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van Leuven N, Zinn MK, Lucassen R, Lipski A, Flemming HC, Bockmühl D. High resolution ITS amplicon melting analysis as a tool to analyse microbial communities of household biofilms in ex-situ models. J Microbiol Methods 2023; 212:106806. [PMID: 37567416 DOI: 10.1016/j.mimet.2023.106806] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/08/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Biofilms are the most common growth types of microorganisms. These complex communities usually consist of different species and are embedded in an extracellular matrix containing polymers, proteins and DNA. This matrix offers protection against different (a)biotic environmental factors and generally increases resistances. Higher resistances against antibiotics are one of the main reasons why biofilms are often associated with healthcare settings. Nevertheless, they are also found in domestic settings, mostly in humid places with abundant nutrients like dishwashers or washing machines. Biofilms in these areas show individual compositions and are influenced for example by temperature, frequency of use or the age of the device. In this study, we introduce a model for the ex-situ cultivation of domestic biofilms from household appliances. Furthermore, we tested the ability of high resolution melting analysis (HRMA) as a tool for analysing these biofilms. Our goal was to maintain a high amount of complexity in the ex-situ biofilms that is characterized by the melting behavior of the contained DNA. Dishwasher and washing machine biofilms were sampled in private households and cultivated for 10 d. After DNA extraction, 16S rDNA was sequenced and melting behavior of the bacterial Internal Transcribed Spacer (ITS) region was analysed. Additionally, testing for independence of continuous new sampling, storage of cultivated biofilms in glycerol stocks and following recultivation of them was done up to three times. Our results show that a high level of complexity could be maintained in the ex-situ biofilms after 10 d of cultivation, although in general the bacterial diversity slightly decreased compared to the original biofilm in most cases. Recultivation of a similar biofilm from glycerol stocks was possible as well with some impact by various factors. Differences in the bacterial composition of biofilms could clearly made visible by HRMA although it was not possible to match peaks to a specific phylogenetic group. Still, HRMA proved to be a less costly and time consuming alternative to sequencing for the characterization of biofilms.
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Affiliation(s)
- Nicole van Leuven
- Rhine-Waal University of Applied Sciences, Faculty of Life Sciences, Kleve, Germany; University of Bonn, Food Microbiology and Hygiene, Bonn, Germany
| | - Marc-Kevin Zinn
- Rhine-Waal University of Applied Sciences, Faculty of Life Sciences, Kleve, Germany; University of Duisburg-Essen, Biofilm Centre, Essen, Germany
| | - Ralf Lucassen
- Rhine-Waal University of Applied Sciences, Faculty of Life Sciences, Kleve, Germany
| | - André Lipski
- University of Bonn, Food Microbiology and Hygiene, Bonn, Germany
| | | | - Dirk Bockmühl
- Rhine-Waal University of Applied Sciences, Faculty of Life Sciences, Kleve, Germany.
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Alirezaei M, Mosawi SH, Afgar A, Zarean M, Movahhed TK, Abbasi V, Fotouhi-Ardakani R. Discrimination of human papillomavirus genotypes using innovative technique nested-high resolution melting. Sci Rep 2022; 12:13943. [PMID: 35977949 PMCID: PMC9382607 DOI: 10.1038/s41598-022-14730-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 06/13/2022] [Indexed: 11/09/2022] Open
Abstract
The prompt detection of human papillomavirus and discrimination of its genotypes by combining conventional methods in new molecular laboratories is essential to achieve the global call of eliminating cervical cancer. After predicting the melting temperature of an approximately 221 bp region of the L1 gene from different HPV genotypes by bioinformatics software, an innovative technique based on the nested- high resolution melting was designed with three approaches and using conventional PCR, qPCR, and diagnostic standards. HPV-positive samples identified by microarray along with diagnostic standards were evaluated by qPCR-HRM and discordant results were subjected to sequencing and analyzed in silico using reference types. In addition to screening for human papillomavirus, nested-qPCR-HRM is one of the modified HRM techniques which can discriminate some genotypes, including 6, 16, 18, 52, 59, 68 and 89. Despite the differences in diagnostic capabilities among HRM, microarray and sequencing, a number of similarities between HRM, and sequencing were diagnostically identified as the gold standard method. However, the bioinformatics analysis and melting temperature studies of the selected region in different HPV genotypes showed that it could be predicted. With numerous HPV genotypes and significant genetic diversity among them, determining the virus genotype is important. Therefore, our goal in this design was to use the specific molecular techniques with several specific primers to increase sensitivity and specificity for discriminating a wide range of HPV genotypes. This approach led to new findings to evaluate the ability of different approaches and procedures in accordance with bioinformatics.
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Affiliation(s)
- Melika Alirezaei
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran
| | | | - Ali Afgar
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehdi Zarean
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tahereh Komeili Movahhed
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran
| | - Vajiheh Abbasi
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran
| | - Reza Fotouhi-Ardakani
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran. .,Department of Medical Biotechnology, School of Medicine, Qom University of Medical Sciences, Qom, Iran.
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3
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Vaupel A, Hommel B, Beule L. High-resolution melting (HRM) curve analysis as a potential tool for the identification of earthworm species and haplotypes. PeerJ 2022; 10:e13661. [PMID: 35782097 PMCID: PMC9248783 DOI: 10.7717/peerj.13661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/10/2022] [Indexed: 01/17/2023] Open
Abstract
Background Earthworm communities are an important component of soil biodiversity and contribute to a number of ecosystem functions such as soil-nutrient cycling. Taxonomic identification is an essential requirement to assess earthworm biodiversity and functionality. Although morphological identification of species is labour-intensive, it is the most commonly used method due to a lack of cost-efficient alternatives. Molecular approaches to identify earthworms at species and haplotype level such as DNA barcoding are gaining popularity in science but are rarely applied in practice. In contrast to barcoding, the differentiation of PCR products based on their thermal denaturation properties using high-resolution melting (HRM) curve analysis is a fast and cost-efficient molecular closed-tube, post-PCR tool that allows identification of taxa. Methods We developed a HRM curve assay to identify eight earthworm species common to agricultural soils in Central Europe (Allolobophora chlorotica, Aporrectodea caliginosa, Apo. limicola, Apo. longa, Apo. rosea, Lumbricus castaneus, L. rubellus, and L. terrestris). For this, a new primer pair targeting a 158-bp long subregion of the cytochrome c oxidase I (COI) gene was designed. Our HRM assay was further tested for the differentiation of COI haplotypes using 28 individuals of the earthworm species Allo. chlorotica. Furthermore, we developed a novel extraction method for DNA from earthworm tissue that is fast and requires minimal consumables and laboratory equipment. Results The developed HRM curve assay allowed identifying all eight earthworm species. Performing the assay on 28 individuals of the earthworm species Allo. chlorotica enabled the distinction among different COI haplotypes. Furthermore, we successfully developed a rapid, robust, scalable, and inexpensive method for the extraction of earthworm DNA from fresh or frozen tissue. Conclusions HRM curve analysis of COI genes has the potential to identify earthworm species and haplotypes and could complement morphological identification, especially for juvenile or damaged individuals. Our rapid and inexpensive DNA extraction method from earthworm tissue helps to reduce the costs of molecular analyses and thereby promote their application in practice.
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Affiliation(s)
- Anna Vaupel
- Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany
| | - Bernd Hommel
- Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany
| | - Lukas Beule
- Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany
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4
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Alkafajy A, Al-Karagoly H, Nikbakht Brujeni G. Comparison of cattle BoLA-DRB3 typing by PCR-RFLP, direct sequencing, and high-resolution DNA melting curve analysis. VETERINARY RESEARCH FORUM : AN INTERNATIONAL QUARTERLY JOURNAL 2020; 11:21-26. [PMID: 32537103 PMCID: PMC7282214 DOI: 10.30466/vrf.2018.90444.2189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/03/2018] [Indexed: 11/01/2022]
Abstract
Major histocompatibility complex (MHC) represents an important genetic marker for manipulation to improve the health and productivity of cattle. It is closely associated with numerous disease susceptibilities and immune responses. Bovine MHC, also called bovine leukocyte antigen (BoLA), is considered as a suitable marker for genetic diversity studies. In cattle, most of the polymorphisms are located in exon 2 of BoLA-DRB3, which encodes the peptide-binding cleft. In this study, the polymorphism of the BoLA-DRB3.2 gene in Holstein's calves was studied using high resolution melting curve analysis (HRM). Observed HRM results were compared to PCR-RFLP and direct sequencing techniques. Eight different HRM and seven different RFLP profiles were identified among the population studied. By comparing to sequencing data, HRM could completely discriminate all genotypes (eight profiles), while the RFLP failed to distinguish between the genotypes *1101/*1001 and *1104/*1501. According to the results, the HRM analysis method gave more accurate results than RFLP by differentiating between the BoLA-DRB3.2 genotypes. Due to the Co-dominant nature of the MHC alleles, HRM technique could be used for investigating the polymorphisms of genotypes and their associations with immune responses.
