Comparison of Polymerase Chain Reaction and Virus Isolation for Detection of Epizootic Hemorrhagic Disease Virus in Clinical Samples from Naturally Infected Deer

We compared our recently reported reverse transcriptase polymerase chain reaction (PCR)-based assay for detection of epizootic hemorrhagic disease virus (EHDV) in clinical samples with different virus isolation (VI) procedures. Thirty-six blood samples and 1 spleen sample from deer were assessed by the EHDV PCR assay and VI in baby hamster kidney (BHK)-21 cells and embryonated chicken eggs (ECE). The EHDV PCR assay detected EHDV RNA from 6 blood samples obtained from deer during 1988–1989 outbreaks of epizootic hemorrhagic disease and from the spleen and blood samples of a deer with clinical hemorrhagic disease in 1992. The 6 blood samples from the 1988–1989 outbreaks and the spleen sample from the 1992 case were VI positive on BHK-21 cell culture. The blood from the same deer with the PCR- and VI-positive spleen was VI negative in BHK-21 cells and ECE. All EHDV isolates were identified as EHDV serotype 2 by a plaque inhibition test. The results of this study indicate that the sensitivity of the previously described EHDV PCR assay is comparable to or greater than that of the VI method in BHK-21 cell culture or ECE. The EHDV PCR assays could provide a superior diagnostic alternative to the current cumbersome and time-consuming VI procedures.

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Rapid, Sensitive Bluetongue Virus Serogroup and Serotype Detection Using Polymerase Chain Reaction

10.32747/1995.7612836.bard ◽

1995 ◽

Author(s):

Bennie Osburn ◽

Marius Ianconescu ◽

Geoffrey Akita ◽

Rozalia Kaufman

Keyword(s):

Cell Culture ◽

Polymerase Chain Reaction ◽

Bluetongue Virus ◽

Animal Health ◽

Clinical Samples ◽

Chain Reaction ◽

Pcr Assay ◽

Diagnostic Pcr ◽

Polymerase Chain ◽

The U.S

The objectives of this proposal were to enhance animal health by 1) development of a BTV serogroup diagnostic assay using polymerase chain reaction (PCR) and 2) development of a BTV serotype specific diagnostic PCR assay. A PCR assay for diagnosis of bluetongue virus (BTV) serogroup from clinical samples meeting the criteria of objective 1 was developed. This PCR assay is more sensitive than virus isolation and has been adopted by both the U.S. and Israeli collaborating laboratories of this project, as well as at least one other U.S. laboratory for routine diagnosis of BTV infection in ruminants. The basic BTV PCR protocol has also become an essential tool in BTV molecular research in both collaborating laboratories. During development of the BTV serotype specific PCR we had the opportunity to investigate a nationwide outbreak of abortions and fatal disease in dogs in the U.S. purportedly due to BTV infection via a BTV contaminated canine vaccine. The BTV serogroup PCR was integral in confirming BTV in tissues from affected dogs and in lots of the suspect vaccine. This led to the first published report of BTV infection in dogs. We discovered that BTV can produce silent persistent infection in canine cell culture. This indicated a need for more stringent screening of biologics for occult BTV infection. A novel mixed cell culture method was developed to identify occult BTV and other occult viral infection cell cultures. Serotype specific primers for PCR detection of all U.S. BTV serotypes and two Israel serotypes (BTV-2 and 10) have been evaluated and are available. A subsequent collaboration would logically include sequencing of the L2 genes of Israel BTV-4, 6 and 16, allowing incorporation of these Israel BTV serotypes into a multiplex PCR assay.

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Detection of Epizootic Hemorrhagic Disease Virus Serotypes 1 and 2 in Cell Culture and Clinical Samples Using Polymerase Chain Reaction

Journal of Veterinary Diagnostic Investigation ◽

10.1177/104063879400600202 ◽

1994 ◽

Vol 6 (2) ◽

pp. 143-147 ◽

Cited By ~ 21

Author(s):

Imadeldin E. Aradaib ◽

Geoffrey Y. Akita ◽

Bennie I. Osburn

Keyword(s):

