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Dehghan Banadaki M, Torabi S, Rockward A, Strike WD, Noble A, Keck JW, Berry SM. Simple SARS-CoV-2 concentration methods for wastewater surveillance in low resource settings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168782. [PMID: 38000737 PMCID: PMC10842712 DOI: 10.1016/j.scitotenv.2023.168782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
Wastewater-based epidemiology (WBE) measures pathogens in wastewater to monitor infectious disease prevalence in communities. Due to the high dilution of pathogens in sewage, a concentration method is often required to achieve reliable biomarker signals. However, most of the current concentration methods rely on expensive equipment and labor-intensive processes, which limits the application of WBE in low-resource settings. Here, we compared the performance of four inexpensive and simple concentration methods to detect SARS-CoV-2 in wastewater samples: Solid Fraction, Porcine Gastric Mucin-conjugated Magnetic Beads, Calcium Flocculation-Citrate Dissolution (CFCD), and Nanotrap® Magnetic Beads (NMBs). The NMBs and CFCD methods yielded the highest concentration performance for SARS-CoV-2 (∼16-fold concentration and ∼ 41 % recovery) and require <45 min processing time. CFCD has a relatively low consumable cost (<$2 per four sample replicates). All methods can be performed with basic laboratory equipment and minimal electricity usage which enables further application of WBE in remote areas and low resource settings.
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Affiliation(s)
| | - Soroosh Torabi
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States
| | - Alexus Rockward
- Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States
| | - William D Strike
- Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States
| | - Ann Noble
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States
| | - James W Keck
- WWAMI School of Medicine, University of Alaska Anchorage, United States
| | - Scott M Berry
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States; Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States.
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2
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Leong NKC, Chu DKW, Chu JTS, Tam YH, Ip DKM, Cowling BJ, Poon LLM. A six-plex droplet digital RT-PCR assay for seasonal influenza virus typing, subtyping, and lineage determination. Influenza Other Respir Viruses 2020; 14:720-729. [PMID: 32519796 PMCID: PMC7578307 DOI: 10.1111/irv.12769] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND There are two influenza A subtypes (H1 and H3) and two influenza B lineages (Victoria and Yamagata) that currently co-circulate in humans. In this study, we report the development of a six-plex droplet digital RT-PCR (ddRT-PCR) assay that can detect HA and M segments of influenza A (H1, H3, and M) and influenza B (Yamagata HA, Victoria HA, and M) viruses in a single reaction mixture. It can simultaneously detect six different nucleic acid targets in a ddRT-PCR platform. METHODS The six-plex ddRT-PCR used in this study is an amplitude-based multiplex assay. The analytical performance of the assay was evaluated. Correlation with standard qRT-PCR methodology was assessed using 55 clinical samples. RESULTS The assay has a wide dynamic range, and it has good reproducibility within and between runs. The limit of quantification of each target in this assay ranged from 15 copies/reaction for influenza B Victoria M gene to 45 copies/reaction for influenza B Yamagata M gene. In addition, this assay can accurately quantify each of these targets in samples containing viral RNAs from two different viruses that were mixed in a highly skewed ratio. Typing, subtyping, and lineage differentiation data of 55 tested clinical respiratory specimens were found to be identical to those deduced from standard monoplex qRT-PCR assays. CONCLUSIONS The six-plex ddRT-PCR test was demonstrated to be highly suitable for detecting dual influenza infection cases. This assay is expected to be a useful diagnostic tool for clinical and research use.
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Affiliation(s)
- Nathaniel K. C. Leong
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Daniel K. W. Chu
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Julie T. S. Chu
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Yat H. Tam
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Dennis K. M. Ip
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Benjamin J. Cowling
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
| | - Leo L. M. Poon
- School of Public HealthLKS Faculty of MedicineThe University of Hong KongHong KongChina
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Goggin RK, Bennett CA, Bassiouni A, Bialasiewicz S, Vreugde S, Wormald PJ, Psaltis AJ. Comparative Viral Sampling in the Sinonasal Passages; Different Viruses at Different Sites. Front Cell Infect Microbiol 2018; 8:334. [PMID: 30283747 PMCID: PMC6156342 DOI: 10.3389/fcimb.2018.00334] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/29/2018] [Indexed: 12/12/2022] Open
Abstract
Background: With the emergence of the microbiome as an important factor in health and disease in the respiratory tract standardised, validated techniques are required for its accurate characterisation. No standardised technique has been reported specifically for viral sampling in the sinonasal passages. Aim: To optimise viral sampling techniques from the sinonasal cavity. Methods: Sterile cytology brushes were used under endoscopic guidance to sample the sinonasal mucosa at time of endoscopic sinus surgery at both the middle and inferior meatuses (MM and IM). DNA and RNA were extracted from the samples and underwent PCR or RT-PCR testing, respectively, for a panel of 15 common upper respiratory tract viruses. Results: Twenty-four adult patients were recruited for this study. 18/24 (75%) patients were positive for virus in at least one site, while 8/24 (33%) were positive for virus at both sites. The mean number of viruses identified at the two sites were similar (0.875 ± 0.899 at the MM vs. 0.750 ± 1.032 at the IM). 6/24 (25%) of patients showed no virus at either site, while 3/24 (12.5%) demonstrated the same viral species at both sites. Conclusion: Although the number of viruses present at different sites with the nasal cavity are similar, discord exists in the viral species between sites. It is therefore recommended that both sites are sampled in the clinical and research setting better to characterise the viral species within the nasal cavity.
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Affiliation(s)
- Rachel K Goggin
- Department of Surgery - Otolaryngology, University of Adelaide, Adelaide, SA, Australia
| | - Catherine A Bennett
- Department of Surgery - Otolaryngology, University of Adelaide, Adelaide, SA, Australia
| | - Ahmed Bassiouni
- Department of Surgery - Otolaryngology, University of Adelaide, Adelaide, SA, Australia
| | - Seweryn Bialasiewicz
- Queensland Paediatric Infectious Diseases Laboratory, Children's Health Queensland, Brisbane, QLD, Australia.,Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Sarah Vreugde
- Department of Surgery - Otolaryngology, University of Adelaide, Adelaide, SA, Australia
| | - Peter-John Wormald
- Department of Surgery - Otolaryngology, University of Adelaide, Adelaide, SA, Australia
| | - Alkis J Psaltis
- Department of Surgery - Otolaryngology, University of Adelaide, Adelaide, SA, Australia
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Terrier O, Carron C, De Chassey B, Dubois J, Traversier A, Julien T, Cartet G, Proust A, Hacot S, Ressnikoff D, Lotteau V, Lina B, Diaz JJ, Moules V, Rosa-Calatrava M. Nucleolin interacts with influenza A nucleoprotein and contributes to viral ribonucleoprotein complexes nuclear trafficking and efficient influenza viral replication. Sci Rep 2016; 6:29006. [PMID: 27373907 PMCID: PMC4931502 DOI: 10.1038/srep29006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 06/09/2016] [Indexed: 01/18/2023] Open
Abstract
Influenza viruses replicate their single-stranded RNA genomes in the nucleus of infected cells and these replicated genomes (vRNPs) are then exported from the nucleus to the cytoplasm and plasma membrane before budding. To achieve this export, influenza viruses hijack the host cell export machinery. However, the complete mechanisms underlying this hijacking remain not fully understood. We have previously shown that influenza viruses induce a marked alteration of the nucleus during the time-course of infection and notably in the nucleolar compartment. In this study, we discovered that a major nucleolar component, called nucleolin, is required for an efficient export of vRNPs and viral replication. We have notably shown that nucleolin interacts with the viral nucleoprotein (NP) that mainly constitutes vRNPs. Our results suggest that this interaction could allow vRNPs to "catch" the host cell export machinery, a necessary step for viral replication.