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Affiliation(s)
- Ala Alkafajy
- PhD Candidate, Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Hassan Al-Karagoly
- PhD Candidate, Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Gholamreza Nikbakht Brujeni
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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Lope P, Maribel H, Egma M, Henri B, Carlos P. Characterization of influenza A(H1N1)pdm09 isolates of Peru using HRM, a post PCR molecular biology method. Bioinformation 2019; 15:640-645. [PMID: 31787813 PMCID: PMC6859703 DOI: 10.6026/97320630015640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 10/06/2019] [Accepted: 10/07/2019] [Indexed: 11/23/2022] Open
Abstract
Influenza caused by A(H1N1)pdm09 is a public health issue with severe conditions in vulnerable populations leading to death. Therefore, it is of interest to characterize and monitor influenza A(H1N1)pdm09 genotypes using High Resolution Melting (HRM), a post PCR molecular biology method. We used HRM analysis (using RotorGene Q thermocycler) to characterize A(H1N1)pdm09 genotypes from several places of Peru. RNA was purified from nasal and pharyngeal swab samples referred to LRNVR-INS, synthesized cDNA, and then the hemagglutinin gene and matrix fragment were amplified. Thus, 287 samples positive for influenza A(H1N1)pdm09 were identified across Peru where places like Lima, Piura, and Arequipa documented highest number of cases. The HRM data was analyzed and results showed different profiles which were further grouped into four genotypes for the HA (A, B, C, D) and 3 for the M (a, b, c) genes. We also report ten genotypes (I-X) of virus using combined HA (hemagglutinin) and M gene profiles representing a national geography. The prevalent genotypes are I and II with a frequency of 35.89% (103) and 29.27% (84), respectively linking with severe acute respiratory infection.
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Affiliation(s)
- Priscila Lope
- Laboratorio de Referencia Nacional de Virus Respiratorio, Centro Nacional de Salud Publica, Instituto Nacional de Salud, Lima, Peru.,Laboratorio de virologia. Universidad Nacional Mayor de San Marcos. Lima. Peru
| | - Huaringa Maribel
- Laboratorio de Referencia Nacional de Virus Respiratorio, Centro Nacional de Salud Publica, Instituto Nacional de Salud, Lima, Peru
| | - Mayta Egma
- Laboratorio de virologia. Universidad Nacional Mayor de San Marcos. Lima. Peru
| | - Bailon Henri
- Laboratorio de Referencia Nacional de Biotecnologia y Biologia Molecular. Centro Nacional de Salud Publica. Instituto Nacional de Salud. Lima. Peru
| | - Padilla Carlos
- Laboratorio de Referencia Nacional de Biotecnologia y Biologia Molecular. Centro Nacional de Salud Publica. Instituto Nacional de Salud. Lima. Peru
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6
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Li YH, Lai CY, Su MC, Cheng JC, Chang YS. Antiviral activity of Portulaca oleracea L. against influenza A viruses. JOURNAL OF ETHNOPHARMACOLOGY 2019; 241:112013. [PMID: 31170517 DOI: 10.1016/j.jep.2019.112013] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 05/25/2019] [Accepted: 06/02/2019] [Indexed: 05/16/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Portulaca oleracea L. is used not only as an edible potherb but also as a traditional remedy to assuage the symptoms of various diseases. The water extract of P. oleracea (WEPO) has been found to effectively alleviate the signs and symptoms of pandemic influenza A virus (IAV) infection. However, the anti-IAV activity of WEPO is still unclear. AIM OF STUDY In this study, we aimed to elucidate the anti-IAV activity of WEPO and investigate the potential mechanisms underlying the anti-H1N1 activity. MATERIALS AND METHODS The cytotoxicity of WEPO and other Chinese herbs was measured using the cell viability test. The anti-IAV activity of WEPO was determined using the plaque reduction assay, real-time reverse transcription-polymerase chain reaction, and immunofluorescence assay. The virucidal activity of WEPO was determined by labeling the virus and using the time-dependent virucidal activity assay. RESULTS The half-maximal effective concentration of WEPO for A/WSN/1933 (H1N1) was very low, with a high selectivity index. The production of circulating H1N1 and H3N2 was suppressed by WEPO. Additionally, the antiviral activity of WEPO was observed in the early stage of IAV infection. Furthermore, WEPO inhibited the binding of virus to cells and exhibited good virucidal activity, significantly decreasing the viral load within 10 min to prevent viral infection. CONCLUSIONS We demonstrate the anti-IAV activity of WEPO and strongly recommend the use of WEPO, as an herbal regimen, to prevent and treat H1N1 infection at an early stage.
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Affiliation(s)
- Yao-Hsuan Li
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, China Medical University, Taichung, Taiwan.
| | - Chun-Yi Lai
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan.
| | - Mei-Chi Su
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan; Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.
| | - Ju-Chien Cheng
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan.
| | - Yuan-Shiun Chang
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, China Medical University, Taichung, Taiwan.
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7
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Zhang Y, Cui Y, An R, Liang X, Li Q, Wang H, Wang H, Fan Y, Dong P, Li J, Cheng K, Wang W, Wang S, Wang G, Xue C, Komiyama M. Topologically Constrained Formation of Stable Z-DNA from Normal Sequence under Physiological Conditions. J Am Chem Soc 2019; 141:7758-7764. [PMID: 30844265 DOI: 10.1021/jacs.8b13855] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Z-DNA, a left-handed duplex, has been shown to form in vivo and regulate expression of the corresponding gene. However, its biological roles have not been satisfactorily understood, mainly because Z-DNA is easily converted to the thermodynamically favorable B-DNA. Here we present a new idea to form stable Z-DNA under normal physiological conditions and achieve detailed analysis on its fundamental features. Simply by mixing two complementary minicircles of single-stranded DNA with no chemical modification, the hybridization spontaneously induces topological constraint which twines one-half of the double-stranded DNA into stable Z-DNA. The formation of Z-conformation with high stability has been proved by using circular dichroism spectroscopy, Z-DNA-specific antibody binding assay, nuclease digestion, etc. Even at a concentration of MgCl2 as low as 0.5 mM, Z-DNA was successfully obtained, avoiding the use of high salt conditions, limited sequences, ancillary additives, or chemical modifications, criteria which have hampered Z-DNA research. The resultant Z-DNA has the potential to be used as a canonical standard sample in Z-DNA research. By using this approach, further developments of Z-DNA science and its applications become highly promising.
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Affiliation(s)
- Yaping Zhang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Yixiao Cui
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Ran An
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Xingguo Liang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , No. 1 Wenhai Road , Qingdao , People's Republic of China
| | - Qi Li
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Haiting Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Hao Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Yiqiao Fan
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Ping Dong
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Jing Li
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Kai Cheng
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Weinan Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Sai Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Guoqing Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , No. 1 Wenhai Road , Qingdao , People's Republic of China
| | - Changhu Xue
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , No. 1 Wenhai Road , Qingdao , People's Republic of China
| | - Makoto Komiyama
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
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8
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Pallandre L, Lesne M, de Boisséson C, Charrier A, Daniel P, Tragnan A, Debeuf B, Chesneau V, Bigarré L. Genetic identification of two Acipenser iridovirus-European variants using high-resolution melting analysis. J Virol Methods 2018; 265:105-112. [PMID: 30586558 DOI: 10.1016/j.jviromet.2018.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/23/2018] [Accepted: 12/15/2018] [Indexed: 11/19/2022]
Abstract
Acipenser iridovirus-European (AcIV-E) is an important pathogen of sturgeons. Two variants differing by single-nucleotide polymorphisms (SNP) in the Major Capsid Protein gene have been described, but without any indication as to their prevalence in farms. To facilitate epidemiological studies, we developed a high-resolution melting (HRM) assay to distinguish between two alleles (var1 and var2) differing by five point substitutions. The HRM assay detected as little as 100 copies of plasmids harboring cloned sequences of var1 and var2, which have melting temperatures (Tm) differing by only 1 °C. The assay was specific of AcIV-E as demonstrated by the absence of signal when testing a related, yet distinct, virus as well as DNA from an AcIV-E-negative sturgeon sample. Experiments with mixtures of two distinct plasmids revealed abnormal melting curve patterns, which showed dips just before the main melting peaks. These dips in the curves were interpreted as the dissociation of heteroduplexes fortuitously created during the PCR step. Screening AciV-E-positive field samples of Russian sturgeons from three farms revealed the presence of var2, based on the Tm. However, for a few samples, the melting curves showed patterns typical of var2 as the dominant viral genome, mixed with another minor variant which proved to be var1. In conclusion, HRM is a simple method to screen for AcIV-E var1 and var2 and can be used on a large scale in Europe to trace these two variants which likely represent two genetic lineages.
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Affiliation(s)
- Laurane Pallandre
- Laboratoire de Ploufragan-Plouzané, ANSES, Technopole Brest Iroise, 29280 Plouzané, France
| | - Mélanie Lesne
- Laboratoires des Pyrénées et des Landes, 40004, Mont-de-Marsan, France
| | - Claire de Boisséson
- Laboratoire de Ploufragan-Plouzané, ANSES, rue des fusillés, 22440, Ploufragan, France
| | - Amélie Charrier
- Laboratoires des Pyrénées et des Landes, 40004, Mont-de-Marsan, France
| | - Patrick Daniel
- Laboratoires des Pyrénées et des Landes, 40004, Mont-de-Marsan, France
| | - Arthur Tragnan
- Groupement de Défense Sanitaire Aquacole Aquitain, 40004, Mont-de-Marsan, France
| | | | | | - Laurent Bigarré
- Laboratoire de Ploufragan-Plouzané, ANSES, Technopole Brest Iroise, 29280 Plouzané, France.
