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Chen L, You S, Wang X, Li D, Ren S, Chen L. Dual carminic acid/hemin-marked DNA probes for simultaneously detecting CV-A16 and EV-A71 based on the mechanism of dimer to monomer transition. Talanta 2023; 265:124884. [PMID: 37392710 DOI: 10.1016/j.talanta.2023.124884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/09/2023] [Accepted: 06/25/2023] [Indexed: 07/03/2023]
Abstract
This study aimed to prepare two hairpin-structure DNA probes by conjugating carminic acid (CA) or hemin into two ends of specific genes of coxsackievirus A16 (CV-A16) and enterovirus A71 (EV-A71) (probeCV-A16-CA and probeEV-A71-hemin). Then, probeCV-A16-CA and probeEV-A71-hemin as the signal molecules were adsorbed onto NH2-MIL-53 (Al) (MOF). Based on these biocomposites, an electrochemical biosensor with dual-signal outputs for simultaneous assay of CV-A16 and EV-A71 was constructed. The stem-loops of probes switched both CA and hemin monomer to dimer, reducing the electrical activity of both CA and hemin. Subsequently, the target-induced opening of the stem-loop switched both CA and hemin dimers to monomers, resulting in two nonoverlapping increasing electrical signals. This sensitively reflected the concentration of targetCV-A16 and targetEV-A17 ranging from 10-10 to 10-15 M with a detection limit of 0.19 and 0.24 fM. This strategy was mainly applied to the simultaneous determination of targetCV-A16 and targetEV-A17 in 100% serum with satisfactory results. The MOF combined with the high loading capacity broke through the intrinsic limitation on sensitivity using the traditional methods. An increase of three orders of magnitude was observed. This study involved simple one-step detection, and only a simple replacement of a gene could trigger its potential in clinical and diagnostic applications.
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Affiliation(s)
- Lili Chen
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Shuang You
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Xiaotong Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Dong Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Shuna Ren
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Lihua Chen
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
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2
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Larivé O, Brandani J, Dubey M, Kohn T. An integrated cell culture reverse transcriptase quantitative PCR (ICC-RTqPCR) method to simultaneously quantify the infectious concentrations of eight environmentally relevant enterovirus serotypes. J Virol Methods 2021; 296:114225. [PMID: 34216645 DOI: 10.1016/j.jviromet.2021.114225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 11/27/2022]
Abstract
Enterovirus (EV) infectivity is typically measured as a bulk parameter, yet EV serotypes vary in their susceptibility to natural and engineered stressors. Here we developed an integrated cell culture reverse transcriptase quantitative PCR (ICC-RTqPCR) method to simultaneously and specifically quantify the infectious concentrations of eight EV serotypes commonly encountered in sewage (coxsackieviruses A9, B1, B2, B3, B4 and B5, and echoviruses 25 and 30). The method uses two cell lines for virus replication and serotype-specific qPCR primers for quantification. Primers were designed to target multiple environmental strains of a given serotype and displayed high specificity. The ICC-RTqPCR method exhibited a linear calibration range between 50 and 1000 (echoviruses) or 5000 (coxsackieviruses) infectious units per mL. Over this range, measurements were not influenced by the presence of non-target serotypes, and calibration slopes were reproducible for different virus batches and cell ages. The ICC-RTqPCR method was able to accurately quantify the infectious concentration of a virus after inactivation by heat, and the concentration of a virus within a wastewater matrix. This method will be valuable to assess the differing fates of EV serotypes in natural or engineered systems, and to portray the associated changes in EV population composition.
