95 % for SARS-CoV-2 and influenza-A respectively. Other targets were in the 80-100 % range. Negative agreement varied between 96.3-100 %. DISCUSSION Lab-developed tests are a key factor for effective clinical diagnostics. The multiplex panel presented in this study demonstrated high performance and provides an easily scalable high-throughput solution for respiratory virus testing, e.g. for testing in high-risk patient populations.
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Affiliation(s)
- Hui Ting Tang
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Dominik Nörz
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Moritz Grunwald
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Katja Giersch
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Susanne Pfefferle
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Nicole Fischer
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Martin Aepfelbacher
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Holger Rohde
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany
| | - Marc Lütgehetmann
- University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, Hamburg, Germany.
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Millward GG, Popelka SM, Gutierrez AG, Kowallis WJ, von Tersch RL, Yerramilli SV. A novel strategy to avoid sensitivity loss in pooled testing for SARS-CoV-2 surveillance: validation using nasopharyngeal swab and saliva samples. Front Public Health 2023; 11:1190308. [PMID: 37637813 PMCID: PMC10450028 DOI: 10.3389/fpubh.2023.1190308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023] Open
Abstract
At the peak of the COVID-19 pandemic, pooled surveillance strategies were employed to alleviate the overwhelming demand for clinical testing facilities. A major drawback of most pooled-testing methods is the dilution of positive samples, which leads to a loss of detection sensitivity and the potential for false negatives. We developed a novel pooling strategy that compensates for the initial dilution with an appropriate concentration during nucleic acid extraction and real-time PCR. We demonstrated the proof of principle using laboratory-created 10-sample pools with one positive and corresponding individual positive samples by spiking a known amount of heat-inactivated SARS-CoV-2 into viral transport medium (VTM) or pooled negative saliva. No Ct difference was observed between a 10-sample pool with one positive vs. the corresponding individually analyzed positive sample by this method, suggesting that there is no detectable loss of sensitivity. We further validated this approach by using nasopharyngeal swab (NPS) specimens and showed that there is no loss of sensitivity. Serial dilutions of the virus were spiked into VTM and pooled with negative saliva in simulated 10-sample pools containing one positive to determine the LOD and process efficiency of this pooling methodology. The LOD of this approach was 10 copies/PCR, and the process efficiencies are ~95%-103% for N1 and ~87%-98% for N2 with samples in different matrices and with two different master mixes tested. Relative to TaqPath 1-step master mix, the TaqMan Fast Virus 1-Step master mix showed better sensitivity for the N2 assay, while the N1 assay showed no Ct difference. Our pooled testing strategy can facilitate large-scale, cost-effective SARS-CoV-2 surveillance screening and maintain the same level of sensitivity when analyzed individually or in a pool. This approach is highly relevant for public health surveillance efforts aimed at mitigating SARS-CoV-2 spread.
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Affiliation(s)
| | | | | | | | | | - Subrahmanyam V. Yerramilli
- Emerging Biological Threats Branch, Molecular Biology Division, Laboratory Sciences, Defense Centers for Public Health - Aberdeen “Formerly the Army Public Health Center”, Aberdeen Proving Ground, Edgewood, MD, United States
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3
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Sikazwe C, Neave MJ, Michie A, Mileto P, Wang J, Cooper N, Levy A, Imrie A, Baird RW, Currie BJ, Speers D, Mackenzie JS, Smith DW, Williams DT. Molecular detection and characterisation of the first Japanese encephalitis virus belonging to genotype IV acquired in Australia. PLoS Negl Trop Dis 2022; 16:e0010754. [PMID: 36409739 PMCID: PMC9721490 DOI: 10.1371/journal.pntd.0010754] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/05/2022] [Accepted: 10/24/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND A fatal case of Japanese encephalitis (JE) occurred in a resident of the Tiwi Islands, in the Northern Territory of Australia in February 2021, preceding the large JE outbreak in south-eastern Australia in 2022. This study reports the detection, whole genome sequencing and analysis of the virus responsible (designated JEV/Australia/NT_Tiwi Islands/2021). METHODS Reverse transcription quantitative PCR (RT-qPCR) testing was performed on post-mortem brain specimens using a range of JE virus (JEV)-specific assays. Virus isolation from brain specimens was attempted by inoculation of mosquito and mammalian cells or embryonated chicken eggs. Whole genome sequencing was undertaken using a combination of Illumina next generation sequencing methodologies, including a tiling amplicon approach. Phylogenetic and selection analyses were performed using alignments of the Tiwi Islands JEV genome and envelope (E) protein gene sequences and publicly available JEV sequences. RESULTS Virus isolation was unsuccessful and JEV RNA was detected only by RT-qPCR assays capable of detecting all JEV genotypes. Phylogenetic analysis revealed that the Tiwi Islands strain is a divergent member of genotype IV (GIV) and is closely related to the 2022 Australian outbreak virus (99.8% nucleotide identity). The Australian strains share highest levels of nucleotide identity with Indonesian viruses from 2017 and 2019 (96.7-96.8%). The most recent common ancestor of this Australian-Indonesian clade was estimated to have emerged in 2007 (95% HPD range: 1998-2014). Positive selection was detected using two methods (MEME and FEL) at several sites in the E and non-structural protein genes, including a single site in the E protein (S194N) unique to the Australian GIV strains. CONCLUSION This case represents the first detection of GIV JEV acquired in Australia, and only the second confirmed fatal human infection with a GIV JEV strain. The close phylogenetic relationship between the Tiwi Islands strain and recent Indonesian viruses is indicative of the origin of this novel GIV lineage, which we estimate has circulated in the region for several years prior to the Tiwi Islands case.
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Affiliation(s)
- Chisha Sikazwe
- PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
| | - Matthew J. Neave
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia
| | - Alice Michie
- PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
| | - Patrick Mileto
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia
| | - Jianning Wang
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia
| | - Natalie Cooper
- PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
| | - Avram Levy
- PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
| | - Allison Imrie
- PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
| | - Robert W. Baird
- Pathology and Infectious Diseases Departments, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Bart J. Currie
- Pathology and Infectious Diseases Departments, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - David Speers
- PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
| | - John S. Mackenzie
- PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
- Faculty of Health Sciences, Curtin University, Bentley, Western Australia, Australia
| | - David W. Smith
- PathWest Laboratory Medicine Western Australia, Nedlands, Western Australia, Australia
- * E-mail: (DWS); (DTW)
| | - David T. Williams
- CSIRO Australian Centre for Disease Preparedness, Geelong, Victoria, Australia
- * E-mail: (DWS); (DTW)
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Urosevic N, Merritt AJ, Inglis TJJ. Plasma cfDNA predictors of established bacteraemic infection. Access Microbiol 2022; 4:acmi000373. [PMID: 36004363 PMCID: PMC9394668 DOI: 10.1099/acmi.0.000373] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/16/2022] [Indexed: 11/18/2022] Open
Abstract
Introduction. Increased plasma cell-free DNA (cfDNA) has been reported for various diseases in which cell death and tissue/organ damage contribute to pathogenesis, including sepsis. Gap Statement. While several studies report a rise in plasma cfDNA in bacteraemia and sepsis, the main source of cfDNA has not been identified. Aim. In this study, we wanted to determine which of nuclear, mitochondrial or bacterial cfDNA is the major contributor to raised plasma cfDNA in hospital subjects with bloodstream infections and could therefore serve as a predictor of bacteraemic disease severity. Methodology. The total plasma concentration of double-stranded cfDNA was determined using a fluorometric assay. The presence of bacterial DNA was identified by PCR and DNA sequencing. The copy numbers of human genes, nuclear β globin and mitochondrial MTATP8, were determined by droplet digital PCR. The presence, size and concentration of apoptotic DNA from human cells were established using lab-on-a-chip technology. Results. We observed a significant difference in total plasma cfDNA from a median of 75 ng ml−1 in hospitalised subjects without bacteraemia to a median of 370 ng ml−1 (P=0.0003) in bacteraemic subjects. The copy numbers of nuclear DNA in bacteraemic also differed between a median of 1.6 copies µl−1 and 7.3 copies µl−1 (P=0.0004), respectively. In contrast, increased mitochondrial cfDNA was not specific for bacteraemic subjects, as shown by median values of 58 copies µl−1 in bacteraemic subjects, 55 copies µl−1 in other hospitalised subjects and 5.4 copies µl−1 in healthy controls. Apoptotic nucleosomal cfDNA was detected only in a subpopulation of bacteraemic subjects with documented comorbidities, consistent with elevated plasma C-reactive protein (CRP) levels in these subjects. No bacterial cfDNA was reliably detected by PCR in plasma of bacteraemic subjects over the course of infection with several bacterial pathogens. Conclusions. Our data revealed distinctive plasma cfDNA signatures in different groups of hospital subjects. The total cfDNA was significantly increased in hospital subjects with laboratory-confirmed bloodstream infections comprising nuclear and apoptotic, but not mitochondrial or bacterial cfDNAs. The apoptotic cfDNA, potentially derived from blood cells, predicted established bacteraemia. These findings deserve further investigation in different hospital settings, where cfDNA measurement could provide simple and quantifiable parameters for monitoring a disease progression.
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Affiliation(s)
- Nadezda Urosevic
- School of Medicine, Faculty of Health & Medical Sciences, The University of Western Australia, Nedlands, WA, Australia
- School of Biomedical Sciences, Faculty of Health & Medical Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Adam J. Merritt
- Department of Microbiology, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, WA, Australia
| | - Timothy J. J. Inglis
- School of Medicine, Faculty of Health & Medical Sciences, The University of Western Australia, Nedlands, WA, Australia
- School of Biomedical Sciences, Faculty of Health & Medical Sciences, The University of Western Australia, Nedlands, WA, Australia
- Department of Microbiology, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, WA, Australia
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5
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Ke W, Lai Q, Yang Y, Qian J, Ji X, He Z. Ratiometric Fluorescence Determination of Avian Influenza a Virus Subtype H1N1 DNA with Functionalized Quantum Dots and Gold Nanoparticles. ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2052306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Wenmin Ke
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Qizhen Lai
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Yixia Yang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Jingjing Qian
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Xinghu Ji
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
| | - Zhike He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, China
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Bhuiyan MU, Snelling T, Sikazwe C, Lang J, Borland M, Martin A, Richmond P, Jaffe A, Smith D, Blyth C. Nasopharyngeal density of respiratory viruses in childhood pneumonia in a highly vaccinated setting: findings from a case-control study. BMJ Open Respir Res 2021; 7:7/1/e000593. [PMID: 32727742 PMCID: PMC7394014 DOI: 10.1136/bmjresp-2020-000593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/18/2020] [Accepted: 06/18/2020] [Indexed: 11/06/2022] Open
Abstract
Background Detection of pneumonia-causing respiratory viruses in the nasopharynx of asymptomatic children has made their actual contribution to pneumonia unclear. We compared nasopharyngeal viral density between children with and without pneumonia to understand if viral density could be used to diagnose pneumonia. Methods Nasopharyngeal swabs (NPS) were collected from hospitalised pneumonia cases at Princess Margaret Hospital (PMH) and contemporaneous age-matched controls at PMH outpatient clinics and a local immunisation clinic in Perth, Australia. The density (copies/mL) of respiratory syncytial virus (RSV), influenza A virus (InfA), human metapneumovirus (HMPV) and rhinovirus in NPS was determined using quantitative PCR. Linear regression analysis was done to assess the trend between viral density and age in months. The association between viral density and disease status was examined using logistic regression. Area under receiver operating characteristic (AUROC) curves were assessed to determine optimal discriminatory viral density cut-offs. Results Through May 2015 to October 2017, 230 pneumonia cases and 230 controls were enrolled. Median nasopharyngeal density for any respiratory virus was not substantially higher in cases than controls (p>0.05 for each). A decreasing density trend with increasing age was observed—the trend was statistically significant for RSV (regression coefficient −0.04, p=0.004) but not for other viruses. After adjusting for demographics and other viral densities, for every log10 copies/mL density increase, the odds of being a case increased by six times for RSV, three times for HMPV and two times for InfA. The AUROC curves were <0.70 for each virus, suggesting poor case–control discrimination based on viral density. Conclusion The nasopharyngeal density of respiratory viruses was not significantly higher in children with pneumonia than those without; however, the odds of being a case increased with increased density for some viruses. The utility of viral density, alone, in defining pneumonia was limited.