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Worasilchai N, Permpalung N, Chindamporn A. High-resolution melting analysis: A novel approach for clade differentiation in Pythium insidiosum and pythiosis. Med Mycol 2018; 56:868-876. [PMID: 29228389 DOI: 10.1093/mmy/myx123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/12/2017] [Indexed: 01/02/2023] Open
Abstract
Pythium insidiosum causes life-threatening human pythiosis. Based on phylogenetic analysis using internal transcribed spacer (ITS) region, mitochondrial cytochrome C oxidase II (COX2) gene, intergenic spacer (IGS) region and exo-1,3-β-glucanase gene (exo1), P. insidiosum is classified into clade ATH, BTH, and CTH related to geographic distribution. At present, polymerase chain reaction in any of these specific regions with DNA sequencing is the only technique to provide clade diagnosis. In this study, P. insidiosum-specific primers targeting COX2 gene were designed and used in real-time quantitative polymerase chain reaction (qPCR) with subsequent high-resolution melting (HRM) to provide rapid identification as well as clade classification for P. insidiosum. Based on the qPCR-HRM method, 15 P. insidiosum isolates could be differentiated from 28 related organisms with 100% specificity and 1 pg limit of detection. This technique was, in addition, directly tested on clinical samples from proved human pythiosis cases: nine corneal scrapes and six arterial clots. The qPCR-HRM results of all nine corneal samples were a 100% match with the results from the conventional PCR at clade level. However, the qPCR-HRM results of arterial clot samples were only matched with the nucleotide sequencing results from the conventional PCR at species level. In conclusion, the qPCR-HRM is a simple one closed tube, inexpensive and user-friendly method to identify P. insidiosum into clade level.
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Affiliation(s)
- Navaporn Worasilchai
- Interdisciplinary Program, Medical Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Nitipong Permpalung
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina, USA
| | - Ariya Chindamporn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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10
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Hashemi S, Mahzounieh M, Sheikhi N, Ebrahimi A. Application of high-resolution melting-curve analysis on pvpA gene for detection and classification of Mycoplasma gallisepticum strains. Microb Pathog 2018; 124:365-371. [PMID: 29959042 DOI: 10.1016/j.micpath.2018.06.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 11/25/2022]
Abstract
Mycoplasma gallisepticum (MG) is an avian species pathogen which causes heavy economic losses in the poultry industry. The purpose of this study was to determine genomic diversity of 14 MG field strains from chicken, Chuker partridge and peacock collected during 2009-2012 in Iran by polymerase chain reaction and partial sequencing of the pvpA gene. A High-Resolution Melting (HRM) technique was also developed and applied to differentiate between field and vaccine strains. Sequencing of the pvpA gene revealed a 51 nucleotide deletion, within DR-1 and DR-2, among MG strains from chicken and partridge whilst 63 nucleotides were deleted in MG strain from peacock. One nucleotide substitution was also observed among chicken MG strains. Phylogenetic analysis of the sequences clustered all of the Iranian MG strains into two clades or phylogeny groups; the strains from chicken and partridge in one group (group 1) and the strain from peacock into another group (group 4). HRM analysis has also produced comparable outcome to those of sequencing; four distinct melting curves which correspond to the three MG strains from chicken, Chukar partridge and peacock and ts-11 vaccine strain. Overall, findings of this study point towards a single source of infection for the chicken and partridge MG strains and likelihood of the strains being native and endemic in Iran. Peacock considered as an exotic species in Iran, hence the genetic distance for the pvpA gene. MG can be transmitted easily among different avian species and this distinct peacock strain may pose a threat to poultry industry. Our findings also show that molecular variation among pvpA gene of MG strains could be revealed using the relatively rapid and affordable HRM technique.
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Affiliation(s)
- Shabnam Hashemi
- Research Institute for Zoonotic Diseases and Department of Pathobiology, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran.
| | - Mohammadreza Mahzounieh
- Research Institute for Zoonotic Diseases and Department of Pathobiology, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
| | - Nariman Sheikhi
- Department of Clinical Sciences, Faculty of Specialized Veterinary Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Azizollah Ebrahimi
- Research Institute for Zoonotic Diseases and Department of Pathobiology, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
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11
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Li PH, Zheng PP, Zhang TF, Wen GY, Shao HB, Luo QP. Fowl adenovirus serotype 4: Epidemiology, pathogenesis, diagnostic detection, and vaccine strategies. Poult Sci 2018; 96:2630-2640. [PMID: 28498980 DOI: 10.3382/ps/pex087] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/20/2017] [Indexed: 12/13/2022] Open
Abstract
Fowl adenovirus (FAdV) serotype-4 is highly pathogenic for chickens, especially for broilers aged 3 to 5 wk, and it has emerged as one of the foremost causes of economic losses to the poultry industry in the last 30 years. The liver is a major target organ of FAdV-4 infections, and virus-infected chickens usually show symptoms of hydropericardium syndrome. The virus is very contagious, and it is spread both vertically and horizontally. It can be isolated from infected liver homogenates and detected by several laboratory diagnostic methods (including an agar gel immunodiffusion test, indirect immunofluorescence assays, counterimmunoelectrophoresis, enzyme-linked immunosorbent assays, restriction endonuclease analyses, polymerase chain reaction (PCR), real-time PCR, and high-resolution melting-curve analyses). Although inactivated vaccines have been deployed widely to control the disease, attenuated live vaccines and subunit vaccines also have been developed, and they are more attractive vaccine candidates. This article provides a comprehensive review of FAdV-4, including its epidemiology, pathogenesis, diagnostic detection, and vaccine strategies.
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Affiliation(s)
- P H Li
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special 1, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China.,Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, China
| | - P P Zheng
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special 1, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China.,Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special 1, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China
| | - T F Zhang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special 1, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China.,Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special 1, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China
| | - G Y Wen
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special 1, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China.,Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special 1, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China
| | - H B Shao
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special 1, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China.,Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special 1, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China
| | - Q P Luo
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special 1, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China.,Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Special 1, Nanhuyaoyuan, Hongshan District, Wuhan, 430064, China
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12
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Development and Validation of a High-Resolution Melting Assay To Detect Azole Resistance in Aspergillus fumigatus. Antimicrob Agents Chemother 2017; 61:AAC.01083-17. [PMID: 28893791 DOI: 10.1128/aac.01083-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/03/2017] [Indexed: 01/04/2023] Open
Abstract
The global emergence of azole-resistant Aspergillus fumigatus strains is a growing public health concern. Different patterns of azole resistance are linked to mutations in cyp51A Therefore, accurate characterization of the mechanisms underlying azole resistance is critical to guide selection of the most appropriate antifungal agent for patients with aspergillosis. This study describes a new sequencing-free molecular screening tool for early detection of the most frequent mutations known to be associated with azole resistance in A. fumigatus PCRs targeting cyp51A mutations at positions G54, Y121, G448, and M220 and targeting different tandem repeats (TRs) in the promoter region were designed. All PCRs were performed simultaneously, using the same cycling conditions. Amplicons were then distinguished using a high-resolution melting assay. For standardization, 30 well-characterized azole-resistant A. fumigatus strains were used, yielding melting curve clusters for different resistance mechanisms for each target and allowing detection of the most frequent azole resistance mutations, i.e., G54E, G54V, G54R, G54W, Y121F, M220V, M220I, M220T, M220K, and G448S, and the tandem repeats TR34, TR46, and TR53 Validation of the method was performed using a blind panel of 80 A. fumigatus azole-susceptible or azole-resistant strains. All strains included in the blind panel were properly classified as susceptible or resistant with the developed method. The implementation of this screening method can reduce the time needed for the detection of azole-resistant A. fumigatus isolates and therefore facilitate selection of the best antifungal therapy in patients with aspergillosis.
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13
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Bowman S, McNevin D, Venables SJ, Roffey P, Richardson A, Gahan ME. Species identification using high resolution melting (HRM) analysis with random forest classification. AUST J FORENSIC SCI 2017. [DOI: 10.1080/00450618.2017.1315835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Sorelle Bowman
- National Centre for Forensic Studies, University of Canberra, Bruce, Australia
| | - Dennis McNevin
- National Centre for Forensic Studies, University of Canberra, Bruce, Australia
| | | | - Paul Roffey
- Forensics, Specialist Operations, Australian Federal Police, Canberra, Australia
| | - Alice Richardson
- National Centre for Epidemiology & Population Health, Australian National University, Canberra, Australia
| | - Michelle E. Gahan
- National Centre for Forensic Studies, University of Canberra, Bruce, Australia
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14
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Ramezanzadeh M, Salehi M, Salehi R. Assessment of high resolution melt analysis feasibility for evaluation of beta-globin gene mutations as a reproducible, cost-efficient and fast alternative to the present conventional method. Adv Biomed Res 2016; 5:71. [PMID: 27169102 PMCID: PMC4854030 DOI: 10.4103/2277-9175.180640] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 09/14/2015] [Indexed: 11/17/2022] Open
Abstract
Background: Beta-thalassemia is the most prevalent monogenic disease throughout the world. It was the first genetic disorder nominated for nation-wide prevention programs involving population screening for heterozygotes and prenatal diagnosis (PND) in Iran. Due to the high prevalence of beta-thalassemia, the shift from conventional mutation detection methods to more recently developed techniques based on novel innovative technologies are essential. We aimed to develop a real-time polymerase chain reaction (PCR) based protocol using high resolution melting (HRM) analysis for diagnosis of common beta-thalassemia mutations. Materials and Methods: Forty DNA samples extracted from peripheral blood of suspected beta-thalassemia carriers participated in this study were subjected to amplification refractory mutation system (ARMS). We then used 20 of these samples for HRM optimization. When 100% sensitivity and specificity was obtained with HRM procedure, we applied the technique for mutation detection on another remaining 20 samples as thalassemia cases with unknown mutations (detected mutations with ARMS-PCR kept confidential). Finally, the HRM procedure applied on 2 chorionic villous sample (CVS) biopsied from 12 weeks gestational age pregnant women for routine PND analysis. Results: In the first step of study, Fr 8/9 (+G), IVSI-1 (G > A), IVSI-5 (G > C), IVSI-110 (G > A), and CD44 (−C) mutations were diagnosed in samples under study using ARMS-PCR technique. Finally, the HRM procedure applied on 20 unknown samples and 2 CVS The results of HRM were in complete concordance with ARMS and confirmed by sequencing. Conclusions: The advantages of HRM analysis over conventional methods is high throughput, rapid, accurate, cost-effective, and reproducible.
