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Liu Y, Wu D, Zhang K, Ren R, Liu Y, Zhang S, Zhang X, Cheng J, Chen L, Huang J. Detection technology and clinical applications of serum viral products of hepatitis B virus infection. Front Cell Infect Microbiol 2024; 14:1402001. [PMID: 39035352 PMCID: PMC11257880 DOI: 10.3389/fcimb.2024.1402001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 06/12/2024] [Indexed: 07/23/2024] Open
Abstract
Viral hepatitis, caused by its etiology, hepatitis virus, is a public health problem globally. Among all infections caused by hepatitis-associated viruses, hepatitis B virus (HBV) infection remains the most serious medical concern. HBV infection particularly affects people in East Asia and Africa, the Mediterranean region, and Eastern Europe, with a prevalence rate of > 2%. Currently, approximately 1 billion people worldwide are infected with HBV, and nearly 30% of them experience chronic infection. Chronic HBV infection can lead to chronic hepatitis B (CHB), liver cirrhosis, and hepatocellular carcinoma (HCC), resulting in the related death of approximately 1 million people annually. Although preventative vaccines and antiviral therapies are currently available, there is no cure for this infection. Clinical testing is not only the gateway for diagnosis of HBV infection, but also crucial for judging the timing of medication, evaluating the effect of antiviral therapy, and predicting the risk of relapse after drug withdrawal in the whole follow-up management of hepatitis B infected persons. With advances in detection technology, it is now possible to measure various viral components in the blood to assess the clinical status of HBV infection. Serum viral products of HBV infection, such as HBV DNA, HBV RNA, hepatitis B surface antigen, hepatitis B e-antigen, and hepatitis B core-related antigen, are non-invasive indicators that are critical for the rapid diagnosis and management of related diseases. Improving the sensitivity of monitoring of these products is essential, and the development of corresponding detection technologies is pivotal in achieving this goal. This review aims to offer valuable insights into CHB infection and references for its effective treatment. We provide a comprehensive and systematic overview of classical and novel methods for detecting HBV serum viral products and discusses their clinical applications, along with the latest research progress in this field.
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Affiliation(s)
- Ying Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Di Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Kui Zhang
- State Key Laboratory of Resource Insects, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Rongrong Ren
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, Zhejiang, China
| | - Yuxuan Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Shuya Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xuanyu Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Jilin Cheng
- Department of Gastroenterology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Liping Chen
- Department of Gastroenterology, Shanghai Geriatric Medical Center, Shanghai, China
| | - Jun Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
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Haynes E, Lorch J, Allender MC. Development and application of a qPCR-based genotyping assay for Ophidiomyces ophidiicola to investigate the epidemiology of ophidiomycosis. PLoS One 2023; 18:e0289159. [PMID: 37535588 PMCID: PMC10399865 DOI: 10.1371/journal.pone.0289159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/12/2023] [Indexed: 08/05/2023] Open
Abstract
Ophidiomycosis (snake fungal disease) is an infectious disease caused by the fungus Ophidiomyces ophidiicola to which all snake species appear to be susceptible. Significant variation has been observed in clinical presentation, progression of disease, and response to treatment, which may be due to genetic variation in the causative agent. Recent phylogenetic analysis based on whole-genome sequencing identified that O. ophidiicola strains from the United States formed a clade distinct from European strains, and that multiple clonal lineages of the clade are present in the United States. The purpose of this study was to design a qPCR-based genotyping assay for O. ophidiicola, then apply that assay to swab-extracted DNA samples to investigate whether the multiple O. ophidiicola clades and clonal lineages in the United States have specific geographic, taxonomic, or temporal predilections. To this end, six full genome sequences of O. ophidiicola representing different clades and clonal lineages were aligned to identify genomic areas shared between subsets of the isolates. Eleven hydrolysis-based Taqman primer-probe sets were designed to amplify selected gene segments and produce unique amplification patterns for each isolate, each with a limit of detection of 10 or fewer copies of the target sequence and an amplification efficiency of 90-110%. The qPCR-based approach was validated using samples from strains known to belong to specific clades and applied to swab-extracted O. ophidiicola DNA samples from multiple snake species, states, and years. When compared to full-genome sequencing, the qPCR-based genotyping assay assigned 75% of samples to the same major clade (Cohen's kappa = 0.360, 95% Confidence Interval = 0.154-0.567) with 67-77% sensitivity and 88-100% specificity, depending on clade/clonal lineage. Swab-extracted O. ophidiicola DNA samples from across the United States were assigned to six different clonal lineages, including four of the six established lineages and two newly defined groups, which likely represent recombinant strains of O. ophidiicola. Using multinomial logistic regression modeling to predict clade based on snake taxonomic group, state of origin, and year of collection, state was the most significant predictor of clonal lineage. Furthermore, clonal lineage was not associated with disease severity in the most intensely sampled species, the Lake Erie watersnake (Nerodia sipedon insularum). Overall, this assay represents a rapid, cost-effective genotyping method for O. ophidiicola that can be used to better understand the epidemiology of ophidiomycosis.