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Affiliation(s)
- Mejbah Uddin Bhuiyan
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Nedlands, Western Australia, Australia .,School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Tom Snelling
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Nedlands, Western Australia, Australia.,Department of Infectious Diseases, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Chisha Sikazwe
- PathWest Laboratory Medical WA, Nedlands, Western Australia, Australia
| | - Jurissa Lang
- PathWest Laboratory Medical WA, Nedlands, Western Australia, Australia
| | - Meredith Borland
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Emergency Department, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Andrew Martin
- Department of General Paediatrics, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Peter Richmond
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Department of General Paediatrics, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Adam Jaffe
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - David Smith
- PathWest Laboratory Medical WA, Nedlands, Western Australia, Australia.,School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Christopher Blyth
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Department of Infectious Diseases, Perth Children's Hospital, Nedlands, Western Australia, Australia
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Tsuneki-Tokunaga A, Kanai K, Itagaki A, Tsuchie H, Okada T, Kasagi M, Tanaka K, Aoki M, Hinay AJA, Kageyama S. Growth capability of epidemic influenza viruses in Japan since the 2009 H1N1 pandemic. Arch Virol 2021; 166:1193-1196. [PMID: 33580378 PMCID: PMC7880649 DOI: 10.1007/s00705-021-04976-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/17/2020] [Indexed: 11/26/2022]
Abstract
The correlation of viral growth capability (n = 156) with the viral load in nasopharyngeal swabs (n = 76) was assessed. Epidemic influenza A/H1N1, A/H3N2, and B viruses showed a wide range of growth capability (104-1011 copies/mL) in Madin-Darby canine kidney cells. The growth was correlated with the nasopharyngeal viral load (r = 0.53). Six selected strains showed growth-dependent cell death (r = 0.96) in a growth kinetics assay. Epidemic influenza viruses exhibit a wide range of growth capability. Growth capability should be considered one of the key factors in disease prognosis.
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Affiliation(s)
- Akeno Tsuneki-Tokunaga
- Division of Virology, Department of Microbiology and Immunology, Tottori University Faculty of Medicine, Yonago, Japan
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
| | - Kyosuke Kanai
- Division of Virology, Department of Microbiology and Immunology, Tottori University Faculty of Medicine, Yonago, Japan
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
| | - Asao Itagaki
- Division of Virology, Department of Microbiology and Immunology, Tottori University Faculty of Medicine, Yonago, Japan
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
| | - Hideaki Tsuchie
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
- Tsuchie Internal Medicine and Pediatric Clinic, Sakaiminato, Japan
| | - Takayoshi Okada
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
- Department of Pediatrics, Tottori Prefectural Kousei Hospital, Kurayoshi, Japan
| | - Masaaki Kasagi
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
- Kasagi Children's Clinic for Health Service, Yonago, Japan
| | - Kiyoshi Tanaka
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
- Tanaka Pediatric Clinic, Tottori, Japan
| | - Miho Aoki
- Division of Virology, Department of Microbiology and Immunology, Tottori University Faculty of Medicine, Yonago, Japan
| | - Alfredo Jr A Hinay
- Division of Virology, Department of Microbiology and Immunology, Tottori University Faculty of Medicine, Yonago, Japan
| | - Seiji Kageyama
- Division of Virology, Department of Microbiology and Immunology, Tottori University Faculty of Medicine, Yonago, Japan.
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan.
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The Diversity and Distribution of Viruses Associated with Culex annulirostris Mosquitoes from the Kimberley Region of Western Australia. Viruses 2020; 12:v12070717. [PMID: 32630711 PMCID: PMC7411826 DOI: 10.3390/v12070717] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/18/2020] [Accepted: 06/30/2020] [Indexed: 12/11/2022] Open
Abstract
Metagenomics revealed an impressive breadth of previously unrecognized viruses. Here, we report the virome of the Culex annulirostris Skuse mosquito, an important vector of pathogenic arboviruses in Australia. Mosquitoes were collected from three sites in the Kimberley region of Western Australia. Unbiased high-throughput sequencing (HTS) revealed the presence of 16 novel viral sequences that share less than 90% identity with known viruses. None were closely related to pathogenic arboviruses. Viruses were distributed unevenly across sites, indicating a heterogeneous Cx. annulirostris virome. Polymerase chain reaction assays confirmed HTS data and identified marked variation between the virus prevalence identified at each site.
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9
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An efficient, reproducible and accurate RT-qPCR based method to determine mumps specific neutralizing antibody. J Virol Methods 2020; 277:113817. [PMID: 31911119 DOI: 10.1016/j.jviromet.2020.113817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 11/29/2019] [Accepted: 01/03/2020] [Indexed: 11/22/2022]
Abstract
INTRODUCTION A resurgence of mumps among fully vaccinated adolescents and young adults globally has led to questions about the longevity of vaccine derived specific immunity. Unfortunately, the ideal serological correlate of immunity to mumps has yet to be identified. However, neutralising antibody titres in serum are used extensively as a surrogate marker of immunity to mumps. Conventional neutralisation tests are technically challenging, thus we developed and validated a high throughput, RT-qPCR microneutralisation (RT-qPCR-MN) method to determine serum neutralising antibody levels to mumps virus strains which avoids a number of the technical limitations of existing methods. METHODS The qPCR-MN assays were thoroughly validated using human serum samples from patients with prior exposure to mumps infection or vaccination. RESULTS Each sample of pooled sera neutralised virus at a constant rate and without significant changes when tested against genotype A (MuV-A) and G (MuV-G) mumps virus concentrations from 200 to 3200 TCID50. The within run and between run variation of the RT-qPCR-MN assays for both genotypes were less than 3 % and 9 % for low and high titre samples, respectively. The correlation between the focus reduction neutralisation test and RT-qPCR-MN was excellent for both MuV-G (r2 = 0.80, 95CI: 0.67-1.00, p < 0.0001) and MuV-A genotypes (r2 = 0.88, 95 %CI 0.69-1.00, p < 0.0001) endpoint determinations. CONCLUSIONS We have developed a RT-qPCR MN assay for mumps virus that is simple, fast, scientifically objective and has high throughput. The assay can be used to provide key insights into the efficacy of mumps vaccination, to help explain the causes for the resurgence of mumps infection in vaccinated populations.
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Williams SH, Levy A, Yates RA, Somaweera N, Neville PJ, Nicholson J, Lindsay MDA, Mackenzie JS, Jain K, Imrie A, Smith DW, Lipkin WI. Discovery of Jogalong virus, a novel hepacivirus identified in a Culex annulirostris (Skuse) mosquito from the Kimberley region of Western Australia. PLoS One 2020; 15:e0227114. [PMID: 31899786 PMCID: PMC6941808 DOI: 10.1371/journal.pone.0227114] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/12/2019] [Indexed: 12/24/2022] Open
Abstract
The discovery of hepaciviruses in non-human hosts has accelerated following the advancement of high-throughput sequencing technology. Hepaciviruses have now been described in reptiles, fish, birds, and an extensive array of mammals. Using metagenomic sequencing on pooled samples of field-collected Culex annulirostris mosquitoes, we discovered a divergent hepacivirus-like sequence, named Jogalong virus, from the Kimberley region in northern Western Australia. Using PCR, we screened the same 300 individual mosquitoes and found just a single positive sample (1/300, 0.33%). Phylogenetic analysis of the hepacivirus NS5B protein places Jogalong virus within the genus Hepacivirus but on a distinct and deeply rooted monophyletic branch shared with duck hepacivirus, suggesting a notably different evolutionary history. Vertebrate barcoding PCR targeting two mitochondrial genes, cytochrome c oxidase subunit I and cytochrome b, indicated that the Jogalong virus-positive mosquito had recently fed on the tawny frogmouth (Podargus strigoides), although it is currently unknown whether this bird species contributes to the natural ecology of this virus.
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Affiliation(s)
- Simon H. Williams
- Center for Infection and Immunity, Mailman School of Public Health of Columbia University, New York, New York, United States of America
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
| | - Avram Levy
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
| | - Rachel A. Yates
- Center for Infection and Immunity, Mailman School of Public Health of Columbia University, New York, New York, United States of America
| | - Nilusha Somaweera
- Environmental Health Directorate, Public and Aboriginal Health Division, Department of Health, Western Australia, Perth, Western Australia, Australia
| | - Peter J. Neville
- Environmental Health Directorate, Public and Aboriginal Health Division, Department of Health, Western Australia, Perth, Western Australia, Australia
| | - Jay Nicholson
- Environmental Health Directorate, Public and Aboriginal Health Division, Department of Health, Western Australia, Perth, Western Australia, Australia
| | - Michael D. A. Lindsay
- Environmental Health Directorate, Public and Aboriginal Health Division, Department of Health, Western Australia, Perth, Western Australia, Australia
| | - John S. Mackenzie
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- Faculty of Health Sciences, Curtin University, Perth, Western Australia, Australia
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health of Columbia University, New York, New York, United States of America
| | - Allison Imrie
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
| | - David W. Smith
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health of Columbia University, New York, New York, United States of America
- * E-mail:
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11
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Smith DW, Barr IG, Loh R, Levy A, Tempone S, O'Dea M, Watson J, Wong FYK, Effler PV. Respiratory Illness in a Piggery Associated with the First Identified Outbreak of Swine Influenza in Australia: Assessing the Risk to Human Health and Zoonotic Potential. Trop Med Infect Dis 2019; 4:tropicalmed4020096. [PMID: 31242646 PMCID: PMC6632059 DOI: 10.3390/tropicalmed4020096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/19/2019] [Accepted: 06/24/2019] [Indexed: 12/15/2022] Open
Abstract
Australia was previously believed to be free of enzootic swine influenza viruses due strict quarantine practices and use of biosecure breeding facilities. The first proven Australian outbreak of swine influenza occurred in Western Australian in 2012, revealing an unrecognized zoonotic risk, and a potential future pandemic threat. A public health investigation was undertaken to determine whether zoonotic infections had occurred and to reduce the risk of further transmission between humans and swine. A program of monitoring, testing, treatment, and vaccination was commenced, and a serosurvey of workers was also undertaken. No acute infections with the swine influenza viruses were detected. Serosurvey results were difficult to interpret due to previous influenza infections and past and current vaccinations. However, several workers had elevated haemagglutination inhibition (HI) antibody levels to the swine influenza viruses that could not be attributed to vaccination or infection with contemporaneous seasonal influenza A viruses. However, we lacked a suitable control population, so this was inconclusive. The experience was valuable in developing better protocols for managing outbreaks at the human–animal interface. Strict adherence to biosecurity practices, and ongoing monitoring of swine and their human contacts is important to mitigate pandemic risk. Strain specific serological assays would greatly assist in identifying zoonotic transmission.
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Affiliation(s)
- David W Smith
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, WA 6009, Australia.
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, WA 6009, Australia.
| | - Ian G Barr
- World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
| | - Richmond Loh
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development, Perth, WA 6151, Australia.
| | - Avram Levy
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, WA 6009, Australia.
| | - Simone Tempone
- Communicable Disease Control Directorate, Department of Health Western Australia, Perth, WA 6004, Australia.
| | - Mark O'Dea
- School of Veterinary Medicine, Murdoch University, Perth, WA 6150, Australia.
| | - James Watson
- CSIRO Australian Animal Health Laboratory, Geelong, VIC 3219, Australia.
| | - Frank Y K Wong
- CSIRO Australian Animal Health Laboratory, Geelong, VIC 3219, Australia.
| | - Paul V Effler
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, WA 6009, Australia.
