101
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Ratcliff RM, Chang G, Kok T, Sloots TP. Molecular diagnosis of medical viruses. Curr Issues Mol Biol 2007; 9:87-102. [PMID: 17489437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
The diagnosis of infectious diseases has been revolutionized by the development of molecular techniques, foremost with the applications of the polymerase chain reaction (PCR). The achievable high sensitivity and ease with which the method can be used to detect any known genetic sequence have led to its wide application in the life sciences. More recently, real-time PCR assays have provided additional major contributions, with the inclusion of an additional fluorescent probe detection system resulting in an increase in sensitivity over conventional PCR, the ability to confirm the amplification product and to quantitate the target concentration. Further, nucleotide sequence analysis of the amplification products has facilitated epidemiological studies of infectious disease outbreaks, and the monitoring of treatment outcomes for infections, in particular with viruses which mutate at high frequency. This review discusses the applications of qualitative and quantitative real-time PCR, nested PCR, multiplex PCR, nucleotide sequence analysis of amplified products and quality assurance with nucleic acid testing (NAT) in diagnostic laboratories.
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Affiliation(s)
- Rodney M Ratcliff
- Infectious Diseases Laboratories, Institute of Medical and Veterinary Science, Frome Road, Adelaide, South Australia.
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102
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Spence L, Brown WJ, Pyne DB, Nissen MD, Sloots TP, McCormack JG, Locke AS, Fricker PA. Incidence, etiology, and symptomatology of upper respiratory illness in elite athletes. Med Sci Sports Exerc 2007; 39:577-86. [PMID: 17414793 DOI: 10.1249/mss.0b013e31802e851a] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
PURPOSE Upper respiratory illness (URI) is the most common medical condition affecting elite athletes. The aims of this study were to identify and evaluate the incidence, pathogenic etiology, and symptomatology of acute URI during a 5-month training and competition period. METHODS Thirty-two elite and 31 recreationally competitive triathletes and cyclists, and 20 sedentary controls (age range 18.0-34.1 yr) participated in a prospective surveillance study. Nasopharyngeal and throat swabs were collected from subjects presenting with two or more defined upper respiratory symptoms. Swabs were analyzed using microscopy, culture, and PCR testing for typical and atypical respiratory pathogens. The Wisconsin Upper Respiratory Symptom Survey (WURSS-44) was used to assess symptomatology and functional impairment. RESULTS Thirty-seven URI episodes were reported in 28 subjects. Incidence rate ratios for illness were higher in both the control subjects (1.93, 95% CI: 0.72-5.18) and elite athletes (4.50, 1.91-10.59) than in the recreationally competitive athletes. Infectious agents were identified in only 11 (two control, three recreationally competitive, and six elite) out of 37 illness episodes. Rhinovirus was the most common respiratory pathogen isolated. Symptom and functional impairment severity scores were higher in subjects with an infectious pathogen episode, particularly on illness days 3-4. CONCLUSION The results confirm a higher rate of URI among elite athletes than recreationally competitive athletes during this training and competition season. However, because pathogens were isolated in fewer than 30% of URI cases, further study is required to uncover the causes of unidentified but symptomatic URI in athletes. Despite the common perception that all URI are infections, physicians should consider both infectious and noninfectious causes when athletes present with symptoms.
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Affiliation(s)
- Luke Spence
- School of Human Movement Studies, The University of Queensland, Brisbane, Australia.
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103
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Gaynor AM, Nissen MD, Whiley DM, Mackay IM, Lambert SB, Wu G, Brennan DC, Storch GA, Sloots TP, Wang D. Identification of a novel polyomavirus from patients with acute respiratory tract infections. PLoS Pathog 2007; 3:e64. [PMID: 17480120 PMCID: PMC1864993 DOI: 10.1371/journal.ppat.0030064] [Citation(s) in RCA: 542] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Accepted: 03/19/2007] [Indexed: 01/08/2023] Open
Abstract
We report the identification of a novel polyomavirus present in respiratory secretions from human patients with symptoms of acute respiratory tract infection. The virus was initially detected in a nasopharyngeal aspirate from a 3-year-old child from Australia diagnosed with pneumonia. A random library was generated from nucleic acids extracted from the nasopharyngeal aspirate and analyzed by high throughput DNA sequencing. Multiple DNA fragments were cloned that possessed limited homology to known polyomaviruses. We subsequently sequenced the entire virus genome of 5,229 bp, henceforth referred to as WU virus, and found it to have genomic features characteristic of the family Polyomaviridae. The genome was predicted to encode small T antigen, large T antigen, and three capsid proteins: VP1, VP2, and VP3. Phylogenetic analysis clearly revealed that the WU virus was divergent from all known polyomaviruses. Screening of 2,135 patients with acute respiratory tract infections in Brisbane, Queensland, Australia, and St. Louis, Missouri, United States, using WU virus–specific PCR primers resulted in the detection of 43 additional specimens that contained WU virus. The presence of multiple instances of the virus in two continents suggests that this virus is geographically widespread in the human population and raises the possibility that the WU virus may be a human pathogen. We have identified a novel virus, referred to as WU virus, in the family Polyomaviridae by screening of human respiratory secretions. Two human polyomaviruses, BK and JC, were identified in 1971 and infect the majority of humans around the world. These two viruses are closely related to each other and are both are pathogenic in immunocompromised individuals. Earlier this year, a third polyomavirus, KI, was described in human clinical specimens, although its pathogenicity and prevalence in humans has not yet been established. The discovery of WU virus brings the number of polyomaviruses detected in humans to four. WU differs from BK and JC significantly in its genome sequence and in its relative tissue tropism, suggesting that it is likely to have unique biological properties. This discovery raises many questions for further investigation, such as, Is WU virus a human pathogen? If so, what kind of disease does it cause? Where in the body does WU virus reside? At what age does infection typically occur? Perhaps most importantly, there are likely to be many more as of yet unidentified viruses infecting the human body.
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Affiliation(s)
- Anne M Gaynor
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michael D Nissen
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
| | - David M Whiley
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
| | - Ian M Mackay
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
| | - Stephen B Lambert
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
| | - Guang Wu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Daniel C Brennan
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Gregory A Storch
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Theo P Sloots
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
| | - David Wang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * To whom correspondence should be addressed. E-mail:
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104
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Bialasiewicz S, Whiley DM, Nissen MD, Sloots TP. Impact of competitive inhibition and sequence variation upon the sensitivity of malaria PCR. J Clin Microbiol 2007; 45:1621-3. [PMID: 17329455 PMCID: PMC1865911 DOI: 10.1128/jcm.02145-06] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2006] [Revised: 11/29/2006] [Accepted: 02/15/2007] [Indexed: 11/20/2022] Open
Abstract
Real-time PCR assays for Plasmodium species utilizing universal and species-specific primers were compared to investigate variables influencing decreased assay sensitivity. Sequence variation in oligomer targets and competitive inhibition of dual-species templates in universal-primer mixes were found to decrease assay sensitivity.
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Affiliation(s)
- Seweryn Bialasiewicz
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Building C28, Back Road, Royal Children's Hospital & Health Service District, Herston, Queensland, Australia 4029.
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105
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M. Whiley D, W. Tapsall J, D. Nissen M, P. Sloots T. Neisseria gonorrhoeae NAAT ? a problem down under. Microbiol Aust 2007. [DOI: 10.1071/ma07007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Nucleic acid amplification tests (NAATs) are used worldwide for the detection of Neisseria gonorrhoeae, either in conjunction with or in place of traditional bacterial culture techniques. There are numerous advantages of gonococcal NAATs, including increased sensitivity, that a viable organism is not needed for detection, and they can be used effectively on non-invasive specimens such as urine and self-collected specimens. For these reasons, NAATs have been particularly useful for patients in remote regions of Australia where sexual health services may not be available and where religious or cultural restrictions otherwise restrict opportunities for specimen collection. Australian studies have been at the forefront of investigating the use of self-collected NAAT specimens and particularly successful at introducing the use of tampon self-collected specimens in remote populations of Indigenous Australians.
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106
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Lum G, Garland SM, Tabrizi S, Harnett G, Smith DW, Sloots TP, Whiley DM, Tapsall JW. Supplemental testing is still required in australia for samples positive for Neisseria gonorrhoeae by nucleic acid detection tests. J Clin Microbiol 2006; 44:4292-4; author reply 4293-4. [PMID: 17088373 PMCID: PMC1698317 DOI: 10.1128/jcm.01577-06] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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107
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Whiley DM, Anderson TP, Barratt K, Beaman MH, Buda PJ, Carter M, Freeman K, Hallsworth P, Limnios EA, Lum G, Merien F, Vernel-Pauillac F, Tapsall JW, Witt MJ, Nissen MD, Sloots TP. Evidence that the gonococcal porA pseudogene is present in a broad range of Neisseria gonorrhoeae strains; suitability as a diagnostic target. Pathology 2006; 38:445-8. [PMID: 17008285 DOI: 10.1080/00313020600928253] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AIMS The primary aim of the study was to determine if the gonococcal porA pseudogene is a stable sequence target for the detection of Neisseria gonorrhoeae by PCR. METHODS A total of 240 gonococcal strains from various geographic locations were tested by porA pseudogene PCR. In addition, porA pseudogene PCR positivity rates were compared with established gonococcal assays in three Australian states. RESULTS All N. gonorrhoeae isolates provided positive results in the porA pseudogene PCR. Positivity rates compared favourably with established gonococcal assays, with increased N. gonorrhoeae detection in the Northern Territory and Western Australia. CONCLUSIONS The results of this multicentre study provide further evidence that the porA pseudogene is highly conserved across a diverse range N. gonorrhoeae strains and is a suitable PCR target for routine detection of N. gonorrhoeae.
