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Liang C, Yang H, Yang X, Long Z, Zhou Y, Wang J, Fan L, Zeng M, Wang Y, Zheng H, Wang Z, Ye P, Lin J, Shi W, Huang H, Yan H, Qian J, Li L, Liu L. Applying improved ddPCR to reliable quantification of MPXV in clinical settings. Microbiol Spectr 2024:e0001824. [PMID: 38757960 DOI: 10.1128/spectrum.00018-24] [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: 01/03/2024] [Accepted: 04/11/2024] [Indexed: 05/18/2024] Open
Abstract
Monkeypox virus (MPXV) poses a global health threat. Droplet digital PCR (ddPCR) holds potential as an accurate diagnostic tool for clinical microbiology. However, there is limited literature on the applicability of ddPCR in clinical settings. In this study, the clinical features of patients with MPXV during the initial outbreak in China in June 2023 were reviewed, and an optimized ddPCR method with dilution and/or inhibitor removal was developed to enhance MPXV detection efficiency. Eighty-two MPXV samples were tested from nine different clinical specimen types, including feces, urine, pharyngeal swabs, anal swabs, saliva, herpes fluid, crust, and semen, and the viral load of each specimen was quantified. A comparative analysis was performed with qPCR to assess sensitivity and specificity and to investigate the characteristics of MPXV infection by analyzing viral loads in different clinical specimens. Consequently, common pharyngeal and gastrointestinal symptoms were observed in patients with MPXV. The optimized ddPCR method demonstrated relatively high sensitivity for MPXV quantification in the clinical materials, with a limit of detection of 0.1 copies/μL. This was particularly evident in low-concentration samples like whole blood, semen, and urine. The optimized ddPCR demonstrated greater detection accuracy compared with normal ddPCR and qPCR, with an area under the curve (AUC) of 0.939. Except for crust samples, viral loads in the specimens gradually decreased as the disease progressed. Virus levels in feces and anal swabs kept a high detection rate at each stage of post-symptom onset, and feces and anal swabs samples may be suitable for clinical diagnosis and continuous monitoring of MPXV. IMPORTANCE The ddPCR technique proved to be a sensitive and valuable tool for accurately quantifying MPXV viral loads in various clinical specimen types. The findings provided valuable insights into the necessary pre-treatment protocols for MPXV diagnosis in ddPCR detection and the potentially suitable sample types for collection. Therefore, such results can aid in comprehending the potential characteristics of MPXV infection and the usage of ddPCR in clinical settings.
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Affiliation(s)
- Chudan Liang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Huiqin Yang
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaofeng Yang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Zhenyu Long
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yuandong Zhou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Jian Wang
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Linjin Fan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Mou Zeng
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yulong Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Haipeng Zheng
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
- The Third People's Hospital of Bijie City, Bijie, Guizhou, China
| | - Zequn Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Pengfei Ye
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Jingyan Lin
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Wendi Shi
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Hongxin Huang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Huijun Yan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
| | - Jun Qian
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Linghua Li
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Linna Liu
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
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2
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Sancha Dominguez L, Cotos Suárez A, Sánchez Ledesma M, Muñoz Bellido JL. Present and Future Applications of Digital PCR in Infectious Diseases Diagnosis. Diagnostics (Basel) 2024; 14:931. [PMID: 38732345 PMCID: PMC11083499 DOI: 10.3390/diagnostics14090931] [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: 03/19/2024] [Revised: 04/19/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
Infectious diseases account for about 3 million deaths per year. The advent of molecular techniques has led to an enormous improvement in their diagnosis, both in terms of sensitivity and specificity and in terms of the speed with which a clinically useful result can be obtained. Digital PCR, or 3rd generation PCR, is based on a series of technical modifications that result in more sensitive techniques, more resistant to the action of inhibitors and capable of direct quantification without the need for standard curves. This review presents the main applications that have been developed for the diagnosis of viral, bacterial, and parasitic infections and the potential prospects for the clinical use of this technology.
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Affiliation(s)
- Laura Sancha Dominguez
- Department of Microbiology, Hospital Universitario de Salamanca, 37007 Salamanca, Spain; (L.S.D.); (A.C.S.)
- Research Group IIMD-16, Institute for Biomedical Research of Salamanca (IBSAL), SACYL, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
| | - Ana Cotos Suárez
- Department of Microbiology, Hospital Universitario de Salamanca, 37007 Salamanca, Spain; (L.S.D.); (A.C.S.)
- Research Group IIMD-16, Institute for Biomedical Research of Salamanca (IBSAL), SACYL, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
| | - María Sánchez Ledesma
- Infectious Diseases Unit, Hospital Universitario de Salamanca, 37007 Salamanca, Spain;
| | - Juan Luis Muñoz Bellido
- Department of Microbiology, Hospital Universitario de Salamanca, 37007 Salamanca, Spain; (L.S.D.); (A.C.S.)
- Research Group IIMD-16, Institute for Biomedical Research of Salamanca (IBSAL), SACYL, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
- Department of Biomedical and Diagnosis Sciences, Faculty of Medicine, Universidad de Salamanca, 37007 Salamanca, Spain
- Center for Research on Tropical Diseases, Universidad de Salamanca (CIETUS), 37007 Salamanca, Spain
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3
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Ju DU, Park D, Kim IH, Kim S, Yoo HM. Development of Human Rhinovirus RNA Reference Material Using Digital PCR. Genes (Basel) 2023; 14:2210. [PMID: 38137032 PMCID: PMC10742479 DOI: 10.3390/genes14122210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The human rhinovirus (RV) is a positive-stranded RNA virus that causes respiratory tract diseases affecting both the upper and lower halves of the respiratory system. RV enhances its replication by concentrating RNA synthesis within a modified host membrane in an intracellular compartment. RV infections often occur alongside infections caused by other respiratory viruses, and the RV virus may remain asymptomatic for extended periods. Alongside qualitative detection, it is essential to accurately quantify RV RNA from clinical samples to explore the relationships between RV viral load, infections caused by the virus, and the resulting symptoms observed in patients. A reference material (RM) is required for quality evaluation, the performance evaluation of molecular diagnostic products, and evaluation of antiviral agents in the laboratory. The preparation process for the RM involves creating an RV RNA mixture by combining RV viral RNA with RNA storage solution and matrix. The resulting RV RNA mixture is scaled up to a volume of 25 mL, then dispensed at 100 µL per vial and stored at -80 °C. The process of measuring the stability and homogeneity of RV RMs was conducted by employing reverse transcription droplet digital polymerase chain reaction (RT-ddPCR). Digital PCR is useful for the analysis of standards and can help to improve measurement compatibility: it represents the equivalence of a series of outcomes for reference materials and samples being analyzed when a few measurement procedures are employed, enabling objective comparisons between quantitative findings obtained through various experiments. The number of copies value represents a measured result of approximately 1.6 × 105 copies/μL. The RM has about an 11% bottle-to-bottle homogeneity and shows stable results for 1 week at temperatures of 4 °C and -20 °C and for 12 months at a temperature of -80 °C. The developed RM can enhance the dependability of RV molecular tests by providing a precise reference value for the absolute copy number of a viral target gene. Additionally, it can serve as a reference for diverse studies.