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Affiliation(s)
- Olivier Terrier
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Coralie Carron
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Benoît De Chassey
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Julia Dubois
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Aurélien Traversier
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Thomas Julien
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Lyon 1, Lyon, France
| | - Gaëlle Cartet
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Anaïs Proust
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Lyon 1, Lyon, France
| | - Sabine Hacot
- Centre de Recherche en Cancérologie de Lyon, UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, Lyon, France and Université de Lyon, Lyon, France
| | - Denis Ressnikoff
- CIQLE, Centre d’imagerie quantitative Lyon-Est, Université Claude Bernard Lyon 1, Lyon, France
| | - Vincent Lotteau
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Bruno Lina
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Hospices Civils de Lyon, Laboratory of Virology, Lyon, France
| | - Jean-Jacques Diaz
- Centre de Recherche en Cancérologie de Lyon, UMR Inserm 1052 CNRS 5286, Centre Léon Bérard, Lyon, France and Université de Lyon, Lyon, France
| | - Vincent Moules
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Lyon 1, Lyon, France
| | - Manuel Rosa-Calatrava
- Virologie et Pathologie Humaine - Team VirPath - Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, Lyon, France
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Lyon 1, Lyon, France
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Weis A, Liang F, Gao J, Barnard RT, Corrie S. RNA and DNA Diagnostics on Microspheres: Current and Emerging Methods. RNA TECHNOLOGIES 2015. [DOI: 10.1007/978-3-319-17305-4_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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A new, multiplex, quantitative real-time polymerase chain reaction system for nucleic acid detection and quantification. Methods Mol Biol 2014; 1039:51-68. [PMID: 24026685 DOI: 10.1007/978-1-62703-535-4_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Quantitative real-time polymerase chain reaction (qPCR) has emerged as a powerful investigative and diagnostic tool with potential to generate accurate and reproducible results. qPCR can be designed to fulfil the four key aspects required for the detection of nucleic acids: simplicity, speed, sensitivity, and specificity. This chapter reports the development of a novel real-time multiplex quantitative PCR technology, dubbed PrimRglo™, with a potential for high-degree multiplexing. It combines the capacity to simultaneously detect many viruses, bacteria, or nucleic acids, in a single reaction tube, with the ability to quantitate viral or bacterial load. The system utilizes oligonucleotide-tagged PCR primers, along with complementary fluorophore-labelled and quencher-labelled oligonucleotides. The analytic sensitivity of PrimRglo technology was compared with the widely used Taqman(®) and SYBR green detection systems.
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7
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Nasal swab samples and real-time polymerase chain reaction assays in community-based, longitudinal studies of respiratory viruses: the importance of sample integrity and quality control. BMC Infect Dis 2014; 14:15. [PMID: 24405747 PMCID: PMC3897990 DOI: 10.1186/1471-2334-14-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 12/20/2013] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Carefully conducted, community-based, longitudinal studies are required to gain further understanding of the nature and timing of respiratory viruses causing infections in the population. However, such studies pose unique challenges for field specimen collection, including as we have observed the appearance of mould in some nasal swab specimens. We therefore investigated the impact of sample collection quality and the presence of visible mould in samples upon respiratory virus detection by real-time polymerase chain reaction (PCR) assays. METHODS Anterior nasal swab samples were collected from infants participating in an ongoing community-based, longitudinal, dynamic birth cohort study. The samples were first collected from each infant shortly after birth and weekly thereafter. They were then mailed to the laboratory where they were catalogued, stored at -80°C and later screened by PCR for 17 respiratory viruses. The quality of specimen collection was assessed by screening for human deoxyribonucleic acid (DNA) using endogenous retrovirus 3 (ERV3). The impact of ERV3 load upon respiratory virus detection and the impact of visible mould observed in a subset of swabs reaching the laboratory upon both ERV3 loads and respiratory virus detection was determined. RESULTS In total, 4933 nasal swabs were received in the laboratory. ERV3 load in nasal swabs was associated with respiratory virus detection. Reduced respiratory virus detection (odds ratio 0.35; 95% confidence interval 0.27-0.44) was observed in samples where the ERV3 could not be identified. Mould was associated with increased time of samples reaching the laboratory and reduced ERV3 loads and respiratory virus detection. CONCLUSION Suboptimal sample collection and high levels of visible mould can impact negatively upon sample quality. Quality control measures, including monitoring human DNA loads using ERV3 as a marker for epithelial cell components in samples should be undertaken to optimize the validity of real-time PCR results for respiratory virus investigations in community-based studies.
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Hackett H, Bialasiewicz S, Jacob K, Bletchly C, Harrower B, Nimmo GR, Nissen MD, Sloots TP, Whiley DM. Screening for H7N9 influenza A by matrix gene-based real-time reverse-transcription PCR. J Virol Methods 2014; 195:123-5. [DOI: 10.1016/j.jviromet.2013.10.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 10/04/2013] [Accepted: 10/04/2013] [Indexed: 11/15/2022]
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9
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Speers DJ, Moss DM, Minney-Smith C, Levy A, Smith DW. Influenza and respiratory syncytial virus are the major respiratory viruses detected from prospective testing of pediatric and adult coronial autopsies. Influenza Other Respir Viruses 2013; 7:1113-21. [PMID: 23855988 PMCID: PMC4634247 DOI: 10.1111/irv.12139] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2013] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND To ascertain the full mortality of influenza and other respiratory viruses, the testing of community autopsy specimens is essential. METHODS Respiratory virus PCR and culture were performed on 2418 fresh unfrozen respiratory samples collected from 1611 coronial cases where the death was either unknown or infection was suspected, from July 2007 to June 2011, to detect the common respiratory viruses in children and adults, using standardized microbiological testing. RESULTS The respiratory virus positive rate was 8·3% (134 cases) with a peak of 28% (42 of 151 cases) in children under 10 years of age. Influenza virus was the commonest respiratory virus (50 cases, 3%), followed by respiratory syncytial virus (RSV) (30 cases, 2%). All tested respiratory viruses were found in children, most commonly adenovirus, enterovirus and RSV, and influenza A and RSV predominated in those over 60 years, but coinfection was uncommon. Almost all influenza cases occurred when influenza was widely circulating in the community but few were diagnosed pre-mortem. Influenza and RSV detection was associated with bronchitis or bronchiolitis in 7 (9%) of the 80 cases and caused pneumonia in 14 (0·8%) deaths overall. CONCLUSIONS Our prospective review of respiratory viruses using standardized testing found a single lower respiratory tract autopsy specimen for respiratory virus PCR would detect most community infections at the time of death.