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Affiliation(s)
- Odile Larivé
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Jade Brandani
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Manupriyam Dubey
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Tamar Kohn
- Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
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3
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Teo FMS, Chu JJH. Diagnosis of human enteroviruses that cause hand, foot and mouth disease. Expert Rev Anti Infect Ther 2016; 14:443-5. [PMID: 27042876 DOI: 10.1586/14787210.2016.1173543] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Fiona Mei Shan Teo
- a Collaborative and Translation Unit for HFMD , Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) , Singapore
| | - Justin Jang Hann Chu
- a Collaborative and Translation Unit for HFMD , Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) , Singapore.,b Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology, Yong Loo Lin School of Medicine , National University of Singapore , Singapore
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Niu P, Qi S, Yu B, Zhang C, Wang J, Li Q, Ma X. Development of a highly sensitive real-time nested RT-PCR assay in a single closed tube for detection of enterovirus 71 in hand, foot, and mouth disease. Arch Virol 2016; 161:3003-10. [PMID: 27475103 PMCID: PMC7086773 DOI: 10.1007/s00705-016-2985-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/11/2016] [Indexed: 12/29/2022]
Abstract
Enterovirus 71 (EV71) is one of the major causative agents of outbreaks of hand, foot, and mouth disease (HFMD). A commercial TaqMan probe-based real-time PCR assay has been widely used for the differential detection of EV71 despite its relatively high cost and failure to detect samples with a low viral load (Ct value > 35). In this study, a highly sensitive real-time nested RT-PCR (RTN RT-PCR) assay in a single closed tube for detection of EV71 in HFMD was developed. The sensitivity and specificity of this assay were evaluated using a reference EV71 stock and a panel of controls consisting of coxsackievirus A16 (CVA16) and common respiratory viruses, respectively. The clinical performance of this assay was evaluated and compared with those of a commercial TaqMan probe-based real-time PCR (qRT-PCR) assay and a traditional two-step nested RT-PCR assay. The limit of detection for the RTN RT-PCR assay was 0.01 TCID50/ml, with a Ct value of 38.3, which was the same as that of the traditional two-step nested RT-PCR assay and approximately tenfold lower than that of the qRT-PCR assay. When testing the reference strain EV71, this assay showed favorable detection reproducibility and no obvious cross-reactivity. The testing results of 100 clinical throat swabs from HFMD-suspected patients revealed that 41 samples were positive for EV71 by both RTN RT-PCR and traditional two-step nested RT-PCR assays, whereas only 29 were EV71 positive by qRT-PCR assay.
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Affiliation(s)
- Peihua Niu
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Shunxiang Qi
- Institute for Viral Disease Control and Prevention, Center for Disease Control and Prevention of Hebei, Shijiazhuang, Hebei, People's Republic of China
| | - Benzhang Yu
- Department of Laboratory Medicine, Shengli Oil Field Central Hospital, Jinan Road, Dongying, Shandong, People's Republic of China
| | - Chen Zhang
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Ji Wang
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Qi Li
- Institute for Viral Disease Control and Prevention, Center for Disease Control and Prevention of Hebei, Shijiazhuang, Hebei, People's Republic of China.
| | - Xuejun Ma
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.
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5
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Yan G, Jun L, Kangchen Z, Yiyue G, Yang Y, Xiaoyu Z, Zhiyang S, Lunbiao C. Rapid and visual detection of human enterovirus coxsackievirus A16 by reverse transcription loop-mediated isothermal amplification combined with lateral flow device. Lett Appl Microbiol 2015; 61:531-7. [PMID: 26399963 DOI: 10.1111/lam.12499] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/13/2015] [Accepted: 09/15/2015] [Indexed: 11/25/2022]
Abstract
UNLABELLED In this study, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) combined with lateral flow device (LFD) technology to rapidly detect CVA16 was developed and evaluated. RT-LAMP assay was optimized to amplify VP1 gene of CVA16. Amplified products were analysed by LFD and capillary electrophoresis. The RT-LAMP-LFD assay showed 100% specificity in detecting CVA16, and showed analytical sensitivity of 0·55 TCID50 per reaction mixture. Comparison of the RT-LAMP-LFD assay with real-time RT-PCR developed previously in clinical specimens showed 93·3% agreement. The RT-LAMP-LFD assay is more sensitive in detecting CVA16 RNA. The RT-LAMP-LFD assay presented here might offer a rapid and simple alternative in clinical diagnosis of CVA16. SIGNIFICANCE AND IMPACT OF THE STUDY Coxsackievirus A16 (CVA16) is one of the major causative agents of hand, foot and mouth disease (HFMD). Rapid and reliable detection and typing of it can limit the spread. We developed a reverse transcription loop-mediated isothermal amplification (RT-LAMP) combined with lateral flow device (LFD) technology to rapidly detect CVA16. The high sensitivity and specificity and its ease of use make this assay ideal for use in resource-limited settings such as primary care facilities and clinical laboratories in developing countries.