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Affiliation(s)
- Mahboubeh Ramezanzadeh
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mansour Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Rasoul Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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15
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Didehdar M, Khansarinejad B, Amirrajab N, Shokohi T. Development of a high-resolution melting analysis assay for rapid and high-throughput identification of clinically important dermatophyte species. Mycoses 2016; 59:442-9. [PMID: 26991756 DOI: 10.1111/myc.12492] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 01/12/2016] [Accepted: 02/02/2016] [Indexed: 11/27/2022]
Abstract
Accurate identification of dermatophyte species is important both for epidemiological studies and for implementing antifungal treatment strategies. Although nucleic acid amplification-based assays have several advantages over conventional mycological methods, a major disadvantage is their high cost. The aim of this study was to develop a rapid and accurate real-time PCR-based high-resolution melting (HRM) assay for differentiation of the most common dermatophyte species. The oligonucleotide primers were designed to amplify highly conserved regions of the dermatophyte ribosomal DNA. Analysis of a panel containing potentially interfering fungi demonstrated no cross reactivity with the assay. To evaluate the performance characteristics of the method, a total of 250 clinical isolates were tested in comparison with the long-established PCR-RFLP method and the results were reassessed using DNA sequencing, as the reference standard method. The assay is able to type dermatophytes using normalised melting peak, difference plot analysis or electrophoresis on agarose gel methods. The results showed that, in comparison to PCR-RFLP, the developed HRM assay was able to differentiate at least 10 common dermatophytes species with a higher speed, throughput and accuracy. These results indicate that the HRM assay will be a useful sensitive, high throughput and cost-effective method for differentiating the most common dermatophyte species.
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Affiliation(s)
- M Didehdar
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran.,Department of Medical Mycology and Parasitology, Arak University of Medical Sciences, Arak, Iran
| | - B Khansarinejad
- Molecular and Medicine Research Center, Arak University of Medical Sciences, Arak, Iran
| | - N Amirrajab
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran.,Department of Laboratory Sciences and Tropical Medicine Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - T Shokohi
- Department of Medical Mycology and Parasitology/Invasive Fungi Research Center (IFRC), Mazandaran University of Medical Sciences, Sari, Iran
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16
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Lineage-specific detection of influenza B virus using real-time polymerase chain reaction with melting curve analysis. Arch Virol 2016; 161:1425-35. [DOI: 10.1007/s00705-016-2802-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 02/19/2016] [Indexed: 11/25/2022]
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17
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Lee E, Kim EJ, Shin YK, Song JY. Design and testing of multiplex RT-PCR primers for the rapid detection of influenza A virus genomic segments: Application to equine influenza virus. J Virol Methods 2015; 228:114-22. [PMID: 26655588 DOI: 10.1016/j.jviromet.2015.11.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 11/12/2015] [Accepted: 11/16/2015] [Indexed: 02/07/2023]
Abstract
The avian influenza A virus causes respiratory infections in animal species. It can undergo genomic recombination with newly obtained genetic material through an interspecies transmission. However, the process is an unpredictable event, making it difficult to predict the emergence of a new pandemic virus and distinguish its origin, especially when the virus is the result of multiple infections. Therefore, identifying a novel influenza is entirely dependent on sequencing its whole genome. Occasionally, however, it can be time-consuming, costly, and labor-intensive when sequencing many influenza viruses. To compensate for the difficulty, we developed a rapid, cost-effective, and simple multiplex RT-PCR to identify the viral genomic segments. As an example to evaluate its performance, H3N8 equine influenza virus (EIV) was studied for the purpose. In developing this protocol to amplify the EIV eight-segments, a series of processes, including phylogenetic analysis based on different influenza hosts, in silico analyses to estimate primer specificity, coverage, and variation scores, and investigation of host-specific amino acids, were progressively conducted to reduce or eliminate the negative factors that might affect PCR amplification. Selectively, EIV specific primers were synthesized with dual priming oligonucleotides (DPO) system to increase primer specificity. As a result, 16 primer pairs were selected to screen the dominantly circulating H3N8 EIV 8 genome segments: PA (3), PB2 (1), PA (3), NP (3), NA8 (2), HA3 (1), NS (1), and M (2). The diagnostic performance of the primers was evaluated with eight sets composing of four segment combinations using viral samples from various influenza hosts. The PCR results suggest that the multiplex RT-PCR has a wide range of applications in detection and diagnosis of newly emerging EIVs. Further, the proposed procedures of designing multiplex primers are expected to be used for detecting other animal influenza A viruses.
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Affiliation(s)
- EunJung Lee
- Viral Disease Division, Animal and Plant Quarantine Agency, 175 Anyang-ro, Manan-gu, Anyang-si, Gyeonggi-do, Republic of Korea
| | - Eun-Ju Kim
- Viral Disease Division, Animal and Plant Quarantine Agency, 175 Anyang-ro, Manan-gu, Anyang-si, Gyeonggi-do, Republic of Korea
| | - Yeun-Kyung Shin
- Viral Disease Division, Animal and Plant Quarantine Agency, 175 Anyang-ro, Manan-gu, Anyang-si, Gyeonggi-do, Republic of Korea
| | - Jae-Young Song
- Viral Disease Division, Animal and Plant Quarantine Agency, 175 Anyang-ro, Manan-gu, Anyang-si, Gyeonggi-do, Republic of Korea.
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18
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Titov I, Tsybanov S, Malogolovkin A. Genotyping of classical swine fever virus using high-resolution melt analysis. J Virol Methods 2015; 224:53-7. [DOI: 10.1016/j.jviromet.2015.08.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 08/17/2015] [Accepted: 08/18/2015] [Indexed: 11/26/2022]
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19
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Identifying the last bloodmeal of questing sheep tick nymphs (Ixodes ricinus L.) using high resolution melting analysis. Vet Parasitol 2015; 210:194-205. [PMID: 25941127 DOI: 10.1016/j.vetpar.2015.04.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 04/02/2015] [Accepted: 04/07/2015] [Indexed: 11/18/2022]
Abstract
The sheep tick, Ixodes ricinus L., is an important hematophagous vector of zoonotic disease of both veterinary and public health importance in Europe. Risk models for tick-borne diseases can be improved by identifying the main hosts of this species in any given area. However, this generalist tick stays on a host for only a few days a year over its life cycle, making the study of its feeding ecology difficult. In contrast, ticks can easily be collected from vegetation when they are questing. Molecular methods have proved to be a reliable alternative to field observation, but most current methods have low sensitivity and/or low identification success (i.e. hosts are only identified to taxonomic levels higher than species). In this study we use Real-time PCR coupled with High Resolution Melting Analysis (HRMA) to identify the source of the last bloodmeal in questing tick nymphs. Twenty of the most important tick hosts were grouped taxonomically and six group-specific primer sets, targeting short mitochondrial DNA regions, were designed de novo. Firstly, we show that these primers successfully amplify target host DNA (from host tissue or engorged ticks), and that HRMA can be used to reliably identify hosts to species (or genera in the case of Sorex and Apodemus). Secondly, the new protocol was tested on field-collected questing nymphs. Bloodmeal source was identified in 65.4% of 52 individuals. In 83.3% of these, the host was identified to species or genera using HRMA alone. Moreover, the primer sets designed here can unequivocally identify mixed bloodmeals. The combination of sensitivity and identification success together with the closed-tube and single step approach that minimizes contamination, make Real-time HRMA a good alternative to current methods for bloodmeal identification.
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20
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Rapid genotyping of beak and feather disease virus using high-resolution DNA melt curve analysis. J Virol Methods 2014; 208:47-55. [DOI: 10.1016/j.jviromet.2014.07.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 07/21/2014] [Accepted: 07/25/2014] [Indexed: 11/21/2022]
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21
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Huang SW, Ho CF, Chan KW, Cheng MC, Shien JH, Liu HJ, Wang CY. The genotyping of Infectious bronchitis virus in Taiwan by a multiplex amplification refractory mutation system reverse transcription polymerase chain reaction. J Vet Diagn Invest 2014; 26:721-33. [DOI: 10.1177/1040638714547735] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Infectious bronchitis virus (IBV; Avian coronavirus) causes acute respiratory and reproductive and urogenital diseases in chickens. Following sequence alignment of IBV strains, a combination of selective primer sets was designed to individually amplify the IBV wild-type and vaccine strains using a multiplex amplification refractory mutation system reverse transcription polymerase chain reaction (ARMS RT-PCR) approach. This system was shown to discriminate the IBV wild-type and vaccine strains. Moreover, an ARMS real-time RT-PCR (ARMS qRT-PCR) was combined with a high-resolution analysis (HRMA) to establish a melt curve analysis program. The specificity of the ARMS RT-PCR and the ARMS qRT-PCR was verified using unrelated avian viruses. Different melting temperatures and distinct normalized and shifted melting curve patterns for the IBV Mass, IBV H120, IBV TW-I, and IBV TW-II strains were detected. The new assays were used on samples of lung and trachea as well as virus from allantoic fluid and cell culture. In addition to being able to detect the presence of IBV vaccine and wild-type strains by ARMS RT-PCR, the IBV Mass, IBV H120, IBV TW-I, and IBV TW-II strains were distinguished using ARMS qRT-PCR by their melting temperatures and by HRMA. These approaches have acceptable sensitivities and specificities and therefore should be able to serve as options when carrying out differential diagnosis of IBV in Taiwan and China.