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Affiliation(s)
- Dong U Ju
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- School of Biomedical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Dongju Park
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Il-Hwan Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Seil Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Hee Min Yoo
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
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4
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Dong T, Wang M, Liu J, Ma P, Pang S, Liu W, Liu A. Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives. Chem Sci 2023; 14:6149-6206. [PMID: 37325147 PMCID: PMC10266450 DOI: 10.1039/d2sc06665c] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced severe public healthcare issues and weakened the global economy significantly. Although SARS-CoV-2 infection is not as fatal as the initial outbreak, many infected victims suffer from long COVID. Therefore, rapid and large-scale testing is critical in managing patients and alleviating its transmission. Herein, we review the recent advances in techniques to detect SARS-CoV-2. The sensing principles are detailed together with their application domains and analytical performances. In addition, the advantages and limits of each method are discussed and analyzed. Besides molecular diagnostics and antigen and antibody tests, we also review neutralizing antibodies and emerging SARS-CoV-2 variants. Further, the characteristics of the mutational locations in the different variants with epidemiological features are summarized. Finally, the challenges and possible strategies are prospected to develop new assays to meet different diagnostic needs. Thus, this comprehensive and systematic review of SARS-CoV-2 detection technologies may provide insightful guidance and direction for developing tools for the diagnosis and analysis of SARS-CoV-2 to support public healthcare and effective long-term pandemic management and control.
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Affiliation(s)
- Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
- School of Pharmacy, Medical College, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Junchong Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Pengxin Ma
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Wanjian Liu
- Qingdao Hightop Biotech Co., Ltd 369 Hedong Road, Hi-tech Industrial Development Zone Qingdao 266112 China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
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5
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Suchy FP, Nishimura T, Seki S, Wilkinson AC, Higuchi M, Hsu I, Zhang J, Bhadury J, Nakauchi H. Streamlined and quantitative detection of chimerism using digital PCR. Sci Rep 2022; 12:10223. [PMID: 35715477 PMCID: PMC9206010 DOI: 10.1038/s41598-022-14467-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 06/07/2022] [Indexed: 12/28/2022] Open
Abstract
Animal chimeras are widely used for biomedical discoveries, from developmental biology to cancer research. However, the accurate quantitation of mixed cell types in chimeric and mosaic tissues is complicated by sample preparation bias, transgenic silencing, phenotypic similarity, and low-throughput analytical pipelines. Here, we have developed and characterized a droplet digital PCR single-nucleotide discrimination assay to detect chimerism among common albino and non-albino mouse strains. In addition, we validated that this assay is compatible with crude lysate from all solid organs, drastically streamlining sample preparation. This chimerism detection assay has many additional advantages over existing methods including its robust nature, minimal technical bias, and ability to report the total number of cells in a prepared sample. Moreover, the concepts discussed here are readily adapted to other genomic loci to accurately measure mixed cell populations in any tissue.
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Affiliation(s)
- Fabian P Suchy
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Toshiya Nishimura
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Shinsuke Seki
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Experimental Animal Division, Bioscience Education and Research Support Center, Akita University, Akita, 010-8543, Japan
| | - Adam C Wilkinson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Maimi Higuchi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ian Hsu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jinyu Zhang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Joydeep Bhadury
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Institute of Biomedicine, Sahlgrenska University Hospital, University of Gothenburg, 41345, Gothenburg, SE, Sweden
| | - Hiromitsu Nakauchi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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6
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Advances in improvement strategies of digital nucleic acid amplification for pathogen detection. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116568] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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7
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Pereira LA, Lapinscki BA, Debur MC, Santos JS, Petterle RR, Nogueira MB, Vidal LRR, De Almeida SM, Raboni SM. Standardization of a high-performance RT-qPCR for viral load absolute quantification of influenza A. J Virol Methods 2021; 301:114439. [PMID: 34942203 DOI: 10.1016/j.jviromet.2021.114439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 12/13/2021] [Accepted: 12/17/2021] [Indexed: 12/26/2022]
Abstract
Influenza is an acute viral infectious respiratory disease worldwide, presenting in different clinical forms, from influenza-like illness (ILI) to severe acute respiratory infection (SARI). Although real-time quantitative polymerase chain reaction (qPCR) is already an important tool for both diagnosis and treatment monitoring of several viral infections, the correlation between the clinical aspects and the viral load of influenza is still unclear. This lack of clarity is primarily due to the low accuracy and reproducibility of the methodologies developed to quantify the influenza virus. Thus, this study aimed to develop and standardize a universal absolute quantification for influenza A by reverse transcription-quantitative PCR (RT-qPCR), using a plasmid DNA. The assay showed efficiency (Eff%) 98.6, determination coefficient (R2) 0.998, linear range 10^1 to 10^10, limit of detection (LOD) 6.77, limit of quantification (LOQ) 20.52 copies/reaction. No inter and intra assay variability was shown, and neither was the matrix effect observed. Serial measurements of clinical samples collected at a 72h interval showed no change in viral load. By contrast, immunocompetent patients have a significantly lower viral load than immunosuppressed ones. Absolute quantification in clinical samples showed some predictors associated with increased viral load: (H1N1)pdm09 (0.045); women (p = 0.049) and asthmatics (p = 0.035). The high efficiency, precision, and previous performance in clinical samples suggest the assay can be used as an accurate universal viral load quantification of influenza A. Its applicability in predicting severity and response to antivirals needs to be evaluated.