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Affiliation(s)
- David M Whiley
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand.
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108
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Whiley DM, Limnios EA, Ray S, Sloots TP, Tapsall JW. Further questions regarding the role of mosaic penA sequences in conferring reduced susceptibility to ceftriaxone in Neisseria gonorrhoeae. Antimicrob Agents Chemother 2006; 51:802-3. [PMID: 17101673 PMCID: PMC1797742 DOI: 10.1128/aac.01307-06] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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109
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Lu X, Chittaganpitch M, Olsen SJ, Mackay IM, Sloots TP, Fry AM, Erdman DD. Real-time PCR assays for detection of bocavirus in human specimens. J Clin Microbiol 2006; 44:3231-5. [PMID: 16954253 PMCID: PMC1594719 DOI: 10.1128/jcm.00889-06] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The recently discovered human bocavirus (HBoV) is the first member of the family Parvoviridae, genus Bocavirus, to be potentially associated with human disease. Several studies have identified HBoV in respiratory specimens from children with acute respiratory disease, but the full spectrum of clinical disease and the epidemiology of HBoV infection remain unclear. The availability of rapid and reliable molecular diagnostics would therefore aid future studies of this novel virus. To address this, we developed two sensitive and specific real-time TaqMan PCR assays that target the HBoV NS1 and NP-1 genes. Both assays could reproducibly detect 10 copies of a recombinant DNA plasmid containing a partial region of the HBoV genome, with a dynamic range of 8 log units (10(1) to 10(8) copies). Eight blinded clinical specimen extracts positive for HBoV by an independent PCR assay were positive by both real-time assays. Among 1,178 NP swabs collected from hospitalized pneumonia patients in Sa Kaeo Province, Thailand, 53 (4.5%) were reproducibly positive for HBoV by one or both targets. Our data confirm the possible association of HBoV infection with pneumonia and demonstrate the utility of these real-time PCR assays for HBoV detection.
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Affiliation(s)
- Xiaoyan Lu
- Respiratory and Gastroenteritis Viruses Branch, Centers for Disease Control and Prevention, 1600 Clifton Road, N.E., Mailstop G04, Atlanta, GA 30333, USA
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110
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Sloots TP, Mackay IM, Bialasiewicz S, Jacob KC, McQueen E, Harnett GB, Siebert DJ, Masters BI, Young PR, Nissen MD. Human metapneumovirus, Australia, 2001-2004. Emerg Infect Dis 2006; 12:1263-6. [PMID: 16965711 PMCID: PMC3291208 DOI: 10.3201/eid1708.051239] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We examined 10,025 respiratory samples collected for 4 years (2001-2004) and found a 7.1% average annual incidence of human metapneumovirus. The epidemic peak of infection was late winter to spring, and genotyping showed a change in predominant viral genotype in 3 of the 4 years.
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Affiliation(s)
- Theo P Sloots
- Queensland Paediatric Infectious Diseases Laboratory, Royal Children's Hospital and Health Service District, Herston Road, Herston, Queensland 4029, Australia.
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111
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Arden KE, McErlean P, Nissen MD, Sloots TP, Mackay IM. Frequent detection of human rhinoviruses, paramyxoviruses, coronaviruses, and bocavirus during acute respiratory tract infections. J Med Virol 2006; 78:1232-40. [PMID: 16847968 PMCID: PMC7167201 DOI: 10.1002/jmv.20689] [Citation(s) in RCA: 292] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Viruses are the major cause of pediatric acute respiratory tract infection (ARTI) and yet many suspected cases of infection remain uncharacterized. We employed 17 PCR assays and retrospectively screened 315 specimens selected by season from a predominantly pediatric hospital-based population. Before the Brisbane respiratory virus research study commenced, one or more predominantly viral pathogens had been detected in 15.2% (n = 48) of all specimens. The Brisbane study made an additional 206 viral detections, resulting in the identification of a microbe in 67.0% of specimens. After our study, the majority of microbes detected were RNA viruses (89.9%). Overall, human rhinoviruses (HRVs) were the most frequently identified target (n = 140) followed by human adenoviruses (HAdVs; n = 25), human metapneumovirus (HMPV; n = 18), human bocavirus (HBoV; n = 15), human respiratory syncytial virus (HRSV; n = 12), human coronaviruses (HCoVs; n = 11), and human herpesvirus-6 (n = 11). HRVs were the sole microbe detected in 37.8% (n = 31) of patients with suspected lower respiratory tract infection (LRTI). Genotyping of the HRV VP4/VP2 region resulted in a proposed subdivision of HRV type A into sublineages A1 and A2. Most of the genotyped HAdV strains were found to be type C. This study describes the high microbial burden imposed by HRVs, HMPV, HRSV, HCoVs, and the newly identified virus, HBoV on a predominantly paediatric hospital population with suspected acute respiratory tract infections and proposes a new formulation of viral targets for future diagnostic research studies.
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Affiliation(s)
- Katherine E. Arden
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Queensland, Australia
| | - Peter McErlean
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Queensland, Australia
| | - Michael D. Nissen
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Queensland, Australia
- Division of Microbiology, Queensland Health Pathology Service, Royal Brisbane Hospitals Campus, Queensland, Australia
- Department of Paediatrics and Child Health, Royal Children's Hospitals, Queensland, Australia
| | - Theo P. Sloots
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Queensland, Australia
- Division of Microbiology, Queensland Health Pathology Service, Royal Brisbane Hospitals Campus, Queensland, Australia
- Department of Paediatrics and Child Health, Royal Children's Hospitals, Queensland, Australia
| | - Ian M. Mackay
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Queensland, Australia
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112
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Sloots TP, Mackay IM, Bialasiewicz S, Jacob KC, McQueen E, Harnett GB, Siebert DJ, Masters IB, Young PR, Nissen MD. Human metapneumovirus, Australia, 2001-2004. Emerg Infect Dis 2006; 12. [PMID: 16965711 PMCID: PMC3291208 DOI: 10.3201/eid1208.051239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
We examined 10,025 respiratory samples collected for 4 years (2001-2004) and found a 7.1% average annual incidence of human metapneumovirus. The epidemic peak of infection was late winter to spring, and genotyping showed a change in predominant viral genotype in 3 of the 4 years.
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Affiliation(s)
- Theo P. Sloots
- Royal Children's Hospital and Health Service District, Brisbane, Queensland, Australia;,Clinical Medical Virology Centre at University of Queensland, Brisbane, Queensland, Australia;,University of Queensland, Brisbane, Queensland, Australia;,Queensland Health Pathology Service, Brisbane, Queensland, Australia
| | - Ian M. Mackay
- Royal Children's Hospital and Health Service District, Brisbane, Queensland, Australia;,Clinical Medical Virology Centre at University of Queensland, Brisbane, Queensland, Australia;,University of Queensland, Brisbane, Queensland, Australia
| | - Seweryn Bialasiewicz
- Royal Children's Hospital and Health Service District, Brisbane, Queensland, Australia;,Clinical Medical Virology Centre at University of Queensland, Brisbane, Queensland, Australia
| | - Kevin C. Jacob
- Royal Children's Hospital and Health Service District, Brisbane, Queensland, Australia;,Clinical Medical Virology Centre at University of Queensland, Brisbane, Queensland, Australia;,University of Queensland, Brisbane, Queensland, Australia
| | - Emily McQueen
- Royal Children's Hospital and Health Service District, Brisbane, Queensland, Australia;,Clinical Medical Virology Centre at University of Queensland, Brisbane, Queensland, Australia
| | | | - David J. Siebert
- Queensland Health Pathology Service, Brisbane, Queensland, Australia
| | - I. Brent Masters
- Royal Children's Hospital and Health Service District, Brisbane, Queensland, Australia
| | - Paul R. Young
- University of Queensland, Brisbane, Queensland, Australia
| | - Michael D. Nissen
- Royal Children's Hospital and Health Service District, Brisbane, Queensland, Australia;,Clinical Medical Virology Centre at University of Queensland, Brisbane, Queensland, Australia;,University of Queensland, Brisbane, Queensland, Australia;,Queensland Health Pathology Service, Brisbane, Queensland, Australia
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113
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114
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Mackay IM, Bialasiewicz S, Jacob KC, McQueen E, Arden KE, Nissen MD, Sloots TP. Genetic diversity of human metapneumovirus over 4 consecutive years in Australia. J Infect Dis 2006; 193:1630-3. [PMID: 16703505 DOI: 10.1086/504260] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Accepted: 01/20/2006] [Indexed: 11/03/2022] Open
Abstract
The molecular epidemiologic profile of human metapneumovirus (hMPV) infection has likely been skewed toward certain genetic subtypes because of assay-design issues, and no comprehensive studies have been conducted to date. Here, reverse-transcription polymerase chain reaction was used to screen 10,319 specimens from patients presenting to hospitals with suspected respiratory tract infections during 2001-2004. After analysis of 727 Australian hMPV strains, 640 were assigned to 1 of 4 previously described subtypes. hMPV was the most common pathogen detected, and subtype B1 was the most common lineage. Concurrent, annual circulation of all 4 hMPV subtypes in our study population was common, with a single, usually different hMPV subtype predominating in each year.
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Affiliation(s)
- Ian M Mackay
- Queensland Paediatric Infectious Disease Laboratory, Royal Children's Hospital, University of Queensland, Queensland, Australia.