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Affiliation(s)
- David J Speers
- Department of Microbiology, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia; School of Medicine and Pharmacology, University of Western Australia, Crawley, WA, Australia
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Liang F, Lai R, Arora N, Zhang KL, Yeh CC, Barnett GR, Voigt P, Corrie SR, Barnard RT. Multiplex–microsphere–quantitative polymerase chain reaction: Nucleic acid amplification and detection on microspheres. Anal Biochem 2013; 432:23-30. [DOI: 10.1016/j.ab.2012.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 09/13/2012] [Accepted: 09/13/2012] [Indexed: 10/27/2022]
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Influenza A viruses control expression of proviral human p53 isoforms p53β and Delta133p53α. J Virol 2012; 86:8452-60. [PMID: 22647703 DOI: 10.1128/jvi.07143-11] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Previous studies have described the role of p53 isoforms, including p53β and Δ133p53α, in the modulation of the activity of full-length p53, which regulates cell fate. In the context of influenza virus infection, an interplay between influenza viruses and p53 has been described, with p53 being involved in the antiviral response. However, the role of physiological p53 isoforms has never been explored in this context. Here, we demonstrate that p53 isoforms play a role in influenza A virus infection by using silencing and transient expression strategies in human lung epithelial cells. In addition, with the help of a panel of different influenza viruses from different subtypes, we also show that infection differentially regulates the expressions of p53β and Δ133p53α. Altogether, our results highlight the role of p53 isoforms in the viral cycle of influenza A viruses, with p53β and Δ133p53α acting as regulators of viral production in a p53-dependent manner.
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Lai R, Liang F, Pearson D, Barnett G, Whiley D, Sloots T, Barnard RT, Corrie SR. PrimRglo: a multiplexable quantitative real-time polymerase chain reaction system for nucleic acid detection. Anal Biochem 2012; 422:89-95. [PMID: 22266293 DOI: 10.1016/j.ab.2011.12.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Revised: 12/26/2011] [Accepted: 12/26/2011] [Indexed: 10/14/2022]
Abstract
We report the development of a new real-time polymerase chain reaction (PCR) detection system that uses oligonucleotide "tagged" PCR primers, a fluorophore-labeled "universal" detection oligonucleotides, and a complementary quenching oligonucleotide. The fluorescence signal decreases as PCR product accumulates due to the increase in detection/quencher hybrid formation as the tagged primer is consumed. We use plasmids containing the influenza A matrix gene and the porA and ctrA genes of Neisseria meningitidis as targets for developing the system. Cycle threshold (Ct) values were generated, and the sensitivity of the new system (dubbed "PrimRglo") compared favorably with the commonly used SYBR green and Taqman detection systems and, unlike the latter system, does not require the design of a new dual-labeled detection oligonucleotide for each new target sequence.
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Affiliation(s)
- Richard Lai
- Biochip Innovations, Mount Gravatt, Queensland 4122, Australia
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13
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Vaccine Effectiveness Against Laboratory-confirmed Influenza in Healthy Young Children: A Case-Control Study. Pediatr Infect Dis J 2011; 30:107-11. [PMID: 21079528 DOI: 10.1097/inf.0b013e318201811c] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND the Western Australian Influenza Vaccine Effectiveness study commenced in 2008 to evaluate a new program to provide free influenza vaccine to all children aged 6 to 59 months. We aimed to assess the protective effect of inactivated influenza vaccination in these children. METHODS We conducted a prospective case-control study in general practices and a hospital emergency department, testing all eligible patients for influenza and a range of other common respiratory viruses. Influenza vaccine effectiveness (VE) against laboratory-confirmed influenza was estimated with cases defined as children with an influenza-like illness who tested positive and controls as those with an influenza-like illness who tested negative for influenza virus. We calculated VE using the adjusted odds ratio from multivariate logistic regression. As a surrogate marker for adequate specimen collection, we explored the difference in VE point estimates defining controls as children in whom another respiratory virus was detected. RESULTS a total of 75 children were enrolled from general practices and 214 through the emergency department, with 12 (27%) and 36 (17%), respectively, having laboratory-confirmed influenza. Using all the influenza-negative controls, the adjusted VE was 58% (95% confidence interval, 9-81). When controls were limited to those with another virus present, the adjusted VE was 68% (95% confidence interval, 26-86). CONCLUSIONS VE estimates were higher when controls included only those children with another respiratory virus detected. Testing for other common respiratory viruses enables the control group to be restricted to those for whom an adequate sample is likely.
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Mulrennan S, Tempone SS, Ling ITW, Williams SH, Gan GC, Murray RJ, Speers DJ. Pandemic influenza (H1N1) 2009 pneumonia: CURB-65 score for predicting severity and nasopharyngeal sampling for diagnosis are unreliable. PLoS One 2010; 5:e12849. [PMID: 20877727 PMCID: PMC2943473 DOI: 10.1371/journal.pone.0012849] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 08/18/2010] [Indexed: 11/19/2022] Open
Abstract
Background From the first case reports of pandemic influenza (H1N1) 2009 it was clear that a significant proportion of infected individuals suffered a primary viral pneumonia. The objective of this study was twofold; to assess the utility of the CURB-65 community acquired pneumonia (CAP) severity index in predicting pneumonia severity and ICU admission, and to assess the relative sensitivity of nasopharyngeal versus lower respiratory tract sampling for the detection of pandemic influenza (H1N1) CAP. Methods A retrospective cohort study of 70 patients hospitalised for pandemic influenza (H1N1) 2009 in an adult tertiary referral hospital. Characteristics evaluated included age, pregnancy status, sex, respiratory signs and symptoms, smoking and alcohol history, CURB-65 score, co-morbidities, disabling sequelae, length of stay and in-hospital mortality outcomes. Laboratory features evaluated included lymphocyte count, C-reactive protein (CRP), nasopharyngeal and lower respiratory tract pandemic influenza (H1N1) 2009 PCR results. Results Patients with pandemic (H1N1) 2009 influenza CAP differed significantly from those without pneumonia regarding length of stay, need for ICU admission, CRP and the likelihood of disabling sequelae. The CURB-65 score did not predict CAP severity or the need for ICU admission (only 2/11 patients admitted to ICU had CURB-65 scores of 2 or 3). Nasopharyngeal specimens for PCR were only 62.9% sensitive in CAP patients compared to 97.8% sensitivity for lower respiratory tract specimens. Conclusions The CURB-65 score does not predict severe pandemic influenza (H1N1) 2009 CAP or need for ICU admission. Lower respiratory tract specimens should be collected when pandemic (H1N1) 2009 influenza CAP is suspected.