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Affiliation(s)
- L A Pereira
- Graduate Program in Internal Medicine and Health Science, Universidade Federal, do Paraná, Curitiba, Brazil
| | - B A Lapinscki
- Graduate Program in Internal Medicine and Health Science, Universidade Federal, do Paraná, Curitiba, Brazil
| | - M C Debur
- Public Health Laboratory, Curitiba, Brazil
| | - J S Santos
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil
| | - R R Petterle
- Sector of Health Sciences, Medical School, Universidade Federal do Paraná, Curitiba, Brazil
| | - M B Nogueira
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil
| | - L R R Vidal
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil
| | - S M De Almeida
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil
| | - S M Raboni
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil; Infectious Diseases Division, Hospital de Clínicas, Universidade Federal do Paraná, Brazil.
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8
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Mori A, Pomari E, Deiana M, Perandin F, Caldrer S, Formenti F, Mistretta M, Orza P, Ragusa A, Piubelli C. Molecular techniques for the genomic viral RNA detection of West Nile, Dengue, Zika and Chikungunya arboviruses: a narrative review. Expert Rev Mol Diagn 2021; 21:591-612. [PMID: 33910444 DOI: 10.1080/14737159.2021.1924059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Molecular technology has played an important role in arboviruses diagnostics. PCR-based methods stand out in terms of sensitivity, specificity, cost, robustness, and accessibility, and especially the isothermal amplification (IA) method is ideal for field-adaptable diagnostics in resource-limited settings (RLS).Areas covered: In this review, we provide an overview of the various molecular methods for West Nile, Zika, Dengue and Chikungunya. We summarize literature works reporting the assessment and use of in house and commercial assays. We describe limitations and challenges in the usage of methods and opportunities for novel approaches such as NNext-GenerationSequencing (NGS).Expert opinion: The rapidity and accuracy of differential diagnosis is essential for a successful clinical management, particularly in co-circulation area of arboviruses. Several commercial diagnostic molecular assays are available, but many are not affordable by RLS and not usable as Point-of-care/Point-of-need (POC/PON) such as RReal-TimeRT-PCR, Array-based methods and NGS. In contrast, the IA-based system fits better for POC/PON but it is still not ideal for the multiplexing detection system. Improvement in the characterization and validation of current molecular assays is needed to optimize their translation to the point of care.
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Affiliation(s)
- Antonio Mori
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy.,Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Elena Pomari
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Michela Deiana
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Francesca Perandin
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Sara Caldrer
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Fabio Formenti
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Manuela Mistretta
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Pierantonio Orza
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Andrea Ragusa
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
| | - Chiara Piubelli
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Verona, Italy
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Kokkoris V, Chagnon PL, Yildirir G, Clarke K, Goh D, MacLean AM, Dettman J, Stefani F, Corradi N. Host identity influences nuclear dynamics in arbuscular mycorrhizal fungi. Curr Biol 2021; 31:1531-1538.e6. [PMID: 33545043 DOI: 10.1016/j.cub.2021.01.035] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/19/2020] [Accepted: 01/12/2021] [Indexed: 02/07/2023]
Abstract
The arbuscular mycorrhizal fungi (AMF) are involved in one of the most ecologically important symbioses on the planet, occurring within the roots of most land plants.1 Knowledge of even basic elements of AM fungal biology is still poor, with the discovery that AMF may in fact have a sexual life cycle being only very recently reported.2-5 AMF produce asexual spores that contain up to several thousand individual haploid nuclei6 of either largely uniform genotypes (AMF homokaryons) or nuclei originating from two parental genotypes2-5 (AMF dikaryons or heterokaryons). In contrast to the sexual dikaryons in the phyla Ascomycota and Basidiomycota,7,8 in which pairs of nuclei coexist in single hyphal compartments, AMF dikaryons carry several thousand nuclei in a coenocytic mycelium. Here, we set out to better understand the dynamics of this unique multinucleate condition by combining molecular analyses with advanced microscopy and modeling. Herein, we report that select AMF dikaryotic strains carry the distinct nucleotypes in equal proportions to one another, whereas others show an unequal distribution of parental nucleotypes. In both cases, the relative proportions within a given strain are inherently stable. Simulation models suggest that AMF dikaryons may be maintained through nuclear cooperation dynamics. Remarkably, we report that these nuclear ratios shift dramatically in response to plant host identity, revealing a previously unknown layer of genetic complexity and dynamism within the intimate interactions that occur between the partners of a prominent terrestrial symbiosis.
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Affiliation(s)
- Vasilis Kokkoris
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada.
| | - Pierre-Luc Chagnon
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montreal, QC H1X 2B2, Canada
| | - Gökalp Yildirir
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Kelsey Clarke
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada
| | - Dane Goh
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Allyson M MacLean
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Jeremy Dettman
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada
| | - Franck Stefani
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON K1A 0C6, Canada
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
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10
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A narrative review of single-nucleotide polymorphism detection methods and their application in studies of Staphylococcus aureus. JOURNAL OF BIO-X RESEARCH 2021. [DOI: 10.1097/jbr.0000000000000071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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11
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Jiang Y, Wang H, Hao S, Chen Y, He J, Liu Y, Chen L, Yu Y, Hua S. Digital PCR is a sensitive new technique for SARS-CoV-2 detection in clinical applications. Clin Chim Acta 2020; 511:346-351. [PMID: 33159953 PMCID: PMC7641518 DOI: 10.1016/j.cca.2020.10.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 10/26/2020] [Indexed: 01/08/2023]
Abstract
Digital PCR is a sensitive new technique for SARS-CoV-2 detection in clinical applications. Digital PCR would substantially reduce the rates of false-negative COVID-19 test results, in particular those pertaining to asymptomatic carriers. Real-time reverse-transcriptase (RT)-PCR is a fast and convenient method for viral nucleic acid detection, but it’s results can be compromised by numerous factors and can yield false-negative results.
The global coronavirus disease 2019 (COVID-19) pandemic has posed great challenges in people’s daily lives. Highly sensitive laboratory techniques played a critical role in clinical COVID-19 diagnosis and management. In this study the feasibility of using a new digital PCR-based detection assay for clinical COVID-19 diagnosis was investigated by comparing its performance with that of RT-PCR. Clinical patient samples and samples obtained from potentially contaminated environments were analyzed. The study included 10 patients with confirmed COVID-19 diagnoses, 32 validated samples of various types derived from different clinical timepoints and sites, and 148 environmentally derived samples. SARS-CoV-2 nucleic acids were more readily detected in respiratory tract samples (35.0%). In analyses of environmentally derived samples, the positivity rate of air samples was higher than that of surface samples, probably due to differences in virus concentrations. Digital PCR detected SARS–CoV–2 in several samples that had previously been deemed negative, including 3 patient-derived samples and 5 environmentally derived samples. In this study digital PCR exhibited higher sensitivity than conventional RT-PCR, suggesting that it may be a useful new method for clinical SARS-CoV-2 detection. Improvement of SARS-CoV-2 detection would substantially reduce the rates of false-negative COVID-19 test results, in particular those pertaining to asymptomatic carriers.