Polymerase Chain Reaction ◽

Cell Cultures ◽

Clinical Samples ◽

Hemorrhagic Disease ◽

Chain Reaction ◽

Pcr Assay ◽

Virus Particles ◽

Agarose Gels ◽

Virus Rna ◽

Polymerase Chain

The potential for the use of the polymerase chain reaction (PCR) in detecting epizootic hemorrhagic disease virus (EHDV) ribonucleic acid in cell cultures and clinical samples was studied. Using oligoribonucleotide primers selected from genome segment 6 of EHDV-2 (Alberta strain), the PCR-based assay resulted in a 387-base pair (bp) PCR product. EHDV RNA from US prototype serotypes 1 and 2 and a number of EHDV field isolates, propagated in cell cultures, were detected by this EHDV PCR-based assay. Amplification products were visualized on ethidium bromide-stained agarose gels or detected by chemiluminescent hybridization. The sensitivity of the PCR assay was 100 fg of virus RNA (equivalent to 6 × 103 virus particles) with ethidium bromide-stained agarose gels. Chemiluminescent hybridization increased the sensitivity of the PCR assay 1,000 times, and specific signals were detected from 0.1 fg of virus RNA (equivalent to 6 virus particles). Amplification product was not detected when the PCR-based assay was applied to RNA from the US bluetongue (BT) virus prototype serotypes 2, 10, 11, 13, and 17 or total nucleic acid extracts from uninfected baby hamster kidney-21 cells, Vero cells, and blood cells from deer that were EHDV seronegative and virus isolation negative. Application of this EHDV PCR-based assay to clinical samples resulted in detection of EHDV RNA from blood and spleen samples from a deer in California with clinical hemorrhagic disease. This EHDV PCR-based assay could provide a rapid, sensitive, and specific assay for detection of EHDV infection in susceptible ruminants.

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Analysis and validation of a highly sensitive one-step nested quantitative real-time polymerase chain reaction assay for specific detection of severe acute respiratory syndrome coronavirus 2

Virology Journal ◽

10.1186/s12985-020-01467-y ◽

2020 ◽

Vol 17 (1) ◽

Author(s):

Yang Zhang ◽

Chunyang Dai ◽

Huiyan Wang ◽

Yong Gao ◽

Tuantuan Li ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Real Time ◽

Quantitative Polymerase Chain Reaction ◽

Clinical Samples ◽

Chain Reaction ◽

Pcr Assay ◽

Qrt Pcr ◽

Highly Sensitive ◽

One Step ◽

Polymerase Chain

Abstract Background Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, is posing a serious threat to global public health. Reverse transcriptase real-time quantitative polymerase chain reaction (qRT-PCR) is widely used as the gold standard for clinical detection of SARS-CoV-2. Due to technical limitations, the reported positive rates of qRT-PCR assay of throat swab samples vary from 30 to 60%. Therefore, the evaluation of alternative strategies to overcome the limitations of qRT-PCR is required. A previous study reported that one-step nested (OSN)-qRT-PCR revealed better suitability for detecting SARS-CoV-2. However, information on the analytical performance of OSN-qRT-PCR is insufficient. Method In this study, we aimed to analyze OSN-qRT-PCR by comparing it with droplet digital PCR (ddPCR) and qRT-PCR by using a dilution series of SARS-CoV-2 pseudoviral RNA and a quality assessment panel. The clinical performance of OSN-qRT-PCR was also validated and compared with ddPCR and qRT-PCR using specimens from COVID-19 patients. Result The limit of detection (copies/ml) of qRT-PCR, ddPCR, and OSN-qRT-PCR were 520.1 (95% CI: 363.23–1145.69) for ORF1ab and 528.1 (95% CI: 347.7–1248.7) for N, 401.8 (95% CI: 284.8–938.3) for ORF1ab and 336.8 (95% CI: 244.6–792.5) for N, and 194.74 (95% CI: 139.7–430.9) for ORF1ab and 189.1 (95% CI: 130.9–433.9) for N, respectively. Of the 34 clinical samples from COVID-19 patients, the positive rates of OSN-qRT-PCR, ddPCR, and qRT-PCR were 82.35% (28/34), 67.65% (23/34), and 58.82% (20/34), respectively. Conclusion In conclusion, the highly sensitive and specific OSN-qRT-PCR assay is superior to ddPCR and qRT-PCR assays, showing great potential as a technique for detection of SARS-CoV-2 in patients with low viral loads.

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Comparison of Virus Isolation and Reverse Transcription Polymerase Chain Reaction Assay for Detection of Bovine Viral Diarrhea Virus in Bulk Milk Tank Samples

Journal of Veterinary Diagnostic Investigation ◽

10.1177/104063870001200219 ◽

2000 ◽

Vol 12 (2) ◽

pp. 184-186 ◽

Cited By ~ 41

Author(s):

R. W. Renshaw ◽

R. Ray ◽

E. J. Dubovi

Keyword(s):