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Affiliation(s)
- Shr-Wei Huang
- Department of Veterinary Medicine, College of Veterinary Medicine (Huang, Ho, Shien, Wang), National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Life Sciences (Liu), National Chung Hsing University, Taichung, Taiwan
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan)
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, Taiwan (Cheng)
| | - Chia-Fang Ho
- Department of Veterinary Medicine, College of Veterinary Medicine (Huang, Ho, Shien, Wang), National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Life Sciences (Liu), National Chung Hsing University, Taichung, Taiwan
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan)
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, Taiwan (Cheng)
| | - Kun-Wei Chan
- Department of Veterinary Medicine, College of Veterinary Medicine (Huang, Ho, Shien, Wang), National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Life Sciences (Liu), National Chung Hsing University, Taichung, Taiwan
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan)
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, Taiwan (Cheng)
| | - Min-Chung Cheng
- Department of Veterinary Medicine, College of Veterinary Medicine (Huang, Ho, Shien, Wang), National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Life Sciences (Liu), National Chung Hsing University, Taichung, Taiwan
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan)
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, Taiwan (Cheng)
| | - Jui-Hung Shien
- Department of Veterinary Medicine, College of Veterinary Medicine (Huang, Ho, Shien, Wang), National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Life Sciences (Liu), National Chung Hsing University, Taichung, Taiwan
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan)
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, Taiwan (Cheng)
| | - Hung-Jen Liu
- Department of Veterinary Medicine, College of Veterinary Medicine (Huang, Ho, Shien, Wang), National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Life Sciences (Liu), National Chung Hsing University, Taichung, Taiwan
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan)
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, Taiwan (Cheng)
| | - Chi-Young Wang
- Department of Veterinary Medicine, College of Veterinary Medicine (Huang, Ho, Shien, Wang), National Chung Hsing University, Taichung, Taiwan
- Graduate Institute of Life Sciences (Liu), National Chung Hsing University, Taichung, Taiwan
- Department of Veterinary Medicine, College of Agriculture, National Chiayi University, Chiayi, Taiwan (Chan)
- Animal Health Research Institute, Council of Agriculture, Executive Yuan, Taiwan (Cheng)
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22
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Komorowska B, Fiore N, Zamorano A, Li R. Simultaneous detection of Cherry necrotic rusty mottle virus and Cherry green ring mottle virus using real-time PCR and high resolution melting analysis. Mol Cell Probes 2014; 28:186-91. [DOI: 10.1016/j.mcp.2014.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/09/2014] [Accepted: 03/12/2014] [Indexed: 11/30/2022]
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23
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Alnuaimi A, Wiesenfeld D, O'Brien-Simpson N, Reynolds E, Peng B, McCullough M. The development and validation of a rapid genetic method for species identification and genotyping of medically important fungal pathogens using high-resolution melting curve analysis. Mol Oral Microbiol 2014; 29:117-30. [DOI: 10.1111/omi.12050] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2014] [Indexed: 11/26/2022]
Affiliation(s)
- A.D. Alnuaimi
- Melbourne Dental School; Oral Health CRC; The University of Melbourne; Melbourne Vic. Australia
| | - D. Wiesenfeld
- Melbourne Dental School; Oral Health CRC; The University of Melbourne; Melbourne Vic. Australia
- Head and Neck Oncology; The Royal Melbourne Hospital; Melbourne Vic. Australia
| | - N.M. O'Brien-Simpson
- Melbourne Dental School; Oral Health CRC; The University of Melbourne; Melbourne Vic. Australia
| | - E.C. Reynolds
- Melbourne Dental School; Oral Health CRC; The University of Melbourne; Melbourne Vic. Australia
| | - B. Peng
- Melbourne Dental School; Oral Health CRC; The University of Melbourne; Melbourne Vic. Australia
| | - M.J. McCullough
- Melbourne Dental School; Oral Health CRC; The University of Melbourne; Melbourne Vic. Australia
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24
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Hata A, Kitajima M, Tajiri-Utagawa E, Katayama H. Development of a high resolution melting analysis for detection and differentiation of human astroviruses. J Virol Methods 2014; 200:29-34. [PMID: 24509176 DOI: 10.1016/j.jviromet.2014.01.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 01/16/2014] [Accepted: 01/21/2014] [Indexed: 11/28/2022]
Abstract
Human astroviruses (AstVs), the common causes of viral gastroenteritis, consist of 8 different sero- or genotypes in which a variety of subtypes have been found. In the present study, a rapid and high-throughput method for detection and sequence-discrimination of AstVs by high resolution melting (HRM) analysis was developed. A newly designed primer set for the assay targeting ORF1b-ORF2 junction region of AstVs successfully reacted with all 8 serotypes of AstVs and allowed genotyping using their amplicons. The HRM assay consists of intercalating dye based real time quantitative PCR (qPCR) and melting curve analysis. The qPCR assay was sensitive enough to detect 1.0×10(1) copies/reaction of AstV serotypes. However, 1.0×10(3) copies/reaction of AstVs gene was required to obtain a sequence-specific difference curve, indicating that pre-amplification is necessary to apply the assay to samples containing low numbers of AstVs. AstVs in clinical specimens were subjected to the HRM assay after pre-amplification. The strains possessing same nucleotide sequences at the target region showed an identical difference curve and those possessing different nucleotide sequences showed a distinguishable difference curve. The newly developed HRM assay is an effective technique for screening of AstVs to quantify and discriminate the strains.
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Affiliation(s)
- Akihiko Hata
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Masaaki Kitajima
- Center for Environmental Sensing and Modeling Singapore-MIT Alliance for Research and Technology 1 CREATE Way, #09-03 CREATE Tower, Singapore 138602
| | - Etsuko Tajiri-Utagawa
- Second Department of Virology, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0012, Japan
| | - Hiroyuki Katayama
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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25
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Zhu Z, Fan H, Qi X, Qi Y, Shi Z, Wang H, Cui L, Zhou M. Development and evaluation of a SYBR green-based real time RT-PCR assay for detection of the emerging avian influenza A (H7N9) virus. PLoS One 2013; 8:e80028. [PMID: 24278234 PMCID: PMC3835827 DOI: 10.1371/journal.pone.0080028] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/27/2013] [Indexed: 11/19/2022] Open
Abstract
Most recently a novel avian-origin influenza A (H7N9) virus emerged in China and has been associated with lots of human infection and fatal cases. Genetic analysis of the viral genome revealed that this reassortant virus might be better adapted to humans than other avian influenza viruses. Molecular diagnostic methods are thus urgently needed in public health laboratories. In this study, a SYBR green-based one-step real time reverse transcription-PCR (RT-PCR) was developed to detect the novel H7N9 virus. The primer pairs on the basis of the hemagglutinin and neuraminidase gene sequences of H7N9 viruses amplified subtype-specific fragments with Tm values of 80.77±0.06°C for H7 and 81.20±0.17°C for N9 respectively. The standard curves showed a dynamic linear range across 6 log units of RNA copy number (106 to 101 copies/ µl) with a detection limit of 10 copies per reaction for both H7 and N9 assays by using serial ten-fold diluted in-vitro transcribed viral RNA. In addition, no cross-reactivity was observed with seasonal H1N1, H1N1 pdm09, H3N2, H5N1 and H9N2 viruses as well as other human respiratory viruses. When the assay was further evaluated in H7N9 virus infected clinical samples, positive amplification signals were obtained in all of the specimens with the accordance between H7 and N9 assays. Therefore, the established SYBR green-based real time RT-PCR assay could provide a rapid, sensitive, specific and reliable alternative approach with lower costs for high throughput screening of suspected samples from humans, animals and environments in first line public health laboratories.
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Affiliation(s)
- Zheng Zhu
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Huan Fan
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Xian Qi
- Department of Acute Infectious Diseases Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yuhua Qi
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Zhiyang Shi
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Hua Wang
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
| | - Lunbiao Cui
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
- * E-mail: (LC); (MZ)
| | - Minghao Zhou
- Institute of Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health, Nanjing, China
- * E-mail: (LC); (MZ)
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Santos GB, Espínola SM, Ferreira HB, Margis R, Zaha A. Rapid detection of Echinococcus species by a high-resolution melting (HRM) approach. Parasit Vectors 2013; 6:327. [PMID: 24517106 PMCID: PMC4029041 DOI: 10.1186/1756-3305-6-327] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 11/05/2013] [Indexed: 12/27/2022] Open
Abstract
Background High-resolution melting (HRM) provides a low-cost, fast and sensitive scanning method that allows the detection of DNA sequence variations in a single step, which makes it appropriate for application in parasite identification and genotyping. The aim of this work was to implement an HRM-PCR assay targeting part of the mitochondrial cox1 gene to achieve an accurate and fast method for Echinococcus spp. differentiation. Findings For melting analysis, a total of 107 samples from seven species were used in this study. The species analyzed included Echinococcus granulosus (n = 41) and Echinococcus ortleppi (n = 50) from bovine, Echinococcus vogeli (n = 2) from paca, Echinococcus oligarthra (n = 3) from agouti, Echinococcus multilocularis (n = 6) from monkey and Echinococcus canadensis (n = 2) and Taenia hydatigena (n = 3) from pig. DNA extraction was performed, and a 444-bp fragment of the cox1 gene was amplified. Two approaches were used, one based on HRM analysis, and a second using SYBR Green Tm-based. In the HRM analysis, a specific profile for each species was observed. Although some species exhibited almost the same melting temperature (Tm) value, the HRM profiles could be clearly discriminated. The SYBR Green Tm-based analysis showed differences between E. granulosus and E. ortleppi and between E. vogeli and E. oligarthra. Conclusions In this work, we report the implementation of HRM analysis to differentiate species of the genus Echinococcus using part of the mitochondrial gene cox1. This method may be also potentially applied to identify other species belonging to the Taeniidae family.