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Affiliation(s)
- Yanfang Jiang
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China.
| | - Haifeng Wang
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China.
| | - Sijia Hao
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China.
| | - Yukun Chen
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China.
| | - Jiaxue He
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China.
| | - Yong Liu
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China.
| | - Liguo Chen
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China.
| | - Yuanhua Yu
- School of Life Science and Technology, Changchun University of Science and Technology, Changchun, China.
| | - Shucheng Hua
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China.
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12
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Navarro Sanchez ME, Devard N, Houy C, Abachin E, Godard S, Esson R, Chareyre A, Nougarede N. Multiplex reverse transcriptase droplet digital PCR for the simultaneous quantification of four dengue serotypes: Proof of concept study. Biologicals 2020; 67:62-68. [DOI: 10.1016/j.biologicals.2020.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/28/2020] [Accepted: 06/01/2020] [Indexed: 10/23/2022] Open
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13
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Rocchigiani AM, Tilocca MG, Portanti O, Vodret B, Bechere R, Di Domenico M, Savini G, Lorusso A, Puggioni G. Development of a Digital RT-PCR Method for Absolute Quantification of Bluetongue Virus in Field Samples. Front Vet Sci 2020; 7:170. [PMID: 32373633 PMCID: PMC7186476 DOI: 10.3389/fvets.2020.00170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/11/2020] [Indexed: 11/24/2022] Open
Abstract
Bluetongue (BT) is a major Office International des Epizooties (OIE)-listed disease of wild and domestic ruminants caused by several serotypes of Bluetongue virus (BTV), a virus with a segmented dsRNA genome belonging to the family Reoviridae, genus Orbivirus. BTV is transmitted through the bites of Culicoides midges. The aim of this study was to develop a new method for quantification of BTV Seg-10 by droplet digital RT-PCR (RTdd-PCR), using nucleic acids purified from complex matrices such as blood, tissues, and midges, that notoriously contain strong PCR inhibitors. First, RTdd-PCR was optimized by using RNAs purified from serially 10-fold dilutions of a BTV-1 isolate (105.43TCID50/ml up to 10−0.57 TCID50/ml) and from the same dilutions spiked into fresh ovine EDTA-blood and spleen homogenate. The method showed a good degree of linearity (R2 ≥ 0.995). The limit of detection (LoD) and the limit of quantification (LoQ) established were 10−0.67TCID50/ml (0.72 copies/μl) and 100.03TCID50/ml (3.05 copies/μl) of BTV-1, respectively. Second, the newly developed test was compared, using the same set of biological samples, to the quantitative RT-PCR (RT-qPCR) detecting Seg-10 assay widely used for the molecular diagnosis of BTV from field samples. Results showed a difference mean of 0.30 log between the two assays with these samples (p < 0.05). Anyway, the analysis of correlation demonstrated that both assays provided similar measurements with a very close agreement between the systems.
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Affiliation(s)
- Angela M Rocchigiani
- Department of Sanità Animale, Istituto Zooprofilattico Sperimentale Della Sardegna, Sassari, Italy
| | - Maria G Tilocca
- Department of Sanità Animale, Istituto Zooprofilattico Sperimentale Della Sardegna, Sassari, Italy
| | - Ottavio Portanti
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale Abruzzo e Molise, Teramo, Italy
| | - Bruna Vodret
- Department of Sanità Animale, Istituto Zooprofilattico Sperimentale Della Sardegna, Sassari, Italy
| | - Roberto Bechere
- Department of Sanità Animale, Istituto Zooprofilattico Sperimentale Della Sardegna, Sassari, Italy
| | - Marco Di Domenico
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale Abruzzo e Molise, Teramo, Italy
| | - Giovanni Savini
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale Abruzzo e Molise, Teramo, Italy
| | - Alessio Lorusso
- OIE Reference Laboratory for Bluetongue, Istituto Zooprofilattico Sperimentale Abruzzo e Molise, Teramo, Italy
| | - Giantonella Puggioni
- Department of Sanità Animale, Istituto Zooprofilattico Sperimentale Della Sardegna, Sassari, Italy
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14
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Salipante SJ, Jerome KR. Digital PCR—An Emerging Technology with Broad Applications in Microbiology. Clin Chem 2019; 66:117-123. [DOI: 10.1373/clinchem.2019.304048] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/18/2019] [Indexed: 01/10/2023]
Abstract
Abstract
BACKGROUND
The PCR and its variant, quantitative PCR (qPCR), have revolutionized the practice of clinical microbiology. Continued advancements in PCR have led to a new derivative, digital PCR (dPCR), which promises to address certain limitations inherent to qPCR.
CONTENT
Here we highlight the important technical differences between qPCR and dPCR, and the potential advantages and disadvantages of each. We then review specific situations in which dPCR has been implemented in clinical microbiology and the results of such applications. Finally, we attempt to place dPCR in the context of other emerging technologies relevant to the clinical laboratory, including next-generation sequencing.
SUMMARY
dPCR offers certain clear advantages over traditional qPCR, but these are to some degree offset by limitations of the technology, at least as currently practiced. Laboratories considering implementation of dPCR should carefully weigh the potential advantages and disadvantages of this powerful technique for each specific application planned.
