A rapid method based on the one-step reverse transcriptase-polymerase chain reaction (RT-PCR) technique for detection of different strains of citrus tristeza virus

2000 ◽  
Vol 148 (7-8) ◽  
pp. 469-475 ◽  
Author(s):  
T. H. Hung ◽  
M. L. Wu ◽  
H. J. Su
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcriptase ◽  
Citrus Tristeza Virus ◽  
Rt Pcr ◽  
Chain Reaction ◽  
One Step ◽  
Polymerase Chain ◽  
The One ◽  
Different Strains ◽  
Tristeza Virus

scholarly journals Development and Application of a Multiplex Reverse-Transcription Polymerase Chain Reaction Assay for Screening a Global Collection of Citrus tristeza virus Isolates

2010 ◽  
Vol 100 (10) ◽  
pp. 1077-1088 ◽  
Author(s):  
Avijit Roy ◽  
G. Ananthakrishnan ◽  
John S. Hartung ◽  
R. H. Brlansky
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcription ◽  
Citrus Tristeza Virus ◽  
Phylogenetic Analyses ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Variable Regions ◽  
Polymerase Chain ◽  
Tristeza Virus ◽  
Citrus Tristeza

The emerging diversity of Citrus tristeza virus (CTV) genotypes has complicated detection and diagnostic measures and prompted the search for new differentiation methods. To simplify the identification and differentiation of CTV genotypes, a multiplex reverse-transcription polymerase chain reaction (RT-PCR) technique for the screening of CTV isolates was developed. Variable regions within the open reading frame (ORF)-1a of diverse CTV genotypes were identified to develop first a simplex (S) and then a hexaplex (H) RT-PCR. CTV isolates have been grouped previously into five genotypes (namely, T3, T30, T36, VT, and B165) based on the nucleotide sequence comparisons and phylogenetic analyses. Nucleotide sequences from GenBank were used to design species and genotype-specific primers (GSPs). The GSPs were initially used for reliable detection of all CTV genotypes using S-RT-PCR. Furthermore, detection of all five recognized CTV genotypes was established using the H-RT-PCR. Six amplicons, one generic to all CTV isolates and one for each of the five recognized genotypes, were identified on the basis of their size and were confirmed by sequence analysis. In all, 175 CTV isolates from 29 citrus-growing countries were successfully analyzed by S- and H-RT-PCR. Of these, 97 isolates contained T36 genotypes, 95 contained T3 genotypes, 76 contained T30 genotypes, 71 contained VT genotypes, and 24 contained B165 genotype isolates. In total, 126 isolates contained mixed infections of 2 to 5 of the known CTV genotypes. Two of the CTV isolates could not be assigned to a known genotype. H-RT-PCR provides a sensitive, specific, reliable, and rapid way to screen for CTV genotypes compared with other methods for CTV genotype detection. Efficient identification of CTV genotypes will facilitate a better understanding of CTV isolates, including the possible interaction of different genotypes in causing or preventing diseases. The methods described can also be used in virus-free citrus propagation programs and in the development of CTV-resistant cultivars.

scholarly journals Mosquito-specific viruses (family Flaviviridae, genus Flavivirus) Diisolasi pada Nyamuk Anopheles vagus di Bali

2021 ◽  
Vol 22 (2) ◽  
pp. 189-197
Author(s):  
Putu Ayu Asri Damayanti ◽  
I Nyoman Mantik Astawa ◽  
Anak Agung Ayu Mirah Adi ◽  
I Made Sudarmaja ◽  
I Kadek Swastika ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcriptase ◽  
Light Trap ◽  
Baby Hamster Kidney ◽  
Rt Pcr ◽  
Chain Reaction ◽  
One Step ◽  
Polymerase Chain ◽  
Anopheles Vagus

Mosquito-specific viruses (MSVs) adalah virus yang hanya dapat bereplikasi pada sel nyamuk. Virus ini terdiri dari berbagai genus, salah satunya yang paling banyak ditemukan adalah dari famili Flaviviridae, genus Flavivirus. Namun, data keberadaan dan karakteristik MSVs dan vektornya di Bali saat ini sangat terbatas. Oleh karena itu, pengamatan untuk memperluas penemuan keragaman vektor dan filogenetik MSVs famili Flaviviridae, genus Flavivirus di Bali dilakukan pada tahun 2016-2018. Nyamuk-nyamuk dewasa ditangkap menggunakan light trap dan dikelompokkan berdasarkan spesies. Isolasi dan propagasi virus dilakukan pada galur sel C6/36 dan baby hamster kidney-21 (BHK-21). Identifikasi virus dilakukan dengan menggunakan one step reverse-transcriptase polymerase chain reaction (RT-PCR). Terdapat dua pool yang berasal dari nyamuk Anopheles vagus menampakan cythopathic effect (CPE) hanya pada galur sel C6/36 dari total 158 pool. Virus yang diisolasi memiliki persentase identity sekuen nukleotida tertinggi 97% dan sekuen asam amino 96% dengan virus Culex theileri Flavivirus isolat JKT-8650 yang diisolasi pada tahun 1981. Selanjutnya, virus dinamakan Mosquito Flavivirus Isolate Bali (MFB) dengan accession numbers KY995166 dan KY290258. Analisis filogenetik menunjukan bahwa MFB berada satu kluster dengan Culex theileri Flavivirus (CTFV) dari Indonesia, Culex Flavivuruses-Myanmar, Culex theileri Flavivirus-Portugal, dan Mosquito Flavivirus-Turki. Terdapat delapan nukelotida dan enam asam amino yang berbeda antara MFB dan CTFV Indonesia. Pada penelitian ini dapat disimpulkan bahwa MSVs dari famili Flaviviridae, genus Flavivirus berhasil diisolasi dari nyamuk An. vagus di Bali.