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Affiliation(s)
- Ellen Haynes
- Wildlife Epidemiology Laboratory, Department of Veterinary Clinical Medicine, University of Illinois College of Veterinary Medicine, Urbana, Illinois, United States of America
- Current affiliation: Southeastern Cooperative Wildlife Disease Study, Department of Population Health, University of Georgia College of Veterinary Medicine, Athens, Georgia, United States of America
| | - Jeffrey Lorch
- U.S. Geological Survey, National Wildlife Health Center, Madison, Wisconsin, United States of America
| | - Matthew C Allender
- Wildlife Epidemiology Laboratory, Department of Veterinary Clinical Medicine, University of Illinois College of Veterinary Medicine, Urbana, Illinois, United States of America
- Chicago Zoological Society, Brookfield Zoo, Brookfield, Illinois, United States of America
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Li M, Lv Y, Cui D, Xu Y, Lin M, Zhang X, Wang Y, Shen C, Xie J. Development and clinical validation of a one-step pentaplex real-time reverse transcription PCR assay for detection of hepatitis virus B, C, E, Treponema pallidum, and a human housekeeping gene. BMC Infect Dis 2023; 23:358. [PMID: 37231355 DOI: 10.1186/s12879-023-08240-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/11/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND With the safety of blood transfusion being a major public health concern, the development of a rapid, sensitive, specific, and cost-effective multiplex PCR assay for simultaneous detection of hepatitis B virus(HBV), hepatitis C virus (HCV), hepatitis E virus (HEV), and Treponema pallidum(T. pallidum) in blood is crucial. METHODS Five primer pairs and probes were designed towards conserved regions of target genes and used to establish a one-step pentaplex real-time reverse transcription PCR(qRT-PCR) assay for simultaneous detection of HBV, HCV, HEV, T. pallidum, and RNase P(housekeeping gene), providing sample quality check. The clinical performance of the assay was further determined with 2400 blood samples from blood donors and patients in Zhejiang province, and compared the results with commercial singleplex qPCR and serological assays. RESULTS The 95% limit of detection(LOD) of HBV, HCV, HEV, and T. pallidum were 7.11 copies/µL, 7.65 copies/µL, 8.45 copies/µL, and 9.06 copies/µL, respectively. Moreover, the assay has good specificity and precision. Compared to the singleplex qPCR assay, the novel assay for detecting HBV, HCV, HEV, and T. pallidum presented 100% clinical sensitivity, specificity, and consistency. Several discrepant results between serological and pentaplex qRT-PCR assays were found. Of 2400 blood samples, there were 2(0.08%) HBsAg positive samples, 3(0.13%) anti-HCV positive samples, 29(1.21%) IgM anti-HEV positive samples and 6(0.25%) anti-T. pallidum positive samples proven negative in nucleic acid detection. 1(0.04%) HBV DNA positive sample and 1(0.04%) HEV RNA positive sample were detected negative by serological testing. CONCLUSIONS The developed pentaplex qRT-PCR is the first assay on simultaneous, sensitive, specific, and reproducible detection of HBV, HCV, HEV, T. pallidum, and RNase P in a single tube. It could detect pathogens in blood during the window period of infection and is a good tool for effectively screening blood donors and early clinical diagnosis.