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Affiliation(s)
- Siobhain Mulrennan
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia.
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15
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Ninove L, Gazin C, Gould EA, Nougairede A, Flahault A, Charrel RN, Zandotti C, de Lamballerie X. A simple method for molecular detection of Swine-origin and human-origin influenza a virus. Vector Borne Zoonotic Dis 2010; 10:237-40. [PMID: 19505254 DOI: 10.1089/vbz.2009.0110] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Here we present a real-time one-step reverse transcriptase-polymerase chain reaction SYBR Green assay derived from the method reported by van Elden and collaborators ( 2001 ) that ensures the rapid, sensitive, and cost-effective detection of both seasonal influenza A virus and emerging (H1N1) swine-origin influenza A virus (S-OIV). In addition to this screening test, which successfully detected both seasonal influenza A virus and S-OIV in human clinical samples, we showed that the probe initially designed by van Elden and collaborators could detect seasonal influenza A virus, but not S-OIV; a new probe was designed and tested that specifically detects S-OIV, but not seasonal influenza A. Both probe-based assays were validated by testing human clinical samples and specifically detected either seasonal influenza virus or S-OIV. Finally, in silico analysis of databases predicted that minor modifications of the van Elden primers would facilitate the use of this assay for the broad spectrum detection of all currently characterized variants of influenza A virus, including avian strains.
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Affiliation(s)
- Laetitia Ninove
- Unité des Virus Emergents, Faculté de Médecine de Marseille, Université de la Méditerranée & Institut de Recherche pour le Développement, Marseille, France
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Rapid detection of respiratory tract viral infections and coinfections in patients with influenza-like illnesses by use of reverse transcription-PCR DNA microarray systems. J Clin Microbiol 2010; 48:3836-42. [PMID: 20739481 DOI: 10.1128/jcm.00733-10] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We prospectively tested 95 nasal swabs or nasopharyngeal aspirates taken from 56 adults and 39 children visiting the Reims University Medical Centre (northern France) for influenza-like illnesses (ILI) during the early stage of the French influenza A/H1N1v pandemic (October 2009). Respiratory samples were tested using a combination of two commercially available reverse transcription-PCR (RT-PCR) DNA microarray systems allowing rapid detection of influenza A virus strains, including the new A/H1N1v strain as well as 20 other common or newly discovered respiratory viruses. Concomitantly, a generic and classical real-time RT-PCR assay was performed to detect all circulating influenza A virus strains in the same samples. Of the 95 respiratory samples tested, 30 (31%) were positive for the detection of influenza A/H1N1v virus infection by both RT-PCR DNA microarray and classical real-time RT-PCR detection assays. Among the infections, 25 (83%) were monoinfections, whereas 5 (17%) were multiple infections associating influenza A/H1N1v virus with coronavirus (CoV), human bocavirus (HBoV), respiratory syncytial virus (RSV), or human rhinoviruses (HRVs). Of the 95 respiratory samples tested, 35 (37%) were positive for respiratory viruses other than influenza A/H1N1v virus. Among these infections, we observed 30 monoinfections (HRVs [63%], parainfluenza viruses [PIVs] [20%]), influenza A/H3N2 virus [6%], coronavirus [4%], and HBoV [4%]) and 5 multiple infections, in which HRVs and PIVs were the most frequently detected viruses. No specific single or mixed viral infections appeared to be associated significantly with secondary hospitalization in infectious disease or intensive care departments during the study period (P > 0.5). The use of RT-PCR DNA microarray systems in clinical virology practice allows the rapid and accurate detection of conventional and newly discovered viral respiratory pathogens in patients suffering from ILI and therefore could be of major interest for development of new epidemiological survey systems for respiratory viral infections.
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Szewczuk E, Thapa K, Anninos T, McPhie K, Higgins G, Dwyer DE, Stanley KK, Iredell JR. Rapid semi-automated quantitative multiplex tandem PCR (MT-PCR) assays for the differential diagnosis of influenza-like illness. BMC Infect Dis 2010; 10:113. [PMID: 20459845 PMCID: PMC2881921 DOI: 10.1186/1471-2334-10-113] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 05/11/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Influenza A, including avian influenza, is a major public health threat in developed and developing countries. Rapid and accurate detection is a key component of strategies to contain spread of infection, and the efficient diagnosis of influenza-like-illness is essential to protect health infrastructure in the event of a major influenza outbreak. METHODS We developed a multiplexed PCR (MT-PCR) assay for the simultaneous diagnosis of respiratory viruses causing influenza-like illness, including the specific recognition of influenza A haemagglutinin subtypes H1, H3, and H5. We tested several hundred clinical specimens in two diagnostic reference laboratories and compared the results with standard techniques. RESULTS The sensitivity and specificity of these assays was higher than individual assays based on direct antigen detection and standard PCR against a range of control templates and in several hundred clinical specimens. The MT-PCR assays provided differential diagnoses as well as potentially useful quantitation of virus in clinical samples. CONCLUSIONS MT-PCR is a potentially powerful tool for the differential diagnosis of influenza-like illness in the clinical diagnostic laboratory.