- Communicable Disease Control Directorate, Department of Health Western Australia, Perth, WA 6004, Australia.
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12
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Kurucz N, Minney-Smith CA, Johansen CA. Arbovirus surveillance using FTA TM cards in modified CO 2 -baited encephalitis virus surveillance traps in the Northern Territory, Australia. JOURNAL OF VECTOR ECOLOGY : JOURNAL OF THE SOCIETY FOR VECTOR ECOLOGY 2019; 44:187-194. [PMID: 31124223 DOI: 10.1111/jvec.12343] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/27/2019] [Indexed: 06/09/2023]
Abstract
In 2016, modified CO2 -baited encephalitis virus surveillance (EVS) traps were evaluated for flavivirus surveillance in the Northern Territory, Australia. The traps were fitted with honey-soaked nucleic acid preservation cards (FTATM ) for mosquitoes to expectorate virus while feeding on the cards. Cards were tested for the presence of selected arboviruses, with two cards testing positive for Kunjin virus and Alfuy, while sentinel chickens tested in parallel also showed Kunjin virus activity at the same time. The results from the cards and vector mosquito feeding rates indicate that CO2 -baited EVS traps coupled with honey-baited FTATM cards are an effective tool for broad-scale arbovirus surveillance.
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Affiliation(s)
- Nina Kurucz
- Medical Entomology, Centre for Disease Control, Department of Health, Darwin, Northern Territory, Australia
| | | | - Cheryl A Johansen
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
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13
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Ho YII, Wong AH, Lai RWM. Comparison of the Cepheid Xpert Xpress Flu/RSV Assay to in-house Flu/RSV triplex real-time RT-PCR for rapid molecular detection of Influenza A, Influenza B and Respiratory Syncytial Virus in respiratory specimens. J Med Microbiol 2018; 67:1576-1580. [PMID: 30207514 DOI: 10.1099/jmm.0.000841] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
This study compared the performance of the commercially available Xpert Xpress Flu/RSV assay to an in-house FluAB/RSV triplex real-time RT-PCR assay for the detection of influenza A/B viruses and respiratory syncitial virus (RSV) from both nasopharyngeal aspirate (NPA) and nasopharyngeal flocked swab (NPS). A total of 20 external quality assurance (EQA) samples and 172 clinical respiratory samples were tested prospectively using both the Xpert Xpress Flu/RSV assay and the in-house FluAB/RSV triplex assay. For the EQA samples, concordance rate was 100 % when tested with both assays. For clinical samples, there was 100 % agreement between the two assays for detection of influenza A and influenza B, 96.7 % agreement for detection of RSV and 99.7 % agreement for negative results. With a shortened turnaround time and good diagnostic performance, application of the Xpert Xpress Flu/RSV assay can facilitate patient triage for prompt implementation of infection control measures and management of high-risk patients during influenza epidemics.
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Affiliation(s)
- Yolanda I I Ho
- Department of Microbiology, Prince of Wales Hospital, Hong Kong, PR China
| | - Ann H Wong
- Department of Microbiology, Prince of Wales Hospital, Hong Kong, PR China
| | - Raymond W M Lai
- Department of Microbiology, Prince of Wales Hospital, Hong Kong, PR China
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14
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Willis GA, Preen DB, Richmond PC, Jacoby P, Effler PV, Smith DW, Robins C, Borland ML, Levy A, Keil AD, Blyth CC. The impact of influenza infection on young children, their family and the health care system. Influenza Other Respir Viruses 2018; 13:18-27. [PMID: 30137663 PMCID: PMC6304317 DOI: 10.1111/irv.12604] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 08/14/2018] [Indexed: 11/29/2022] Open
Abstract
Background Influenza is a major cause of respiratory illness in young children. Assessing the impact of infection on children and the community is required to guide immunisation policies. Objectives To describe the impact of laboratory‐proven influenza in young children and to compare its impact with that of other respiratory viruses on the child, their family and the health care system. Methods Preschool children presenting for care or admission to a tertiary paediatric hospital during the 2008‐2014 influenza seasons were tested for respiratory virus by polymerase chain reaction and culture. Parental surveys were used to determine the impact of infection on illness duration, medication use, absenteeism and health service utilisation. Multivariate regression analyses were used to assess the impact of influenza and to evaluate the association between influenza status and outcomes. Results Among 1191 children assessed, 238 had influenza. Among children with influenza, 87.8% were administered antipyretics and 40.9% antibiotics. 28.6% had secondary complications. 65.4% of children missed school/day care, and 53.4% of parents missed work. When influenza and other viruses were compared, significant differences were noted including duration of illness (influenza: 9.54 days, other viruses: 8.50 days; P = 0.005) and duration of absenteeism for both the child (23.1 vs 17.3 hours; P = 0.015) and their parents (28.5 vs 22.7 hours; P = 0.012). Conclusions Influenza infection in young children has a significant impact on medication use, absenteeism and the use of health care service. Significant differences are identified when compared with other ILI. These data demonstrate that influenza prevention strategies including immunisation are likely to have wide and significant impacts.
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Affiliation(s)
- Gabriela A Willis
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, West Perth, Western Australia, Australia.,Department of Health, Population Health Services, Hobart, Tasmania, Australia
| | - David B Preen
- School of Population Health, University of Western Australia, Crawley, Western Australia, Australia
| | - Peter C Richmond
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, West Perth, Western Australia, Australia.,School of Pediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia.,Department of General Pediatrics, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Peter Jacoby
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, West Perth, Western Australia, Australia
| | - Paul V Effler
- Department of Health, Communicable Disease Control Directorate, Shenton Park, Western Australia, Australia
| | - David W Smith
- School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Western Australia, Australia.,Department of Microbiology, QEII Medical Centre, PathWest Laboratory Medicine, Nedlands, Western Australia, Australia
| | - Christine Robins
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, West Perth, Western Australia, Australia
| | - Meredith L Borland
- Emergency Department, Perth Children's Hospital, Perth, Western Australia, Australia.,School of Primary Aboriginal and Rural Healthcare, University of Western Australia, Perth, Western Australia, Australia
| | - Avram Levy
- School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Western Australia, Australia.,Department of Microbiology, QEII Medical Centre, PathWest Laboratory Medicine, Nedlands, Western Australia, Australia
| | - Anthony D Keil
- Department of Microbiology, PathWest Laboratory Medicine, Princess Margaret Hospital, Nedlands, Western Australia, Australia
| | - Christopher C Blyth
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, West Perth, Western Australia, Australia.,School of Pediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia.,Department of Microbiology, PathWest Laboratory Medicine, Princess Margaret Hospital, Nedlands, Western Australia, Australia.,Department of Infectious Diseases, Perth Children's Hospital, Perth, Western Australia, Australia
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15
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Dayakar S, Pillai HR, Thulasi VP, Jayalekshmi D, Nair RR. Comparative Study of Molecular Approaches for the Detection of Influenza Virus from Patient Samples Using Real-time PCR: Prospective Disease Burden Study in Kerala (India) from 2010 to 2016. Curr Infect Dis Rep 2018; 20:24. [DOI: 10.1007/s11908-018-0632-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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16
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Bhuiyan MU, Snelling TL, West R, Lang J, Rahman T, Borland ML, Thornton R, Kirkham LA, Sikazwe C, Martin AC, Richmond PC, Smith DW, Jaffe A, Blyth CC. Role of viral and bacterial pathogens in causing pneumonia among Western Australian children: a case-control study protocol. BMJ Open 2018; 8:e020646. [PMID: 29549211 PMCID: PMC5857668 DOI: 10.1136/bmjopen-2017-020646] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/27/2017] [Accepted: 02/12/2018] [Indexed: 12/28/2022] Open
Abstract
INTRODUCTION Pneumonia is the leading cause of childhood morbidity and mortality globally. Introduction of the conjugate Haemophilus influenzae B and multivalent pneumococcal vaccines in developed countries including Australia has significantly reduced the overall burden of bacterial pneumonia. With the availability of molecular diagnostics, viruses are frequently detected in children with pneumonia either as primary pathogens or predispose to secondary bacterial infection. Many respiratory pathogens that are known to cause pneumonia are also identified in asymptomatic children, so the true contribution of these pathogens to childhood community-acquired pneumonia (CAP) remains unclear. Since the introduction of pneumococcal vaccines, very few comprehensive studies from developed countries have attempted to determine the bacterial and viral aetiology of pneumonia. We aim to determine the contribution of bacteria and viruses to childhood CAP to inform further development of effective diagnosis, treatment and preventive strategies. METHODS AND ANALYSIS We are conducting a prospective case-control study (PneumoWA) where cases are children with radiologically confirmed pneumonia admitted to Princess Margaret Hospital for Children (PMH) and controls are healthy children identified from PMH outpatient clinics and from local community immunisation clinics. The case-control ratio is 1:1 with 250 children to be recruited in each arm. Nasopharyngeal swabs are collected from both cases and controls to detect the presence of viruses and bacteria by PCR; pathogen load will be assessed by quantitative PCR. The prevalence of pathogens detected in cases and controls will be compared, the OR of detection and population attributable fraction to CAP for each pathogen will be determined; relationships between pathogen load and disease status and severity will be explored. ETHICS AND DISSEMINATION This study has been approved by the human research ethics committees of PMH, Perth, Australia (PMH HREC REF 2014117EP). Findings will be disseminated at research conferences and in peer-reviewed journals.
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Affiliation(s)
- Mejbah Uddin Bhuiyan
- Division of Paediatrics, Faculty of Health and Medical Sciences, School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Australia
| | - Thomas L Snelling
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Australia
- Department of Infectious Diseases, Princess Margaret Hospital for Children, Perth, Australia
| | - Rachel West
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Australia
| | - Jurissa Lang
- PathWest Laboratory Medicine WA, Perth, Australia
| | - Tasmina Rahman
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Australia
- Faculty of Health and Medical Sciences, School of Biomedical Science, The University of Western Australia, Perth, Australia
| | - Meredith L Borland
- Department of Infectious Diseases, Princess Margaret Hospital for Children, Perth, Australia
| | - Ruth Thornton
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Australia
- Faculty of Health and Medical Sciences, School of Biomedical Science, The University of Western Australia, Perth, Australia
| | - Lea-Ann Kirkham
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Australia
- Faculty of Health and Medical Sciences, School of Biomedical Science, The University of Western Australia, Perth, Australia
| | | | - Andrew C Martin
- Department of Infectious Diseases, Princess Margaret Hospital for Children, Perth, Australia
| | - Peter C Richmond
- Division of Paediatrics, Faculty of Health and Medical Sciences, School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
- Department of Infectious Diseases, Princess Margaret Hospital for Children, Perth, Australia
| | | | - Adam Jaffe
- Faculty of Medicine, School of Women's and Children's Health, University of New South Wales, Sydney, Australia
| | - Christopher C Blyth
- Division of Paediatrics, Faculty of Health and Medical Sciences, School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Australia
- Department of Infectious Diseases, Princess Margaret Hospital for Children, Perth, Australia
- PathWest Laboratory Medicine WA, Perth, Australia
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17
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Faddy HM, Tran TV, Hoad VC, Seed CR, Viennet E, Chan HT, Harley R, Hewlett E, Hall RA, Bielefeldt-Ohmann H, Flower RLP, Prow NA. Ross River virus in Australian blood donors: possible implications for blood transfusion safety. Transfusion 2018; 58:485-492. [PMID: 29350414 DOI: 10.1111/trf.14472] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 10/05/2017] [Accepted: 10/13/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND Emerging transfusion-transmissible pathogens, including arboviruses such as West Nile, Zika, dengue, and Ross River viruses, are potential threats to transfusion safety. The most prevalent arbovirus in humans in Australia is Ross River virus (RRV); however, prevalence varies substantially around the country. Modeling estimated a yearly risk of 8 to 11 potentially RRV-viremic fresh blood components nationwide. This study aimed to measure the occurrence of RRV viremia among donors who donated at Australian collection centers located in areas with significant RRV transmission during one peak season. STUDY DESIGN AND METHODS Plasma samples were collected from donors (n = 7500) who donated at the selected collection centers during one peak season. Viral RNA was extracted from individual samples, and quantitative reverse transcription-polymerase chain reaction was performed. RESULTS Regions with the highest rates of RRV transmission were not areas where donor centers were located. We did not detect RRV RNA among 7500 donations collected at the selected centers, resulting in a zero risk estimate with a one-sided 95% confidence interval of 0 to 1 in 2019 donations. CONCLUSION Our results suggest that the yearly risk of collecting a RRV-infected blood donation in Australia is low and is at the lower range of previous risk modeling. The majority of Australian donor centers were not in areas known to be at the highest risk for RRV transmission, which was not taken into account in previous models based on notification data. Therefore, we believe that the risk of RRV transfusion transmission in Australia is acceptably low and appropriately managed through existing risk management, including donation restrictions and recall policies.