scholarly journals Detection and Isolate Differentiation of Citrus tristeza virus in Infected Field Trees Based on Reverse Transcription-Polymerase Chain Reaction

Plant Disease ◽  
2004 ◽  
Vol 88 (6) ◽  
pp. 625-629 ◽  
Author(s):  
Zhipeng Huang ◽  
Phyllis A. Rundell ◽  
Xiong Guan ◽  
Charles A. Powell
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcription ◽  
Citrus Tristeza Virus ◽  
Sweet Orange ◽  
Enzyme Linked Immunosorbent Assay ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Tristeza Virus ◽  
Citrus Tristeza

Reverse transcription-polymerase chain reaction (RT-PCR) was compared with enzyme-linked immunosorbent assay (ELISA) and direct tissue blot immunoassay (DTBIA) for detection of non-decline-inducing and decline-inducing isolates of Citrus tristeza virus (CTV) in 21 field sweet orange and grapefruit plants on sour orange rootstock in Fort Pierce, FL. Among these samples, seven, six, and eight were infected with decline-inducing, non-decline-inducing, and both decline-inducing and non-decline-inducing isolates of CTV, respectively. However, there was not a good correlation between field symptoms and detection of the decline-inducing isolate. The results confirmed that RT-PCR is not only able to detect and differentiate decline-inducing and non-decline-inducing isolates of CTV in Florida, but also can detect both isolate types in a single field sweet orange or grapefruit tree. For most samples, results from RT-PCR, ELISA, and DTBIA were the same. However, the 320-bp fragments produced only from decline-inducing isolates were amplified from two sweet orange and two grapefruit samples that did not react with decline-inducing CTV-specific monoclonal antibody MCA13 in ELISA or DTBIA, indicating that RT-PCR has a higher sensitivity than these immunological tests for field sweet orange or grapefruit samples. Thus, RT-PCR is a simple, rapid, and specific procedure for CTV identification applicable to both research and diagnostic needs.

scholarly journals Discrimination Between Mild and Severe Citrus tristeza virus Isolates with a Rapid and Highly Specific Real-Time Reverse Transcription-Polymerase Chain Reaction Method Using TaqMan LNA Probes

2009 ◽  
Vol 99 (3) ◽  
pp. 307-315 ◽  
Author(s):  
S. Ruiz-Ruiz ◽  
P. Moreno ◽  
J. Guerri ◽  
S. Ambrós
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Reverse Transcription ◽  
Citrus Tristeza Virus ◽  
Dynamic Range ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Tristeza Virus ◽  
Citrus Tristeza

Severe isolates of Citrus tristeza virus (CTV) inducing seedling yellows (SY) and/or stem pitting (SP) in grapefruit or sweet orange are a major threat for the citrus industry worldwide. Identification of these CTV variants was achieved by quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) using a general primer set and three TaqMan locked nucleic acids (LNA) probes targeting sequences characteristic of severe, mild (non-SY, non-SP), and T36-like isolates. Successful amplification was achieved from fresh or silica-desiccated CTV-infected samples and all isolates but one reacted with one or more probes. Standard curves using RNA transcripts homologous to the three probes allowed a reproducible quantitative assay, with a wide dynamic range of detection starting with 102 copies. RT-PCR assays with homologous and heterologous transcript RNA mixes demonstrated that each probe reacted only with its cognate sequence which was detected even at ratios below 2.5%. Analysis of 56 pathogenically distinct CTV isolates from 20 countries showed that mild isolates reacted only with the mild probe, whereas severe SP and SY isolates reacted with the severe-SP or the T36-like probes, respectively, and often with a second probe. This procedure can be useful to identify and control potentially dangerous CTV isolates in areas affected only by mild isolates.