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Affiliation(s)
- Elektra Szewczuk
- Centre for Infectious Diseases and Microbiology, University of Sydney, Westmead Hospital, Westmead NSW 2145, Australia
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Ilinykh PA, Shestopalova EM, Khripko YI, Durimanov AG, Sharshov KA, Shestopalov AM. Detection of influenza A virus RNA in birds by optimized Real—Time PCR system. ASIAN PAC J TROP MED 2010. [DOI: 10.1016/s1995-7645(10)60082-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Bouscambert Duchamp M, Casalegno J, Gillet Y, Frobert E, Bernard E, Escuret V, Billaud G, Valette M, Javouhey E, Lina B, Floret D, Morfin F. Pandemic A(H1N1)2009 influenza virus detection by real time RT-PCR : is viral quantification useful? Clin Microbiol Infect 2010; 16:317-21. [DOI: 10.1111/j.1469-0691.2010.03169.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Murray RJ, Robinson JO, White JN, Hughes F, Coombs GW, Pearson JC, Tan HL, Chidlow G, Williams S, Christiansen KJ, Smith DW. Community-acquired pneumonia due to pandemic A(H1N1)2009 influenzavirus and methicillin resistant Staphylococcus aureus co-infection. PLoS One 2010; 5:e8705. [PMID: 20090931 PMCID: PMC2806836 DOI: 10.1371/journal.pone.0008705] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Accepted: 12/19/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Bacterial pneumonia is a well described complication of influenza. In recent years, community-onset methicillin-resistant Staphylococcus aureus (cMRSA) infection has emerged as a contributor to morbidity and mortality in patients with influenza. Since the emergence and rapid dissemination of pandemic A(H1N1)2009 influenzavirus in April 2009, initial descriptions of the clinical features of patients hospitalized with pneumonia have contained few details of patients with bacterial co-infection. METHODOLOGY/PRINCIPAL FINDINGS Patients with community-acquired pneumonia (CAP) caused by co-infection with pandemic A(H1N1)2009 influenzavirus and cMRSA were prospectively identified at two tertiary hospitals in one Australian city during July to September 2009, the period of intense influenza activity in our region. Detailed characterization of the cMRSA isolates was performed. 252 patients with pandemic A(H1N1)2009 influenzavirus infection were admitted at the two sites during the period of study. Three cases of CAP due to pandemic A(H1N1)2009/cMRSA co-infection were identified. The clinical features of these patients were typical of those with S. aureus co-infection or sequential infection following influenza. The 3 patients received appropriate empiric therapy for influenza, but inappropriate empiric therapy for cMRSA infection; all 3 survived. In addition, 2 fatal cases of CAP caused by pandemic A(H1N1)2009/cMRSA co-infection were identified on post-mortem examination. The cMRSA infections were caused by three different cMRSA clones, only one of which contained genes for Panton-Valentine Leukocidin (PVL). CONCLUSIONS/SIGNIFICANCE Clinicians managing patients with pandemic A(H1N1)2009 influenzavirus infection should be alert to the possibility of co-infection or sequential infection with virulent, antimicrobial-resistant bacterial pathogens such as cMRSA. PVL toxin is not necessary for the development of cMRSA pneumonia in the setting of pandemic A( H1N1) 2009 influenzavirus co-infection.
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Affiliation(s)
- Ronan J Murray
- Division of Microbiology and Infectious Diseases, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre, Perth, Western Australia, Australia.
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Duplex real-time reverse transcriptase PCR assays for rapid detection and identification of pandemic (H1N1) 2009 and seasonal influenza A/H1, A/H3, and B viruses. J Clin Microbiol 2010; 48:862-6. [PMID: 20071557 DOI: 10.1128/jcm.01435-09] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Reports of a novel influenza virus type A (H1N1), now designated by the World Health Organization as pandemic (H1N1) 2009, emerged from the United States and Mexico in April 2009. The management of the pandemic in Australia required rapid and reliable testing of large numbers of specimens for the novel influenza strain and differentiation from seasonal influenza strains. A real-time reverse transcriptase PCR (RT-PCR) assay for the detection of pandemic (H1N1) 2009 was designed and used with existing real-time RT-PCR assays for seasonal influenza viruses A and B. MS2 coliphage was added to all samples and amplified as a quality control. Three duplex RT-PCR assays, each containing two primer pairs and corresponding 5' nuclease probes, were initially evaluated on control material and stored samples and showed high sensitivity and specificity. More than 11,000 clinical samples were then tested for influenza A and B matrix gene targets and specific hemagglutinin gene targets for seasonal influenza A/H1, A/H3, and pandemic A (H1N1) 2009. Minimum sensitivities and specificities were 98.8% and 100%, respectively, for pandemic (H1N1) 2009, 81.5% and 98.9% for seasonal A/H1, and 96.3% and 99.6% for A/H3. Automated sample extraction facilitated the rapid processing of samples so that the assays allowed accurate, rapid, and cost-effective screening of large numbers of clinical samples.
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A Novel Duplex Real-Time Reverse-Transcription PCR Assay for the Detection of Influenza A and the Novel Influenza A(H1N1) Strain. Viruses 2009; 1:1204-8. [PMID: 21994590 PMCID: PMC3185501 DOI: 10.3390/v1031204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 11/28/2009] [Accepted: 12/04/2009] [Indexed: 11/28/2022] Open
Abstract
Timely implementation of antiviral treatment and other public health based responses are dependent on accurate and rapid diagnosis of the novel pandemic influenza A(H1N1) strain. In this study we developed a duplex real-time PCR (RT-PCR) (dFLU-TM) assay for the simultaneous detection of a broad range of influenza A subtypes and specific detection of the novel H1N1 2009 pandemic strain. The assay was compared to the combined results of two previously described monoplex RT-PCR assays using 183 clinical samples and 10 seasonal influenza A isolates. Overall, the results showed that the dFLU-TM RT-PCR method is suitable for detection of influenza A, including the novel H1N1 pandemic strain, in clinical samples.
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Muradrasoli S, Mohamed N, Belák S, Czifra G, Herrmann B, Berencsi G, Blomberg J. Broadly targeted triplex real-time PCR detection of influenza A, B and C viruses based on the nucleoprotein gene and a novel "MegaBeacon" probe strategy. J Virol Methods 2009; 163:313-22. [PMID: 19879296 PMCID: PMC7172653 DOI: 10.1016/j.jviromet.2009.10.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2006] [Revised: 09/19/2009] [Accepted: 10/20/2009] [Indexed: 11/19/2022]
Abstract
A PCR assay that covers animal and human influenza A, B and C viruses, i.e., most of Orthomyxoviridae, is needed. Influenza types are distinguished based on differences in the nucleoprotein (NP) present in the virus. Conserved NP regions were therefore used to design a TaqMan-based triplex reverse transcription real-time PCR method. Variability of influenza A within the probe target region mandated the development of a novel molecular beacon, the "Mega" molecular beacon (MegaBeacon; MegB), for the detection of influenza A with this method. MegaBeacon is a mismatch-tolerant molecular beacon that is also a TaqMan probe. The triplex method (3QPCR-MegB) was evaluated with influenza A isolates covering 18 HxNx combinations, two influenza B isolates, and five Japanese influenza C isolates, as well as influenza A, B and C synthetic DNA targets. One to ten viral RNA and cDNA genome equivalents were detected per PCR reaction for influenza A, B and C. Seventy-one human nasopharyngeal aspirates from respiratory infections yielded 30 influenza A, 11 influenza B and 0 influenza C with 3QPCR-MegB, where immunofluorescence (IF) found 28 influenza A and 10 influenza B. 3QPCR-MegB was more mismatch-tolerant than a variant PCR with an influenza A TaqMan probe (3QPCR) and is a sensitive and rational method to detect influenza viruses of animal and human origin. MegaBeacon probes hold promise for variable target nucleic acids.