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Affiliation(s)
- Helen M Faddy
- Research and Development, Australian Red Cross Blood Service, Brisbane, Queensland, Australia.,School of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Thu V Tran
- Research and Development, Australian Red Cross Blood Service, Brisbane, Queensland, Australia
| | - Veronica C Hoad
- Clinical Services and Research, Australian Red Cross Blood Service, Brisbane, Queensland, Australia
| | - Clive R Seed
- Clinical Services and Research, Australian Red Cross Blood Service, Brisbane, Queensland, Australia
| | - Elvina Viennet
- Research and Development, Australian Red Cross Blood Service, Brisbane, Queensland, Australia
| | - Hiu-Tat Chan
- Clinical Services and Research, Australian Red Cross Blood Service, Brisbane, Queensland, Australia
| | - Robert Harley
- Clinical Services and Research, Australian Red Cross Blood Service, Brisbane, Queensland, Australia
| | - Elise Hewlett
- Research and Development, Australian Red Cross Blood Service, Brisbane, Queensland, Australia.,Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Roy A Hall
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Helle Bielefeldt-Ohmann
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Robert L P Flower
- Research and Development, Australian Red Cross Blood Service, Brisbane, Queensland, Australia
| | - Natalie A Prow
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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18
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Saito M, Tsukagoshi H, Takahashi Y, Saruki N. Multiplex one-step real-time PCR detection for influenza viruses, AH1pdm09, AH3 and B. Infect Dis (Lond) 2017; 50:634-636. [PMID: 29235912 DOI: 10.1080/23744235.2017.1416164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Mariko Saito
- a Gunma Prefectural Institute of Public Health and Environmental Sciences , Maebashi-shi , Gunma , Japan
| | - Hiroyuki Tsukagoshi
- a Gunma Prefectural Institute of Public Health and Environmental Sciences , Maebashi-shi , Gunma , Japan
| | - Yu Takahashi
- a Gunma Prefectural Institute of Public Health and Environmental Sciences , Maebashi-shi , Gunma , Japan
| | - Nobuhiro Saruki
- a Gunma Prefectural Institute of Public Health and Environmental Sciences , Maebashi-shi , Gunma , Japan
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19
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Lim FJ, Wake ZV, Levy A, Tempone S, Moore HC, Richmond PC, de Klerk N, Conway NT, Keil AD, Effler PV, Smith DW, Blyth CC. Viral Etiology and the Impact of Codetection in Young Children Presenting With Influenza-Like Illness. J Pediatric Infect Dis Soc 2017; 6:260-266. [PMID: 27440506 PMCID: PMC7107488 DOI: 10.1093/jpids/piw042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 06/28/2016] [Indexed: 01/17/2023]
Abstract
BACKGROUND Children with acute respiratory tract infection (ARTI) frequently exhibit virus-virus codetection, yet the clinical significance of ARTI remains contentious. Using data from a prospective cohort of children with influenza-like illness, we examined the virology of ARTI and determined the clinical impact of virus-virus codetection. METHODS Children aged 6 to 59 months who presented to a tertiary pediatric hospital between influenza seasons 2008 and 2012 with fever and acute respiratory symptoms were enrolled, and nasal samples were collected. Respiratory viruses were identified by culture and polymerase chain reaction. We compared demographics, presenting symptoms, and clinical outcomes of children with a single-virus infection and those in whom 2 or more viruses were detected (virus-virus codetection). We used logistic regression models and estimated marginal means to calculate the adjusted odds ratios and probabilities of symptom presentation, prescription of antibiotics, and hospitalization. RESULTS Of 2356 children, a virus was detected in 1630 (69.2%) of them; rhinovirus (40.8%), influenza (29.5%), and respiratory syncytial virus (26.4%) were detected most commonly. Two or more viruses were detected in 25% of these children. After we adjusted for demographic factors, children with virus-virus codetection had greater odds of presenting with cough (adjusted odds ratio [aOR], 1.9; 95% confidence interval [CI], 1.2-3.1) and rhinorrhea (aOR, 1.8; 95% CI, 1.1-2.9) than those with a single-virus infection, although both symptoms were common. Children with influenza and respiratory syncytial virus combined had the highest probability of hospitalization (55%; 95% CI, 35%-73%), which was significantly greater than for those with influenza infection alone (22%; 95% CI, 16%-29%). CONCLUSIONS Overall, virus-virus codetection has limited impact on clinical severity among children with influenza-like illness. However, infection with specific pathogen pairs might be associated with more severe outcomes. Routine diagnostics to identify specific viruses should be restricted to common pathogens.
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Affiliation(s)
- Faye J Lim
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, West Perth;
,Correspondence: F. J. Lim, Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, PO Box 855, West Perth, WA 6872, Australia ()
| | - Zoe V Wake
- Department of General Paediatrics;
,Department of Infectious Diseases
| | - Avram Levy
- PathWest Laboratory Medicine WA, QEII Medical Centre, Nedlands;
,School of Pathology and Laboratory Medicine, Crawley
| | - Simone Tempone
- PathWest Laboratory Medicine WA, QEII Medical Centre, Nedlands
| | - Hannah C Moore
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, West Perth
| | - Peter C Richmond
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, West Perth;
,Department of General Paediatrics;
,School of Paediatrics and Child Health, University of Western Australia
| | - Nicholas de Klerk
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, West Perth
| | - Nicholas T Conway
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, West Perth
| | - Anthony D Keil
- Department of Microbiology, PathWest Laboratory Medicine WA, Princess Margaret Hospital for Children, Perth, and
| | - Paul V Effler
- Communicable Disease Control Directorate, Department of Health, Grace Vaughan House, Shenton Park, Australia
| | - David W Smith
- PathWest Laboratory Medicine WA, QEII Medical Centre, Nedlands;
,School of Pathology and Laboratory Medicine, Crawley
| | - Christopher C Blyth
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, West Perth;
,Department of Infectious Diseases;
,School of Paediatrics and Child Health, University of Western Australia;
,Department of Microbiology, PathWest Laboratory Medicine WA, Princess Margaret Hospital for Children, Perth, and
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20
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Otto CC, Kaplan SE, Stiles J, Mikhlina A, Lee C, Babady NE, Tang YW. Rapid Molecular Detection and Differentiation of Influenza Viruses A and B. J Vis Exp 2017. [PMID: 28190065 DOI: 10.3791/54312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Influenza is a contagious respiratory illness caused by influenza viruses A and B in humans and causes a significant amount of morbidity and mortality every year. The Influenza A and B assay was the first CLIA-waived molecular rapid flu test available. The Influenza A and B test works by employing isothermal amplification with influenza-specific primers followed by target detection with molecular beacon probes. Here, the performance of the Influenza A and B assay on frozen, archived nasopharyngeal swab (NPS) specimens stored in viral transport medium (VTM) were compared to a respiratory panel assay. The performance of the Influenza A and B assay was evaluated by comparing the results to the respiratory panel reference method. The sensitivity for total influenza virus A was 67.5% (95% CI (CI), 56.6-78.5) and the specificity was 86.9% (CI, 71.0-100). For influenza virus B testing, the sensitivity and specificity were 90.2% (CI, 68.5-100) and 98.8% (CI, 68.5-100), respectively. This system has the advantage of a significantly shorter test time than any other currently available molecular assay and the simple, pipette-free procedure runs on a fully integrated, closed, small-footprint system. Overall, the Influenza A and B assay evaluated in this study has the potential to serve as a point-of-care rapid influenza diagnostic test.
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Affiliation(s)
- Caitlin C Otto
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center
| | - Samuel E Kaplan
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center
| | - Jeffrey Stiles
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center
| | - Albina Mikhlina
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center
| | - Cindy Lee
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center
| | - N Esther Babady
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center
| | - Yi-Wei Tang
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center;
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21
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Francis JR, Richmond P, Robins C, Lindsay K, Levy A, Effler PV, Borland M, Blyth CC. An observational study of febrile seizures: the importance of viral infection and immunization. BMC Pediatr 2016; 16:202. [PMID: 27914475 PMCID: PMC5135752 DOI: 10.1186/s12887-016-0740-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/26/2016] [Indexed: 11/24/2022] Open
Abstract
Background Febrile seizures are common in young children. Annual peaks in incidence mirror increased respiratory virus activity during winter. Limited virological data are available using modern diagnostic techniques for children with febrile seizures. We aimed to determine the frequency of detection of specific viral pathogens in children with febrile seizures, to describe risk factors including recent vaccination and clinical features associated with specific etiologies. Methods An observational study was performed. Children aged 6 months to 5 years presenting to the Emergency Department of a tertiary children’s hospital in Western Australia with febrile seizures were enrolled between March 2012 and October 2013. Demographic, clinical data and vaccination history were collected, and virological testing was performed on per-nasal and per-rectal samples. Results One hundred fifty one patients (72 female; median age 1.7y; range 6 m-4y9m) were enrolled. Virological testing was completed for 143/151 (95%). At least one virus was detected in 102/143 patients (71%). The most commonly identified were rhinoviruses (31/143, 22%), adenovirus (30/151, 21%), enteroviruses, (28/143, 20%), influenza (19/143, 13%) and HHV6 (17/143, 12%). More than one virus was found in 48/143 (34%). No significant clinical differences were observed when children with a pathogen identified were compared with those with no pathogen detected. Febrile seizures occurred within 14 days of vaccine administration in 16/151 (11%). Conclusion At least one virus was detected in over two thirds of cases tested (commonly picornaviruses, adenovirus and influenza). Viral co-infections were frequently identified. Febrile seizures occurred infrequently following immunization.
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Affiliation(s)
- Joshua R Francis
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia. .,Department of Paediatrics, Royal Darwin Hospital, Darwin, NT, Australia. .,Department of General Paediatrics, Princess Margaret Hospital, Perth, WA, Australia.
| | - Peter Richmond
- Department of General Paediatrics, Princess Margaret Hospital, Perth, WA, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia.,Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Christine Robins
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Katie Lindsay
- PathWest Laboratory Medicine, Princess Margaret Hospital, Perth, WA, Australia
| | - Avram Levy
- PathWest Laboratory Medicine, QEII Medical Centre, Perth, WA, Australia.,School of Pathology and Laboratory Medicine, University of Western Australia, Perth, WA, Australia
| | - Paul V Effler
- Communicable Disease Control, Department of Health, Perth, WA, Australia
| | - Meredith Borland
- School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia.,Emergency Department, Princess Margaret Hospital, Perth, WA, Australia.,School of Primary, Rural and Aboriginal Health Care, University of Western Australia, Perth, WA, Australia
| | - Christopher C Blyth
- School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia.,Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia.,PathWest Laboratory Medicine, Princess Margaret Hospital, Perth, WA, Australia.,Department of Infectious Diseases, Princess Margaret Hospital, Perth, WA, Australia
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Lei C, Zhang H, Liu Y, Du X. Net-flow Fingerprint Model Based on Optimization Theory. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2016. [DOI: 10.1007/s13369-016-2073-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
BACKGROUND Data demonstrating the effectiveness of inactivated trivalent influenza vaccine (TIV) for children at increased risk of severe disease are limited. Our objective was to determine the effectiveness of TIV in children with risk factors for severe disease and to compare vaccine uptake, parental attitudes and prescriber recommendations in children with and without risk factors for severe disease. METHODS Children aged 6-59 months presenting for emergency care (2008 to 2014) with an influenza-like illness were eligible. Influenza polymerase chain reaction/culture was performed on nasopharyngeal samples. Vaccination status was confirmed via the national register and/or vaccine providers. The test-negative design was used to estimate vaccine effectiveness (VE). Risk factors, parental attitudes and prescriber recommendations were assessed by parental questionnaire. RESULTS Two thousand seven hundred twenty-three children were recruited. Risk factors for severe disease included comorbid medical conditions (11.6%), preterm birth (13.0%) and indigeneity (5.0%). Influenza was identified in 546 (20.1%) participants. Overall VE (2008 and 2010 to 2014) was 70.0% (95% confidence interval: 47.7 to 82.9); VE for children with medical comorbidities, children born preterm and children <2 years were 82.5% (14.6 to 96.4), 79.2% (10.9 to 95.1) and 84.7% (49.6 to 95.3), respectively. After adverse events in 2010, the number of children fully vaccinated with TIV declined significantly. This included children with and without risk factors for severe disease. Attitudes were similar in parents of children with and without risk factors for severe disease. CONCLUSIONS VE for TIV in young children with and without risk factors for severe disease was ≥70%. Despite this, participation in the preschool influenza vaccination program remains low with parents and prescribers unconvinced of the benefits and safety of TIV.