scholarly journals A meta-analysis of accuracy and sensitivity of chest CT and RT-PCR in COVID-19 diagnosis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Fatemeh Khatami ◽  
Mohammad Saatchi ◽  
Seyed Saeed Tamehri Zadeh ◽  
Zahra Sadat Aghamir ◽  
Alireza Namazi Shabestari ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcriptase ◽  
Ct Scan ◽  
Predictive Value ◽  
Meta Analysis ◽  
Chest Ct ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Chest Ct Scan

AbstractNowadays there is an ongoing acute respiratory outbreak caused by the novel highly contagious coronavirus (COVID-19). The diagnostic protocol is based on quantitative reverse-transcription polymerase chain reaction (RT-PCR) and chests CT scan, with uncertain accuracy. This meta-analysis study determines the diagnostic value of an initial chest CT scan in patients with COVID-19 infection in comparison with RT-PCR. Three main databases; PubMed (MEDLINE), Scopus, and EMBASE were systematically searched for all published literature from January 1st, 2019, to the 21st May 2020 with the keywords "COVID19 virus", "2019 novel coronavirus", "Wuhan coronavirus", "2019-nCoV", "X-Ray Computed Tomography", "Polymerase Chain Reaction", "Reverse Transcriptase PCR", and "PCR Reverse Transcriptase". All relevant case-series, cross-sectional, and cohort studies were selected. Data extraction and analysis were performed using STATA v.14.0SE (College Station, TX, USA) and RevMan 5. Among 1022 articles, 60 studies were eligible for totalizing 5744 patients. The overall sensitivity, specificity, positive predictive value, and negative predictive value of chest CT scan compared to RT-PCR were 87% (95% CI 85–90%), 46% (95% CI 29–63%), 69% (95% CI 56–72%), and 89% (95% CI 82–96%), respectively. It is important to rely on the repeated RT-PCR three times to give 99% accuracy, especially in negative samples. Regarding the overall diagnostic sensitivity of 87% for chest CT, the RT-PCR testing is essential and should be repeated to escape misdiagnosis.

scholarly journals Use of immunodot blot and multiplex reverse transcriptase-polymerase chain reaction in dengue virus detection in macerates of Aedes aegypti larvae

2012 ◽  
Vol 3 (1) ◽  
pp. 13
Author(s):  
Aline T.A. Chagas ◽  
Michelle D. Oliveira ◽  
Jose M.S. Mezencio ◽  
Eduardo A.M. Silva ◽  
Leandro L. Oliveira ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Aedes Aegypti ◽  
Dengue Virus ◽  
Reverse Transcriptase ◽  
Epidemiological Surveillance ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Denv Serotypes ◽  
Polymerase Chain ◽  
Pcr Techniques

The <em>Dengue virus</em> is the main arbovirus that affects man in terms of morbidity and mortality. The detection of the virus is very important for epidemiological surveillance, so here we propose to standardize and compare the immunodot blot (IDB) and multiplex reverse transcriptase-polymerase chain reaction (M-RT-PCR) techniques to detect and characterize the dengue virus (DENV) serotypes in samples of <em>Aedes aegypti</em> larvae. Thus, the IDB and M-RT-PCR techniques were standardized using macerated samples of larvae collected in nature. The use of monoclonal antibodies in IDB has not shown great results, but DENV detection through this method was possible using polyclonal antibodies. The distinction of serotypes 1, 2 and 3 was carried out by M-RT-PCR.

scholarly journals Deteksi Molekuler Virus Dengue dan Chikungunya pada Nyamuk Aedes spp. di Kecamatan Cilongok

2020 ◽  
Vol 2 (2) ◽  
pp. 181
Author(s):  
Dwi Iva Fitriana ◽  
Endang Srimurni Kusmintarsih ◽  
Trisnowati Budi Ambarningrum
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcriptase ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain

DBD dan chikungunya merupakan salah satu penyakit yang masih menjadi masalah di Indonesia. Kecamatan Cilongok merupakan salah kecamatan endemis DBD dan pernah mengalami KLB chikungunya. Deteksi virus pada nyamuk sebelum menginfeksi manusia penting sebagai peringatan dini dalam upaya pencegahan wabah di daerah endemis. Tujuan penelitian ini adalah mengetahui infeksi virus Dengue dan Chikungunya pada nyamuk Aedes spp. yang ditangkap. Penelitian ini dilakukan di empat desa di Kecamatan Cilongok yang meliputi Desa Cilongok, Pernasidi, Kalisari, dan Jatisaba, pengambilan sampel dilakukan secara purposive. Deteksi virus Dengue dan Chikungunya pada nyamuk dilakukan menggunakan metode Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR). Hasil positifitas virus dianalisis secara deskriptif untuk menggambarkan potensi transmisi virus. Hasil penelitian menunjukkan bahwa nyamuk Aedes spp. yang tertangkap tidak mengandung virus Dengue dan Chikungunya.  

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