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115
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Mackay IM, Harnett G, Jeoffreys N, Bastian I, Sriprakash KS, Siebert D, Sloots TP. Detection and discrimination of herpes simplex viruses, Haemophilus ducreyi, Treponema pallidum, and Calymmatobacterium (Klebsiella) granulomatis from genital ulcers. Clin Infect Dis 2006; 42:1431-8. [PMID: 16619156 DOI: 10.1086/503424] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Accepted: 01/17/2006] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Genital ulcer disease (GUD) is commonly caused by pathogens for which suitable therapies exist, but clinical and laboratory diagnoses may be problematic. This collaborative project was undertaken to address the need for a rapid, economical, and sensitive approach to the detection and diagnosis of GUD using noninvasive techniques to sample genital ulcers. METHODS The genital ulcer disease multiplex polymerase chain reaction (GUMP) was developed as an inhouse nucleic acid amplification technique targeting serious causes of GUD, namely, herpes simplex viruses (HSVs), H. ducreyi, Treponema pallidum, and Klebsiella species. In addition, the GUMP assay included an endogenous internal control. Amplification products from GUMP were detected by enzyme linked amplicon hybridization assay (ELAHA). RESULTS GUMP-ELAHA was sensitive and specific in detecting a target microbe in 34.3% of specimens, including 1 detection of HSV-1, three detections of HSV-2, and 18 detections of T. pallidum. No H. ducreyi has been detected in Australia since 1998, and none was detected here. No Calymmatobacterium (Klebsiella) granulomatis was detected in the study, but there were 3 detections during ongoing diagnostic use of GUMP-ELAHA in 2004 and 2005. The presence of C. granulomatis was confirmed by restriction enzyme digestion and nucleotide sequencing of the 16S rRNA gene for phylogenetic analysis. CONCLUSIONS GUMP-ELAHA permitted comprehensive detection of common and rare causes of GUD and incorporated noninvasive sampling techniques. Data obtained by using GUMP-ELAHA will aid specific treatment of GUD and better define the prevalence of each microbe among at-risk populations with a view to the eradication of chancroid and donovanosis in Australia.
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Affiliation(s)
- Ian M Mackay
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Queensland, Australia.
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116
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Tan EL, Chow VTK, Kumarasinghe G, Lin RTP, Mackay IM, Sloots TP, Poh CL. Specific detection of enterovirus 71 directly from clinical specimens using real-time RT-PCR hybridization probe assay. Mol Cell Probes 2006; 20:135-40. [PMID: 16460910 DOI: 10.1016/j.mcp.2005.11.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2005] [Accepted: 11/15/2005] [Indexed: 10/25/2022]
Abstract
Enterovirus 71 (EV71) is one of the main causative agents of hand, foot and mouth disease (HFMD) in young children. Infections caused by EV71 could lead to many complications, ranging from brainstem encephalitis to pulmonary oedema, resulting in high mortality. Thus, rapid detection of the virus is required to enable measures to be implemented in preventing widespread transmission. Based on primers and probes targeting at the VP1 region, a real-time reverse-transcriptase polymerase chain reaction (RT-PCR) hybridization probe assay was developed for specific detection of EV71 from clinical specimens. Quantitative analysis showed that the assay was able to detect as low as 5 EV71 viral copies and EV71 was detected from 46 of the 55 clinical specimens obtained from pediatric patients suffering from HFMD during the period from 2000 to 2003 in Singapore. This study showed that the single tube real-time RT-PCR assay developed in this study can be applied as a rapid and sensitive method for specific detection of EV71 directly from clinical specimens.
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Affiliation(s)
- Eng Lee Tan
- Department of Microbiology, Faculty of Medicine, National University of Singapore, Singapore
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117
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Herd KA, Mahalingam S, Mackay IM, Nissen M, Sloots TP, Tindle RW. Cytotoxic T-lymphocyte epitope vaccination protects against human metapneumovirus infection and disease in mice. J Virol 2006; 80:2034-44. [PMID: 16439559 PMCID: PMC1367143 DOI: 10.1128/jvi.80.4.2034-2044.2006] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human metapneumovirus (hMPV) has emerged as an important human respiratory pathogen causing upper and lower respiratory tract infections in young children and older adults. In addition, hMPV infection is associated with asthma exacerbation in young children. Recent epidemiological evidence indicates that hMPV may cocirculate with human respiratory syncytial virus (hRSV) and mediate clinical disease similar to that seen with hRSV. Therefore, a vaccine for hMPV is highly desirable. In the present study, we used predictive bioinformatics, peptide immunization, and functional T-cell assays to define hMPV cytotoxic T-lymphocyte (CTL) epitopes recognized by mouse T cells restricted through several major histocompatibility complex class I alleles, including HLA-A*0201. We demonstrate that peptide immunization with hMPV CTL epitopes reduces viral load and immunopathology in the lungs of hMPV-challenged mice and enhances the expression of Th1-type cytokines (gamma interferon and interleukin-12 [IL-12]) in lungs and regional lymph nodes. In addition, we show that levels of Th2-type cytokines (IL-10 and IL-4) are significantly lower in hMPV CTL epitope-vaccinated mice challenged with hMPV. These results demonstrate for the first time the efficacy of an hMPV CTL epitope vaccine in the control of hMPV infection in a murine model.
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Affiliation(s)
- Karen A Herd
- Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Herston Road, Herston QLD 4029, Australia
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118
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Whiley DM, Sloots TP. Sequence variation in primer targets affects the accuracy of viral quantitative PCR. J Clin Virol 2006; 34:104-7. [PMID: 16157260 DOI: 10.1016/j.jcv.2005.02.010] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2005] [Revised: 02/24/2005] [Accepted: 02/25/2005] [Indexed: 11/16/2022]
Abstract
This study was designed to assess the effect of sequence mismatches between primers and their targets on viral quantitative PCR. Numerous primers were constructed incorporating various mismatches with a target sequence on the BKV T antigen gene. When using these primers in standard Taqman two-step cycling conditions, as few as two mismatches in a single primer increased cycle threshold values and significantly influenced the calculation of viral load.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Herston, Qld 4029, Australia
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119
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Abstract
Nucleic acid amplification tests (NAATs) for the detection of Neisseria gonorrhoeae became available in the early 1990s. Although offering several advantages over traditional detection methods, N. gonorrhoeae NAATs do have some limitations. These include cost, risk of carryover contamination, inhibition, and inability to provide antibiotic resistance data. In addition, there are sequence-related limitations that are unique to N. gonorrhoeae NAATs. In particular, false-positive results are a major consideration. These primarily stem from the frequent horizontal genetic exchange occurring within the Neisseria genus, leading to commensal Neisseria species acquiring N. gonorrhoeae genes. Furthermore, some N. gonorrhoeae subtypes may lack specific sequences targeted by a particular NAAT. Therefore, NAAT false-negative results because of sequence variation may occur in some gonococcal populations. Overall, the N. gonorrhoeae species continues to present a considerable challenge for molecular diagnostics. The need to evaluate N. gonorrhoeae NAATs before their use in any new patient population and to educate physicians on the limitations of these tests is emphasized in this review.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital & Health Service District, Herston Road, Herston, Queensland, Australia 4029.
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120
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Lum G, Freeman K, Nguyen NL, Limnios EA, Tabrizi SN, Carter I, Chambers IW, Whiley DM, Sloots TP, Garland SM, Tapsall JW. A cluster of culture positive gonococcal infections but with false negative cppB gene based PCR. Sex Transm Infect 2005; 81:400-2. [PMID: 16199739 PMCID: PMC1745040 DOI: 10.1136/sti.2004.013805] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVES To describe the prevalence and characteristics of isolates of Neisseria gonorrhoeae grown from urine samples that produced negative results with nucleic acid amplification assays (NAA) targeting the cppB gene. METHODS An initial cluster of culture positive, but cppB gene based NAA negative, gonococcal infections was recognised. Urine samples and suspensions of gonococci isolated over 9 months in the Northern Territory of Australia were examined using cppB gene based and other non-cppB gene based NAA. The gonococcal isolates were phenotyped by determining the auxotype/serovar (A/S) class and genotyped by pulsed field gel electrophoresis (PFGE). RESULTS 14 (9.8%) of 143 gonococci isolated were of A/S class Pro(-/)Brpyut, indistinguishable on PFGE and negative in cppB gene based, but not other, NAA. CONCLUSIONS This cluster represents a temporal and geographic expansion of a gonococcal subtype lacking the cppB gene with consequent loss of sensitivity of NAA dependent on amplification of this target. Gonococci lacking the cppB gene have in the past been more commonly associated with the PAU-/PCU- auxotype, a gonococcal subtype hitherto infrequently encountered in Australia. NAA based on the cppB gene as a target may produce false positive as well as false negative NAA. This suggests that unless there is continuing comparison with culture to show their utility, cppB gene based NAA should be regarded as suboptimal for use either as a diagnostic or supplemental assay for diagnosis of gonorrhoea, and NAA with alternative amplification targets should be substituted.