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Chen L, Tian Y, Chen S, Liesenfeld O. Performance of the Cobas(®) Influenza A/B Assay for Rapid Pcr-Based Detection of Influenza Compared to Prodesse ProFlu+ and Viral Culture. Eur J Microbiol Immunol (Bp) 2015; 5:236-45. [PMID: 26716012 PMCID: PMC4681351 DOI: 10.1556/1886.2015.00046] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 11/13/2015] [Indexed: 12/18/2022] Open
Abstract
Rapid and accurate diagnosis of influenza is important for patient management and infection control. We determined the performance of the cobas® Influenza A/B assay, a rapid automated nucleic acid assay performed on the cobas® Liat System for qualitative detection of influenza A and influenza B from nasopharyngeal (NP) swab specimens. Retrospective frozen and prospectively collected NP swabs from patients with signs and symptoms of influenza collected in universal transport medium (UTM) were tested at multiple sites including CLIA-waived sites using the cobas® Influenza A/B assay. Results were compared to the Prodesse Pro-Flu+ assay and to viral culture. Compared to the Prodesse ProFlu+ Assay, sensitivities of the cobas® Influenza A/B assay for influenza A and B were 97.7 and 98.6%, respectively; specificity was 99.2 and 99.4%. Compared to viral culture, the cobas® Influenza A/B assay showed sensitivities of 97.5 and 96.9% for influenza virus A and B, respectively; specificities were 97.9% for both viruses. Polymerase chain reaction (PCR)/sequencing showed that the majority of viral culture negative but cobas® Influenza A/B positive results were true positive results, indicating that the cobas® Influenza A/B assay has higher sensitivity compared to viral culture. In conclusion, the excellent accuracy, rapid time to result, and remarkable ease of use make the cobas® Influenza A/B nucleic acid assay for use on the cobas® Liat System a highly suitable point-of-care solution for the management of patients with suspected influenza A and B infection.
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Affiliation(s)
- L Chen
- Roche Molecular Systems , Marlborough 01752, MA, USA
| | - Y Tian
- Roche Molecular Systems , Marlborough 01752, MA, USA
| | - S Chen
- Roche Molecular Systems , Marlborough 01752, MA, USA
| | - O Liesenfeld
- Medical and Scientific Affairs, Roche Molecular Systems , Pleasanton 94588, CA, USA
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25
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Zhou L, Gong R, Lu X, Zhang Y, Tang J. Development of a Multiplex Real-Time PCR Assay for the Detection of Treponema pallidum, HCV, HIV-1, and HBV. Jpn J Infect Dis 2015; 68:481-7. [PMID: 25866106 DOI: 10.7883/yoken.jjid.2014.416] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Treponema pallidum, hepatitis C virus (HCV), human immunodeficiency virus (HIV)-1, and hepatitis B virus (HBV) are major causes of sexually transmitted diseases passed through blood contact. The development of a sensitive and efficient method for detection is critical for early diagnosis and for large-scale screening of blood specimens in China. This study aims to establish an assay to detect these pathogens in clinical serum specimens. We established a TaqMan-locked nucleic acid (LNA) real-time polymerase chain reaction (PCR) assay for rapid, sensitive, specific, quantitative, and simultaneous detection and identification. The copy numbers of standards of these 4 pathogens were quantified. Standard curves were generated by determining the mean cycle threshold values versus 10-fold serial dilutions of standards over a range of 10(6) to 10(1) copies/μL, with the lowest detection limit of the assay being 10(1) copies/μL. The assay was applied to 328 clinical specimens and compared with enzyme-linked immunosorbent assay (ELISA) and commercial nucleic acid testing (NAT) methods. The assay identified 39 T. pallidum-, 96 HCV-, 13 HIV-1-, 123 HBV-, 5 HBV/HCV-, 1 T. pallidum/HBV-, 1 HIV-1/HCV-, and 1 HIV-1/T. pallidum-positive specimens. The high sensitivity of the assay confers strong potential for its use as a highly reliable, cost-effective, and useful molecular diagnostic tool for large-scale screening of clinical specimens. This assay will assist in the study of the pathogenesis and epidemiology of sexually transmitted blood diseases.
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Affiliation(s)
- Li Zhou
- ABSL-III Laboratory at Center for Animal Experiment, State Key Laboratory of Virology, Wuhan University School of Medicine
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26
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Mikel P, Vasickova P, Kralik P. Methods for Preparation of MS2 Phage-Like Particles and Their Utilization as Process Control Viruses in RT-PCR and qRT-PCR Detection of RNA Viruses From Food Matrices and Clinical Specimens. FOOD AND ENVIRONMENTAL VIROLOGY 2015; 7:96-111. [PMID: 25711389 PMCID: PMC7090958 DOI: 10.1007/s12560-015-9188-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 02/19/2015] [Indexed: 06/04/2023]
Abstract
RNA viruses are pathogenic agents of many serious infectious diseases affecting humans and animals. The detection of pathogenic RNA viruses is based on modern molecular methods, of which the most widely used methods are the reverse transcription polymerase chain reaction (RT-PCR) and the real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). All steps of RT-PCR and qRT-PCR should be strictly controlled to ensure the validity of obtained results. False-negative results may be caused not only by inhibition of RT or/and PCR steps but also by failure of the nucleic acid extraction step, particularly in the case of viral RNA extraction. The control of nucleic acid extraction generally involves the utilization of a non-pathogenic virus (process control virus) of similar structural properties to those of the target virus. Although in clinical samples the use of such process control virus is only recommended, in other kinds of settings such as food matrices its use is necessary. Currently, several different process control viruses are used for these purposes. Process control viruses can also be constructed artificially using technology for production of MS2 phage-like particles, which have many advantages in comparison with other used controls and are especially suited for controlling the detection and quantification of certain types of RNA viruses. The technology for production of MS2 phage-like particles is theoretically well established, uses the knowledge gained from the study of the familiar bacteriophage MS2 and utilizes many different approaches for the construction of the various process control viruses. Nevertheless, the practical use of MS2 phage-like particles in routine diagnostics is relatively uncommon. The current situation with regard to the use of MS2 phage-like particles as process control viruses in detection of RNA viruses and different methods of their construction, purification and use are summarized and discussed in this review.
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Affiliation(s)
- P Mikel
- Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic,
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27
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Influenza vaccine effectiveness estimates for Western Australia during a period of vaccine and virus strain stability, 2010 to 2012. Vaccine 2014; 32:6312-8. [PMID: 25223268 DOI: 10.1016/j.vaccine.2014.08.066] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 07/04/2014] [Accepted: 08/27/2014] [Indexed: 11/22/2022]
Abstract
During 2010-2012 the strain composition of the influenza vaccine in the Southern Hemisphere did not change, but the circulating virus type/subtype did. We pooled data for these years from the Western Australian sentinel medical practice surveillance system for influenza to estimate vaccine effectiveness (VE) by influenza virus type and subtype. A case test-negative design was used with VE estimated as (1-odds ratio)×100%. There were 2182 patients included in the analysis across the 3 years studied. The predominant subtype was A/H1pdm09 in 2010 and 2011, and A/H3 in 2012. The overall adjusted VE estimate against all influenza for 2010-2012 was 51% (95% CI: 36, 63). Estimates were highest against A/H1pdm09 at 74% (95% CI: 47, 87), followed by 56% (95% CI: 33, 71) for influenza B and lowest against A/H3 at 39% (95% CI: 13, 57). When analyses were restricted to compare influenza-positive patients with patients who tested positive for a non-influenza virus, overall adjusted VE was 59% (95% CI: 39, 72). These results suggest moderate protection against influenza by vaccination in Western Australia over the period 2010-2012, and are consistent with findings from other settings.
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Evaluation of Alere i Influenza A&B for rapid detection of influenza viruses A and B. J Clin Microbiol 2014; 52:3339-44. [PMID: 24989611 DOI: 10.1128/jcm.01132-14] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Rapid and accurate diagnosis of influenza is important for infection control, as well as for patient management. Alere i Influenza A&B is an isothermal nucleic acid amplification-based integrated system for detection and differentiation of influenza virus A and influenza virus B. The performance of the Alere i Influenza A&B was screened using frozen nasopharyngeal-swab specimens collected in viral transport medium (VTM) that were originally tested fresh with the FilmArray Respiratory Panel (RP) assay during the 2012-2013 influenza outbreak. In total, 360 VTM specimens were selected for Alere i Influenza A&B testing: 40 influenza virus A H1N1-2009 (influenza virus A-1), 40 influenza virus A H3N2 (influenza virus A-3), 37 influenza virus A "equivocal" or "no subtype detected" (influenza virus A-u), 41 influenza virus B, and 202 influenza virus-negative specimens, as initially determined by the FilmArray RP assay. The Alere assay showed sensitivities of 87.2%, 92.5%, 25.0%, and 97.4% for influenza virus A-1, influenza virus A-3, influenza virus A-u, and influenza virus B, respectively, after discordant resolution by Prodesse ProFLU+ PCR. The specificities were 100% for both influenza virus A and influenza virus B. In general, the Alere i Influenza A&B provided good sensitivity, although the assay did show poorer sensitivity with samples determined to have low influenza virus A titers by Prodesse ProFlu+ PCR (a mean real-time PCR threshold cycle [CT] value of 31.9 ± 2.0), which included the majority of the samples called influenza virus A "equivocal" or "no subtype detected" by a single BioFire FilmArray RP test. The integrated, rapid, and simple characteristics of the Alere i Influenza A&B assay make it a potential candidate for point-of-care testing, with a test turnaround time of less than 15 min.