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Affiliation(s)
- Miaomiao Li
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yan Lv
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Dawei Cui
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yushan Xu
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Mengjiao Lin
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | | | - Yongjun Wang
- Key Laboratory of Blood Safety Research of Zhejiang Province, Zhejiang Province Blood Center, Hangzhou, 310052, China
| | - Cuifen Shen
- Department of Clinical Laboratory, Huzhou Central Hospital, Huzhou, 313000, China.
| | - Jue Xie
- Department of Blood Transfusion, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
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Wu Y, Liu B, Liu Z, Zhang P, Mu X, Tong Z. Construction, Characterization, and Application of a Nonpathogenic Virus-like Model for SARS-CoV-2 Nucleocapsid Protein by Phage Display. Toxins (Basel) 2022; 14:toxins14100683. [PMID: 36287952 PMCID: PMC9607219 DOI: 10.3390/toxins14100683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022] Open
Abstract
With the outbreak and spread of COVID-19, a deep investigation of SARS-CoV-2 is urgent. Direct usage of this virus for scientific research could provide reliable results and authenticity. However, it is strictly constrained and unrealistic due to its high pathogenicity and infectiousness. Considering its biosafety, different systems and technologies have been employed in immunology and biomedical studies. In this study, phage display technology was used to construct a nonpathogenic model for COVID-19 research. The nucleocapsid protein of SARS-CoV-2 was fused with the M13 phage capsid p3 protein and expressed on the M13 phages. After validation of its successful expression, its potential as the standard for qPCR quantification and affinity with antibodies were confirmed, which may show the possibility of using this nonpathogenic bacteriophage to replace the pathogenic virus in scientific research concerning SARS-CoV-2. In addition, the model was used to develop a system for the classification and identification of different samples using ATR–FTIR, which may provide an idea for the development and evaluation of virus monitoring equipment in the future.
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Wei Z, Wang X, Feng H, Ji F, Bai D, Dong X, Huang W. Isothermal nucleic acid amplification technology for rapid detection of virus. Crit Rev Biotechnol 2022; 43:415-432. [PMID: 35156471 DOI: 10.1080/07388551.2022.2030295] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
While the research field and industrial market of in vitro diagnosis (IVD) thrived during and post the COVID-19 pandemic, the development of isothermal nucleic acid amplification test (INAAT) based rapid diagnosis was engendered in a global wised large measure as a problem-solving exercise. This review systematically analyzed the recent advances of INAAT strategies with practical case for the real-world scenario virus detection applications. With the qualities that make INAAT systems useful for making diagnosis relevant decisions, the key performance indicators and the cost-effectiveness of enzyme-assisted methods and enzyme-free methods were compared. The modularity of nucleic acid amplification reactions that can lead to thresholding signal amplifications using INAAT reagents and their methodology design were examined, alongside the potential application with rapid test platform/device integration. Given that clinical practitioners are, by and large, unaware of many the isothermal nucleic acid test advances. This review could bridge the arcane research field of different INAAT systems and signal output modalities with end-users in clinic when choosing suitable test kits and/or methods for rapid virus detection.
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Affiliation(s)
- Zhenting Wei
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- North Sichuan Medical College, Nanchong, China
| | - Xiaowen Wang
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- North Sichuan Medical College, Nanchong, China
| | - Huhu Feng
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
| | - Fanpu Ji
- Department of Infectious Diseases, The 2nd Hospital of Xi'an Jiaotong University, Nanchong, China
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The 2nd Hospital of Xi'an Jiaotong University, Nanchong, China
- Division of Gastroenterology and Hepatology, Stanford University Medical Center, Nanchong, China
| | - Dan Bai
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- Research and Development Institute of Northwestern Polytechnical University in Shenzhen, Northwestern Polytechnical University, Nanchong, China
| | - Xiaoping Dong
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Nanchong, China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Nanchong, China
| | - Wei Huang