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Affiliation(s)
- G Lum
- Department of Microbiology, Royal Darwin Hospital, Casuarina, Northern Territory, Australia
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121
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Whiley DM, Sloots TP. Comparison of three in-house multiplex PCR assays for the detection of Neisseria gonorrhoeae and Chlamydia trachomatis using real-time and conventional detection methodologies. Pathology 2005; 37:364-70. [PMID: 16194847 DOI: 10.1080/00313020500254552] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AIMS To develop and evaluate multiplex PCR assays for Chlamydia trachomatis and Neisseria gonorrhoeae, using real-time and conventional PCR detection methodologies. METHODS Two real-time multiplex PCR assays, using nuclease (TaqMan-ABI7500) and hybridisation (LightCycler) probe formats, and a third assay using conventional PCR with solid-phase hybridisation and colour detection, were developed. The porA pseudogene was targeted for N. gonorrhoeae, and the major outer membrane protein gene for C. trachomatis. A total of 145 urogenital specimens were tested in all assays, and the results were compared with the Roche Cobas Amplicor assay. RESULTS There was little difference in clinical sensitivity and specificity, result discrimination and test cost for the three in-house assays. Our results showed that competitive inhibition of the PCR occurred in some samples that were positive for both organisms. CONCLUSIONS These results highlight the suitability and versatility of three multiplex PCR methods for the detection of C. trachomatis and N. gonorrhoeae.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Brisbane, Queensland, Australia.
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122
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Whiley DM, Sloots TP. A 5'-nuclease real-time reverse transcriptase-polymerase chain reaction assay for the detection of a broad range of influenza A subtypes, including H5N1. Diagn Microbiol Infect Dis 2005; 53:335-7. [PMID: 16269224 DOI: 10.1016/j.diagmicrobio.2005.08.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2005] [Accepted: 08/02/2005] [Indexed: 11/30/2022]
Abstract
A 5'-nuclease real-time reverse transcriptase-polymerase chain reaction assay was developed for the detection of influenza type A and was validated using a range of influenza A subtypes, including avian strains, and 126 nasopharyngeal aspirate samples. The results show the assay is suitable for screening for influenza A infections, particularly in regions where avian strains may be circulating.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Queensland, 4029 Australia.
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Sloots TP, McErlean P, Speicher DJ, Arden KE, Nissen MD, Mackay IM. Evidence of human coronavirus HKU1 and human bocavirus in Australian children. J Clin Virol 2005; 35:99-102. [PMID: 16257260 PMCID: PMC7108338 DOI: 10.1016/j.jcv.2005.09.008] [Citation(s) in RCA: 280] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Accepted: 09/22/2005] [Indexed: 11/17/2022]
Abstract
Undiagnosed cases of respiratory tract disease suspected of an infectious aetiology peak during the winter months. Since studies applying molecular diagnostic assays usually report reductions in the number of undiagnosed cases of infectious disease compared to traditional techniques, we applied PCR assays to investigate the role of two recently described viruses, namely human coronavirus (HCoV) HKU1 and human bocavirus (HBoV), in a hospital-based paediatric population. Both viruses were found among Australia children with upper or lower respiratory tract disease during the autumn and winter of 2004, contributing to 21.1% of all microbial diagnoses, with individual incidences of 3.1% (HCoV-HKU1) and 5.6% (HBoV) among 324 specimens. HBoV was found to coincide with another virus in more than half of all instances and displayed a single genetic lineage, whilst HCoV-HKU1 was more likely to occur in the absence of another microbe and strains could be divided into two genetic lineages which we propose be termed HCoV-HKU1 type A and type B. Children under the age of 2 years were most at risk of infection by these viruses which contribute significantly to the microbial burden among patients with respiratory tract disease during the colder months.
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Affiliation(s)
- Theo P. Sloots
- Queensland Paediatric Infectious Diseases Laboratory, CVRU, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Herston Road, Herston, Queensland 4029, Australia
- Clinical and Medical Virology Centre, University of Queensland, Queensland, Australia
- Division of Microbiology, Queensland Health Pathology Service, Royal Brisbane Hospitals Campus, Queensland, Australia
- Department of Paediatrics and Child Health, Royal Children's Hospitals, Queensland, Australia
| | - Peter McErlean
- Queensland Paediatric Infectious Diseases Laboratory, CVRU, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Herston Road, Herston, Queensland 4029, Australia
- Clinical and Medical Virology Centre, University of Queensland, Queensland, Australia
| | - David J. Speicher
- Queensland Paediatric Infectious Diseases Laboratory, CVRU, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Herston Road, Herston, Queensland 4029, Australia
- Clinical and Medical Virology Centre, University of Queensland, Queensland, Australia
| | - Katherine E. Arden
- Queensland Paediatric Infectious Diseases Laboratory, CVRU, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Herston Road, Herston, Queensland 4029, Australia
- Clinical and Medical Virology Centre, University of Queensland, Queensland, Australia
| | - Michael D. Nissen
- Queensland Paediatric Infectious Diseases Laboratory, CVRU, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Herston Road, Herston, Queensland 4029, Australia
- Clinical and Medical Virology Centre, University of Queensland, Queensland, Australia
- Division of Microbiology, Queensland Health Pathology Service, Royal Brisbane Hospitals Campus, Queensland, Australia
- Department of Paediatrics and Child Health, Royal Children's Hospitals, Queensland, Australia
| | - Ian M. Mackay
- Queensland Paediatric Infectious Diseases Laboratory, CVRU, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Herston Road, Herston, Queensland 4029, Australia
- Clinical and Medical Virology Centre, University of Queensland, Queensland, Australia
- Corresponding author. Tel.: +61 3636 8716; fax: +61 3636 1401.
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124
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Arden KE, Nissen MD, Sloots TP, Mackay IM. New human coronavirus, HCoV-NL63, associated with severe lower respiratory tract disease in Australia. J Med Virol 2005; 75:455-62. [PMID: 15648064 PMCID: PMC7166768 DOI: 10.1002/jmv.20288] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
A new human coronavirus, HCoV‐NL63, was associated recently with bronchiolitis. The current study aimed to examine retrospectively stored specimens for the presence of HCoV‐NL63 using nested RT‐PCR assays targeting the 1a and 1b genes. The study population was composed of patients with acute respiratory disease warranting presentation to Queensland hospitals. HCoV‐NL63 was detected in the nasopharyngeal aspirates (NPA) of 16 of 840 specimens representing 766 patients (2%). HCoV‐NL63 positive individuals were diagnosed most commonly with lower respiratory tract (LRT) disease (81%). The clinical diagnosis was commonly supported by an abnormal chest X‐ray (56%) together with respiratory distress (50%), wheeze (44%), and râles (25%) on first presentation with HCoV‐NL63 infection. All patients positive for HCoV‐NL63 required admission to hospital. Among 38% of HCoV‐NL63 positive specimens a second pathogen was detected. Sequencing of amplicon from gene 1b revealed more than 99% nucleotide homology with the viral type strains while sequencing amplicon from gene 1a permitted the grouping of viral strains. It was shown that HCoV‐NL63 is associated with severe LRT disease in an Australian hospital setting during the cooler months of the year. We propose that HCoV‐NL63 is a global and seasonal pathogen of both children and adults associated with severe LRT illness. J. Med. Virol. 75:455–462, 2005. © 2005 Wiley‐Liss, Inc.
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Affiliation(s)
- Katherine E. Arden
- Clinical Virology and Molecular Microbiology Research Units, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Queensland, Australia
| | - Michael D. Nissen
- Clinical Virology and Molecular Microbiology Research Units, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Queensland, Australia
- Division of Microbiology, Queensland Health Pathology Service, Royal Brisbane Hospitals Campus, Queensland, Australia
- Department of Paediatrics and Child Health, Royal Children's Hospitals, Queensland, Australia
| | - Theo P. Sloots
- Clinical Virology and Molecular Microbiology Research Units, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Queensland, Australia
- Division of Microbiology, Queensland Health Pathology Service, Royal Brisbane Hospitals Campus, Queensland, Australia
- Department of Paediatrics and Child Health, Royal Children's Hospitals, Queensland, Australia
| | - Ian M. Mackay
- Clinical Virology and Molecular Microbiology Research Units, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Queensland, Australia
- Clinical and Medical Virology Centre, University of Queensland, Queensland, Australia
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125
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Whiley DM, Sloots TP. Sequence variation can affect the performance of minor groove binder TaqMan probes in viral diagnostic assays. J Clin Virol 2005; 35:81-3. [PMID: 16002331 DOI: 10.1016/j.jcv.2005.05.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2005] [Revised: 05/16/2005] [Accepted: 05/18/2005] [Indexed: 11/16/2022]
Abstract
A minor groove binder (MGB) TaqMan real-time PCR assay was developed for the detection of respiratory syncytial virus (RSV) in clinical specimens. Upon evaluation of the assay, notable differences were observed in the overall fluorescent response obtained from RSV positive specimens, with some linear amplification curves deviating only slightly from baseline fluorescence. Sequencing of the probes targets in these RSV strains revealed single base mismatches with the MGB TaqMan probe. Overall, these results highlight the usefulness of MGB TaqMan probes for the detection of mismatches, but suggest that MGB Taqman probes have limitations for routine screening for uncharacterised viral strains.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital & Health Service District, Herston Road, Herston, Qld 4029, Australia.