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Deyde VM, Sampath R, Gubareva LV. RT-PCR/electrospray ionization mass spectrometry approach in detection and characterization of influenza viruses. Expert Rev Mol Diagn 2014; 11:41-52. [DOI: 10.1586/erm.10.107] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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30
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Zang Y, Du D, Ge P, Xu Y, Liu X, Zhang Y, Su W, Kiseleva I, Rudenko L, Xu F, Kong W, Jiang C. Development of one-step real-time PCR assay for titrating trivalent live attenuated influenza vaccines. Hum Vaccin Immunother 2014; 10:3642-8. [PMID: 25483696 PMCID: PMC4514063 DOI: 10.4161/hv.34453] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 07/31/2014] [Accepted: 08/13/2014] [Indexed: 12/28/2022] Open
Abstract
Traditionally, infectivity of a trivalent live attenuated influenza vaccines (LAIVs) is titrated by determining the 50% egg infectious dose assay (EID50) or plaque forming units (PFU), which requires specific monoclonal antibodies to neutralize 2 strains while estimating the titer of the non-neutralized strain. Compared to this time-consuming, laborious, subjective and variable process, reverse transcription-quantitative real-time PCR (RT-qPCR) technology has advantages of rapidity, sensitivity, reproducibility and reduced contamination, thus has been applied widely for detecting pathogens and measuring viral titers. In this study, the critical harvest time was determined to be 18 h post-infection (hpi) for type A influenza and 12 hpi for type B influenza, but no significant difference between titers at 12 hpi and 18 hpi for the type B strain was observed. In conclusion, trivalent LAIVs can be titrated simultaneously within 24 h by this one-step RT-qPCR assay, which yielded titers comparable to those obtained by the traditional EID50 assay. Therefore, the RT-qPCR assay may be used as a highly specific, sensitive, precise and rapid alternative to the EID50 assay for titering LAIVs.
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Key Words
- 50% egg infectious dose assay
- CV%, coefficient of variation
- Ct, Cycle threshold
- E, efficiency
- EID50, 50% egg infectious dose assay
- HA, hemagglutinin
- LAIVs, live attenuated influenza vaccines
- NA, neuraminidase
- R2, Correlation coefficient values
- RT-qPCR, reverse transcription-quantitative real-time PCR
- SD, standard deviation
- hpi, hour post-infection
- infectivity
- live attenuated influenza vaccine
- quantitative real-time PCR
- titration
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Affiliation(s)
- Yang Zang
- National Engineering Laboratory for AIDS Vaccine; School of Life Sciences; Jilin University; Changchun, China
| | - Dongchuan Du
- National Engineering Laboratory for AIDS Vaccine; School of Life Sciences; Jilin University; Changchun, China
| | - Peng Ge
- Changchun BCHT Biotechnology Company; Changchun, China
| | - Yongqing Xu
- National Engineering Laboratory for AIDS Vaccine; School of Life Sciences; Jilin University; Changchun, China
| | - Xintao Liu
- Changchun BCHT Biotechnology Company; Changchun, China
| | - Yan Zhang
- National Engineering Laboratory for AIDS Vaccine; School of Life Sciences; Jilin University; Changchun, China
| | - Weiheng Su
- National Engineering Laboratory for AIDS Vaccine; School of Life Sciences; Jilin University; Changchun, China
| | - Irina Kiseleva
- Institute of Experimental Medicine; RAMS; St. Petersburg, Russia
| | - Larisa Rudenko
- Institute of Experimental Medicine; RAMS; St. Petersburg, Russia
| | - Fei Xu
- National Engineering Laboratory for AIDS Vaccine; School of Life Sciences; Jilin University; Changchun, China
- Changchun BCHT Biotechnology Company; Changchun, China
| | - Wei Kong
- National Engineering Laboratory for AIDS Vaccine; School of Life Sciences; Jilin University; Changchun, China
- Key Laboratory for Molecular Enzymology & Engineering; Ministry of Education; Jilin University; Changchun, China
- Changchun BCHT Biotechnology Company; Changchun, China
| | - Chunlai Jiang
- National Engineering Laboratory for AIDS Vaccine; School of Life Sciences; Jilin University; Changchun, China
- Key Laboratory for Molecular Enzymology & Engineering; Ministry of Education; Jilin University; Changchun, China
- Changchun BCHT Biotechnology Company; Changchun, China
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Fantoni A, Arena C, Corrias L, Salez N, de Lamballerie XN, Amoros JP, Blanchon T, Varesi L, Falchi A. Genetic drift of influenza A(H3N2) viruses during two consecutive seasons in 2011-2013 in Corsica, France. J Med Virol 2013; 86:585-91. [PMID: 24105757 DOI: 10.1002/jmv.23745] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2013] [Indexed: 11/11/2022]
Abstract
The 2011-2012 and 2012-2013 post-pandemic influenza outbreaks were characterized by variability in the A(H3N2) influenza viruses, resulting in low to moderate vaccine effectiveness (VE). The aim of this study was to investigate the molecular evolution and vaccine strain match of the A(H3N2) influenza viruses, having been circulated throughout the population of the French Corsica Island in 2011-2012 and again in 2012-2013. Clinical samples from 31 patients with confirmed A(H3N2) influenza viruses were collected by general practitioners (GPs) over these two consecutive seasons. An analysis of genetic distance and antigenic drift was conducted. Based on a hemagglutinin (HA) aminoacid sequence analysis, the Corsican A(H3N2) viruses fell into the A/Victoria/208/2009 genetic clade, group 3. All influenza viruses were characterized by at least four fixed amino acid mutations which were: N145S (epitope A); Q156H and V186G (epitope B) Y219S (epitope D), with respect to the A/Perth/16/2009 (reference vaccine strain for the 2011-2012) and the A/Victoria/361/2011 (reference vaccine strain for the 2012-2013). Using the p(epitope) model, the percentages of the perfect match VE estimated against circulated strains declined within and between seasons, with estimations of <50%. Overall, these results seem to indicate an antigenic drift of the A(H3N2) influenza viruses which were circulated in Corsica. These findings highlight the importance of the continuous and careful surveillance of genetic changes in the HA domain during seasonal influenza epidemics, in order to provide information on newly emerging genetic variants.
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Affiliation(s)
- Anais Fantoni
- INSERM, U707, Paris, France; Laboratory of Virology, EA 7310, University of Corsica, Corte, France
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Tsuneki A, Itagaki A, Tsuchie H, Tokuhara M, Okada T, Narai S, Kasagi M, Tanaka K, Kageyama S. Reduced replication capacity of influenza A(H1N1)pdm09 virus during the 2010-2011 winter season in Tottori, Japan. J Med Virol 2013; 85:1871-7. [DOI: 10.1002/jmv.23700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2013] [Indexed: 12/20/2022]
Affiliation(s)
- Akeno Tsuneki
- Division of Virology; Department of Microbiology and Immunology; Tottori University Faculty of Medicine; Yonago City Japan
- Tottori Infectious Diseases Forum; Tottori Prefecture Japan
| | - Asao Itagaki
- Division of Virology; Department of Microbiology and Immunology; Tottori University Faculty of Medicine; Yonago City Japan
- Tottori Infectious Diseases Forum; Tottori Prefecture Japan
| | - Hideaki Tsuchie
- Tottori Infectious Diseases Forum; Tottori Prefecture Japan
- Tsuchie Internal Medicine and Pediatric Clinic; Sakaiminato City Japan
| | - Misato Tokuhara
- Division of Virology; Department of Microbiology and Immunology; Tottori University Faculty of Medicine; Yonago City Japan
| | - Takayoshi Okada
- Tottori Infectious Diseases Forum; Tottori Prefecture Japan
- Department of Pediatrics; Tottori Prefectural Kousei Hospital; Kurayoshi City Japan
| | - Sakae Narai
- Tottori Infectious Diseases Forum; Tottori Prefecture Japan
- Department of Pediatrics; Tottori Prefectural Kousei Hospital; Kurayoshi City Japan
| | - Masaaki Kasagi
- Tottori Infectious Diseases Forum; Tottori Prefecture Japan
- Kasagi Children's Clinic for Health Service; Yonago City Japan
| | - Kiyoshi Tanaka
- Tottori Infectious Diseases Forum; Tottori Prefecture Japan
- Tanaka Pediatric Clinic; Tottori City Japan
| | - Seiji Kageyama
- Division of Virology; Department of Microbiology and Immunology; Tottori University Faculty of Medicine; Yonago City Japan
- Tottori Infectious Diseases Forum; Tottori Prefecture Japan
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Speers DJ, Moss DM, Minney-Smith C, Levy A, Smith DW. Influenza and respiratory syncytial virus are the major respiratory viruses detected from prospective testing of pediatric and adult coronial autopsies. Influenza Other Respir Viruses 2013; 7:1113-21. [PMID: 23855988 PMCID: PMC4634247 DOI: 10.1111/irv.12139] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2013] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND To ascertain the full mortality of influenza and other respiratory viruses, the testing of community autopsy specimens is essential. METHODS Respiratory virus PCR and culture were performed on 2418 fresh unfrozen respiratory samples collected from 1611 coronial cases where the death was either unknown or infection was suspected, from July 2007 to June 2011, to detect the common respiratory viruses in children and adults, using standardized microbiological testing. RESULTS The respiratory virus positive rate was 8·3% (134 cases) with a peak of 28% (42 of 151 cases) in children under 10 years of age. Influenza virus was the commonest respiratory virus (50 cases, 3%), followed by respiratory syncytial virus (RSV) (30 cases, 2%). All tested respiratory viruses were found in children, most commonly adenovirus, enterovirus and RSV, and influenza A and RSV predominated in those over 60 years, but coinfection was uncommon. Almost all influenza cases occurred when influenza was widely circulating in the community but few were diagnosed pre-mortem. Influenza and RSV detection was associated with bronchitis or bronchiolitis in 7 (9%) of the 80 cases and caused pneumonia in 14 (0·8%) deaths overall. CONCLUSIONS Our prospective review of respiratory viruses using standardized testing found a single lower respiratory tract autopsy specimen for respiratory virus PCR would detect most community infections at the time of death.
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Affiliation(s)
- David J Speers
- Department of Microbiology, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia; School of Medicine and Pharmacology, University of Western Australia, Crawley, WA, Australia
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Choi JH, Kim MS, Lee JY, Lee NJ, Kwon D, Kang MG, Kang C. Development and evaluation of multiplex real-time RT-PCR assays for seasonal, pandemic A/H1pdm09 and avian A/H5 influenza viruses detection. J Microbiol 2013; 51:252-7. [PMID: 23625229 PMCID: PMC7091309 DOI: 10.1007/s12275-013-2452-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 01/02/2013] [Indexed: 10/26/2022]
Abstract
Since the pandemic influenza A (H1N1) 2009 ((H1N1)pdm09) virus spread all over the world, the (H1N1)pdm09 virus has been circulating with seasonal influenza viruses. We developed rapid and sensitive one-step multiplex real-time RT-PCR assays (rRT-PCR) for simultaneous detection of influenza viruses currently circulating in humans, and the avian A/H5 virus. The detection limit of each assay was 4.8 to 1 copies per reaction and no cross-reactivity with other major respiratory pathogens was found. Analytical positive predictive value (PPV), negative predictive value (NPV) sensitivity and specificity were 100%, 94.1%, 93.7% and 100%, respectively. Clinical evaluation revealed that 1,976 (16.5%) of 11,963 throat swabs from patients with respiratory symptoms were confirmed as 1,651 (83.6%) A/H1pdm09, 308 (15.6%) A/H3 and 17 (0.8%) B virus during the 2010-2011 influenza season. Collectively, the multiplex rRT-PCR assays described here provide a practical tool for reliable implementation of influenza surveillance and diagnosis.
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Affiliation(s)
- Jang-Hoon Choi
- Division of Influenza Virus, Center for Infectious Disease, Korea National Institute of Health, Korea Center for Disease Control and Prevention, Osong 363-951, Republic of Korea
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Pecoraro HL, Spindel ME, Bennett S, Lunn KF, Landolt GA. Evaluation of virus isolation, one-step real-time reverse transcription polymerase chain reaction assay, and two rapid influenza diagnostic tests for detecting canine Influenza A virus H3N8 shedding in dogs. J Vet Diagn Invest 2013; 25:402-6. [PMID: 23536615 DOI: 10.1177/1040638713480500] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Sustained transmission of canine Influenza A virus (CIV) H3N8 among U.S. dogs underscores the threat influenza continues to pose to canine health. Because rapid and accurate detection of infection is critical to the diagnosis and control of CIV, the 2 main objectives of the current study were to estimate and compare the sensitivities of CIV testing methods on canine swab samples and to evaluate the performance of Flu Detect™ (Synbiotics Corp., Kansas City, MO) for detecting CIV nasal shedding in high-risk shelter dogs. To address the first objective, nasal and pharyngeal swab samples were collected from 124 shelter and household dogs seen by Colorado State University Veterinary Teaching Hospital clinicians for canine infectious respiratory disease between April 2006 and March 2007 and tested for CIV shedding using virus isolation, the rapid influenza diagnostic test Directigen Flu A+B™ (BD Diagnostic Systems, Sparks, MD), and real-time reverse transcription polymerase chain reaction (RT-PCR). For the second objective, 1,372 dogs with unknown respiratory health status were sampled from 6 U.S. shelters from December 2009 to November 2010. Samples were tested for presence of CIV using real-time RT-PCR and Flu Detect. Using a stochastic latent class modeling approach, the median sensitivities of virus isolation, rapid influenza diagnostic test, and real-time RT-PCR were 72%, 65%, and 95%, respectively. The Flu Detect test performed poorly for detecting CIV nasal shedding compared to real-time RT-PCR. In conclusion, the real-time RT-PCR has the highest sensitivity for detecting virus nasal shedding and can be used as a rapid diagnostic test for CIV.