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Affiliation(s)
- G Yan
- Department of Neonatology, Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
| | - L Jun
- Department of Emergency, Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
| | - Z Kangchen
- Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing, China
| | - G Yiyue
- Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing, China
| | - Y Yang
- Department of Neonatology, Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
| | - Z Xiaoyu
- Department of Neonatology, Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
| | - S Zhiyang
- Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing, China
| | - C Lunbiao
- Key Laboratories of Enteric Pathogenic Microbiology (Ministry of Health), Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing, China
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6
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Zhang S, Wang J, Yan Q, He S, Zhou W, Ge S, Xia N. A one-step, triplex, real-time RT-PCR assay for the simultaneous detection of enterovirus 71, coxsackie A16 and pan-enterovirus in a single tube. PLoS One 2014; 9:e102724. [PMID: 25029500 PMCID: PMC4100918 DOI: 10.1371/journal.pone.0102724] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 05/16/2014] [Indexed: 01/22/2023] Open
Abstract
The recent, ongoing epidemic of hand, foot, and mouth disease (HFMD), which is caused by enterovirus infection, has affected millions of children and resulted in thousands of deaths in China. Enterovirus 71 (EV71) and coxsackie A16 (CA16) are the two major distinct pathogens for HFMD. However, EV71 is more commonly associated with neurologic complications and even fatalities. Therefore, simultaneously detecting and differentiating EV71 and CA16 specifically from other enteroviruses for diagnosing HFMD is important. Here, we developed a one-step, triplex, real-time RT-PCR assay for the simultaneous detection of EV71, CA16, and pan-enterovirus (EVs) in a single tube with an internal amplification control. The detection results for the serially diluted viruses indicate that the lower limit of detection for this assay is 0.001–0.04 TCID50/ml, 0.02 TCID50/ml, and 0.001 TCID50/ml for EVs, EV71, and CA16, respectively. After evaluating known HFMD virus stocks of 17 strains of 16 different serotypes, this assay showed a favorable detection spectrum and no obvious cross-reactivity. The results for 141 clinical throat swabs from HFMD-suspected patients demonstrated sensitivities of 98.4%, 98.7%, and 100% for EVs, EV71, and CA16, respectively, and 100% specificity for each virus. The application of this one-step, triplex, real-time RT-PCR assay in clinical units will contribute to HFMD surveillance and help to identify causative pathogen in patients with suspected HFMD.
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Affiliation(s)
- Shiyin Zhang
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Life Science, Xiamen University, Xiamen, Fujian, China
| | - Jin Wang
- Xiamen Innovax Biotech Co., LTD, Xiamen, Fujian, China
| | - Qiang Yan
- Xiamen Innovax Biotech Co., LTD, Xiamen, Fujian, China
| | - Shuizhen He
- Xiamen Center for Disease Control and Prevention, Fujian, China
| | - Wenbin Zhou
- Xiamen Innovax Biotech Co., LTD, Xiamen, Fujian, China
| | - Shengxiang Ge
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Life Science, Xiamen University, Xiamen, Fujian, China
- School of Public Health, Xiamen University, Xiamen, China
- * E-mail:
| | - Ningshao Xia
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Life Science, Xiamen University, Xiamen, Fujian, China
- School of Public Health, Xiamen University, Xiamen, China
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7
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Xu J, Cao L, Su L, Dong N, Yu M, Ju J. A new accurate assay for Coxsackievirus A 16 by fluorescence detection of isothermal RNA amplification. J Virol Methods 2013; 193:459-62. [PMID: 23872269 DOI: 10.1016/j.jviromet.2013.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 06/30/2013] [Accepted: 07/10/2013] [Indexed: 11/24/2022]
Abstract
Coxsackievirus A 16 (CA16) is one of the most common causes of hand, foot, and mouth disease (HFMD) worldwide. Without a vaccine or antiviral drug early, rapid, and accurate detection is critical for preventing and controlling HFMD. A simultaneous amplification and testing (SAT) assay was developed for detecting CA16 based on isothermal RNA amplification with fluorescence using standard, real-time PCR equipment. Primers and probes were designed to target the VP1 region of CA16. Virus strains and clinical specimens were used to evaluate the diagnostic performance characteristics of the assay. The assay detected as few as 10 copies of CA16 RNA transcripts. Using real-time PCR plus sequencing as the reference standard, the sensitivity and specificity of the SAT-CA16 assay were 100% and 99.2%, respectively. These findings indicate that SAT-CA16 is a rapid and reliable method for detecting CA16.