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126
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Tapsall JW, Limnios EA, Nguyen NL, Carter I, Lum G, Freeman K, Tabrizi SN, Garland SM, Whiley DM, Sloots TP, Chambers IW. Cryptic-plasmid-free gonococci may contribute to failure of cppB gene-based assays to confirm results of BD ProbeTEC PCR for identification of Neisseria gonorrhoeae. J Clin Microbiol 2005; 43:2036-7. [PMID: 15815057 PMCID: PMC1081405 DOI: 10.1128/jcm.43.4.2036-2037.2005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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127
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128
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Whiley DM, Buda PP, Freeman K, Pattle NI, Bates J, Sloots TP. A real-time PCR assay for the detection of Neisseria gonorrhoeae in genital and extragenital specimens. Diagn Microbiol Infect Dis 2005; 52:1-5. [PMID: 15878435 DOI: 10.1016/j.diagmicrobio.2004.12.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2004] [Accepted: 12/20/2004] [Indexed: 11/23/2022]
Abstract
A Neisseria gonorrhoeae LightCycler (NGpapLC) assay targeting the porA pseudogene was compared with bacterial culture for detection of N. gonorrhoeae in 636 clinical specimens (216 cervical, 185 urethral, 196 throat, and 39 rectal swab specimens). The specificity of the NGpapLC assay was further investigated by testing a bacterial reference panel comprising several Neisseria species. Overall, 19 (3.0%) specimens were positive and 613 (96.4%) specimens were negative by both methods. Four (0.6%) specimens were positive by the NGpapLC assay only. For the cervical and urethral swabs, the NGpapLC provided 100% sensitivity and 100% specificity compared with bacterial culture. Following discrepant analysis, the clinical sensitivity and specificity of the NGpapLC for throat and rectal swabs was also 100%. For the bacterial panel, only N. gonorrhoeae isolates provided positive results. The results show the NGpapLC assay is suitable for use on a range of clinical specimens and could improve detection of pharyngeal N. gonorrhoeae.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Queensland 4029, Australia
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129
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O'Carroll MR, Syrmis MW, Wainwright CE, Greer RM, Mitchell P, Coulter C, Sloots TP, Nissen MD, Bell SC. Clonal strains of Pseudomonas aeruginosa in paediatric and adult cystic fibrosis units. Eur Respir J 2005; 24:101-6. [PMID: 15293611 DOI: 10.1183/09031936.04.00122903] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Despite recent reports of clonal strains of Pseudomonas aeruginosa in cystic fibrosis (CF) units, the need for routine microbiological surveillance remains contentious. Sputum was collected prospectively from productive patients attending the regional paediatric and adult CF units in Brisbane, Australia. All P. aeruginosa isolates were typed using pulsed-field gel electrophoresis. Spirometry, anthropometrics, hospitalisations and antibiotic sensitivity data were recorded. The first 100 sputum samples (first 50 patients at each clinic) harboured 163 isolates of P. aeruginosa. A total of 39 patients shared a common strain (pulsotype 2), 20 patients shared a strain with at least one other patient and 41 patients harboured unique strains. Eight patients shared a strain identical to a previously reported Australian transmissible strain (pulsotype 1). Compared with the unique strain group, patients harbouring pulsotype 2 were younger and had poorer lung function. Treatment requirements were similar in these two groups, as were the rates of multiresistance. In conclusion, 59% of patients harboured a clonal strain, supporting the need for routine microbiological surveillance. In contrast to previously described clonal strains, the dominant pulsotype was indistinguishable from nonclonal strains with respect to both colonial morphology and multiresistance. The clinical significance of clonal strains remains uncertain and requires longitudinal study.
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Affiliation(s)
- M R O'Carroll
- Adult Cystic Fibrosis Unit, The Prince Charles Hospital, Chermside, Australia
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130
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Punch G, Syrmis MW, Rose BR, Harbour C, Bye PTP, Nissen MD, Elkins MR, Sloots TP. Method for detection of respiratory viruses in the sputa of patients with cystic fibrosis. Eur J Clin Microbiol Infect Dis 2005; 24:54-7. [PMID: 15616837 PMCID: PMC7088139 DOI: 10.1007/s10096-004-1273-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Since the role of respiratory viruses in lung exacerbations of patients with cystic fibrosis has been hampered by the difficulty of detecting viruses in viscous sputum specimens, a multiplex reverse transcriptase PCR (RT-PCR) assay combined with colorimetric amplicon detection was tested for the identification of seven common respiratory viruses in the sputa of cystic fibrosis patients. Of 52 sputa from 38 patients, 12 (23%) samples from 12 patients were positive for a respiratory virus (4 for influenza B, 3 for parainfluenza 1, 3 for influenza A and 2 for respiratory syncytial virus). These results suggest that the RT-PCR method carried out on sputum may provide a convenient means of investigating the role of virus infection in lung exacerbations of cystic fibrosis patients.
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Affiliation(s)
- G Punch
- Department of Infectious Diseases and Immunology, University of Sydney, Parramatta Road, Camperdown, New South Wales 2006, Australia
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131
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Mackay IM, Bialasiewicz S, Waliuzzaman Z, Chidlow GR, Fegredo DC, Laingam S, Adamson P, Harnett GB, Rawlinson W, Nissen MD, Sloots TP. Use of the P gene to genotype human metapneumovirus identifies 4 viral subtypes. J Infect Dis 2004; 190:1913-8. [PMID: 15529254 DOI: 10.1086/425013] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2003] [Accepted: 05/24/2004] [Indexed: 11/03/2022] Open
Abstract
This study, conducted during 2001-2003, undertook the screening of patients with acute infectious respiratory-tract disease. A random selection of positive specimens was used for sequencing studies of the human metapneumovirus (hMPV) nucleoprotein gene and the phosphoprotein (P) gene. Australian and international sequences were compared, and a global classification scheme was developed. The hMPV P gene was an ideal molecular target for the detection and genotyping of hMPV. The region contained conserved sequences for reverse-transcriptase-polymerase chain-reaction primers and adequate variability to permit the accurate genotyping of the virus into 2 main lineages and 4 sublineages. Establishing viral identity is essential for the linking of genotype and disease severity.
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Affiliation(s)
- Ian M Mackay
- Clinical Virology and Molecular Microbiology Research Units, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and University of Queensland, Herston Road, Herston, Queensland 4029, Australia.
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132
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Syrmis MW, O'Carroll MR, Sloots TP, Coulter C, Wainwright CE, Bell SC, Nissen MD. Rapid genotyping of Pseudomonas aeruginosa isolates harboured by adult and paediatric patients with cystic fibrosis using repetitive-element-based PCR assays. J Med Microbiol 2004; 53:1089-1096. [PMID: 15496385 DOI: 10.1099/jmm.0.45611-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, the suitability of two repetitive-element-based PCR (rep-PCR) assays, enterobacterial repetitive intergenic consensus (ERIC)-PCR and BOX-PCR, to rapidly characterize Pseudomonas aeruginosa strains isolated from patients with cystic fibrosis (CF) was examined. ERIC-PCR utilizes paired sequence-specific primers and BOX-PCR a single primer that target highly conserved repetitive elements in the P. aeruginosa genome. Using these rep-PCR assays, 163 P. aeruginosa isolates cultured from sputa collected from 50 patients attending an adult CF clinic and 50 children attending a paediatric CF clinic were typed. The results of the rep-PCR assays were compared to the results of PFGE. All three assays revealed the presence of six major clonal groups shared by multiple patients attending either of the CF clinics, with the dominant clonal group infecting 38 % of all patients. This dominant clonal group was not related to the dominant clonal group detected in Sydney or Melbourne (pulsotype 1), nor was it related to the dominant groups detected in the UK. In all, PFGE and rep-PCR identified 58 distinct clonal groups, with only three of these shared between the two clinics. The results of this study showed that both ERIC-PCR and BOX-PCR are rapid, highly discriminatory and reproducible assays that proved to be powerful surveillance screening tools for the typing of clinical P. aeruginosa isolates recovered from patients with CF.