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Affiliation(s)
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, WA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
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15
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McMullen A, Martinez-Hernandez F, Martinez-Garcia M. Absolute quantification of infecting viral particles by chip-based digital polymerase chain reaction. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:855-860. [PMID: 31659846 DOI: 10.1111/1758-2229.12804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/25/2019] [Accepted: 10/25/2019] [Indexed: 06/10/2023]
Abstract
In silico and empirical quantification of viruses is paramount for obtaining information on viral populations that have a major impact on biogeochemical cycles. The uncultured Pelagibacter virus vSAG 37-F6 discovered via single-virus genomics is one of the most abundant and cosmopolitan marine viruses; however, little is understood about its temporal variation. Here, we estimated the absolute number of infecting 37-F6 viruses in coastal bacterioplankton from the Mediterranean Sea by using a novel, feasible SYBR Green I chip-based digital PCR (SYBR dPCR) technique, not implemented before for enumerating (uncultured) microbes. Quantitative SYBR dPCR estimated 450-3480 genome copies of virus 37-F6 in cells/mL (i.e. infecting viruses) and a total of ≈10-400 putative infected cells/mL with a potential C release of 0.12-4.9 pg/ml in the analysed samples. Considering that virus 37-F6 is ubiquitous and abundant in all Tara samples, an enormous amount of C could be transformed by this virus through the 'viral shunt'. Thus, this SYBR dPCR technique has enabled the absolute quantification of an ecologically relevant uncultured virus in nature and the estimation of its potential contribution on biogeochemical cycles. Overall, our study also shows that this approach has a broad applicability for quantifying any other target loci in Microbiology and Virology.
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Affiliation(s)
- Africa McMullen
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | | | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
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16
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Clinical correlation of influenza and respiratory syncytial virus load measured by digital PCR. PLoS One 2019; 14:e0220908. [PMID: 31479459 PMCID: PMC6720028 DOI: 10.1371/journal.pone.0220908] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/25/2019] [Indexed: 02/07/2023] Open
Abstract
Acute respiratory tract infections are a major cause of respiratory morbidity and mortality in pediatric patients worldwide. However, accurate viral and immunologic markers to predict clinical outcomes of this patient population are still lacking. Droplet digital PCR assays for influenza and respiratory syncytial virus (RSV) were designed and performed in 64 respiratory samples from 23 patients with influenza virus infection and 73 samples from 19 patients with RSV infection. Samples of patients with hematologic malignancies, solid tumors, or sickle cell disease were included. Clinical information from institutional medical records was reviewed to assess disease severity. Samples from patients with fever or respiratory symptoms had a significantly higher viral loads than those from asymptomatic patients. Samples from patients with influenza virus and RSV infection collected at presentation had significantly higher viral loads than those collected from patients after completing a course of oseltamivir or ribavirin, respectively. RSV loads correlated positively with clinical symptoms in patients ≤5 years of age, whereas influenza viral loads were associated with clinical symptoms, irrespective of age. Patients receiving antivirals for influenza and RSV had a significant reduction in viral loads after completing therapy. Digital PCR offers an effective method to monitor the efficacy of antiviral treatment for respiratory tract infections in immunocompromised hosts.
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17
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Martinez-Hernandez F, Garcia-Heredia I, Lluesma Gomez M, Maestre-Carballa L, Martínez Martínez J, Martinez-Garcia M. Droplet Digital PCR for Estimating Absolute Abundances of Widespread Pelagibacter Viruses. Front Microbiol 2019; 10:1226. [PMID: 31244789 PMCID: PMC6581686 DOI: 10.3389/fmicb.2019.01226] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/16/2019] [Indexed: 12/14/2022] Open
Abstract
Absolute abundances of prokaryotes are typically determined by FISH. Due to the lack of a universal conserved gene among all viruses, metagenomic fragment recruitment is commonly used to estimate the relative viral abundance. However, the paucity of absolute virus abundance data hinders our ability to fully understand how viruses drive global microbial populations. The cosmopolitan marine Pelagibacter ubique is host for the highly widespread HTVC010P pelagiphage isolate and the extremely abundant uncultured virus vSAG 37-F6 recently discovered by single-virus genomics. Here we applied droplet digital PCR (ddPCR) to calculate the absolute abundance of these pelagiphage genotypes in the Mediterranean Sea and the Gulf of Maine. Abundances were between 360 and 8,510 virus mL-1 and 1,270–14,400 virus mL-1 for vSAG 37-F6 and HTVC010P, respectively. Illumina PCR-amplicon sequencing corroborated the absence of ddPCR non-specific amplifications for vSAG 37-F6, but showed an overestimation of 6% for HTVC010P from off-targets, genetically unrelated viruses. Absolute abundances of both pelagiphages, two of the most abundance marine viruses, suggest a large viral pelagiphage diversity in marine environments, and show the efficiency and power of ddPCR to disentangle the structure of marine viral communities. Results also highlight the need for a standardized workflow to obtain accurate quantification that allows cross data comparison.
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Affiliation(s)
| | | | - Monica Lluesma Gomez
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Lucia Maestre-Carballa
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | | | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
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18
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Yuan D, Cui M, Yu S, Wang H, Jing R. Droplet digital PCR for quantification of PML-RARα in acute promyelocytic leukemia: a comprehensive comparison with real-time PCR. Anal Bioanal Chem 2019; 411:895-903. [PMID: 30617397 DOI: 10.1007/s00216-018-1508-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/09/2018] [Accepted: 11/21/2018] [Indexed: 11/26/2022]
Abstract
Real-time quantitative PCR (qPCR) has been widely implemented for molecular testing, but there are still some inherent limitations that hamper its usefulness. Droplet digital PCR (ddPCR), which can provide direct, standards-free quantification, has recently received increasing attention. In our study, a comprehensive comparison of ddPCR with qPCR in relation to the quantification of PML-RARα was performed to evaluate the diagnostic potential of ddPCR. Results showed that ddPCR displayed significant concordance with qPCR in the detection of PML-RARα in clinical samples, but showed advantages over qPCR in terms of precision, limit of detection (LOD), and other basic performance parameters. A study of the feasibility of duplexing also indicated that ddPCR could simultaneously quantify the target PML-RARα and the clinical common reference gene ABL in a reaction, in contrast to qPCR. Moreover, ddPCR was more tolerant than qPCR of inhibition, and was shown to be able to quantify inhibition-prone samples. Another advantage of using ddPCR in clinical applications is that it will yield accurate results for patients with PML-RARα levels that fluctuate around the LOD of qPCR. Therefore, ddPCR is considered to have the potential to become a reliable alternative technique for quantifying PML-RARα. Graphical abstract ᅟ.
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Affiliation(s)
- Dandan Yuan
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No 20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Ming Cui
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No 20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Shuping Yu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No 20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Huimin Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No 20, Xisi Road, Nantong, 226001, Jiangsu, China.
| | - Rongrong Jing
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No 20, Xisi Road, Nantong, 226001, Jiangsu, China.