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Affiliation(s)
- Jin Xu
- Laboratory Medicine Center, Children's Hospital of Fudan University, Shanghai 201102, China.
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8
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The development and application of the two real-time RT-PCR assays to detect the pathogen of HFMD. PLoS One 2013; 8:e61451. [PMID: 23637836 PMCID: PMC3630163 DOI: 10.1371/journal.pone.0061451] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 03/08/2013] [Indexed: 11/19/2022] Open
Abstract
Large-scale Hand, Foot, and Mouth Disease (HFMD) outbreaks have frequently occurred in China since 2008, affecting more than one million children and causing several hundred children deaths every year. The pathogens of HFMD are mainly human enteroviruses (HEVs). Among them, human enterovirus 71 (HEV71) and coxsackievirus A16 (CVA16) are the most common pathogens of HFMD. However, other HEVs could also cause HFMD. To rapidly detect HEV71 and CVA16, and ensure detection of all HEVs causing HFMD, two real-time hybridization probe-based RT-PCR assays were developed in this study. One is a multiplex real-time RT-PCR assay, which was developed to detect and differentiate HEV71 specifically from CVA16 directly from clinical specimens within 1–2 h, and the other is a broad-spectrum real-time RT-PCR assay, which targeted almost all HEVs. The experiments confirmed that the two assays have high sensitivity and specificity, and the sensitivity was up to 0.1 TCID50/ml for detection of HEVs, HEV71, and CVA16, respectively. A total of 213 clinical specimens were simultaneously detected by three kinds of assays, including the two real-time RT-PCR assays, direct conventional RT-PCR assay, and virus isolation assay on human rhabdomyosarcoma cells (RD cells). The total positive rate of both HEV71 and CVA16 was 69.48% with real-time RT-PCR assay, 47.42% with RT-PCR assay, and 34.58% with virus isolation assay. One HFMD clinical specimen was positive for HEV, but negative for HEV71 or CVA16, which was identified as Echovirus 11 (Echo11) by virus isolation, RT-PCR, and sequencing for the VP1 gene. The two real-time RT-PCR assays had been applied in 31 provincial HFMD labs to detect the pathogens of HFMD, which has contributed to the rapid identification of the pathogens in the early stages of HFMD outbreaks, and helped to clarify the etiologic agents of HFMD in China.
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Abstract
Enteroviruses are positive stranded RNA viruses belonging to the genus Enterovirus of the Picornaviridae family. Human enteroviruses are transmitted through the fecal-oral route and have been shown to cause mild to life-threatening diseases. Various diagnostic methods have been developed to detect enteroviruses from clinical specimens but many were impeded by requirements for special reagents, lengthy procedures, low sensitivity or cross-reactivity. This chapter describes rapid and highly sensitive methods of enteroviral detection directly from clinical specimens based on a conventional one-step Reverse Transcription polymerase chain reaction (RT-PCR) and a one-step real-time RT-PCR.