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Affiliation(s)
| | | | | | | | - Arnaldo Zaha
- Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Caixa Postal 15005, CEP 91501-970, Porto Alegre, RS, Brazil.
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Hasiów-Jaroszewska B, Komorowska B. A new method for detection and discrimination of Pepino mosaic virus isolates using high resolution melting analysis of the triple gene block 3. J Virol Methods 2013; 193:1-5. [DOI: 10.1016/j.jviromet.2013.04.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 04/22/2013] [Accepted: 04/29/2013] [Indexed: 11/30/2022]
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Kalthoff D, Beer M, Hoffmann B. High resolution melting analysis: rapid and precise characterisation of recombinant influenza A genomes. Virol J 2013; 10:284. [PMID: 24028349 PMCID: PMC3847122 DOI: 10.1186/1743-422x-10-284] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 09/09/2013] [Indexed: 01/23/2023] Open
Abstract
Background High resolution melting analysis (HRM) is a rapid and cost-effective technique for the characterisation of PCR amplicons. Because the reverse genetics of segmented influenza A viruses allows the generation of numerous influenza A virus reassortants within a short time, methods for the rapid selection of the correct recombinants are very useful. Methods PCR primer pairs covering the single nucleotide polymorphism (SNP) positions of two different influenza A H5N1 strains were designed. Reassortants of the two different H5N1 isolates were used as a model to prove the suitability of HRM for the selection of the correct recombinants. Furthermore, two different cycler instruments were compared. Results Both cycler instruments generated comparable average melting peaks, which allowed the easy identification and selection of the correct cloned segments or reassorted viruses. Conclusions HRM is a highly suitable method for the rapid and precise characterisation of cloned influenza A genomes.
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Affiliation(s)
- Donata Kalthoff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, Greifswald-Insel Riems, 17493, Germany.
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Hartmann NM, Dartscht M, Szewzyk R, Selinka HC. Monitoring of adenovirus serotypes in environmental samples by combined PCR and melting point analyses. Virol J 2013; 10:190. [PMID: 23758742 PMCID: PMC3706342 DOI: 10.1186/1743-422x-10-190] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 05/17/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Human adenoviruses are promising candidates for addressing health risks associated with enteric viruses in environmental waters. Relatively harmless but common, these DNA viruses persist within the population and are generally considered extremely stable, remaining infectious in water for long periods of time. Group-specific or single species detection of human adenoviruses in environmental samples is usually based on polymerase chain reaction assays. Simultaneous identification of specific species or serotypes needs additional processing. Here we present a simple molecular approach for the monitoring of serotypic diversity in the human adenovirus populations in contaminated water sites. METHODS Diversity patterns of human adenoviruses in environmental samples, collected in an outdoor artificial stream and pond simulation system, were analyzed using a closed tube polymerase chain reaction method with subsequent melting point analysis. RESULTS Human adenovirus serotype 41 was the most prominent adenovirus serotype detected in environmental water samples, but melting point analyses indicated the presence of additional adenovirus serotypes. CONCLUSIONS Based on investigations with spiked and environmental samples, a combination of qPCR and melting point analysis was shown to identify adenovirus serotypes in sewage contaminated water.
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Affiliation(s)
- Nils Marten Hartmann
- German Federal Environment Agency (UBA, Umweltbundesamt), Division II 1.4 Microbiological Risks, Corrensplatz 1, 14195 Berlin, Germany
| | - Melanie Dartscht
- German Federal Environment Agency (UBA, Umweltbundesamt), Division II 1.4 Microbiological Risks, Corrensplatz 1, 14195 Berlin, Germany
| | - Regine Szewzyk
- German Federal Environment Agency (UBA, Umweltbundesamt), Division II 1.4 Microbiological Risks, Corrensplatz 1, 14195 Berlin, Germany
| | - Hans-Christoph Selinka
- German Federal Environment Agency (UBA, Umweltbundesamt), Division II 1.4 Microbiological Risks, Corrensplatz 1, 14195 Berlin, Germany
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High-resolution melting molecular signatures for rapid identification of human papillomavirus genotypes. PLoS One 2012; 7:e42051. [PMID: 22916117 PMCID: PMC3423390 DOI: 10.1371/journal.pone.0042051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 07/02/2012] [Indexed: 11/21/2022] Open
Abstract
Background Genotyping of human papillomarvirus (HPV) is crucial for patient management in a clinical setting. This study accesses the combined use of broad-range real-time PCR and high-resolution melting (HRM) analysis for rapid identification of HPV genotypes. Methods Genomic DNA sequences of 8 high-risk genotypes (HPV16/18/39/45/52/56/58/68) were subject to bioinformatic analysis to select for appropriate PCR amplicon. Asymmetric broad-range real-time PCR in the presence of HRM dye and two unlabeled probes specific to HPV16 and 18 was employed to generate HRM molecular signatures for HPV genotyping. The method was validated via assessment of 119 clinical HPV isolates. Results A DNA fragment within the L1 region was selected as the PCR amplicon ranging from 215–221 bp for different HPV genotypes. Each genotype displayed a distinct HRM molecular signature with minimal inter-assay variability. According to the HRM molecular signatures, HPV genotypes can be determined with one PCR within 3 h from the time of viral DNA isolation. In the validation assay, a 91% accuracy rate was achieved when the genotypes were in the database. Concomitantly, the HRM molecular signatures for additional 6 low-risk genotypes were established. Conclusions This assay provides a novel approach for HPV genotyping in a rapid and cost-effective manner.
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Ganopoulos I, Madesis P, Zambounis A, Tsaftaris A. High-resolution melting analysis allowed fast and accurate closed-tube genotyping of Fusarium oxysporum formae speciales complex. FEMS Microbiol Lett 2012; 334:16-21. [PMID: 22670678 DOI: 10.1111/j.1574-6968.2012.02610.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 05/22/2012] [Accepted: 05/31/2012] [Indexed: 11/30/2022] Open
Abstract
The fungus Fusarium oxysporum is a highly complex species composed by many strains put together into groups called formae speciales. As it is difficult and laborious to discriminate Fusarium formae specials via biochemical or phenotypic methods, it is very important to develop novel, rapid, and simple to perform identification methods. Herein, real-time PCR assay [using universal internal transcribed spacer (ITS) primers] coupled with high-resolution melting (HRM) analysis was developed for identifying and distinguishing F. oxysporum formae speciales complex. The melting curve analysis of these amplicons specifically classified all isolates into seven F. oxysporum formae speciales and generated seven HRM curve profiles. The smallest DNA sequence difference recognized in this study was one nucleotide. The results presented show that HRM curve analysis of Fusarium ITS sequences is a simple, quick, and reproducible method that allows both the identification of seven F. oxysporum formae speciales and at the same time their screening for variants. Our genotyping assay uses the combined information of simultaneously acquired HRM data from an unlabeled probe and the full-length amplicon. Finally, the completion of both reaction and analysis in a closed tube saves time by eliminating the separate steps and reduces the risk of contamination.
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Affiliation(s)
- Ioannis Ganopoulos
- Department of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, Greece
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Sepúlveda D, Cárdenas C, Carmona M, Marshall SH. Novel strategy to evaluate infectious salmon anemia virus variants by high resolution melting. PLoS One 2012; 7:e37265. [PMID: 22719837 PMCID: PMC3373561 DOI: 10.1371/journal.pone.0037265] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 04/18/2012] [Indexed: 12/29/2022] Open
Abstract
Genetic variability is a key problem in the prevention and therapy of RNA-based virus infections. Infectious Salmon Anemia virus (ISAv) is an RNA virus which aggressively attacks salmon producing farms worldwide and in particular in Chile. Just as with most of the Orthomyxovirus, ISAv displays high variability in its genome which is reflected by a wider infection potential, thus hampering management and prevention of the disease. Although a number of widely validated detection procedures exist, in this case there is a need of a more complex approach to the characterization of virus variability. We have adapted a procedure of High Resolution Melting (HRM) as a fine-tuning technique to fully differentiate viral variants detected in Chile and projected to other infective variants reported elsewhere. Out of the eight viral coding segments, the technique was adapted using natural Chilean variants for two of them, namely segments 5 and 6, recognized as virulence-associated factors. Our work demonstrates the versatility of the technique as well as its superior resolution capacity compared with standard techniques currently in use as key diagnostic tools.