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19
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Maggi F, Pistello M, Antonelli G. Future management of viral diseases: role of new technologies and new approaches in microbial interactions. Clin Microbiol Infect 2018; 25:136-141. [PMID: 30502490 DOI: 10.1016/j.cmi.2018.11.015] [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] [Received: 08/22/2018] [Revised: 11/03/2018] [Accepted: 11/10/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND New technologies allow rapid detecting and counting of virus genomes in clinical specimens, defining susceptibility to specific antivirals, pinpointing molecular sequences correlated to virulence traits, and identifying viral and host factors driving resolution or chronicity of infections. As a result, during the past three decades the diagnostic virology laboratory has become crucial for patient care and an integral component of the multifarious armamentarium for patient management. This change in paradigm has caused obsolescence of methods once considered the reference standard of infectious disease diagnosis that were used to detect whole or specific components of virions in the specimen. OBJECTIVES This review provides an overview of standard and novel technologies applied to molecular diagnosis of viral infections and illustrates some crucial points for correcting interpretation of the laboratory data. SOURCES Peer-reviewed literature of topics pertinent to this review. CONTENT AND IMPLICATIONS New technologies are reinventing the way virologic diagnoses are made, with a conversion to new, simpler-to-use platforms. Although indicated for the same purpose, not all methods are equal and can yield different results. Further, tests identifying multiple analytes at once can detect microorganisms present or activated as a result of pathologic processes triggered by other pathogens or noninfectious causes. Thus, new directions will have to be taken in the way in which the diagnoses of viral diseases are performed. This represents a breakthrough in the clinical virology laboratory.
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Affiliation(s)
- F Maggi
- Department of Translational Research, Retrovirus Center and Virology Section, University of Pisa, Pisa, Italy; Virology Division, Pisa University Hospital, Pisa, Italy
| | - M Pistello
- Department of Translational Research, Retrovirus Center and Virology Section, University of Pisa, Pisa, Italy; Virology Division, Pisa University Hospital, Pisa, Italy
| | - G Antonelli
- Department of Molecular Medicine, Laboratory of Virology and Pasteur Institute-Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy; Microbiology and Virology Unit, Sapienza University Hospital 'Policlinico Umberto I,' Rome, Italy.
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20
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Bosman KJ, Wensing AMJ, Pijning AE, van Snippenberg WJ, van Ham PM, de Jong DMC, Hoepelman AIM, Nijhuis M. Development of sensitive ddPCR assays to reliably quantify the proviral DNA reservoir in all common circulating HIV subtypes and recombinant forms. J Int AIDS Soc 2018; 21:e25185. [PMID: 30375818 PMCID: PMC6138437 DOI: 10.1002/jia2.25185] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/17/2018] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION The latent reservoir is the main barrier on the road to HIV cure, and clinical approaches towards eradication are often evaluated by their effect on proviral DNA. To ensure inclusiveness and representativeness in HIV cure studies, proviral DNA quantification assays that are able to detect all common circulating HIV clades are urgently needed. Here, three HIV DNA assays targeting three different genomic regions were evaluated for their sensitivity and subtype-tolerance using digital PCR. METHODS A subtype-B-specific assay targeting gag (GAG) and two assays targeting conserved sequences in ltr and pol (LTR and JO) were assessed for their sensitivity and subtype-tolerance in digital PCR (Bio-Rad QX200), using a panel of serially diluted subtype reference plasmids as well as a panel of clinical isolates. Both panels represent subtypes A, B, C, D, F, G and circulating recombinant forms (CRFs) AE and AG, which together are responsible for 94% of HIV infections worldwide. RESULTS HIV subtype was observed to greatly affect HIV DNA quantification results. Robust regression analysis of the serially diluted plasmid panel showed that the GAG assay was only able to linearly quantify subtype B, D and G isolates (4/13 reference plasmids, average R2 = 0.99), whereas LTR and JO were able to quantify all tested isolates (13/13 reference plasmids, respective average R2 = 0.99 and 0.98). In the clinical isolates panel, isolates were considered detectable if all replicates produced a positive result. The GAG assay could detect HIV DNA in four out of five subtype B and one out of two subtype D isolates, whereas the LTR and JO assays detected HIV DNA in all twenty-nine tested isolates. LTR and JO results were found to be equally precise but more precise than GAG. CONCLUSIONS The results demonstrate the need for a careful validation of proviral reservoir quantification assays prior to investigations into non-B subtype reservoirs. The LTR and JO assays can sensitively and reliably quantify HIV DNA in a panel that represents the worldwide most prevalent subtypes and CRFs (A, B, C, D, AE, F, G and AG), justifying their application in future trials aimed at global HIV cure.
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Affiliation(s)
- Kobus J Bosman
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Annemarie MJ Wensing
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Aster E Pijning
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | | | - Petra M van Ham
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Dorien MC de Jong
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Andy IM Hoepelman
- Department of Internal Medicine and Infectious DiseasesUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Monique Nijhuis
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
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21
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Vynck M, Vandesompele J, Thas O. On determining the power of digital PCR experiments. Anal Bioanal Chem 2018; 410:5731-5739. [PMID: 29961092 DOI: 10.1007/s00216-018-1212-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 11/28/2022]
Abstract
The experimental design that will be carried out to evaluate a nucleic acid quantification hypothesis determines the cost and feasibility of digital polymerase chain reaction (digital PCR) studies. Experiment design involves the calculation of the number of technical measurement replicates and the determination of the characteristics of those replicates, and this in accordance with the capabilities of the available digital PCR platform. Available digital PCR power analyses suffer from one or more of the following limitations: narrow scope, unrealistic assumptions, no sufficient detail for replication, lack of source code and user-friendly software. Here, we discuss the nature of six parameters that affect the statistical power, i.e., desired effect size, total number of partitions, fraction of positive partitions, number of replicate measurements, between-replicate variance, and significance level. We also show to what extent these parameters affect power, and argue that careful design of experiments is needed to achieve the desired power. A web tool, dPowerCalcR, that allows interactive calculation of statistical power and optimization of the experimental design is available.