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Affiliation(s)
- Chit Laa Poh
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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10
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Xu F, He D, He S, Wu B, Guan L, Niu J, Li L, Li C, Weng Z, Yan Q, Yang L, Ge S, Cheng T, Chen Y, Zhang J, Xia N. Development of an IgM-capture ELISA for Coxsackievirus A16 infection. J Virol Methods 2010; 171:107-10. [PMID: 20970457 DOI: 10.1016/j.jviromet.2010.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Revised: 10/08/2010] [Accepted: 10/14/2010] [Indexed: 11/19/2022]
Abstract
Diagnosis of Coxsackievirus A16 (CA16) infection in China relies mainly on reverse transcription-polymerase chain reaction (RT-PCR) that require expensive equipment and special trained personnel, thus making its wide application in health care settings unlikely. In this study, a novel IgM anti-CA16 assay was developed for the detection of IgM antibodies to CA16 in serum. The responses and diagnostic value of IgM for the CA16 infection were assessed by testing 1970 serum samples. The results showed that sensitivity of IgM test was 84.6% (259/306, 95% CI: 80.1-88.5), and specificity in control subjects and patients with CA16 HFMD was 99.2% (1508/1520, 95% CI: 98.6-99.6) and 90.3% (14/144, 95% CI: 84.2-94.6), respectively. The IgM positive rate reached 56.3% in the sera collected within the first day after onset, increased continuously to 95.3% at day 5 to day 7 after onset, and then reached 100% after more than 8 days. The cross-reaction rate in patients infected with other non-CA16 enteroviruses was 9.7% (14/144). These results suggest that the IgM anti-CA16 assay offers a rapid, convenient, and reliable method to detect acute CA16 infections.
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Affiliation(s)
- Feihai Xu
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, Xiamen University, Xiamen, China
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11
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Development of multiplex real-time hybridization probe reverse transcriptase polymerase chain reaction for specific detection and differentiation of Enterovirus 71 and Coxsackievirus A16. Diagn Microbiol Infect Dis 2008; 61:294-301. [DOI: 10.1016/j.diagmicrobio.2008.02.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2007] [Revised: 01/14/2008] [Accepted: 02/13/2008] [Indexed: 11/22/2022]
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12
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Perera D, Yusof MA, Podin Y, Ooi MH, Thao NTT, Wong KK, Zaki A, Chua KB, Malik YA, Tu PV, Tien NTK, Puthavathana P, McMinn PC, Cardosa MJ. Molecular phylogeny of modern coxsackievirus A16. Arch Virol 2007; 152:1201-8. [PMID: 17308978 DOI: 10.1007/s00705-006-0934-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2006] [Accepted: 12/21/2006] [Indexed: 10/23/2022]
Abstract
A phylogenetic analysis of VP1 and VP4 nucleotide sequences of 52 recent CVA16 strains demonstrated two distinct CVA16 genogroups, A and B, with the prototype strain being the only member of genogroup A. CVA16 G-10, the prototype strain, showed a nucleotide difference of 27.7-30.2% and 19.9-25.2% in VP1 and VP4, respectively, in relation to other CVA16 strains, which formed two separate lineages in genogroup B with nucleotide variation of less than 13.4% and less than 16.3% in VP1 and VP4, respectively. Lineage 1 strains circulating before 2000 were later displaced by lineage 2 strains.
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Affiliation(s)
- D Perera
- Institute of Health and Community Medicine, Universiti Malaysia Sarawak, Sarawak, Malaysia
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13
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14
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Li L, He Y, Yang H, Zhu J, Xu X, Dong J, Zhu Y, Jin Q. Genetic characteristics of human enterovirus 71 and coxsackievirus A16 circulating from 1999 to 2004 in Shenzhen, People's Republic of China. J Clin Microbiol 2005; 43:3835-9. [PMID: 16081920 PMCID: PMC1233905 DOI: 10.1128/jcm.43.8.3835-3839.2005] [Citation(s) in RCA: 180] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genetic and phylogenetic characteristics of human enterovirus 71 (EV71) and coxsackievirus A16 (CA16) sampled from children with hand, foot, and mouth disease in Shenzhen, People's Republic of China, over a 6-year period (1999 to 2004) were examined with reverse transcription-PCR and DNA sequencing. Out of 147 stool specimens, 60 showed positive signals when screened with EV71- and CA16-specific primers. EV71 was identified in 19 specimens, and CA16 was identified in 41 specimens; coinfection by EV71 and CA16 was not observed. Phylogenetic analysis of all EV71 strains isolated from the mainland Chinese samples established C4 as the predominant genotype. Only one other known strain (3254-TAI-98; AF286531), isolated in Taiwan in 1998, was identified as belonging to genotype C4. Phylogenetic analysis of CA16 strains allowed us to identify three new genetic lineages (A, B, and C), with lineage C recently predominating in Asian countries, such as the People's Republic of China, Malaysia, and Japan. These new observations indicate that CA16 circulating in the People's Republic of China is genetically diverse, and additional surveillance is warranted.