- Frontiers Science Center for Flexible Electronics (FSCFE), Institute of Flexible Electronics (IFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Xi'an Key Laboratory of Special Medicine and Health Engineering, Northwestern Polytechnical University, Xi'an, China
- Research and Development Institute of Northwestern Polytechnical University in Shenzhen, Northwestern Polytechnical University, Nanchong, China
- Institute of Advanced Materials (IAM), Nanjing Tech University, Nanchong, China
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Chen X, Tan Y, Wang S, Wu X, Liu R, Yang X, Wang Y, Tai J, Li S. A CRISPR-Cas12b-Based Platform for Ultrasensitive, Rapid, and Highly Specific Detection of Hepatitis B Virus Genotypes B and C in Clinical Application. Front Bioeng Biotechnol 2021; 9:743322. [PMID: 34692662 PMCID: PMC8529042 DOI: 10.3389/fbioe.2021.743322] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 08/31/2021] [Indexed: 12/13/2022] Open
Abstract
Hepatitis B virus (HBV) is one of the most dangerous and prevalent agents that causes acute and chronic liver diseases in humans. Genotyping plays an important role in determining clinical outcomes and response to antiviral treatment in HBV-infected patients. Here, we first devised a CRISPR-based testing platform, termed "CRISPR-HBV," for ultrasensitive, highly specific, and rapid detection of two major HBV genotypes (HBV-B and HBV-C) in clinical application. The CRISPR-HBV employed multiple cross displacement amplification (MCDA) for rapid preamplification and then Cas12b-based detection for decoding the targets. Finally, the detection result was read out with real-time fluorescence and a lateral flow biosensor. The sensitivity of CRISPR-HBV was 10 copies per test. The specificity was one hundred percent, and no cross reactions were observed in other HBV genotypes and pathogens. The whole detection process, including DNA template extraction (15 min), preamplification reaction of MCDA (30 min at 65°C), CRISPR-Cas12b-based detection (5 min at 37°C), and results readout (∼2 min), could be completed within 1 h. The feasibility of the CRISPR-HBV assay for genotyping HBV-B and -C as successfully validated with clinical samples. Hence, the CRISPR-HBV assay has remarkable potential to develop a point-of-care testing for identifying and distinguishing HBV genotypes B and C in clinical settings, especially in resource-scarcity countries.
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Affiliation(s)
- Xu Chen
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Yan Tan
- Guizhou Provincial Center for Clinical Laboratory, Guiyang, China
| | - Shuoshi Wang
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Xueli Wu
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Rui Liu
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Xinggui Yang
- Public Health School, Guizhou Medical University, Guiyang, China
| | - Yi Wang
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China
| | - Jun Tai
- Department of Otolaryngology, Head and Neck Surgery, Children's Hospital Capital Institute of Pediatrics, Beijing, China
| | - Shijun Li
- Guizhou Provincial Centre for Disease Control and Prevention, Guiyang, China
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Hulaniuk ML, Corach D, Trinks J, Caputo M. A simple and rapid approach for human herpesvirus type 8 subtype characterization using single base extension. Lett Appl Microbiol 2021; 73:308-317. [PMID: 34048079 DOI: 10.1111/lam.13515] [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: 02/12/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/28/2022]
Abstract
Sequence analysis of the ORFK1 of human herpesvirus type 8 (HHV-8) allows the identification of six major subtypes (A-F), which are related to human migrations and the clinical progression of Kaposi's sarcoma. Sequencing and subsequent phylogenetic analysis of ORFK1 is considered to be the most reliable method for HHV-8 genotyping. However, it exhibits challenges and limitations. Herein, we designed and validated a single base extension (SBE) protocol for characterization of HHV-8 ORFK1 subtypes. A nested polymerase chain reaction (PCR) protocol was carried out to amplify a small 294-bp PCR product encompassing four single nucleotide polymorphisms at positions 360, 406, 465 and 527 of the HHV-8 genome. Finally, a multiplex SBE technique was developed and validated in 20 samples previously genotyped by phylogenetic analysis. The patterns obtained in this reaction could successfully discriminate between ORFK1 subtypes. The typing results obtained completely matched with those of the 'gold standard' method in all analysed samples. This method can reliably identify HHV-8 subtypes A, B and C, which are the most prevalent ones worldwide, and the remaining subtypes (D, E and F). SBE can be useful as an efficient, rapid and low-cost screening method for viral genotyping in a single tube, particularly samples with low-quality DNA, and with easy data interpretation.