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Affiliation(s)
- Dagoberto Sepúlveda
- Laboratorio de Patógenos Acuícolas, Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Constanza Cárdenas
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Marisela Carmona
- Laboratorio de Patógenos Acuícolas, Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Sergio H. Marshall
- Laboratorio de Patógenos Acuícolas, Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- * E-mail:
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Ruskova L, Raclavsky V. The potential of high resolution melting analysis (hrma) to streamline, facilitate and enrich routine diagnostics in medical microbiology. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2012; 155:239-52. [PMID: 22286809 DOI: 10.5507/bp.2011.045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Routine medical microbiology diagnostics relies on conventional cultivation followed by phenotypic techniques for identification of pathogenic bacteria and fungi. This is not only due to tradition and economy but also because it provides pure culture needed for antibiotic susceptibility testing. This review focuses on the potential of High Resolution Melting Analysis (HRMA) of double-stranded DNA for future routine medical microbiology. METHODS AND RESULTS Search of MEDLINE database for publications showing the advantages of HRMA in routine medical microbiology for identification, strain typing and further characterization of pathogenic bacteria and fungi in particular. The results show increasing numbers of newly-developed and more tailor-made assays in this field. For microbiologists unfamiliar with technical aspects of HRMA, we also provide insight into the technique from the perspective of microbial characterization. CONCLUSIONS We can anticipate that the routine availability of HRMA in medical microbiology laboratories will provide a strong stimulus to this field. This is already envisioned by the growing number of medical microbiology applications published recently. The speed, power, convenience and cost effectiveness of this technology virtually predestine that it will advance genetic characterization of microbes and streamline, facilitate and enrich diagnostics in routine medical microbiology without interfering with the proven advantages of conventional cultivation.
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Affiliation(s)
- Lenka Ruskova
- Department of Microbiology, Palacky University Olomouc, Czech Republic
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High-resolution melting analysis for the rapid detection of fluoroquinolone and streptomycin resistance in Mycobacterium tuberculosis. PLoS One 2012; 7:e31934. [PMID: 22363772 PMCID: PMC3283711 DOI: 10.1371/journal.pone.0031934] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 01/18/2012] [Indexed: 01/13/2023] Open
Abstract
Background Molecular methods for the detection of drug-resistant tuberculosis are potentially more rapid than conventional culture-based drug susceptibility testing, facilitating the commencement of appropriate treatment for patients with drug resistant tuberculosis. We aimed to develop and evaluate high-resolution melting (HRM) assays for the detection of mutations within gyrA, rpsL, and rrs, for the determination of fluoroquinolone and streptomycin resistance in Mycobacterium tuberculosis (MTB). Methodology/Principal Findings A blinded series of DNA samples extracted from a total of 92 clinical isolates of MTB were analyzed by HRM analysis, and the results were verified using DNA sequencing. The sensitivity and specificity of the HRM assays in comparison with drug susceptibility testing were 74.1% and 100.0% for the detection of fluoroquinolone resistance, and 87.5% and 100.0% for streptomycin resistance. Five isolates with low level resistance to ofloxacin had no mutations detected in gyrA, possibly due to the action of efflux pumps, or false negativity due to mixed infections. One fluoroquinolone-resistant isolate had a mutation in a region of gyrA not encompassed by our assay. Six streptomycin-resistant strains had undetectable mutations by HRM and DNA sequencing, which may be explained by the fact that not all streptomycin-resistant isolates have mutations within rpsL and rrs, and suggesting that other targets may be involved. Conclusion The HRM assays described here are potentially useful adjunct tests for the efficient determination of fluoroquinolone and streptomycin resistance in MTB, and could facilitate the timely administration of appropriate treatment for patients infected with drug-resistant TB.
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Universal PCR coupled with high-resolution melting analysis for rapid detection and identification of microorganism. ACTA ACUST UNITED AC 2012. [DOI: 10.1097/mrm.0b013e32834f9e62] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Hsiao CC, Chang J, Wu JY, Liu WH, Han SY, Chen PJ, Yeh SH. High-resolution melting and real-time PCR for quantification and detection of drug-resistant HBV mutants in a single amplicon. Antivir Ther 2011; 17:291-303. [PMID: 22301217 DOI: 10.3851/imp2022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2011] [Indexed: 10/14/2022]
Abstract
BACKGROUND Antiviral therapy by nucleoside/nucleotide analogues (NAs) effectively reduces HBV replication in chronic hepatitis B (CHB) patients. Because long-term NA treatments will eventually select for drug-resistant mutants, early detection of mutants and frequent monitoring of viral loads is crucial for successful NA therapy. Because no efficient test for one-tube quantification and qualification of various HBV-resistant mutants exists, we propose to use high-resolution melting (HRM) analysis in combination with real-time PCR to achieve this unmet need. METHODS We developed a single amplicon for detecting HBV mutants resistant to lamivudine (LMV), adefovir (ADV) and entecavir (ETV), which are commonly used for CHB treatment. Our design consists of two steps: real-time PCR for viral quantification, and hybridization probe HRM analysis for detection of specific drug-resistant mutants. RESULTS Assay quantification was accurate (R=0.98) for viral loads from 10(3) to 10(9) copies/ml. HRM analysis produced distinct melting temperatures that clearly distinguished the mutants, rtM204V/I (LMV), rtA181V and rtN236T (ADV), and rtT184G and rtM250V (ETV), from their respective wild types. The assay detected mutants at only 10-25% of the HBV population. The clinical applicability of this assay was tested in a pilot study with serial samples from patients receiving LMV treatment. CONCLUSIONS Flexibility, speed and cost-efficiency are additional benefits unique to our assay. The clinical sample results further support the feasibility of applying our design to frequent and long-term monitoring of CHB patients receiving NA treatments in the clinical setting.
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Affiliation(s)
- Chia-Chieh Hsiao
- NTU Center for Genomic Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
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Matsuda Y, Qazi Y, Iwaki Y. A rapid and efficient method BK polyomavirus genotyping by high-resolution melting analysis. J Med Virol 2011; 83:2128-34. [DOI: 10.1002/jmv.22239] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Molecular Detection of Respiratory Viruses. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Chang SS, Hsu HL, Cheng JC, Tseng CP. An efficient strategy for broad-range detection of low abundance bacteria without DNA decontamination of PCR reagents. PLoS One 2011; 6:e20303. [PMID: 21637859 PMCID: PMC3102696 DOI: 10.1371/journal.pone.0020303] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 04/29/2011] [Indexed: 02/04/2023] Open
Abstract
Background Bacterial DNA contamination in PCR reagents has been a long standing problem that hampers the adoption of broad-range PCR in clinical and applied microbiology, particularly in detection of low abundance bacteria. Although several DNA decontamination protocols have been reported, they all suffer from compromised PCR efficiency or detection limits. To date, no satisfactory solution has been found. Methodology/Principal Findings We herein describe a method that solves this long standing problem by employing a broad-range primer extension-PCR (PE-PCR) strategy that obviates the need for DNA decontamination. In this method, we first devise a fusion probe having a 3′-end complementary to the template bacterial sequence and a 5′-end non-bacterial tag sequence. We then hybridize the probes to template DNA, carry out primer extension and remove the excess probes using an optimized enzyme mix of Klenow DNA polymerase and exonuclease I. This strategy allows the templates to be distinguished from the PCR reagent contaminants and selectively amplified by PCR. To prove the concept, we spiked the PCR reagents with Staphylococcus aureus genomic DNA and applied PE-PCR to amplify template bacterial DNA. The spiking DNA neither interfered with template DNA amplification nor caused false positive of the reaction. Broad-range PE-PCR amplification of the 16S rRNA gene was also validated and minute quantities of template DNA (10–100 fg) were detectable without false positives. When adapting to real-time and high-resolution melting (HRM) analytical platforms, the unique melting profiles for the PE-PCR product can be used as the molecular fingerprints to further identify individual bacterial species. Conclusions/Significance Broad-range PE-PCR is simple, efficient, and completely obviates the need to decontaminate PCR reagents. When coupling with real-time and HRM analyses, it offers a new avenue for bacterial species identification with a limited source of bacterial DNA, making it suitable for use in clinical and applied microbiology laboratories.
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Affiliation(s)
- Shy-Shin Chang
- Graduate Institute of Clinical Medical Sciences, Department of Medicine, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan, Republic of China
- Department of Medicine, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan, Republic of China
- Department of Family Medicine and Emergency Medicine, Chang Gung Memorial Hospital, Tao-Yuan, Taiwan, Republic of China
| | - Hsung-Ling Hsu
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Tao-Yuan, Taiwan, Republic of China
| | - Ju-Chien Cheng
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Republic of China
| | - Ching-Ping Tseng
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Tao-Yuan, Taiwan, Republic of China
- Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan, Republic of China
- * E-mail:
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Alonso M, Navarro Y, Barletta F, Martínez Lirola M, Gotuzzo E, Bouza E, García de Viedma D. A novel method for the rapid and prospective identification of Beijing Mycobacterium tuberculosis strains by high-resolution melting analysis. Clin Microbiol Infect 2011; 17:349-57. [PMID: 20384709 DOI: 10.1111/j.1469-0691.2010.03234.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genotypic analysis of Mycobacterium tuberculosis (MTB) has enabled the definition of several lineages. The Beijing family, which is considered highly virulent and transmissible, has been associated with resistance in certain settings and involved in severe outbreaks, making it one of the most closely-monitored lineages. Therefore, rapid prospective identification of Beijing MTB strains could be relevant. In the present study, we evaluate a real-time PCR followed by high-resolution melting (HRM) based on the identification of a single nucleotide polymorphism (SNP) in the Rv2629 gene which defines Beijing lineage (A191C for Beijing genotype and A191A for non-Beijing genotype). This combined methodology efficiently differentiated Beijing and non-Beijing strains in 100% of the isolates from a collection of reference strains without requiring specific DNA probes. Additionally, HRM was able to assign a Beijing/non-Beijing genotype in 90.9% of the respiratory specimens assayed. Its applicability was tested on a Peruvian sample of circulating MTB strains, in which it identified 10.7% as belonging to the Beijing genotype; this proportion reached 20% in the North Lima area. HRM analysis of the A191C SNP is a rapid, reliable, and sensitive method for the efficient prospective survey of high-risk Beijing MTB strains, even in developing settings where MTB culture is often not available.