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Affiliation(s)
- Linlin Li
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese CDC, Beijing, Department of Microbiology, Shenzhen Center for Disease Control and Prevention, Shenzhen, People's Republic of China
| | - Yaqing He
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese CDC, Beijing, Department of Microbiology, Shenzhen Center for Disease Control and Prevention, Shenzhen, People's Republic of China
| | - Hong Yang
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese CDC, Beijing, Department of Microbiology, Shenzhen Center for Disease Control and Prevention, Shenzhen, People's Republic of China
| | - Junping Zhu
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese CDC, Beijing, Department of Microbiology, Shenzhen Center for Disease Control and Prevention, Shenzhen, People's Republic of China
| | - Xingye Xu
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese CDC, Beijing, Department of Microbiology, Shenzhen Center for Disease Control and Prevention, Shenzhen, People's Republic of China
| | - Jie Dong
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese CDC, Beijing, Department of Microbiology, Shenzhen Center for Disease Control and Prevention, Shenzhen, People's Republic of China
| | - Yafang Zhu
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese CDC, Beijing, Department of Microbiology, Shenzhen Center for Disease Control and Prevention, Shenzhen, People's Republic of China
| | - Qi Jin
- State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese CDC, Beijing, Department of Microbiology, Shenzhen Center for Disease Control and Prevention, Shenzhen, People's Republic of China
- Corresponding author. Mailing address: State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese CDC, No. 6 Rongjing East Street, Yi zhuang, Beijing 100176, China. Phone: 86 10 67876915. Fax: 86 10 67877736. E-mail:
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15
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Singh S, Chow VTK, Phoon MC, Chan KP, Poh CL. Direct detection of enterovirus 71 (EV71) in clinical specimens from a hand, foot, and mouth disease outbreak in Singapore by reverse transcription-PCR with universal enterovirus and EV71-specific primers. J Clin Microbiol 2002; 40:2823-7. [PMID: 12149336 PMCID: PMC120643 DOI: 10.1128/jcm.40.8.2823-2827.2002] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A recent outbreak of hand, foot, and mouth disease in Singapore in 2000 affected several thousand children and resulted in four deaths. The aim of this study was to determine the applicability of reverse transcription-PCR (RT-PCR) with universal pan-enterovirus primers and enterovirus 71 (EV71) type-specific primers for the direct detection of enteroviruses in clinical specimens derived from this outbreak. With the universal primers, EV71 RNA sequences were successfully detected by RT-PCR and direct sequencing in 71% of positive specimens. Three pairs of EV71 type-specific primers were evaluated for rapid detection of EV71 directly from clinical specimens and cell culture isolates. By using a seminested RT-PCR strategy, specific identification of EV71 sequences directly in clinical specimens was achieved, with a detection rate of 53%. In contrast, cell culture could isolate EV71 in only 20% of positive specimens. EV71 was detected directly from brain, heart, and lung specimens of two deceased siblings. Although more than one type of enterovirus was identified in clinical specimens from this outbreak, 90% of the enteroviruses were confirmed as EV71. The data demonstrate the clinical applicability of pan-enterovirus and seminested RT-PCR for the detection of EV71 RNA directly from clinical specimens in an outbreak situation.
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Affiliation(s)
- Sunita Singh
- Programme in Infectious Diseases, Department of Microbiology, Faculty of Medicine, National University of Singapore, Singapore 117597
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