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Affiliation(s)
- M L Hulaniuk
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), Buenos Aires, Argentina
| | - D Corach
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Buenos Aires, Argentina
| | - J Trinks
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - M Caputo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Buenos Aires, Argentina
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Laidoudi Y, Davoust B, Varloud M, Niang EHA, Fenollar F, Mediannikov O. Development of a multiplex qPCR-based approach for the diagnosis of Dirofilaria immitis, D. repens and Acanthocheilonema reconditum. Parasit Vectors 2020; 13:319. [PMID: 32571427 PMCID: PMC7309989 DOI: 10.1186/s13071-020-04185-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/13/2020] [Indexed: 12/17/2022] Open
Abstract
Background Dirofilaria immitis, D. repens and Acanthocheilonema reconditum are the main causative agents of zoonotic canine filariosis. Methods We developed a combined multiplex approach for filaria and Wolbachia detection using the 28S-based pan-filarial and 16S-based pan-Wolbachia qPCRs, respectively, involving a fast typing method of positive samples using triplex qPCR targeting A. reconditum, D. immitis and D. repens, and a duplex qPCR targeting Wolbachia of D. immitis and D. repens. The approach was complemented by a duplex qPCR for the differential diagnosis of heartworms (D. immitis and Angiostrongylus vasorum) and pan-filarial cox1 and pan-Wolbachia ftsZ PCRs to identify other filarial parasites and their Wolbachia, respectively. A total of 168 canine blood and sera samples were used to validate the approach. Spearmanʼs correlation was used to assess the association between filarial species and the strain of Wolbachia. Positive samples for both the heartworm antigen-test after heating sera and at least one DNA-positive for D. immitis and its Wolbachia were considered true positive for heartworm infection. Indeed, the presence of D. repens DNA or that of its Wolbachia as well as A. reconditum DNA indicates true positive infections. Results The detection limit for Wolbachia and filariae qPCRs ranged from 5 × 10−1 to 1.5 × 10−4 mf/ml of blood. When tested on clinical samples, 29.2% (49/168) tested positive for filariae or Wolbachia DNA. Filarial species and Wolbachia genotypes were identified by the combined multiplex approach from all positive samples. Each species of Dirofilaria was significantly associated with a specific genotype of Wolbachia. Compared to the true positives, the approach showed excellent agreement (k = 0.98–1). Unlike D. immitis DNA, no A. vasorum DNA was detected by the duplex qPCR. The immunochromatographic test for heartworm antigen showed a substantial (k = 0.6) and a weak (k = 0.15) agreements before and after thermal pre-treatment of sera, respectively. Conclusions The proposed approach is a reliable tool for the exploration and diagnosis of occult and non-occult canine filariosis. The current diagnosis of heartworm disease based on antigen detection should always be confirmed by qPCR essays. Sera heat pre-treatment is not effective and strongly discouraged.![]()
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Affiliation(s)
- Younes Laidoudi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UMR Aix-Marseille University, IRD, APHM, IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France
| | - Bernard Davoust
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UMR Aix-Marseille University, IRD, APHM, IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France
| | - Marie Varloud
- Ceva Santé Animale, 10 Avenue de la Ballastière, 33500, Libourne, France
| | - El Hadji Amadou Niang
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UMR Aix-Marseille University, IRD, APHM, IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France
| | - Florence Fenollar
- IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France.,VITROME, UMR Aix-Marseille University, IRD, SSA, APHM, IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France
| | - Oleg Mediannikov
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UMR Aix-Marseille University, IRD, APHM, IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France. .,IHU Méditerranée Infection, 19-21, Bd Jean Moulin, 13005, Marseille, France.