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Affiliation(s)
- Melanie W Syrmis
- Clinical Virology and Molecular Microbiology Research Unit, Sir Albert Sakzewksi Virus Research Centre, Royal Children's Hospital and Clinical Medical Virology Centre, University of Queensland, Herston, Queensland, Australia 4029 2,6Department of Paediatrics and Child Health2 and Department of Medicine6, University of Queensland, Brisbane, Queensland, Australia 3Adult Cystic Fibrosis Unit, The Prince Charles Hospital, Brisbane, Queensland, Australia 4Department of Respiratory Medicine, Royal Children's Hospital, Brisbane, Queensland, Australia 5Department of Microbiology, Queensland Health Pathology Service, The Prince Charles Hospital Campus, Brisbane, Queensland, Australia
| | - Mark R O'Carroll
- Clinical Virology and Molecular Microbiology Research Unit, Sir Albert Sakzewksi Virus Research Centre, Royal Children's Hospital and Clinical Medical Virology Centre, University of Queensland, Herston, Queensland, Australia 4029 2,6Department of Paediatrics and Child Health2 and Department of Medicine6, University of Queensland, Brisbane, Queensland, Australia 3Adult Cystic Fibrosis Unit, The Prince Charles Hospital, Brisbane, Queensland, Australia 4Department of Respiratory Medicine, Royal Children's Hospital, Brisbane, Queensland, Australia 5Department of Microbiology, Queensland Health Pathology Service, The Prince Charles Hospital Campus, Brisbane, Queensland, Australia
| | - Theo P Sloots
- Clinical Virology and Molecular Microbiology Research Unit, Sir Albert Sakzewksi Virus Research Centre, Royal Children's Hospital and Clinical Medical Virology Centre, University of Queensland, Herston, Queensland, Australia 4029 2,6Department of Paediatrics and Child Health2 and Department of Medicine6, University of Queensland, Brisbane, Queensland, Australia 3Adult Cystic Fibrosis Unit, The Prince Charles Hospital, Brisbane, Queensland, Australia 4Department of Respiratory Medicine, Royal Children's Hospital, Brisbane, Queensland, Australia 5Department of Microbiology, Queensland Health Pathology Service, The Prince Charles Hospital Campus, Brisbane, Queensland, Australia
| | - Chris Coulter
- Clinical Virology and Molecular Microbiology Research Unit, Sir Albert Sakzewksi Virus Research Centre, Royal Children's Hospital and Clinical Medical Virology Centre, University of Queensland, Herston, Queensland, Australia 4029 2,6Department of Paediatrics and Child Health2 and Department of Medicine6, University of Queensland, Brisbane, Queensland, Australia 3Adult Cystic Fibrosis Unit, The Prince Charles Hospital, Brisbane, Queensland, Australia 4Department of Respiratory Medicine, Royal Children's Hospital, Brisbane, Queensland, Australia 5Department of Microbiology, Queensland Health Pathology Service, The Prince Charles Hospital Campus, Brisbane, Queensland, Australia
| | - Claire E Wainwright
- Clinical Virology and Molecular Microbiology Research Unit, Sir Albert Sakzewksi Virus Research Centre, Royal Children's Hospital and Clinical Medical Virology Centre, University of Queensland, Herston, Queensland, Australia 4029 2,6Department of Paediatrics and Child Health2 and Department of Medicine6, University of Queensland, Brisbane, Queensland, Australia 3Adult Cystic Fibrosis Unit, The Prince Charles Hospital, Brisbane, Queensland, Australia 4Department of Respiratory Medicine, Royal Children's Hospital, Brisbane, Queensland, Australia 5Department of Microbiology, Queensland Health Pathology Service, The Prince Charles Hospital Campus, Brisbane, Queensland, Australia
| | - Scott C Bell
- Clinical Virology and Molecular Microbiology Research Unit, Sir Albert Sakzewksi Virus Research Centre, Royal Children's Hospital and Clinical Medical Virology Centre, University of Queensland, Herston, Queensland, Australia 4029 2,6Department of Paediatrics and Child Health2 and Department of Medicine6, University of Queensland, Brisbane, Queensland, Australia 3Adult Cystic Fibrosis Unit, The Prince Charles Hospital, Brisbane, Queensland, Australia 4Department of Respiratory Medicine, Royal Children's Hospital, Brisbane, Queensland, Australia 5Department of Microbiology, Queensland Health Pathology Service, The Prince Charles Hospital Campus, Brisbane, Queensland, Australia
| | - Michael D Nissen
- Clinical Virology and Molecular Microbiology Research Unit, Sir Albert Sakzewksi Virus Research Centre, Royal Children's Hospital and Clinical Medical Virology Centre, University of Queensland, Herston, Queensland, Australia 4029 2,6Department of Paediatrics and Child Health2 and Department of Medicine6, University of Queensland, Brisbane, Queensland, Australia 3Adult Cystic Fibrosis Unit, The Prince Charles Hospital, Brisbane, Queensland, Australia 4Department of Respiratory Medicine, Royal Children's Hospital, Brisbane, Queensland, Australia 5Department of Microbiology, Queensland Health Pathology Service, The Prince Charles Hospital Campus, Brisbane, Queensland, Australia
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Whiley DM, Crisante ME, Syrmis MW, Mackay IM, Sloots TP. Detection of Neisseria Meningitidis in clinical samples by a duplex real-time PCR targeting the porA and ctrA genes. ACTA ACUST UNITED AC 2004; 7:141-5. [PMID: 15068383 DOI: 10.1007/bf03260030] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
BACKGROUND In recent years PCR has proven to be a highly sensitive and specific method for the diagnosis of infections caused by Neisseria meningitidis. STUDY DESIGN We developed and evaluated a N. meningitidis LightCycler real-time duplex PCR (NM-LCdPCR) capable of simultaneously detecting and distinguishing between two separate genes on the N. meningitidis genome. METHODS The NM-LCdPCR was developed on the LightCycler platform (Roche Diagnostics, Castle Hill, NSW, Australia) and comprised two primer pairs and two hybridization probe sets, enabling the detection of both the porA and ctrA genes within the same reaction mix. To distinguish between the fluorescence emitted by each hybridization probe set, each downstream probe was labeled with a different fluorophore (either LC-Red640 or LC-Red705). The results obtained by the NM-LCdPCR were then compared with the results obtained by a mono-specific LightCycler assay targeting the porA gene only (porA-LCPCR). PATIENTS One-hundred and forty-eight clinical samples from patients with suspected meningococcal infection were evaluated. RESULTS The results of the NM-LCdPCR and porA-LCPCR gave 100% agreement; N. meningitidis DNA was detected in 25 samples whereas 123 samples were negative by both assays. The breakdown of the NM-LCdPCR results show that both genes were detected in 26 of the 28 positive samples. DISCUSSION By targeting two separate N. meningitidis genes, the NM-LCdPCR has the potential to prevent the false-positive results which may arise from sequence variation. In addition, the ability to detect and discriminate between the two different N. meningitidis genes within the same reaction mix offers a rapid means for confirming the presence of N. meningitidis DNA in clinical samples, thereby reducing the need for subsequent confirmatory assays to be performed. CONCLUSIONS The sensitivity and specificity of the NM-LCdPCR assay, combined with its ability to detect and discriminate both the N. meningitidis porA and ctrA genes, make it suitable for the diagnosis of N. meningitidis infections in the routine clinical laboratory.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Herston, and Clinical Medical Virology Centre, University of Queensland, Brisbane, Queensland, Australia
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Boivin G, Mackay I, Sloots TP, Madhi S, Freymuth F, Wolf D, Shemer-Avni Y, Ludewick H, Gray GC, LeBlanc E. Global genetic diversity of human metapneumovirus fusion gene. Emerg Infect Dis 2004; 10:1154-7. [PMID: 15207075 PMCID: PMC3323143 DOI: 10.3201/eid1006.031097] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We analyzed 64 human metapneumovirus strains from eight countries. Phylogenetic analysis identified two groups (A and B, amino acid identity 93%-96%) and four subgroups. Although group A strains predominated, accounting for 69% of all strains, as many B as A strains were found in persons >3 years of age.
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Affiliation(s)
- Guy Boivin
- Centre Hospitalier Universitaire de Québec and Laval University, Sainte-Foy, Quebec City, Canada.
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135
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Whiley DM, Mackay IM, Syrmis MW, Witt MJ, Sloots TP. Detection and differentiation of herpes simplex virus types 1 and 2 by a duplex LightCycler PCR that incorporates an internal control PCR reaction. J Clin Virol 2004; 30:32-8. [PMID: 15072751 DOI: 10.1016/j.jcv.2003.08.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2003] [Revised: 08/12/2003] [Accepted: 08/15/2003] [Indexed: 11/27/2022]
Abstract
BACKGROUND In recent years polymerase chain reaction (PCR) has proven to be a highly sensitive and specific method for the diagnosis of herpes simplex virus (HSV) infections. The advent of real-time HSV PCR protocols now enables rapid result turnaround times with minimal hands-on time. OBJECTIVES In this study, we developed a real-time duplex PCR assay (HSVgD-dPCR) comprising of HSV and internal control PCR reactions. STUDY DESIGN Using the LightCycler, the HSVgD-dPCR targeted the HSV glycoprotein D gene and HSV typing was performed by melting curve analysis. The internal control PCR reaction targeted sequences of the DNA of the human endogenous retrovirus (ERV-3). In total, 300 swab specimens, from patients with suspected HSV infection, were tested by the HSVgD-dPCR assay. The results were then compared to the results obtained by another HSV LightCycler assay, which utilized published primer and probe sequences targeting the HSV DNA polymerase gene (Dpol-HSV-LCPCR). RESULTS Overall, 91 (30.3%) specimens were positive and 204 (68.0%) specimens were negative for HSV by both LightCycler assays. In addition, four (1.3%) specimens were positive by Dpol-HSV-LCPCR and negative by HSVgD-dPCR, whereas one (0.3%) specimen was positive by HSVgD-dPCR and negative by Dpol-HSV-LCPCR. The presence of HSV in these five specimens was confirmed by conventional PCR. Melting curve analysis by the HSVgD-dPCR assay enabled all HSV positive specimens to be typed, whereas sequence variation prevented three HSV positive specimens from being typed by the Dpol-HSV-LCPCR. Using the ERV-3 PCR, 5% specimens were found to contain inhibitory substances. CONCLUSIONS By developing the HSVgD-dPCR we have enhanced the diagnostic utility of real-time detection of HSV by incorporating an internal control reaction and by accurately typing a greater proportion of HSV positive specimens.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital & Health Service District, Herston Road, Herston, Queensland 4029, Australia
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Whiley DM, Buda PJ, Bayliss J, Cover L, Bates J, Sloots TP. A new confirmatory Neisseria gonorrhoeae real-time PCR assay targeting the porA pseudogene. Eur J Clin Microbiol Infect Dis 2004; 23:705-10. [PMID: 15248092 DOI: 10.1007/s10096-004-1170-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The Roche Cobas Amplicor system is widely used for the detection of Neisseria gonorrhoeae but is known to cross react with some commensal Neisseria spp. Therefore, a confirmatory test is required. The most common target for confirmatory tests is the cppB gene of N. gonorrhoeae. However, the cppB gene is also present in other Neisseria spp. and is absent in some N. gonorrhoeae isolates. As a result, laboratories targeting this gene run the risk of obtaining both false-positive and false-negative results. In the study presented here, a newly developed N. gonorrhoeae LightCycler assay (NGpapLC) targeting the N. gonorrhoeae porA pseudogene was tested. The NGpapLC assay was used to test 282 clinical samples, and the results were compared to those obtained using a testing algorithm combining the Cobas Amplicor System (Roche Diagnostics, Sydney, Australia) and an in-house LightCycler assay targeting the cppB gene (cppB-LC). In addition, the specificity of the NGpapLC assay was investigated by testing a broad panel of bacteria including isolates of several Neisseria spp. The NGpapLC assay proved to have comparable clinical sensitivity to the cppB-LC assay. In addition, testing of the bacterial panel showed the NGpapLC assay to be highly specific for N. gonorrhoeae DNA. The results of this study show the NGpapLC assay is a suitable alternative to the cppB-LC assay for confirmation of N. gonorrhoeae-positive results obtained with Cobas Amplicor.