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Affiliation(s)
- Shaman Muradrasoli
- Section of Clinical Virology, Department of Medical Sciences, Uppsala University, Sweden
| | - Nahla Mohamed
- Section of Clinical Virology, Department of Medical Sciences, Uppsala University, Sweden
| | - Sándor Belák
- Department of Virology, National Veterinary Institute and Swedish University of Agricultural Sciences, Ultuna, Uppsala, Sweden
| | - György Czifra
- Department of Virology, National Veterinary Institute and Swedish University of Agricultural Sciences, Ultuna, Uppsala, Sweden
| | - Björn Herrmann
- Section of Clinical Virology, Department of Medical Sciences, Uppsala University, Sweden
| | | | - Jonas Blomberg
- Section of Clinical Virology, Department of Medical Sciences, Uppsala University, Sweden
- Corresponding author at: Section of Clinical Virology, Department of Medical Sciences, Uppsala University, Academic Hospital, 751 85 Uppsala, Sweden. Tel.: +46 18 6115593; fax: +46 18 551012.
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Detection of novel influenza A(H1N1) virus by real-time RT-PCR. J Clin Virol 2009; 45:203-4. [DOI: 10.1016/j.jcv.2009.05.032] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 05/22/2009] [Indexed: 11/22/2022]
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An economical tandem multiplex real-time PCR technique for the detection of a comprehensive range of respiratory pathogens. Viruses 2009; 1:42-56. [PMID: 21994537 PMCID: PMC3185464 DOI: 10.3390/v1010042] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 06/02/2009] [Accepted: 06/05/2009] [Indexed: 12/14/2022] Open
Abstract
This study used real-time PCR assays to screen small sample volumes for a comprehensive range of 35 respiratory pathogens. Initial thermocycling was limited to 20 cycles to avoid competition for reagents, followed by a secondary real-time multiplex PCR. Supplementary semi-nested human metapneumovirus and picornavirus PCR assays were required to complete the acute respiratory pathogen profile. Potential pathogens were detected in 85 (70%) of pernasal aspirates collected from 121 children with acute respiratory symptoms. Multiple pathogens were detected in 29 (24%) of those samples. The tandem multiplex real-time PCR was an efficient method for the rapid detection of multiple pathogens.
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Universal detection and identification of avian influenza virus by use of resequencing microarrays. J Clin Microbiol 2009; 47:988-93. [PMID: 19279171 DOI: 10.1128/jcm.01346-08] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Zoonotic microbes have historically been, and continue to emerge as, threats to human health. The recent outbreaks of highly pathogenic avian influenza virus in bird populations and the appearance of some human infections have increased the concern of a possible new influenza pandemic, which highlights the need for broad-spectrum detection methods for rapidly identifying the spread or outbreak of all variants of avian influenza virus. In this study, we demonstrate that high-density resequencing pathogen microarrays (RPM) can be such a tool. The results from 37 influenza virus isolates show that the RPM platform is an effective means for detecting and subtyping influenza virus, while simultaneously providing sequence information for strain resolution, pathogenicity, and drug resistance without additional analysis. This study establishes that the RPM platform is a broad-spectrum pathogen detection and surveillance tool for monitoring the circulation of prevalent influenza viruses in the poultry industry and in wild birds or incidental exposures and infections in humans.
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Wang W, Ren P, Mardi S, Hou L, Tsai C, Chan KH, Cheng P, Sheng J, Buchy P, Sun B, Toyoda T, Lim W, Peiris JSM, Zhou P, Deubel V. design of multiplexed detection assays for identification of avian influenza a virus subtypes pathogenic to humans by SmartCycler real-time reverse transcription-PCR. J Clin Microbiol 2009; 47:86-92. [PMID: 18971359 PMCID: PMC2620859 DOI: 10.1128/jcm.01090-08] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 08/13/2008] [Accepted: 10/13/2008] [Indexed: 11/20/2022] Open
Abstract
Influenza A virus (IAV) epidemics are the result of human-to-human or poultry-to-human transmission. Tracking seasonal outbreaks of IAV and other avian influenza virus (AIV) subtypes that can infect humans, aquatic and migratory birds, poultry, and pigs is essential for epidemiological surveillance and outbreak alerts. In this study, we performed four real-time reverse transcription-PCR (rRT-PCR) assays for identification of the IAV M and hemagglutinin (HA) genes from six known AIVs infecting pigs, birds, and humans. IAV M1 gene-positive samples tested by single-step rRT-PCR and a fluorogenic Sybr green I detection system were further processed for H5 subtype identification by using two-primer-set multiplex and Sybr green I rRT-PCR assays. H5 subtype-negative samples were then tested with either a TaqMan assay for subtypes H1 and H3 or a TaqMan assay for subtypes H2, H7, and H9 and a beacon multiplex rRT-PCR identification assay. The four-tube strategy was able to detect 10 RNA copies of the HA genes of subtypes H1, H2, H3, H5, and H7 and 100 RNA copies of the HA gene of subtype H9. At least six H5 clades of H5N1 viruses isolated in Southeast Asia and China were detected by that test. Using rRT-PCR assays for the M1 and HA genes in 202 nasopharyngeal swab specimens from children with acute respiratory infections, we identified a total of 39 samples positive for the IAV M1 gene and subtypes H1 and H3. When performed with a portable SmartCycler instrument, the assays offer an efficient, flexible, and reliable platform for investigations of IAV and AIV in remote hospitals and in the field.
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Affiliation(s)
- Wei Wang
- Chinese Academy of Sciences, Institut Pasteur of Shanghai, Shanghai Institute of Biological Sciences, 411 Hefei Road, 200025 Shanghai, People's Republic of China
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Abstract
SUMMARY Clinical laboratories historically diagnose seven or eight respiratory virus infections using a combination of techniques including enzyme immunoassay, direct fluorescent antibody staining, cell culture, and nucleic acid amplification tests. With the discovery of six new respiratory viruses since 2000, laboratories are faced with the challenge of detecting up to 19 different viruses that cause acute respiratory disease of both the upper and lower respiratory tracts. The application of nucleic acid amplification technology, particularly multiplex PCR coupled with fluidic or fixed microarrays, provides an important new approach for the detection of multiple respiratory viruses in a single test. These multiplex amplification tests provide a sensitive and comprehensive approach for the diagnosis of respiratory tract infections in individual hospitalized patients and the identification of the etiological agent in outbreaks of respiratory tract infection in the community. This review describes the molecular methods used to detect respiratory viruses and discusses the contribution that molecular testing, especially multiplex PCR, has made to our ability to detect respiratory viruses and to increase our understanding of the roles of various viral agents in acute respiratory disease.
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Stelzer-Braid S, Escott R, Baleriola C, Kirkland P, Robertson P, Catton M, Rawlinson WD. Proficiency of nucleic acid tests for avian influenza viruses, Australasia. Emerg Infect Dis 2008; 14:1126-8. [PMID: 18598638 PMCID: PMC2600363 DOI: 10.3201/eid1407.071098] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
An avian influenza quality assurance program was used to provide information for laboratories on the sensitivity and specificity of their avian influenza nucleic acid testing. Most laboratories were able to correctly detect clinically relevant amounts of influenza virus (H5N1), and results improved as each subsequent panel was tested.