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Affiliation(s)
- Heidi L Pecoraro
- Departments of Microbiology, Immunology, and Pathology, Colorado State University, 300 West Drake Road, Fort Collins, CO 80523, USA
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36
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Conway NT, Wake ZV, Richmond PC, Smith DW, Keil AD, Williams S, Kelly H, Carcione D, Effler PV, Blyth CC. Clinical Predictors of Influenza in Young Children: The Limitations of "Influenza-Like Illness". J Pediatric Infect Dis Soc 2013; 2:21-9. [PMID: 26619439 PMCID: PMC7537662 DOI: 10.1093/jpids/pis081] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 07/16/2012] [Indexed: 11/15/2022]
Abstract
BACKGROUND Influenza-like illness (ILI) definitions have been infrequently studied in young children. Despite this, clinical definitions of ILI play an important role in influenza surveillance. This study aims to identify clinical predictors of influenza infection in children ≤5 years old from which age-specific ILI definitions are then constructed. METHODS Children aged 6-59 months with a history of fever and acute respiratory symptoms were recruited in the Western Australia Influenza Vaccine Effectiveness (WAIVE) Study. Clinical data and per-nasal specimens were obtained from all children. Logistic regression identified significant predictors of influenza infection. Different ILI definitions were compared for diagnostic accuracy. RESULTS Children were recruited from 2 winter influenza seasons (2008-2009; n = 944). Of 919 eligible children, 179 (19.5%) had laboratory-confirmed influenza infection. Predictors of infection included increasing age, lack of influenza vaccination, lower birth weight, fever, cough, and absence of wheeze. An ILI definition comprising fever ≥38°C, cough, and no wheeze had 58% sensitivity (95% confidence interval [CI], 50-66), 60% specificity (95% CI, 56-64), 26% positive predictive value (95% CI, 21-31), and 86% negative predictive value (95% CI, 82-89). The addition of other symptoms or higher fever thresholds to ILI definition had little impact. The Centers for Disease Control and Prevention definition of ILI (presence of fever [≥37.8°C] and cough and/or sore throat) was sensitive (92%; 95% CI, 86-95), yet lacked specificity (10%; 95% CI, 8-13) in this population. CONCLUSIONS Influenza-like illness is a poor predictor of laboratory-confirmed influenza infection in young children but can be improved using age-specific data. Incorporating age-specific ILI definitions and/or diagnostic testing into influenza surveillance systems will improve the accuracy of epidemiological data.
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Affiliation(s)
- Nicholas T. Conway
- Vaccine Trials Group, Telethon Institute for Child Health Research, Perth, Western Australia
,Child Health, University of Dundee, Scotland
,Corresponding Author: Dr. Nicholas Conway, Child Health, MACHS Building, Ninewells Hospital, Dundee, Scotland, UK DD1 9SY. E-mail:
| | - Zoe V. Wake
- Department of Paediatric and Adolescent Medicine, Princess Margaret Hospital for Children
| | - Peter C. Richmond
- Vaccine Trials Group, Telethon Institute for Child Health Research, Perth, Western Australia
,Department of Paediatric and Adolescent Medicine, Princess Margaret Hospital for Children,School of Paediatrics and Child Health, University of Western Australia, Perth
| | - David W. Smith
- PathWest Laboratory Medicine WA, QEII Medical Centre, Nedlands
,School of Pathology and Laboratory Medicine, University of Western Australia, Perth
| | - Anthony D. Keil
- Department of Microbiology, PathWest Laboratory Medicine, Princess Margaret Hospital for Children, Perth, Western Australia
| | - Simon Williams
- PathWest Laboratory Medicine WA, QEII Medical Centre, Nedlands
| | - Heath Kelly
- Victorian Infectious Diseases Reference Laboratory, North Melbourne, Victoria, Australia
| | - Dale Carcione
- Communicable Disease Control Directorate, Department of Health, Perth, Western Australia
| | - Paul V. Effler
- Communicable Disease Control Directorate, Department of Health, Perth, Western Australia
| | - Christopher C. Blyth
- Vaccine Trials Group, Telethon Institute for Child Health Research, Perth, Western Australia
,Department of Paediatric and Adolescent Medicine, Princess Margaret Hospital for Children,School of Paediatrics and Child Health, University of Western Australia, Perth
,Department of Microbiology, PathWest Laboratory Medicine, Princess Margaret Hospital for Children, Perth, Western Australia
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Shulman LM, Hindiyeh M, Muhsen K, Cohen D, Mendelson E, Sofer D. Evaluation of four different systems for extraction of RNA from stool suspensions using MS-2 coliphage as an exogenous control for RT-PCR inhibition. PLoS One 2012; 7:e39455. [PMID: 22815706 PMCID: PMC3397973 DOI: 10.1371/journal.pone.0039455] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 05/21/2012] [Indexed: 12/30/2022] Open
Abstract
Knowing when, and to what extent co-extracted inhibitors interfere with molecular RNA diagnostic assays is of utmost importance. The QIAamp Viral RNA Mini Kit (A); MagNA Pure LC2.0 Automatic extractor (B); KingFisher (C); and NucliSENS EasyMag (D) RNA extraction systems were evaluated for extraction efficiency and co-purification of inhibitors from stool suspensions. Real-Time Reverse Transcriptase Polymerase Chain Reaction (rRT-PCR) of MS-2 coliphage spiked into each system's lysis buffer served as an external control for both. Cycle thresholds (Cts) of the MS2 were determined for RNA extracted from stool suspensions containing unknown (n = 93) or varying amounts of inhibitors (n = 92). Stool suspensions from the latter group were also used to determine whether MS-2 and enterovirus rRT-PCR inhibitions were correlated. Specifically 23 RNA extracts from stool suspensions were spiked with enterovirus RNA after extraction and 13 of these stool suspension were spiked with intact enterovirus before extraction. MS2 rRT-PCR inhibition varied for RNAs extracted by the different systems. Inhibition was noted in 12 (13.0%), 26 (28.3%), 7 (7.6%), and 7 (7.6%) of the first 93 RNA extracts, and 58 (63.0%), 55 (59.8%), 37 (40.2%) and 30 (32.6%) of the second 92 extracts for A, B, C, and D, respectively. Furthermore, enterovirus rRT-PCR inhibition correlated with MS2 rRT-PCR inhibition for added enterovirus RNA or virus particles. In conclusion, rRT-PCR for MS-2 RNA is a good predictor of inhibition of enterovirus RNA extracted from stool suspensions. EasyMag performed the best, however all four extraction methods were suitable provided that external controls identified problematic samples.
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Affiliation(s)
- Lester M Shulman
- Central Virology Laboratory, Public Health Services, Israel Ministry of Health, Sheba Medical Center, Tel Hashomer, Israel.
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Tham NT, Hang VTT, Khanh TH, Viet DC, Hien TT, Farrar J, Chau NVV, van Doorn HR. Comparison of the Roche RealTime ready Influenza A/H1N1 Detection Set with CDC A/H1N1pdm09 RT-PCR on samples from three hospitals in Ho Chi Minh City, Vietnam. Diagn Microbiol Infect Dis 2012; 74:131-6. [PMID: 22785431 DOI: 10.1016/j.diagmicrobio.2012.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 05/29/2012] [Accepted: 06/02/2012] [Indexed: 11/28/2022]
Abstract
Real-time polymerase chain reaction (PCR) can be considered the gold standard for detection of influenza viruses due to its high sensitivity and specificity. Roche has developed the RealTime ready Influenza A/H1N1 Detection Set, consisting of a generic influenza virus A PCR targeting the M2 gene (M2 PCR) and a specific PCR targeting the hemagglutinin (HA) of A/H1N1-pdm09 (HA PCR, 2009 H1N1), with the intention to make a reliable, rapid, and simple test to detect and quantify 2009 H1N1 in clinical samples. We evaluated this kit against the US Centers for Disease Control and Prevention (USCDC)/World Health Organization real-time PCR for influenza virus using 419 nose and throat swabs from 210 patients collected in 3 large hospitals in Ho Chi Minh City, Vietnam. In the per-patient analysis, when compared to CDC PCR, the sensitivity and specificity of the M2 PCR were 85.8% and 97.6%, respectively; the sensitivity and specificity of HA PCR were 88.2% and 100%, respectively. In the per-sample analysis, the sensitivity and specificity in nose swabs were higher than those in throat swabs for both M2 and HA PCRs. The viral loads as determined with the M2 and HA PCRs correlated well with the Ct values of the CDC PCR. Compared with the CDC PCR, the kit has a reasonable sensitivity and very good specificity for the detection and quantification of influenza A virus and A/H1N1-pdm09. However, given the current status of 2009 H1N1, a kit that can detect all circulating seasonal influenza viruses would be preferable.
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Affiliation(s)
- Nguyen thi Tham
- Oxford University Clinical Research Unit-Vietnam, Wellcome Trust Major Overseas Program, Ho Chi Minh City, Vietnam
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Grant KA, Fielding JE, Mercer GN, Carcione D, Lopez L, Smith DW, Huang QS, Kelly HA. Comparison of the pandemic H1N1 2009 experience in the Southern Hemisphere with pandemic expectations. Aust N Z J Public Health 2012. [DOI: 10.1111/j.1753-6405.2012.00886.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Chidlow GR, Laing IA, Harnett GB, Greenhill AR, Phuanukoonnon S, Siba PM, Pomat WS, Shellam GR, Smith DW, Lehmann D. Respiratory viral pathogens associated with lower respiratory tract disease among young children in the highlands of Papua New Guinea. J Clin Virol 2012; 54:235-9. [PMID: 22595309 PMCID: PMC3383990 DOI: 10.1016/j.jcv.2012.04.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 04/03/2012] [Accepted: 04/17/2012] [Indexed: 11/18/2022]
Abstract
Background Acute lower respiratory tract infections (ALRI) commonly result in fatal outcomes in the young children of Papua New Guinea (PNG). However, comprehensive studies of the viral aetiology of ALRI have not been conducted in PNG for almost 30 years. Objectives To determine the viruses associated with ALRI among children living in the PNG highlands using sensitive molecular detection techniques. Study design Pernasal swabs were collected routinely between 1 week and 18 months of age and also during episodes of ALRI, as part of a neonatal pneumococcal conjugate vaccine trial. A tandem multiplex real-time PCR assay was used to test for a comprehensive range of respiratory viruses in samples collected from 221 young children. Picornavirus typing was supported by DNA sequence analysis. Results Recognized pathogenic respiratory viruses were detected in 198/273 (73%) samples collected from children with no evidence of ALRI and 69/80 (86%) samples collected during ALRI episodes. Human rhinoviruses (HRV) species A, B and C were detected in 152 (56%) samples from non-ALRI children and 50 (63%) samples collected during ALRI episodes. Partial structural region sequences for two new species C rhinoviruses were added to the GenBank database. ALRI was associated with detection of adenovirus species B (p < 0.01) or C (p < 0.05), influenza A (p < 0.0001) or respiratory syncytial virus (p < 0.0001). Multiple viruses were detected more often during ALRI episodes (49%) than when children displayed no symptoms of ALRI (18%) (p < 0.0001). Conclusions The burden of infection with respiratory viruses remains significant in young children living in the PNG highlands.