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Affiliation(s)
- D M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Clinical Medical Virology Centre, University of Queensland, Herston, Brisbane, Australia
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Whiley DM, LeCornec GM, Baddeley A, Savill J, Syrmis MW, Mackay IM, Siebert DJ, Burns D, Nissen M, Sloots TP. Detection and differentiation of Plasmodium species by polymerase chain reaction and colorimetric detection in blood samples of patients with suspected malaria. Diagn Microbiol Infect Dis 2004; 49:25-9. [PMID: 15135496 DOI: 10.1016/j.diagmicrobio.2003.10.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2003] [Accepted: 10/24/2003] [Indexed: 11/20/2022]
Abstract
Polymerase chain reaction (PCR) is now recognized as a sensitive and specific method for detecting Plasmodium species in blood. In this study, we tested 279 blood samples, from patients with suspected malaria, by a PCR assay utilizing species-specific colorimetric detection, and compared the results to light microscopy. Overall, both assays were in agreement for 270 of the 279 specimens. P. vivax was detected in 131 (47.0%) specimens, P. falciparum in 64 (22.9%) specimens, P. ovale in 6 (2.1%) specimens, and P. malariae in 5 (1.8%) specimens. Both P. falciparum and P. vivax were detected in a further 10 (3.6%) specimens, and 54 (19.3%) specimens were negative by both assays. In the remaining nine specimens, microscopy either failed to detect the parasite or incorrectly identified the species present. In summary, the sensitivity, specificity and simplicity of the PCR assay makes it particularly suitable for use in a diagnostic laboratory.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Clinical Medical Virology Centre, University of Queensland, Brisbane, Queensland, Australia
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Syrmis MW, Whiley DM, Thomas M, Mackay IM, Williamson J, Siebert DJ, Nissen MD, Sloots TP. A sensitive, specific, and cost-effective multiplex reverse transcriptase-PCR assay for the detection of seven common respiratory viruses in respiratory samples. J Mol Diagn 2004; 6:125-31. [PMID: 15096568 PMCID: PMC1867476 DOI: 10.1016/s1525-1578(10)60500-4] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2004] [Indexed: 10/18/2022] Open
Abstract
Cell culture and direct fluorescent antibody (DFA) assays have been traditionally used for the laboratory diagnosis of respiratory viral infections. Multiplex reverse transcriptase polymerase chain reaction (m-RT-PCR) is a sensitive, specific, and rapid method for detecting several DNA and RNA viruses in a single specimen. We developed a m-RT-PCR assay that utilizes multiple virus-specific primer pairs in a single reaction mix combined with an enzyme-linked amplicon hybridization assay (ELAHA) using virus-specific probes targeting unique gene sequences for each virus. Using this m-RT-PCR-ELAHA, we examined the presence of seven respiratory viruses in 598 nasopharyngeal aspirate (NPA) samples from patients with suspected respiratory infection. The specificity of each assay was 100%. The sensitivity of the DFA was 79.7% and the combined DFA/culture amplified-DFA (CA-DFA) was 88.6% when compared to the m-RT-PCR-ELAHA. Of the 598 NPA specimens screened by m-RT-PCR-ELAHA, 3% were positive for adenovirus (ADV), 2% for influenza A (Flu A) virus, 0.3% for influenza B (Flu B) virus, 1% for parainfluenza type 1 virus (PIV1), 1% for parainfluenza type 2 virus (PIV2), 5.5% for parainfluenza type 3 virus (PIV3), and 21% for respiratory syncytial virus (RSV). The enhanced sensitivity, specificity, rapid result turnaround time and reduced expense of the m-RT-PCR-ELAHA compared to DFA and CA-DFA, suggests that this assay would be a significant improvement over traditional assays for the detection of respiratory viruses in a clinical laboratory.
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Affiliation(s)
- Melanie W Syrmis
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Queensland, Australia
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Mackay IM, Gardam T, Arden KE, McHardy S, Whiley DM, Crisante E, Sloots TP. Co-detection and discrimination of six human herpesviruses by multiplex PCR-ELAHA. J Clin Virol 2004; 28:291-302. [PMID: 14522068 DOI: 10.1016/s1386-6532(03)00072-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Herpesviruses are a significant cause of human morbidity. Traditional approaches to the identification of these viruses require infectious or at least antigenic virus. Multiplex PCR (mPCR) is capable of simultaneously amplifying a range of targets from a single preparation of nucleic acids and when combined with a suitable detection assay, it is capable of discriminating each of the amplicons. OBJECTIVES Several methods have been described in the literature, however, they lack one or more significant design features required to suitably control a routinely applied nucleic acid amplification assay. We aimed to design a multiplex herpesvirus PCR that could co-amplify eight human herpesvirus targets plus an internal control (IC) molecule in a single tube. STUDY DESIGN Primers were designed to target the DNA polymerase genes of each of the human herpesviruses. Synthetic controls were developed to act as templates for the evaluation of assay sensitivity and specificity and for development of an in-house competitive quantitative PCR. Amplicon was discriminated using a simplified enzyme linked amplicon hybridisation assay (ELAHA). RESULTS AND CONCLUSIONS For routine diagnostic use we reduced the number of herpesviral targets from 8 to 6 in order to maintain adequate clinical sensitivity. The ELAHA proved more sensitive than agarose gel electrophoresis. Additionally, 36 cytomegalovirus positive patients were examined with an in-house quantitative PCR-ELAHA which was developed to confirm that that the mPCR's co-detection limit of 10(2) copy of synthetic template per millilitre was relevant for use in detecting virus from clinical samples. The mPCR-ELAHA was then applied to the screening of 174 patient specimens resulting in a specificity of 98% and a sensitivity of 93%. This preliminary study demonstrated that the mPCR-ELAHA was a complete approach to the detection of herpesviruses from a range of clinical samples and disease states.
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Affiliation(s)
- Ian M Mackay
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Australia.
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Whiley DM, Arden KE, Mackay IM, Syrmis MW, Sloots TP. Simultaneous detection and differentiation of human polyomaviruses JC and BK by a rapid and sensitive PCR-ELAHA assay and a survey of the JCV subtypes within an Australian population. J Med Virol 2004; 72:467-72. [PMID: 14748071 DOI: 10.1002/jmv.20005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Human polyomaviruses JCV and BKV can cause several clinical manifestations in immunocompromised hosts, including progressive multifocal leukoencephalopathy (PML) and haemorrhagic cystitis. Molecular detection by polymerase chain reaction (PCR) is recognised as a sensitive and specific method for detecting human polyomaviruses in clinical samples. In this study, we developed a PCR assay using a single primer pair to amplify a segment of the VP1 gene of JCV and BKV. An enzyme linked amplicon hybridisation assay (ELAHA) using species-specific biotinylated oligonucleotide probes was used to differentiate between JCV and BKV. This assay (VP1-PCR-ELAHA) was evaluated and compared to a PCR assay targeting the human polyomavirus T antigen gene (pol-PCR). DNA sequencing was used to confirm the polyomavirus species identified by the VP1-PCR-ELAHA and to determine the subtype of each JCV isolate. A total of 297 urine specimens were tested and human polyomavirus was detected in 105 specimens (35.4%) by both PCR assays. The differentiation of JCV and BKV by the VP1-PCR-ELAHA showed good agreement with the results of DNA sequencing. Further, DNA sequencing of the JCV positive specimens showed the most prevalent JCV subtype in our cohort was 2a (27%) followed by 1b (20%), 1a (15%), 2c (14%), 4 (14%) and 2b (10%). The results of this study show that the VP1-PCR-ELAHA is a sensitive, specific and rapid method for detecting and differentiating human polyomaviruses JC and BK and is highly suitable for routine use in the clinical laboratory.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Queensland, Australia
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141
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Whiley DM, Syrmis MW, Mackay IM, Sloots TP. Preliminary Comparison of Three LightCycler PCR Assays for the Detection of Herpes Simplex Virus in Swab Specimens. Eur J Clin Microbiol Infect Dis 2003; 22:764-7. [PMID: 14605937 DOI: 10.1007/s10096-003-1031-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Three Herpes Simplex Virus LightCycler polymerase chain reaction assays were compared for the detection of herpes simplex virus in 48 swab specimens. The assays comprised of one in-house assay and two commercial kits: the Artus HSV LC RealArt PCR kit and the Roche LightCycler HSV 1/2 Detection kit. On the whole, the three assays had comparable sensitivities. However, differentiation of herpes simplex virus types 1 and 2 by melting curve analysis was problematic in all assays. Overall, the results highlight the limitations of typing herpes simplex virus by melting curve analysis.
