1
|
Wong SSY, Yip CCY, Sridhar S, Leung KH, Cheng AKW, Fung AMY, Lam HY, Chan KH, Chan JFW, Cheng VCC, Tang BSF, Yuen KY. Comparative evaluation of a laboratory-developed real-time PCR assay and RealStar® Adenovirus PCR Kit for quantitative detection of human adenovirus. Virol J 2018; 15:149. [PMID: 30261891 PMCID: PMC6161464 DOI: 10.1186/s12985-018-1059-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 09/19/2018] [Indexed: 12/17/2022] Open
Abstract
Background Human adenoviruses are common causes of community-acquired respiratory tract and enteric infections. Severe disseminated infections with high mortality rates may be seen in immunocompromised individuals. An accurate and cost-effective quantitative assay is essential not only for laboratory diagnosis of adenoviral infections, but also for monitoring of response to antiviral treatment. The diagnostic performance of an in-house quantitative polymerase chain reaction assay was compared to a commercial system. Methods The analytical sensitivity, specificity, linearity, precision and accuracy of an in-house adenovirus quantitative polymerase chain reaction assay were evaluated against the RealStar® Adenovirus PCR Kit (Altona Diagnostics GmbH, Hamburg, Germany), using 122 clinical specimens and 18 proficiency testing samples. Results Linear regression analysis of the quantitative results by the in-house assay showed the dynamic range from 2.60 to 9 log10 (plasma) and 2.94 to 9 log10 (viral transport medium) copies/mL, with the coefficient of determination (R2) of 0.996 and 0.998, respectively. A dilution series demonstrated the limits of detection and lower limits of quantification for plasma were 2.06 log10 and 2.60 log10 copies/mL and those for viral transport medium were 2.31 log10 and 2.94 log10 copies/mL respectively. The precision of the in-house assay was highly reproducible among runs with coefficients of variance ranging from 0.07 to 3.21% for plasma and 0.17% to 2.11% for viral transport medium. A comparison of 52 matched samples showed an excellent correlation between the quantitative viral loads measured by the in-house assay and the RealStar® Adenovirus PCR Kit (R2 = 0.984), with an average bias of − 0.16 log10 copies/mL. Conclusions The in-house adenovirus assay is a sensitive and reliable assay with lower cost for the detection and quantification of adenoviral DNA when compared to the RealStar® Adenovirus PCR Kit. Electronic supplementary material The online version of this article (10.1186/s12985-018-1059-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Samson S Y Wong
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Cyril C Y Yip
- Department of Microbiology, Queen Mary Hospital, Hong Kong, China
| | - Siddharth Sridhar
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Kit-Hang Leung
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Andrew K W Cheng
- Department of Microbiology, Queen Mary Hospital, Hong Kong, China
| | - Ami M Y Fung
- Department of Microbiology, Queen Mary Hospital, Hong Kong, China
| | - Ho-Yin Lam
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Kwok-Hung Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Jasper F W Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | | | - Bone S F Tang
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Kwok-Yung Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong, China. .,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China. .,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China. .,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China. .,Department of Microbiology, Queen Mary Hospital, Hong Kong, China. .,The Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong, China.
| |
Collapse
|
2
|
Wang J, Yu P, Xie Z, Yan T, Chen C, Shen X, Chen X, Li L, Wang X, Sun S, Ma X. A resequencing pathogen microarray method for high-throughput molecular diagnosis of multiple etiologies associated with central nervous system infection. Arch Virol 2017; 162:3769-3778. [PMID: 28913577 PMCID: PMC7087039 DOI: 10.1007/s00705-017-3550-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/01/2017] [Indexed: 12/28/2022]
Abstract
Central nervous system infection (CNSI) results in significant health and economic burdens worldwide, but the diversity of causative pathogens makes differential diagnosis very difficult. Although PCR and real-time fluorescent quantitative PCR (q-PCR) assays are widely applied for pathogen detection, they are generally optimized for the detection of a single or limited number of targets and are not suitable for the diagnosis of numerous CNSI agents. In this study, we describe the development of a resequencing pathogen microarray (RPM-IVDC4) method for the simultaneous detection of viruses, bacteria, fungi and parasites that cause CNSI. The test panel of this assay included more than 100 microorganism species across 45 genera and 30 families. The analytical specificity and sensitivity were examined using a panel of positive reference strains, and the clinical performance was evaluated using 432 clinical samples by comparing the results with q-PCR assays. Our results demonstrated good performance of the RPM-IVDC4 assay in terms of sensitivity, specificity and detection range, suggesting that the platform can be further developed for high-throughput CNSI diagnosis.
Collapse
Affiliation(s)
- Ji Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Panhui Yu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Neurology Department, Children's Hospital of Hebei Province, Shijiazhuang, China
| | - Zhengde Xie
- MOE Key Laboratory of Major Diseases in Children, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Tengfei Yan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,No. 1 Hospital of Shijiazhuang, Shijiazhuang, China
| | - Chen Chen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xinxin Shen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiangpeng Chen
- MOE Key Laboratory of Major Diseases in Children, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Lixin Li
- No. 1 Hospital of Shijiazhuang, Shijiazhuang, China
| | - Xiuxia Wang
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Suzhen Sun
- Neurology Department, Children's Hospital of Hebei Province, Shijiazhuang, China.