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Affiliation(s)
- Glenys R Chidlow
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, Australia.
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Abstract
INTRODUCTION Influenza virus infections cause significant morbidity, and the unique ability of these viruses to undergo antigenic drift and shift means that it is critical for current laboratory assays to keep pace with these changes for accurate diagnosis. New subtypes have the potential to evolve into pandemics hence accurate virus subtyping is also essential. AREAS COVERED In this article, the authors review the current techniques available to detect influenza virus. EXPERT OPINION The biggest gains in improving on influenza diagnostics may lie in reappraising our current approach and optimizing all existing steps in influenza detection: pre-analytical, analytical, post-analytical. In addition, we must foster close collaboration between governments, surveillance networks and frontline diagnostic laboratories, and utilize advances in information technology to facilitate these interactions and to disseminate crucial information.
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Affiliation(s)
- Matthew C Gray
- Department of Microbiology and Infectious Diseases, Sydney South West Pathology Service -Liverpool , Locked Bag 7090, Liverpool BC, NSW, 1871 , Australia +0061 2 9828 5124 ; +0061 2 9828 5129 ;
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Evaluation of real-time reverse transcriptase PCR assays for detection of pandemic influenza A/H1N1 2009 virus. J Clin Microbiol 2011; 49:3444-5. [PMID: 21878586 DOI: 10.1128/jcm.00974-11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Myers CA, Kasper MR, Yasuda CY, Savuth C, Spiro DJ, Halpin R, Faix DJ, Coon R, Putnam SD, Wierzba TF, Blair PJ. Dual infection of novel influenza viruses A/H1N1 and A/H3N2 in a cluster of Cambodian patients. Am J Trop Med Hyg 2011; 85:961-3. [PMID: 22049058 PMCID: PMC3205650 DOI: 10.4269/ajtmh.2011.11-0098] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 06/06/2011] [Indexed: 11/07/2022] Open
Abstract
During the early months of 2009, a novel influenza A/H1N1 virus (pH1N1) emerged in Mexico and quickly spread across the globe. In October 2009, a 23-year-old male residing in central Cambodia was diagnosed with pH1N1. Subsequently, a cluster of four influenza-like illness cases developed involving three children who resided in his home and the children's school teacher. Base composition analysis of internal genes using reverse transcriptase polymerase chain reaction and electrospray ionization mass spectrometry revealed that specimens from two of the secondary victims were coinfected with influenza A/H3N2 and pH1N1. Phylogenetic analysis of the hemagglutinin genes from these isolated viruses showed that they were closely related to existing pH1N1 and A/H3N2 viruses circulating in the region. Genetic recombination was not evident within plaque-purified viral isolates on full genome sequencing. This incident confirms dual influenza virus infections and highlights the risk of zoonotic and seasonal influenza viruses to coinfect and possibly, reassort where they cocirculate.
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Inglis TJJ, Merritt AJ, Levy A, Vietheer P, Bradbury R, Scholler A, Chidlow G, Smith DW. Deployable laboratory response to influenza pandemic; PCR assay field trials and comparison with reference methods. PLoS One 2011; 6:e25526. [PMID: 22022407 PMCID: PMC3192042 DOI: 10.1371/journal.pone.0025526] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 09/05/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The influenza A/H1N1/09 pandemic spread quickly during the Southern Hemisphere winter in 2009 and reached epidemic proportions within weeks of the official WHO alert. Vulnerable population groups included indigenous Australians and remote northern population centres visited by international travellers. At the height of the Australian epidemic a large number of troops converged on a training area in northern Australia for an international exercise, raising concerns about their potential exposure to the emerging influenza threat before, during and immediately after their arrival in the area. Influenza A/H1N1/09 became the dominant seasonal variant and returned to Australia during the Southern winter the following year. METHODS A duplex nucleic acid amplification assay was developed within weeks of the first WHO influenza pandemic alert, demonstrated in northwestern Australia shortly afterwards and deployed as part of the pathology support for a field hospital during a military exercise during the initial epidemic surge in June 2009. RESULTS The nucleic acid amplification assay was twice as sensitive as a point of care influenza immunoassay, as specific but a little less sensitive than the reference laboratory nucleic acid amplification assay. Repetition of the field assay with blinded clinical samples obtained during the 2010 winter influenza season demonstrated a 91.7% congruence with the reference laboratory method. CONCLUSIONS Rapid in-house development of a deployable epidemic influenza assay allowed a flexible laboratory response, effective targeting of limited disease control resources in an austere military environment, and provided the public health laboratory service with a set of verification tools for resource-limited settings. The assay method was suitable for rapid deployment in time for the 2010 Northern winter.
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Affiliation(s)
- Timothy J J Inglis
- Division of Microbiology and Infectious Diseases, PathWest Laboratory Medicine WA, QEII Medical Centre, Nedlands, Western Australia, Australia.
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Curd E, Pollinger J, Toffelmier E, Smith T. Rapid influenza A detection and quantitation in birds using a one-step real-time reverse transcriptase PCR and High Resolution Melting. J Virol Methods 2011; 176:125-30. [DOI: 10.1016/j.jviromet.2011.05.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 05/16/2011] [Accepted: 05/25/2011] [Indexed: 10/18/2022]
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Bilder L, Machtei E, Shenhar Y, Kra-Oz Z, Basis F. Salivary Detection of H1N1 Virus: A Clinical Feasibility Investigation. J Dent Res 2011; 90:1136-9. [DOI: 10.1177/0022034511413283] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
The fast and efficient transportation among continents will continue to play a role in the spread of airborne pandemics. The objective of this study was to detect H1N1 virus in the saliva of individuals who visited the emergency department and were diagnosed as having H1N1 influenza. Nasopharyngeal swabs and saliva samples from those who presented to the emergency department with flu-like symptoms were sent to the laboratory. RNA was extracted from both samples. Real-time RT-PCR tests were performed, and the saliva and nasopharyngeal swab tests were compared. Samples were drawn from 26 individuals. A positive nasopharyngeal swab test and salivary test was found in 14 persons, and negative tests were found in 12 persons. Saliva sampling for H1N1 has excellent predictive value, is highly accurate and reliable, and is more convenient than the nasopharyngeal swab. Clinical trial with the Helsinki Committee at Rambam Health Care Campus, registration number 036309-RMB.
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Affiliation(s)
| | | | | | | | - F. Basis
- Emergency Department, Rambam Health Care Campus, The Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, P.O. Box 9602, Haifa, 31096, Israel
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Nakauchi M, Yoshikawa T, Nakai H, Sugata K, Yoshikawa A, Asano Y, Ihira M, Tashiro M, Kageyama T. Evaluation of reverse transcription loop-mediated isothermal amplification assays for rapid diagnosis of pandemic influenza A/H1N1 2009 virus. J Med Virol 2011; 83:10-5. [PMID: 21108334 DOI: 10.1002/jmv.21934] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Two genetic diagnosis systems using reverse transcription-loop-mediated isothermal amplification (RT-LAMP) technology were evaluated: one for detecting the HA gene of the pandemic influenza A/H1N1 2009 virus (H1pdm RT-LAMP) and the other for detecting the matrix gene of the influenza A virus (TypeA RT-LAMP). The competence of these two RT-LAMP assay kits for the diagnosis of the pandemic influenza A/H1N1 2009 virus was compared using real-time RT-PCR assays developed recently on viruses isolated and clinical specimens collected from patients with suspected infection. TypeA RT-LAMP and H1pdm RT-LAMP showed almost the same sensitivity as real-time RT-PCR for viruses isolated. The sensitivity and specificity of TypeA RT-LAMP and H1pdm RT-LAMP were 96.3% and 88.9%, respectively, for clinical specimens. Considering that the ability of the two RT-LAMP assay kits for detection of the pandemic influenza A/H1N1 2009 virus was comparable to that of the real-time RT-PCR assays, and that the assays were completed within 1 hr and did not require any expensive equipment, these two RT-LAMP assays are promising rapid diagnostic tests for the pandemic influenza A/H1N1 2009 virus at the hospital bedside.
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Affiliation(s)
- Mina Nakauchi
- Influenza Virus Research Center, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
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Evaluation of twelve real-time reverse transcriptase PCR primer-probe sets for detection of pandemic influenza A/H1N1 2009 virus. J Clin Microbiol 2011; 49:1434-40. [PMID: 21289144 DOI: 10.1128/jcm.01914-10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Real-time reverse transcriptase PCR (rRT-PCR) assays have greatly contributed to the detection, control, and prevention of the pandemic influenza A/H1N1 2009 virus. To improve the rRT-PCR assays for detection of pandemic influenza A/H1N1 2009 virus, we evaluated the sensitivity, specificity, and performance of 12 rRT-PCR primer-probe sets [SW (a) to SW (l)] using a panel of virus strains and clinical specimens. These primer-probe sets were derived from published work and designed for detecting the hemagglutinin (HA) or the neuraminidase (NA) gene of the pandemic influenza A/H1N1 2009 virus. A primer-probe set, SW (CDC), developed by the Centers for Disease Control and Prevention (U.S. CDC) to target the HA gene of pandemic influenza A/H1N1 2009 virus, was used as a referee method. Our results demonstrated that although all primer-probe sets in this study had as high as 98.4 to 100% in silico coverage, some of the primer-probe sets had better specificity, sensitivity, and amplification efficiency than others. Two primer-probe sets, SW (h) and SW (l), which target the NA gene of pandemic influenza A/H1N1 2009 virus, were highly sensitive (10(4) copies/reaction), had high detection rates (56/60, P = 0.134, and 59/60, P = 1.000), and showed ideal specificity compared with SW (CDC). In addition, a cocktail of primer-probe sets targeted to the HA and NA genes displayed higher detection sensitivity than primer-probe sets targeting HA or NA alone, indicating that for practical applications, a combination of primer-probes targeting HA and NA genes is the best option for the detection of pandemic influenza A/H1N1 2009 virus.
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Abstract
PURPOSE OF REVIEW The 2009 H1N1 pandemic focused attention on the speed and accuracy of influenza diagnostic methods. This review provides an update on current tests and new developments. RECENT FINDINGS Widely used rapid antigen tests and immunofluorescence tests were generally less sensitive for 2009 H1N1 influenza than for seasonal influenza. In addition, marked variability was reported for the same tests in different settings and patient groups. The advantages of molecular testing gained wide recognition, namely high sensitivity, speed compared with culture, ability to assess viral load and to identify subtype. Although adoption of influenza molecular testing can be expected to accelerate, immunoassays and rapid cultures performed on site retain advantages for many facilities. Falsely negative results were seen with all methods, especially for samples collected very early or late. SUMMARY Influenza diagnostic test performance can be adversely affected by viral genetic and antigenic changes and should be re-assessed annually. Variability in sensitivity and specificity of the same test in different settings highlights the need for each laboratory to ensure optimal procedures and work with clinicians to improve sample quality. Manufacturers have been motivated to improve immunoassays and develop simpler and faster multiplex molecular tests, hopefully in advance of the next pandemic.
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Shahinas D, Lau R, Khairnar K, Hancock D, Pillai DR. Artesunate misuse and Plasmodium falciparum malaria in traveler returning from Africa. Emerg Infect Dis 2011; 16:1608-10. [PMID: 20875294 PMCID: PMC3294389 DOI: 10.3201/eid1610.100116] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Co-infection with seasonal influenza A (H1N1) and pandemic (H1N1) 2009 could result in reassortant viruses that may acquire new characteristics of transmission, virulence, and oseltamivir susceptibility. Results from oseltamivir-sensitivity testing on viral culture suggested the possibility of co-infections with oseltamivir-resistant (seasonal A [H1N1]) and -susceptible (pandemic [H1N1] 2009) viruses.
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