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Affiliation(s)
- D M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Herston Road, 4029 Herston, Queensland, Australia
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143
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Mackay IM, Jacob KC, Woolhouse D, Waller K, Syrmis MW, Whiley DM, Siebert DJ, Nissen M, Sloots TP. Molecular assays for detection of human metapneumovirus. J Clin Microbiol 2003; 41:100-5. [PMID: 12517833 PMCID: PMC149567 DOI: 10.1128/jcm.41.1.100-105.2003] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The recent description of the respiratory pathogen human metapneumovirus (hMPV) has highlighted a deficiency in current diagnostic techniques for viral agents associated with acute lower respiratory tract infections. We describe two novel approaches to the detection of viral RNA by use of reverse transcriptase PCR (RT-PCR). The PCR products were identified after capture onto a solid-phase medium by hybridization with a sequence-specific, biotinylated oligonucleotide probe. The assay was applied to the screening of 329 nasopharyngeal aspirates sampled from patients suffering from respiratory tract disease. These samples were negative for other common microbial causes of respiratory tract disease. We were able to detect hMPV sequences in 32 (9.7%) samples collected from Australian patients during 2001. To further reduce result turnaround times we designed a fluorogenic TaqMan oligoprobe and combined it with the existing primers for use on the LightCycler platform. The real-time RT-PCR proved to be highly reproducible and detected hMPV in an additional 6 out of 62 samples (9.6%) tested during the comparison of the two diagnostic approaches. We found the real-time RT-PCR to be the test of choice for future investigation of samples for hMPV due to its speed, reproducibility, specificity, and sensitivity.
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Affiliation(s)
- Ian M Mackay
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Brisbane, Queensland, Australia
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144
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Whiley DM, Syrmis MW, Mackay IM, Sloots TP. Detection of human respiratory syncytial virus in respiratory samples by LightCycler reverse transcriptase PCR. J Clin Microbiol 2002; 40:4418-22. [PMID: 12454129 PMCID: PMC154614 DOI: 10.1128/jcm.40.12.4418-4422.2002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Laboratory diagnosis of human respiratory syncytial virus (hRSV) infections has traditionally been performed by virus isolation in cell culture and the direct fluorescent-antibody assay (DFA). Reverse transcriptase PCR (RT-PCR) is now recognized as a sensitive and specific alternative for detection of hRSV in respiratory samples. Using the LightCycler instrument, we developed a rapid RT-PCR assay for the detection of hRSV (the LC-RT-PCR) with a pair of hybridization probes that target the hRSV L gene. In the present study, 190 nasopharyngeal aspirate samples from patients with clinically recognized respiratory tract infections were examined for hRSV. The results were then compared to the results obtained with a testing algorithm that combined DFA and a culture-augmented DFA (CA-DFA) assay developed in our laboratory. hRSV was detected in 77 (41%) specimens by LC-RT-PCR and in 75 (39%) specimens by the combination of DFA and CA-DFA. All specimens that were positive by the DFA and CA-DFA testing algorithm were positive by the LC-RT-PCR. The presence of hRSV RNA in the two additional LC-RT-PCR-positive specimens was confirmed by a conventional RT-PCR method that targets the hRSV N gene. The sensitivity of LC-RT-PCR was 50 PFU/ml; and this, together with its high specificity and rapid turnaround time, makes the LC-RT-PCR suitable for the detection of hRSV in clinical specimens.
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Affiliation(s)
- David M. Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Clinical Medical Virology Centre, Department of Paediatric and Child Health, University of Queensland, Microbiology Division, Queensland Health Pathology Service, Royal Brisbane Hospital Campus, Brisbane, Queensland, Australia
| | - Melanie W. Syrmis
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Clinical Medical Virology Centre, Department of Paediatric and Child Health, University of Queensland, Microbiology Division, Queensland Health Pathology Service, Royal Brisbane Hospital Campus, Brisbane, Queensland, Australia
| | - Ian M. Mackay
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Clinical Medical Virology Centre, Department of Paediatric and Child Health, University of Queensland, Microbiology Division, Queensland Health Pathology Service, Royal Brisbane Hospital Campus, Brisbane, Queensland, Australia
| | - Theo P. Sloots
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Clinical Medical Virology Centre, Department of Paediatric and Child Health, University of Queensland, Microbiology Division, Queensland Health Pathology Service, Royal Brisbane Hospital Campus, Brisbane, Queensland, Australia
- Corresponding author. Mailing address: Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Herston Rd., Herston, Queensland 4029, Australia. Phone: 61-7-3636 8833. Fax: 61-7-36361401. E-mail:
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Abstract
The focus of rapid diagnosis of infectious diseases of children in the last decade has shifted from variations of the conventional laboratory techniques of antigen detection, microscopy and culture to that of molecular diagnosis of infectious agents. Pediatricians will need to be able to interpret the use, limitations and results of molecular diagnostic techniques as they are increasingly integrated into routine clinical microbiology laboratory protocols. PCR is the best known and most successfully implemented diagnostic molecular technology to date. It can detect specific infectious agents and determine their virulence and antimicrobial genotypes with greater speed, sensitivity and specificity than conventional microbiology methods. Inherent technical limitations of PCR are present, although they are reduced in laboratories that follow suitable validation and quality control procedures. Variations of PCR together with advances in nucleic acid amplification technology have broadened its diagnostic capabilities in clinical infectious disease to now rival and even surpass traditional methods in some situations. Automation of all components of PCR is now possible. The completion of the genome sequencing projects for significant microbial pathogens, in combination with PCR and DNA chip technology, will revolutionize the diagnosis and management of infectious diseases.
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Affiliation(s)
- Michael D Nissen
- Department of Infectious Diseases, Royal Children's Hospital-Brisbane, Herston, Australia
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146
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147
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Abstract
The detection of Neisseria gonorrhoeae by the polymerase chain reaction (PCR) is now recognized as a sensitive and specific method of diagnosing infection by the organism. In this Study 152 urine specimens were examined for N. gonorrhoeae by a real-time PCR method using the LightCycler platform and results were compared to an "in-house" PCR assay using an ELISA-based detection method. N. gonorrhoeae DNA was detected in 29 (19%) specimens by LightCycler PCR (LC-PCR) and in 31 (20%) specimens by the "in house" PCR method. The LightCycler assay proved to be specific and 94% sensitive when compared to the "in house" PCR method. These features combined with the rapid turn-around time for results makes the LC-PCR particularly suitable for the detection of N. gonorrhoeae in a routine clinical laboratory.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Brisbane, Queensland, Australia
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148
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Abstract
Human polyomaviruses JC and BK may cause several clinical manifestations in immunocompromised hosts, including progressive multifocal leukoencephalopathy and hemorrhagic cystitis. Molecular detection by PCR is recognized as a sensitive and specific method for detecting human polyomaviruses in clinical samples. In this study, a real-time PCR assay using the LightCycler platform was evaluated and compared to an "in-house" PCR assay using a conventional detection method. A total of 122 urine specimens were tested, and human polyomavirus was detected in 49 specimens (40%) by both conventional PCR and LightCycler PCR. The remaining 73 specimens (60%) were found negative by both assays. For 46 of the 49 positive specimens, LightCycler PCR and conventional PCR identified the same polyomavirus type. These samples included 30 samples with JC virus (JCV), 14 samples with BK virus (BKV), and 2 samples in which both viruses were detected. In the remaining three samples, both JCV and BKV were detected by the conventional assay, but only JCV was detected by the LightCycler assay. The results of this study show that the LightCycler PCR assay displays sensitivity and specificity similar to those of a conventional PCR assay. These data, combined with its rapid turnaround time for results and decreased hands-on time, make the LightCycler PCR assay highly suitable for the rapid detection and differentiation of JCV and BKV in the clinical laboratory.
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Affiliation(s)
- D M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Queensland, Australia
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149
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Abstract
Current methods to detect transduction efficiency during the routine use of integrating retroviral vectors in gene therapy applications may require the use of radioactivity and usually rely upon subjective determination of the results. We have developed two competitive quantitative assays that use an enzyme-linked, amplicon hybridization assay (ELAHA) to detect the products of PCR-amplified regions of transgene from cells transduced with Moloney murine leukemia virus vectors. The quantitative assays (PCR-ELAHA) proved to be simple, rapid, and sensitive, avoiding the need for Southern hybridization, complex histochemical stains, or often subjective and time-consuming tissue culture and immunofluorescence assays. The PCR-ELAHA systems can rapidly detect proviral DNA from any retroviral vector carrying the common selective and marker genes neomycin phosphotransferase and green fluorescent protein, and the methods described are equally applicable to other sequences of interest, providing a cheaper alternative to the evolving real-time PCR methods. The results revealed the number of copies of retrovector provirus present per stably transduced cell using vectors containing either one or both qPCR targets.
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Affiliation(s)
- I M Mackay
- Gene Therapy Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital, Herston Road, Herston, Queensland 4029, Australia.
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Lott WB, Takyar SS, Tuppen J, Crawford DH, Harrison M, Sloots TP, Gowans EJ. Vitamin B12 and hepatitis C: molecular biology and human pathology. Proc Natl Acad Sci U S A 2001; 98:4916-21. [PMID: 11296247 PMCID: PMC33138 DOI: 10.1073/pnas.081072798] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cobalamins are stored in high concentrations in the human liver and thus are available to participate in the regulation of hepatotropic virus functions. We show that cyanocobalamin (vitamin B12) inhibited the HCV internal ribosome entry site (IRES)-dependent translation of a reporter gene in vitro in a dose-dependent manner without significantly affecting the cap-dependent mechanism. Vitamin B12 failed to inhibit translation by IRES elements from encephalomyocarditis virus (EMCV) or classical swine fever virus (CSFV). We also demonstrate a relationship between the total cobalamin concentration in human sera and HCV viral load (a measure of viral replication in the host). The mean viral load was two orders of magnitude greater when the serum cobalamin concentration was above 200 pM (P < 0.003), suggesting that the total cobalamin concentration in an HCV-infected liver is biologically significant in HCV replication.
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Affiliation(s)
- W B Lott
- Clinical Medical Virology Research Centre, University of Queensland, St. Lucia, Queensland 4067, Australia.
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