| | - Xuejun Ma
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| |
Collapse
|
3
|
Li Y, Zhou W, Zhao Y, Wang Y, Xie Z, Lou Y, Tan W. Molecular typing and epidemiology profiles of human adenovirus infection among paediatric patients with severe acute respiratory infection in China. PLoS One 2015; 10:e0123234. [PMID: 25856575 PMCID: PMC4391708 DOI: 10.1371/journal.pone.0123234] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 03/02/2015] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Human adenoviruses (HAdVs) have been recognised as pathogens that cause a broad spectrum of diseases. The studies on HAdV infection among children with severe acute respiratory infection (SARI) are limited. OBJECTIVE To investigate the prevalence, epidemiology, and genotype of HAdV among children with SARI in China. STUDY DESIGN Nasopharyngeal aspirates (NPAs) or induced sputum (IS) was collected from hospitalised children with SARIs in Beijing (representing Northern China; n = 259) and Zhejiang Province (representing Eastern China; n = 293) from 2007 to 2010. The prevalence of HAdV was screened by polymerase chain reaction (PCR), followed by sequence typing of PCR fragments that targeted the second half of the hexon gene. In addition, co-infection with other human respiratory viruses, related epidemiological profiles and clinical presentations were investigated. RESULTS AND CONCLUSIONS In total, 76 (13.8%) of 552 SARI patients were positive for HAdV, and the infection rates of HAdV in Northern and Eastern China were 20.1% (n = 52) and 8.2% (n = 24), respectively. HAdV co-infection with other respiratory viruses was frequent (infection rates: Northern China, 90.4%; Eastern China, 70.8%). The peak seasons for HAdV-B infection was winter and spring. Additionally, members of multiple species (Human mastadenovirus B, C, D and E) were circulating among paediatric patients with SARI, of which HAdV-B (34/52; 65.4%) and HAdV-C (20/24, 83.3%) were the most predominant in Northern and Eastern China, respectively. These findings provide a benchmark for future epidemiology and prevention strategies for HAdV.
Collapse
Affiliation(s)
- Yamin Li
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Weimin Zhou
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Yanjie Zhao
- Institute of Medical Virology, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yanqun Wang
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Zhengde Xie
- Beijing Pediatric Research Institute, BCH-CMU, Beijing, China
| | - Yongliang Lou
- Institute of Medical Virology, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Wenjie Tan
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
- * E-mail:
| |
Collapse
|
4
|
Yoo SM, Lee SY. DNA microarray for the identification of pathogens causing bloodstream infections. Expert Rev Mol Diagn 2014; 10:263-8. [DOI: 10.1586/erm.10.23] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
5
|
Berthet N, Paulous S, Coffey LL, Frenkiel MP, Moltini I, Tran C, Matheus S, Ottone C, Ungeheuer MN, Renaudat C, Caro V, Dussart P, Gessain A, Desprès P. Resequencing microarray method for molecular diagnosis of human arboviral diseases. J Clin Virol 2012; 56:238-43. [PMID: 23219893 DOI: 10.1016/j.jcv.2012.10.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 10/31/2012] [Indexed: 12/29/2022]
Abstract
BACKGROUND Resequencing DNA microarray (RMA) technology uses probes designed to identify a panel of viral sequences. It can be used for detecting emerging viruses by revealing the nucleotide polymorphisms within the target of interest. OBJECTIVES/STUDY DESIGN As a new tool for molecular diagnosis of arbovirus infection, high density PathogenID v2.0 RMA (PID2-RMA) was assessed for the detection and genetic analysis of dengue, West Nile, and Chikungunya viruses in spiked blood samples or sera from individuals infected with dengue virus. Viral RNAs extracted from biological samples were retrotranscribed into cDNA and amplified using the Phi 29 polymerase-based method. This amplified cDNA was used for hybridization on PID2-RMA. RESULTS A good specificity of RMA-based detection was demonstrated using a panel of arboviruses including Dengue, West Nile and Chikungunya viruses. This technology was also efficient for the detection and genetic analysis of the different serotypes of dengue virus in sera of infected patients. Furthermore, the mixing of dengue, West Nile and Chikungunya prototype viruses within a single sample of human blood did not interfere with the sensitivity of PID2-RMA. CONCLUSIONS Our data show that high density PID2-RMA was suitable for the identification of medically important arboviruses. It appears to be particularly adapted to the genetic analysis of dengue, West Nile, and Chikungunya viruses in urgent clinical situations where the rapid identification and characterization of the pathogen is essential.
Collapse
Affiliation(s)
- N Berthet
- Institut Pasteur, Epidemiology and Physiopathology of Oncogenic Viruses Unit, 28 rue du Docteur Roux, F75015 Paris, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Woo PCY, Lau SKP, Lee P, Miao J, Fung AMY, Choi GKY, Ellis-Behnke R, Yuen KY. Resequencing microarray for detection of human adenoviruses in patients with community-acquired gastroenteritis: a proof-of-concept study. J Med Microbiol 2010; 59:1387-1390. [PMID: 20671084 DOI: 10.1099/jmm.0.023796-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Patrick C Y Woo
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong SAR
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR
| | - Susanna K P Lau
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong SAR
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR
| | - Paul Lee
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR
| | - Ji Miao
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR
| | - Ami M Y Fung
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR
| | - Garnet K Y Choi
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR
| | - Rutledge Ellis-Behnke
- Department of Brain & Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Anatomy, The University of Hong Kong, Hong Kong SAR
| | - Kwok-Yung Yuen
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong SAR
| |
Collapse
|
7
|
Pooling the wrong conclusion. J Clin Virol 2010; 47:387. [DOI: 10.1016/j.jcv.2010.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Accepted: 01/22/2010] [Indexed: 11/22/2022]
|