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Lambert SB, Whiley DM, O'Neill NT, Andrews EC, Canavan FM, Bletchly C, Siebert DJ, Sloots TP, Nissen MD. Comparing nose-throat swabs and nasopharyngeal aspirates collected from children with symptoms for respiratory virus identification using real-time polymerase chain reaction. Pediatrics 2008; 122:e615-20. [PMID: 18725388 DOI: 10.1542/peds.2008-0691] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES The objective of this study was to calculate sensitivity values for the detection of major respiratory viruses of childhood by using combined nose-throat swabs and nasopharyngeal aspirates. METHODS Children who had symptoms and presented to a pediatric teaching hospital and had a diagnostic respiratory specimen collected were enrolled, and paired nose-throat swab and nasopharyngeal aspirate specimens were collected. Parents were asked to collect the nose-throat swab specimen in the first instance but could defer to a health care worker if unwilling. Nose-throat swab collectors were asked to rate perceived quality of collection. All nasopharyngeal aspirates were collected by a health care worker by using a standard protocol. Real-time polymerase chain reaction for 8 respiratory viruses was performed in our hospital's diagnostic laboratory. RESULTS Paired nose-throat swab/nasopharyngeal aspirate specimens were collected during 303 illnesses, with at least 1 respiratory virus identified in 186 (61%). For the major pathogens of childhood, influenza A virus and respiratory syncytial virus, collection by using the nose-throat swab had a sensitivity of 91.9% and 93.1%, respectively. A health care worker collected 219 (72%) of the nose-throat swab specimens; concordance with the nasopharyngeal aspirate was not related to health care worker collection or perceived quality of collection. CONCLUSIONS Nose-throat swab specimens, in combination with sensitive molecular testing, are a less invasive diagnostic respiratory specimen with adequate sensitivity for use in the clinic and hospital outpatient settings and large-scale community studies through parent collection. For children who present to a hospital in which an avian or pandemic strain of influenza virus is reasonably part of the differential diagnosis, nasopharyngeal aspirates or a similar collection technique (eg, nasal washes) should continue to be used.
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Affiliation(s)
- Stephen B Lambert
- MBBS, Queensland Paediatric Infectious Diseases Laboratory, Royal Children's Hospital, Herston Queensland 4029, Australia.
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Chantratita W, Sukasem C, Kaewpongsri S, Srichunrusami C, Pairoj W, Thitithanyanont A, Chaichoune K, Ratanakron P, Songserm T, Damrongwatanapokin S, Landt O. Qualitative detection of avian influenza A (H5N1) viruses: a comparative evaluation of four real-time nucleic acid amplification methods. Mol Cell Probes 2008; 22:287-93. [PMID: 18672052 DOI: 10.1016/j.mcp.2008.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2008] [Revised: 05/13/2008] [Accepted: 06/11/2008] [Indexed: 11/16/2022]
Abstract
The aim of this study was to determine the performance of real-time amplification based methods - NASBA, TaqMan, RT-FRET, and RT-PCR LUXtrade mark formats - for the detection of influenza A (H5N1) virus RNA. In an analysis of 54 samples obtained from a range of animal species in Thailand during the period 2003-2006, results showed that the NASBA (H5=98.2%, N1=96.3%), TaqMan (H5=98.2%, N1=96.3%) and FRET (H5=98.2%, N1=96.3%) had significantly higher rates of positive detection than LUX (H5=94.4%, N1=50.0%; P<0.001) for influenza A, H5 and N1 isolates. There were no false-positive results from any methods used in the negative-control group of samples. The limits of analytical detection were at least 10copies/reaction in real-time NASBA and LUX assays, while FRET and TaqMan assay appeared to be less sensitive at > or =100copies/reaction. The assays were relatively specific without cross-reactivity to a number of other influenza strains or viral pathogens. In conclusion, our study demonstrated that real-time NASBA, TaqMan and FRET assays can be used to detect influenza A (H5N1) from a wide range of hosts, and be specific for H5N1 samples obtained during different outbreaks (2003-2006). All assays provided the benefit of rapid influenza H5N1 identification for early diagnosis, in the range of hours, and they are well suited to high throughput analyses.
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Affiliation(s)
- Wasun Chantratita
- Virology and Molecular Microbiology Unit, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand.
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Kerby MB, Freeman S, Prachanronarong K, Artenstein AW, Opal SM, Tripathi A. Direct sequence detection of structured h5 influenza viral RNA. J Mol Diagn 2008; 10:225-35. [PMID: 18403607 DOI: 10.2353/jmoldx.2008.070094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe the development of sequence-specific molecular beacons (dual-labeled DNA probes) for identification of the H5 influenza subtype, cleavage motif, and receptor specificity when hybridized directly with in vitro transcribed viral RNA (vRNA). The cloned hemagglutinin segment from a highly pathogenic H5N1 strain, A/Hanoi/30408/2005(H5N1), isolated from humans was used as template for in vitro transcription of sense-strand vRNA. The hybridization behavior of vRNA and a conserved subtype probe was characterized experimentally by varying conditions of time, temperature, and Mg2+ to optimize detection. Comparison of the hybridization rates of probe to DNA and RNA targets indicates that conformational switching of influenza RNA structure is a rate-limiting step and that the secondary structure of vRNA dominates the binding kinetics. The sensitivity and specificity of probe recognition of other H5 strains was calculated from sequence matches to the National Center for Biotechnology Information influenza database. The hybridization specificity of the subtype probes was experimentally verified with point mutations within the probe loop at five locations corresponding to the other human H5 strains. The abundance frequencies of the hemagglutinin cleavage motif and sialic acid recognition sequences were experimentally tested for H5 in all host viral species. Although the detection assay must be coupled with isothermal amplification on the chip, the new probes form the basis of a portable point-of-care diagnostic device for influenza subtyping.