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Affiliation(s)
- M Alonso
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorìo Marañón, Madrid, Spain
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Arancia S, Sandini S, De Bernardis F, Fortini D. Rapid, simple, and low-cost identification of Candida species using high-resolution melting analysis. Diagn Microbiol Infect Dis 2011; 69:283-5. [DOI: 10.1016/j.diagmicrobio.2010.10.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 09/29/2010] [Accepted: 10/05/2010] [Indexed: 11/28/2022]
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Detection of hemagglutinin variants of the pandemic influenza A (H1N1) 2009 virus by pyrosequencing. J Clin Microbiol 2011; 49:1307-12. [PMID: 21307217 DOI: 10.1128/jcm.02424-10] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
For influenza viruses, pyrosequencing has been successfully applied to the high-throughput detection of resistance markers in genes encoding the drug-targeted M2 protein and neuraminidase. In this study, we expanded the utility of this assay to the detection of multiple receptor binding variants of the hemagglutinin protein of influenza viruses directly in clinical specimens. Specifically, a customized pyrosequencing protocol that permits detection of virus variants with the D, G, N, or E amino acid at position 222 in the hemagglutinin of the 2009 pandemic influenza A (H1N1) virus was developed. This customized pyrosequencing protocol was applied to the analysis of 241 clinical specimens. The use of the optimized nucleotide dispensation order allowed detection of mixtures of variants in 10 samples (4.1%) which the standard cyclic nucleotide dispensation protocol failed to detect. The optimized pyrosequencing protocol is expected to provide a more accurate tool in the analysis of virus variant composition.
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A new method for detection of pandemic influenza virus using High Resolution Melting analysis of the neuraminidase gene. J Virol Methods 2011; 171:284-6. [DOI: 10.1016/j.jviromet.2010.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 10/01/2010] [Accepted: 10/07/2010] [Indexed: 11/22/2022]
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Li JH, Yin YP, Zheng HP, Zhong MY, Peng RR, Wang B, Chen XS. A high-resolution melting analysis for genotyping urogenital Chlamydia trachomatis. Diagn Microbiol Infect Dis 2010; 68:366-74. [DOI: 10.1016/j.diagmicrobio.2010.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Revised: 07/16/2010] [Accepted: 07/21/2010] [Indexed: 11/26/2022]
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Mader E, Ruzicka J, Schmiderer C, Novak J. Quantitative high-resolution melting analysis for detecting adulterations. Anal Biochem 2010; 409:153-5. [PMID: 20946863 DOI: 10.1016/j.ab.2010.10.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Revised: 10/01/2010] [Accepted: 10/01/2010] [Indexed: 11/17/2022]
Abstract
Admixtures of different plant species are a common problem in raw materials for medicinal use. Two exemplary assays were developed to admixtures in Helleborus niger with high-resolution melting analysis. HRM proved to be a very sensitive tool in detecting admixtures, able to detect a ratio of 1:1000 with unknown species, and of 1:200,000 with Veratrum nigrum. The example proves the ability of HRM for quantification in multiplex PCR. The method is not limited to detecting adulterations. It can also be used to quantify a specific target by integrating a second amplicon in the assay as internal standard.
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Affiliation(s)
- Eduard Mader
- Institute for Applied Botany, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Wien, Austria.
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Senapin S, Molthathong S, Phiwsaiya K, Jaengsanong C, Chuchird N. Application of high resolution melt (HRM) analysis for duplex detection of Macrobrachium rosenbergii nodavirus (MrNV) and extra small virus (XSV) in shrimp. Mol Cell Probes 2010; 24:291-7. [DOI: 10.1016/j.mcp.2010.06.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 06/08/2010] [Accepted: 06/09/2010] [Indexed: 11/30/2022]
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Montgomery JL, Sanford LN, Wittwer CT. High-resolution DNA melting analysis in clinical research and diagnostics. Expert Rev Mol Diagn 2010; 10:219-40. [PMID: 20214540 DOI: 10.1586/erm.09.84] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Among nucleic acid analytical methods, high-resolution melting analysis is gaining more and more attention. High-resolution melting provides simple, homogeneous solutions for variant scanning and genotyping, addressing the needs of today's overburdened laboratories with rapid turnaround times and minimal cost. The flexibility of the technique has allowed it to be adopted by a wide range of disciplines for a variety of applications. In this review we examine the broad use of high-resolution melting analysis, including gene scanning, genotyping (including small amplicon, unlabeled probe and snapback primers), sequence matching and methylation analysis. Four major application arenas are examined to demonstrate the methods and approaches commonly used in particular fields. The appropriate usage of high-resolution melting analysis is discussed in the context of known constraints, such as sample quality and quantity, with a particular focus placed on proper experimental design in order to produce successful results.
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Affiliation(s)
- Jesse L Montgomery
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT 84132, USA
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Use of a high-resolution melt assay to characterize codon 54 of the cyp51A gene of Aspergillus fumigatus on a Rotor-Gene 6000 instrument. Antimicrob Agents Chemother 2010; 54:2248-51. [PMID: 20194699 DOI: 10.1128/aac.01712-09] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A high-resolution melt (HRM) assay using a Rotor-Gene 6000 instrument was developed to characterize the codon for glycine 54 in the cyp51A genes from 13 reference isolates and 12 clinical isolates of Aspergillus fumigatus. Mutations in this codon confer reduced susceptibility to itraconazole and posaconazole. The assay is simple to perform, and a result of "wild type" or "mutant" is available after approximately 1 h following DNA extraction using commercially available reagents and conventional primers.
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Ugo V, Tondeur S, Menot ML, Bonnin N, Le Gac G, Tonetti C, Mas VMD, Lecucq L, Kiladjian JJ, Chomienne C, Dosquet C, Parquet N, Darnige L, Porneuf M, Escoffre-Barbe M, Giraudier S, Delabesse E, Cassinat B. Interlaboratory development and validation of a HRM method applied to the detection of JAK2 exon 12 mutations in polycythemia vera patients. PLoS One 2010; 5:e8893. [PMID: 20126644 PMCID: PMC2811183 DOI: 10.1371/journal.pone.0008893] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 12/28/2009] [Indexed: 11/29/2022] Open
Abstract
Background Myeloproliferative disorders are characterized by clonal expansion of normal mature blood cells. Acquired mutations giving rise to constitutive activation of the JAK2 tyrosine kinase has been shown to be present in the majority of patients. Since the demonstration that the V617F mutation in the exon 14 of the JAK2 gene is present in about 90% of patients with Polycythemia Vera (PV), the detection of this mutation has become a key tool for the diagnosis of these patients. More recently, additional mutations in the exon 12 of the JAK2 gene have been described in 5 to 10% of the patients with erythrocytosis. According to the updated WHO criteria the presence of these mutations should be looked for in PV patients with no JAK2 V617F mutation. Reliable and accurate methods dedicated to the detection of these highly variable mutations are therefore necessary. Methods/Findings For these reasons we have defined the conditions of a High Resolution DNA Melting curve analysis (HRM) method able to detect JAK2 exon 12 mutations. After having validated that the method was able to detect mutated patients, we have verified that it gave reproducible results in repeated experiments, on DNA extracted from either total blood or purified granulocytes. This HRM assay was further validated using 8 samples bearing different mutant sequences in 4 different laboratories, on 3 different instruments. Conclusion The assay we have developed is thus a valid method, adapted to routine detection of JAK2 exon 12 mutations with highly reproducible results.
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Affiliation(s)
- Valerie Ugo
- CHU BREST, Laboratoire d'Hematologie, Brest, France
- INSERM U613, Brest, France
| | - Sylvie Tondeur
- CHU Montpellier, Laboratoire d'Hématologie, Hôpital Saint-Eloi, Montpellier, France
| | | | - Nadine Bonnin
- AP-HP, Unite de Biologie Cellulaire, Hopital Saint-Louis, Paris, France
| | | | - Carole Tonetti
- AP-HP, Laboratoire d'Hematologie, Hopital Henri Mondor, Creteil, France
| | | | - Lydie Lecucq
- CHU BREST, Laboratoire d'Hematologie, Brest, France
| | - Jean-Jacques Kiladjian
- AP-HP, Hematology Department, Hopital Avicenne, Bobigny, France
- PV-Nord Group, Hopital Saint-Louis, Paris, France
| | - Christine Chomienne
- AP-HP, Unite de Biologie Cellulaire, Hopital Saint-Louis, Paris, France
- PV-Nord Group, Hopital Saint-Louis, Paris, France
| | - Christine Dosquet
- AP-HP, Unite de Thérapie Cellulaire, Hopital Saint-Louis, Paris, France
| | - Nathalie Parquet
- AP-HP, Unite de Thérapie Cellulaire, Hopital Saint-Louis, Paris, France
- PV-Nord Group, Hopital Saint-Louis, Paris, France
| | - Luc Darnige
- AP-HP, Laboratoire d'Hematologie, Hopital Europeen G. Pompidou, Paris, France
| | - Marc Porneuf
- CH Le Foll, Service d'Hématologie, Saint Brieuc, France
| | | | | | - Eric Delabesse
- CHU Toulouse, Laboratoire d'Hematologie, Hôpital Purpan, Toulouse, France
| | - Bruno Cassinat
- AP-HP, Unite de Biologie Cellulaire, Hopital Saint-Louis, Paris, France
- PV-Nord Group, Hopital Saint-Louis, Paris, France
- * E-mail:
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