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Affiliation(s)
- Matthijs Vynck
- Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.,Bioinformatics Institute Ghent: from Nucleotides to Networks (BIG N2N), Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.,Biogazelle, Technologiepark 3, 9052, Zwijnaarde, Belgium
| | - Olivier Thas
- Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.,Bioinformatics Institute Ghent: from Nucleotides to Networks (BIG N2N), Ghent University, Coupure Links 653, 9000, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.,National Institute for Applied Statistics Research Australia (NIASRA), School of Mathematics and Applied Statistics, University of Wollongong, Wollongong, NSW, 2522, Australia
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22
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Denis JA, Guillerm E, Coulet F, Larsen AK, Lacorte JM. The Role of BEAMing and Digital PCR for Multiplexed Analysis in Molecular Oncology in the Era of Next-Generation Sequencing. Mol Diagn Ther 2018; 21:587-600. [PMID: 28667577 DOI: 10.1007/s40291-017-0287-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BEAMing polymerase chain reaction (PCR) and digital PCR (dPCR) are used for robust and accurate quantification of nucleic acids. These methods are particularly well suited for the identification of very small fractions (<1%) of variant copies such as the presence of mutant genes in a predominantly wild-type background. BEAMing and dPCR are increasingly used in diverse fields including bacteriology, virology, non-invasive prenatal testing, and oncology, in particular for the molecular analysis of liquid biopsies. In this review, we present the principles of BEAMing and dPCR as well as the trends of future technical development, focusing on the possibility of developing multiplexed mutation analysis. Finally, we will discuss why such techniques will remain useful despite the ever-decreasing costs and increased automatization of next-generation sequencing (NGS), using molecular characterization of cancer cells as an example.
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Affiliation(s)
- Jérôme Alexandre Denis
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France. .,Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine, INSERM, UMRS 938, 75571, Paris Cedex 12, France. .,Department of Endocrine and Oncological Biochemistry, AP-HP, University Hospitals of Pitié-Salpétrière - Charles Foix, 75651, Paris, France.
| | - Erell Guillerm
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,INSERM, UMRS 938 Centre de Recherche Saint-Antoine, "Instability of Microsatellites and Cancers", Team approved by the National League Against Cancer, 75571, Paris Cedex 12, France.,Departement of Genetics, Unit of Molecular Oncogenetics and Angiogenetics, AP-HP, University Hospitals of Pitié-Salpétrière - Charles Foix, 75651, Paris Cedex, France
| | - Florence Coulet
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,INSERM, UMRS 938 Centre de Recherche Saint-Antoine, "Instability of Microsatellites and Cancers", Team approved by the National League Against Cancer, 75571, Paris Cedex 12, France.,Departement of Genetics, Unit of Molecular Oncogenetics and Angiogenetics, AP-HP, University Hospitals of Pitié-Salpétrière - Charles Foix, 75651, Paris Cedex, France
| | - Annette K Larsen
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine, INSERM, UMRS 938, 75571, Paris Cedex 12, France
| | - Jean-Marc Lacorte
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,INSERM, UMR_S 1166, Research Institute of Cardiovascular Disease, Metabolism and Nutrition, 75013, Paris, France.,Department of Endocrine and Oncological Biochemistry, AP-HP, University Hospitals of Pitié-Salpétrière - Charles Foix, 75651, Paris, France
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23
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Kint S, De Spiegelaere W, De Kesel J, Vandekerckhove L, Van Criekinge W. Evaluation of bisulfite kits for DNA methylation profiling in terms of DNA fragmentation and DNA recovery using digital PCR. PLoS One 2018; 13:e0199091. [PMID: 29902267 PMCID: PMC6002050 DOI: 10.1371/journal.pone.0199091] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/31/2018] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is one of the most important epigenetic modifications in the regulation of gene transcription. The current gold standard to study this modification is bisulfite sequencing. Although multiple commercial bisulfite treatment kits provide good conversion efficiencies, DNA loss and especially DNA fragmentation remain troublesome. This hampers DNA methylation profiling of long DNA sequences. Here, we explored the performance of twelve commercial bisulfite kits by an in-depth comparison of DNA fragmentation using gel electrophoresis, qPCR and digital PCR, DNA recovery by spectroscopic measurements and digital PCR and conversion efficiency by next generation sequencing. The results show a clear performance difference between the bisulfite kits, and depending on the specific goal of the study, the most appropriate kit might differ. Moreover, we demonstrated that digital PCR is a valuable method to monitor both DNA fragmentation as well as DNA recovery after bisulfite treatment.
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Affiliation(s)
- Sam Kint
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
- * E-mail:
| | - Ward De Spiegelaere
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Jonas De Kesel
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Wim Van Criekinge
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Vynck M, Thas O. Reducing Bias in Digital PCR Quantification Experiments: The Importance of Appropriately Modeling Volume Variability. Anal Chem 2018; 90:6540-6547. [DOI: 10.1021/acs.analchem.8b00115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthijs Vynck
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent 9000, Belgium
| | - Olivier Thas
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent 9000, Belgium
- National Institute for Applied Statistics Research Australia (NIASRA), University of Wollongong, Wollongong, NSW 2522, Australia
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25
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Comparison of reverse-transcriptase qPCR and droplet digital PCR for the quantification of dengue virus nucleic acid. Biologicals 2018; 52:49-54. [DOI: 10.1016/j.biologicals.2018.01.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 10/13/2017] [Accepted: 01/19/2018] [Indexed: 11/21/2022] Open
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26
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Rutsaert S, Bosman K, Trypsteen W, Nijhuis M, Vandekerckhove L. Digital PCR as a tool to measure HIV persistence. Retrovirology 2018; 15:16. [PMID: 29378600 PMCID: PMC5789538 DOI: 10.1186/s12977-018-0399-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/19/2018] [Indexed: 11/12/2022] Open
Abstract
Although antiretroviral therapy is able to suppress HIV replication in infected patients, the virus persists and rebounds when treatment is stopped. In order to find a cure that can eradicate the latent reservoir, one must be able to quantify the persisting virus. Traditionally, HIV persistence studies have used real-time PCR (qPCR) to measure the viral reservoir represented by HIV DNA and RNA. Most recently, digital PCR is gaining popularity as a novel approach to nucleic acid quantification as it allows for absolute target quantification. Various commercial digital PCR platforms are nowadays available that implement the principle of digital PCR, of which Bio-Rad’s QX200 ddPCR is currently the most used platform in HIV research. Quantification of HIV by digital PCR is proving to be a valuable improvement over qPCR as it is argued to have a higher robustness to mismatches between the primers-probe set and heterogeneous HIV, and forfeits the need for a standard curve, both of which are known to complicate reliable quantification. However, currently available digital PCR platforms occasionally struggle with unexplained false-positive partitions, and reliable segregation between positive and negative droplets remains disputed. Future developments and advancements of the digital PCR technology are promising to aid in the accurate quantification and characterization of the persistent HIV reservoir.