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Affiliation(s)
- Matthew B Kerby
- Chemical and Biochemical Engineering Laboratory, Brown University, Providence, RI, USA
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Influenza detection and subtyping by reverse transcriptase polymerase chain reaction–restriction fragment length polymorphism for laboratory surveillance in Brazil. Diagn Microbiol Infect Dis 2008; 60:445-7. [DOI: 10.1016/j.diagmicrobio.2007.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Revised: 11/28/2007] [Accepted: 11/30/2007] [Indexed: 11/21/2022]
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Zourob M, Elwary S, Turner A. Micro and Nanopatterning for Bacteria- and Virus-Based Biosensing Applications. PRINCIPLES OF BACTERIAL DETECTION: BIOSENSORS, RECOGNITION RECEPTORS AND MICROSYSTEMS 2008. [PMCID: PMC7121747 DOI: 10.1007/978-0-387-75113-9_32] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Current technologies capable of rapidly and accurately detecting the presence of infectious diseases and toxic compounds in the human body and the environment are inadequate and new, novel techniques are required to ensure the safety of the general population. To develop these technologies, researchers must broaden their scope of interest and investigate scientific areas that have yet to be fully explored. Lithography is a common name given to technologies designed to print materials onto smooth surfaces. More specifically, micropatterning encompasses the selective binding of materials to surfaces in organized microscale arrays. The selective micropatterning of bacteria and viruses is currently an exciting area of research in the field of biomedical engineering and can potentially offer attractive qualities to biosensing applications in terms of increased sensing accuracy and reliability. This chapter focuses on briefly introducing the reader to the fundamentals of bacterial and viral surface interactions and describing several different micropatterning techniques and their advantages and disadvantages in the field of biosensing. The application of these techniques in healthcare and environmental settings is also discussed.
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Affiliation(s)
| | - Souna Elwary
- Consultant to Biophage Pharma Inc, Montreal, Canada
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Lu YY, Yan JY, Feng Y, Xu CP, Shi W, Mao HY. Rapid detection of H5 avian influenza virus by TaqMan-MGB real-time RT-PCR. Lett Appl Microbiol 2007; 46:20-5. [PMID: 17944840 PMCID: PMC7197896 DOI: 10.1111/j.1472-765x.2007.02253.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aims: Real‐time reverse transcription‐polymerase chain reaction (RT‐PCR) assay based on a TaqMan‐minor groove binder (MGB) probe was developed for the rapid detection of avian influenza virus subtype H5. Methods and Results: Conserved regions in the haemagglutinin genes of avian influenza viruses subtype H5 served as targets for the primers and TaqMan‐MGB probe design. Concentrations of primers and probe were optimized to improve the sensitivity and specificity of the reactions. A plasmid containing the haemagglutinin gene was constructed and in vitro transcribed for a quantitative assay of copy numbers of the target gene. The results revealed that the optimal concentration of primers and probe was 640 and 480 nmol l−1, respectively. The threshold of 100 copies of target molecules could be detected. The linear range for detection was determined as 102 to 108 molecules in reaction. Conclusions: It took less than 3 h to complete the detection from viral RNA extraction, with good sensitivity and repeatability. Significance and Impact of the Study: Real‐time RT‐PCR assay with MGB probe was an effective means for quick and quantitative laboratory detection and monitoring of H5 avian influenza viruses.
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Affiliation(s)
- Y Y Lu
- Institute of Virology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China.
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Abstract
PURPOSE OF REVIEW Molecular techniques offer the promise of improving diagnosis of lower respiratory tract infections. This review focuses on currently used molecular diagnostic techniques for various types of pneumonia and highlights potential future applications of this technology. RECENT FINDINGS Lower respiratory tract infections result in a high degree of morbidity and mortality, but a definitive microbiologic diagnosis is often not obtained by traditional culture or serologic methods. In addition, culture of certain organisms may be difficult or require extended periods of time. Molecular techniques have the potential to improve diagnostic yield and decrease time to pathogen identification. These techniques are also helpful in the determination of drug sensitivity and the understanding of transmission and outbreaks. Most currently used techniques employ some variation of the polymerase chain reaction. Limitations include high costs, the need for specialized equipment, and problems with false-positive and -negative results. SUMMARY Molecular diagnosis of pneumonia has the potential to improve identification of pathogens in patients with suspected lower respiratory tract infection. Limitations of molecular techniques currently prevent their widespread use, but future developments will likely lead to inclusion of these tests in routine diagnostic evaluations.
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Affiliation(s)
- Yvonne R Chan
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
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Dawson ED, Moore CL, Smagala JA, Dankbar DM, Mehlmann M, Townsend MB, Smith CB, Cox NJ, Kuchta RD, Rowlen KL. MChip: a tool for influenza surveillance. Anal Chem 2007; 78:7610-5. [PMID: 17105150 DOI: 10.1021/ac061739f] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The design and characterization of a low-density microarray for subtyping influenza A is presented. The microarray consisted of 15 distinct oligonucleotides designed to target only the matrix gene segment of influenza A. An artificial neural network was utilized to automate microarray image interpretation. The neural network was trained to recognize fluorescence image patterns for 68 known influenza viruses and subsequently used to identify 53 unknowns in a blind study that included 39 human patient samples and 14 negative control samples. The assay exhibited a clinical sensitivity of 95% and clinical specificity of 92%.
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Affiliation(s)
- Erica D Dawson
- Department of Chemistry and Biochemistry, UCB 215, University of Colorado at Boulder, Boulder, Colorado 80309, USA
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Pourmand N, Diamond L, Garten R, Erickson JP, Kumm J, Donis RO, Davis RW. Rapid and highly informative diagnostic assay for H5N1 influenza viruses. PLoS One 2006; 1:e95. [PMID: 17183727 PMCID: PMC1762361 DOI: 10.1371/journal.pone.0000095] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Accepted: 11/20/2006] [Indexed: 11/19/2022] Open
Abstract
A highly discriminative and information-rich diagnostic assay for H5N1 avian influenza would meet immediate patient care needs and provide valuable information for public health interventions, e.g., tracking of new and more dangerous variants by geographic area as well as avian-to-human or human-to-human transmission. In the present study, we have designed a rapid assay based on multilocus nucleic acid sequencing that focuses on the biologically significant regions of the H5N1 hemagglutinin gene. This allows the prediction of viral strain, clade, receptor binding properties, low- or high-pathogenicity cleavage site and glycosylation status. H5 HA genes were selected from nine known high-pathogenicity avian influenza subtype H5N1 viruses, based on their diversity in biologically significant regions of hemagglutinin and/or their ability to cause infection in humans. We devised a consensus pre-programmed pyrosequencing strategy, which may be used as a faster, more accurate alternative to de novo sequencing. The available data suggest that the assay described here is a reliable, rapid, information-rich and cost-effective approach for definitive diagnosis of H5N1 avian influenza. Knowledge of the predicted functional sequences of the HA will enhance H5N1 avian influenza surveillance efforts.
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MESH Headings
- Animals
- Base Sequence
- Birds
- DNA Primers/genetics
- DNA, Viral/genetics
- Genes, Viral
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Humans
- Influenza A Virus, H5N1 Subtype/genetics
- Influenza A Virus, H5N1 Subtype/isolation & purification
- Influenza A Virus, H5N1 Subtype/pathogenicity
- Influenza in Birds/virology
- Influenza, Human/diagnosis
- Influenza, Human/transmission
- Influenza, Human/virology
- Molecular Sequence Data
- Phylogeny
- Polymerase Chain Reaction/methods
- Sequence Analysis, RNA/methods
- Virology/methods
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Affiliation(s)
- Nader Pourmand
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America.
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