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Kim H, Hur M, Bae E, Lee KA, Lee WI. Performance evaluation of cobas HBV real-time PCR assay on Roche cobas 4800 System in comparison with COBAS AmpliPrep/COBAS TaqMan HBV Test. Clin Chem Lab Med 2019; 56:1133-1139. [PMID: 29455185 DOI: 10.1515/cclm-2017-1133] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/17/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND Hepatitis B virus (HBV) nucleic acid amplification testing (NAAT) is important for the diagnosis and management of HBV infection. We evaluated the analytical performance of the cobas HBV NAAT (Roche Diagnostics GmbH, Mannheim, Germany) on the cobas 4800 System in comparison with COBAS AmpliPrep/COBAS TaqMan HBV Test (CAP/CTM HBV). METHODS Precision was evaluated using three levels of cobas HBV/HCV/HIV-1 Control Kit, and linearity was evaluated across the anticipated measuring range (10.0-1.0×109 IU/mL) at seven levels using clinical samples. Detection capability, including limit of blank (LOB), limit of detection (LOD) and limit of quantitation (LOQ), was verified using the 4th WHO International Standard for HBV DNA for NAT (NIBSC code: 10/266). Correlation between the two systems was compared using 205 clinical samples (102 sera and 103 EDTA plasma). RESULTS Repeatability and total imprecision (coefficient of variation) ranged from 0.5% to 3.8% and from 0.5% to 3.5%, respectively. Linearity (coefficient of determination, R2) was 0.999. LOB, LOD and LOQ were all acceptable within the observed proportion rate (85%). Correlation was very high between the two systems in both serum and plasma samples (correlation coefficient [r]=0.995). CONCLUSIONS The new cobas HBV real-time PCR assay on the cobas 4800 System showed reliable analytical performances.
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Affiliation(s)
- Hanah Kim
- Department of Laboratory Medicine, School of Medicine, Konkuk University, Seoul, Republic of Korea
| | - Mina Hur
- Department of Laboratory Medicine, School of Medicine, Konkuk University, Seoul, Republic of Korea
| | - Eunsin Bae
- Department of Laboratory Medicine, Veterans Healthcare System Medical Center, Seoul, Republic of Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Woo-In Lee
- Department of Laboratory Medicine, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
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Epidemiology and Molecular Detection of HAV, HBV, and HCV in Patients with Acute Hepatitis Symptoms in Ahvaz. Jundishapur J Microbiol 2018. [DOI: 10.5812/jjm.63317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Singh A, Mankotia DS, Irshad M. A Single-step Multiplex Quantitative Real Time Polymerase Chain Reaction Assay for Hepatitis C Virus Genotypes. J Transl Int Med 2017; 5:34-42. [PMID: 28680837 DOI: 10.1515/jtim-2017-0010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND AND OBJECTIVES The variable response of hepatitis C virus (HCV) genotypes towards anti-viral treatment requires prior information on the genotype status before planning a therapeutic strategy. Although assays for typing or subtyping of HCV are available, however, a fast and reliable assay system is still needed. The present study was planned to develop a single-step multiplex quantitative real time polymerase chain reaction (qPCR) assay to determine HCV genotypes in patients' sera. METHODS The conserved sequences from 5' UTR, core and NS5b regions of HCV genome were used to design primers and hydrolysis probes labeled with fluorophores. Starting with the standardization of singleplex (qPCR) for each individual HCV-genotype, the experimental conditions were finally optimized for the development of multiplex assay. The sensitivity and specificity were assessed both for singleplex and multiplex assays. Using the template concentration of 102 copies per microliter, the value of quantification cycle (Cq) and the limit of detection (LOD) were also compared for both singleplex and multiplex assays. Similarly, the merit of multiplex assay was also compared with sequence analysis and restriction fragment length polymorphism (RFLP) techniques used for HCV genotyping. In order to find the application of multiplex qPCR assay, it was used for genotyping in a panel of 98 sera positive for HCV RNA after screening a total number of 239 patients with various liver diseases. RESULTS The results demonstrated the presence of genotype 1 in 26 of 98 (26.53%) sera, genotype 3 in 65 (66.32%) and genotype 4 in 2 (2.04%) sera samples, respectively. One sample showed mixed infection of genotype 1 and 3. Five samples could not show the presence of any genotype. Genotypes 2, 5 and 6 could not be detected in these sera samples. The analysis of sera by singleplex and RFLP indicated the results of multiplex to be comparable with singleplex and with clear merit of multiplex over RFLP. In addition, the results of multiplex assay were also found to be comparable with those from sequence analysis. The sensitivity, specificity, Cq values and LOD values were compared and found to be closely associated both for singleplex and multiplex assays. CONCLUSION The multiplex qPCR assay was found to be a fast, specific and sensitive method that can be used as a technique of choice for HCV genotyping in all routine laboratories.
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Affiliation(s)
- Akanksha Singh
- Clinical Biochemistry Division, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Dhananjay Singh Mankotia
- Clinical Biochemistry Division, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi-110029, India
| | - Mohammad Irshad
- Clinical Biochemistry Division, Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi-110029, India
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