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Affiliation(s)
- Sofie Rutsaert
- HIV Cure Research Center, Department of Internal Medicine, Ghent University, Ghent, Belgium
| | - Kobus Bosman
- Department of Medical Microbiology, Virology, UMC Utrecht, Utrecht, The Netherlands
| | - Wim Trypsteen
- HIV Cure Research Center, Department of Internal Medicine, Ghent University, Ghent, Belgium
| | - Monique Nijhuis
- Department of Medical Microbiology, Virology, UMC Utrecht, Utrecht, The Netherlands
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine, Ghent University, Ghent, Belgium.
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27
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Vynck M, Vandesompele J, Thas O. Quality control of digital PCR assays and platforms. Anal Bioanal Chem 2017; 409:5919-5931. [PMID: 28799053 DOI: 10.1007/s00216-017-0538-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/11/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
Digital polymerase chain reaction (digital PCR, dPCR) is a direct nucleic acid quantification method, thus requiring no standard curves unlike quantitative real-time PCR (qPCR). Nevertheless, evaluation of the linear dynamic range, accuracy, and precision of an assay or platform is recommended, as there are several potential causes of important non-linearity, bias, and imprecision. Ignoring these quality issues may lead to erroneous quantification. This necessitates an approach akin to the construction of standard curves. We study the pitfalls associated with the evaluation of such an experiment, and provide guidelines for the assessment of linearity, accuracy, and precision in dPCR experiments. We present simulation results and a case study supporting the importance of a thorough evaluation. Further, typically presented plots and statistics may not reveal problems with linearity, accuracy, or precision. We find that a robust weighted least-squares approach is highly advisable, yet may also suffer from an inflated false-positive rate. The proposed assessments are also applicable to other analyses, such as the comparison of results obtained from qPCR and dPCR. A web tool for quality evaluation, dPCalibRate, is available.
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Affiliation(s)
- Matthijs Vynck
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.,Bioinformatics Institute Ghent: from Nucleotides to Networks (BIG N2N), Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.,Biogazelle, Technologiepark 3, 9052, Zwijnaarde, Belgium
| | - Olivier Thas
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.,Bioinformatics Institute Ghent: from Nucleotides to Networks (BIG N2N), Ghent University, Coupure Links 653, 9000, Ghent, Belgium.,National Institute for Applied Statistics Research Australia (NIASRA), School of Mathematics and Applied Statistics, University of Wollongong, NSW, 2522, Australia
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Abstract
Digital PCR (dPCR) is an important new tool for use in the clinical microbiology laboratory. Its advantages over quantitative PCR (qPCR), including absolute quantification without a standard curve, improved precision, improved accuracy in the presence of inhibitors, and more accurate quantitation when amplification efficiency is low, make dPCR the assay of choice for several specimen testing applications. This minireview will discuss the advantages and disadvantages of dPCR compared to qPCR, its applications in clinical microbiology, and considerations for implementation of the method in a clinical laboratory.
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29
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Superiority of Digital Reverse Transcription-PCR (RT-PCR) over Real-Time RT-PCR for Quantitation of Highly Divergent Human Rhinoviruses. J Clin Microbiol 2016; 55:442-449. [PMID: 27881615 DOI: 10.1128/jcm.01970-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/16/2016] [Indexed: 01/31/2023] Open
Abstract
Human rhinoviruses (HRV) comprise 3 species representing more than 150 genotypes. As an important human respiratory pathogen, molecular detection is an indispensable tool for diagnosis and surveillance. However, the sequence diversity of HRV genotypes poses challenges for developing robust molecular methods that detect all genotypes with equal efficiencies. This study compares the accuracies of reverse transcription-quantitative PCR (RT-qPCR) and reverse transcription-digital PCR (RT-dPCR) for quantifying HRV RNA using genotype-specific primers and probes and a consensus primer/probe set targeting the 5' noncoding region of HRV. When using consensus primers and probes for the quantification of HRV, RT-dPCR outperformed RT-qPCR by consistently and accurately quantifying HRV RNAs across more genotype groups, despite the presence of up to 2 target-sequence mismatches within the primer or probe binding region. Because it does not rely on amplification efficiency, which can be affected by sequence mismatches in primer/probe binding regions, RT-dPCR may be the optimal molecular method for future HRV quantification studies and for quantitating other viruses with high sequence diversity.
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Stahl T, Rothe C, Böhme MU, Kohl A, Kröger N, Fehse B. Digital PCR Panel for Sensitive Hematopoietic Chimerism Quantification after Allogeneic Stem Cell Transplantation. Int J Mol Sci 2016; 17:ijms17091515. [PMID: 27618030 PMCID: PMC5037792 DOI: 10.3390/ijms17091515] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 08/10/2016] [Accepted: 08/31/2016] [Indexed: 12/05/2022] Open
Abstract
Accurate and sensitive determination of hematopoietic chimerism is a crucial diagnostic measure after allogeneic stem cell transplantation to monitor engraftment and potentially residual disease. Short tandem repeat (STR) amplification, the current “gold standard” for chimerism assessment facilitates reliable accuracy, but is hampered by its limited sensitivity (≥1%). Digital PCR (dPCR) has been shown to combine exact quantification and high reproducibility over a very wide measurement range with excellent sensitivity (routinely ≤0.1%) and thus represents a promising alternative to STR analysis. We here aimed at developing a whole panel of digital-PCR based assays for routine diagnostic. To this end, we tested suitability of 52 deletion/insertion polymorphisms (DIPs) for duplex analysis in combination with either a reference gene or a Y-chromosome specific PCR. Twenty-nine DIPs with high power of discrimination and good performance were identified, optimized and technically validated. We tested the newly established assays on retrospective patient samples that were in parallel also measured by STR amplification and found excellent correlation. Finally, a screening plate for initial genotyping with DIP-specific duplex dPCR assays was designed for convenient assay selection. In conclusion, we have established a comprehensive dPCR system for precise and high-sensitivity measurement of hematopoietic chimerism, which should be highly useful for clinical routine diagnostics.
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Affiliation(s)
- Tanja Stahl
- Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
| | | | | | - Aloisa Kohl
- Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
| | - Nicolaus Kröger
- Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
| | - Boris Fehse
- Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
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