Infected Animal ◽

Virus Isolation ◽

Rt Pcr ◽

Chain Reaction ◽

Pcr Assay ◽

Diarrhea Virus ◽

Bulk Milk ◽

Polymerase Chain ◽

Viral Diarrhea Virus ◽

Bulk Milk Tank

The use of a reverse transcriptase polymerase chain reaction (RT-PCR) assay to screen bulk milk tank samples for bovine viral diarrhea virus (BVDV) has proven to be a sensitive and economical means to evaluate the lactating animals in a herd. The assay is capable of detecting the presence of a single persistently infected animal within a group of several hundred cows. Over a 3–year period, 144 samples from 97 farms were tested for BVDV using an RT-PCR assay in conjunction with a classical virus isolation (VI) procedure to measure the relative effectiveness of the techniques. Virus could be detected with both methods when the milk from a single persistently infected animal was diluted 1:600 with the milk from a herd of BVDV-negative animals. Based on individual farms, there was an overall prevalence of 12.4% BVDV infection, and the correlation between the 2 assays was 95.9%. In terms of sensitivity, specificity, and turnaround time, RT-PCR was superior to VI. However, of the 17 samples that were VI positive, 4 were RT-PCR negative. RT-PCR may not detect all naturally occurring BVDV isolates because they may contain minor sequence variations in the primer regions. VI and RT-PCR are both suitable for detection of BVDV in bulk milk samples when used independently, but to increase the probability of successful detection and to provide cross-checks against assay contamination, it is desirable to utilize both methods in parallel.

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Evaluation of Amplification Targets for the Specific Detection ofBordetella pertussisUsing Real-Time Polymerase Chain Reaction

Canadian Journal of Infectious Diseases and Medical Microbiology ◽

10.1155/2014/763128 ◽

2014 ◽

Vol 25 (4) ◽

pp. 217-221 ◽

Cited By ~ 7

Author(s):

Mohammad Rubayet Hasan ◽

Rusung Tan ◽

Ghada N Al-Rawahi ◽

Eva Thomas ◽

Peter Tilley

Keyword(s):

Polymerase Chain Reaction ◽

Real Time ◽

Target Genes ◽

Reference Panel ◽

Superior Performance ◽

Clinical Samples ◽

Analytical Sensitivity ◽

Chain Reaction ◽

Pcr Assay ◽

Polymerase Chain

BACKGROUND:Bordetella pertussisinfections continue to be a major public health challenge in Canada. Polymerase chain reaction (PCR) assays to detectB pertussisare typically based on the multicopy insertion sequence IS481, which offers high sensitivity but lacks species specificity.METHODS: A novelB pertussisreal-time PCR assay based on the porin gene was tested in parallel with several previously published assays that target genes such as IS481,ptx-promoter, pertactin and a putative thialase. The assays were evaluated using a reference panel of common respiratory bacteria including differentBordetellaspecies and 107 clinical nasopharyngeal specimens. Discrepant results were confirmed by sequencing the PCR products.RESULTS: Analytical sensitivity was highest for the assay targeting the IS481element; however, the assay lacked specificity forB pertussisin the reference panel and in the clinical samples. False-positive results were also observed with assays targeting theptx-promoter and pertactin genes. A PCR assay based on the thialase gene was highly specific but failed to detect all reference strains ofB pertussis. However, a novel assay targeting the porin gene demonstrated high specificity forB pertussisboth in the reference panel and in clinical samples and, based on sequence-confirmed results, correctly predicted allB pertussis-positive cases in clinical samples. According to Probit regression analysis, the 95% detection limit of the new assay was 4 colony forming units/reaction.CONCLUSION: A novel porin assay forB pertussisdemonstrated superior performance and may be useful for improved molecular detection ofB pertussisin clinical specimens.

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Systematic Review and Meta-analysis of Real-time Polymerase Chain Reaction assay for the detection of COVID-19 from clinical samples in low-and middle-income countries: Protocol

10.21203/rs.3.rs-960246/v1 ◽

2021 ◽

Author(s):

Emmanuel Oladipo Babafemi

Keyword(s):

Systematic Review ◽

Polymerase Chain Reaction ◽

Real Time ◽

Meta Analysis ◽

Clinical Samples ◽

Rt Pcr ◽

Chain Reaction ◽

Pcr Assay ◽

Middle Income ◽

Polymerase Chain

Abstract Background: COVID-19 has spread globally since its discovery in Hubei province, China in December 2019 and became pandemic in 2020. COVID-19 is a new betacoronavirus and a variant of severe acute respiratory syndrome coronavirus 2 (SARA- CoV-2). Rapid, accurate and reliable diagnosis of COVID-19 will prevent the spread and allow for appropriate management. The main objective of this systematic review is to identify, appraise and summarise the published evidence on the diagnostic performance and effectiveness of SARS-CoV-2 virus in the diagnosis of current or previous COVID-19 using real-time polymerase chain reaction (RT-PCR) assay in low-and middle-income countries (LMICs). Methods: We will search MEDLINE/PubMed, EMBASE, BIOSIS, LILACS, Cochrane Infectious Diseases Group Specialised Register (CIDG SR), Global Health, and CINAHL for published studies for the diagnosis of COVID-19 using real-time polymerase chain reaction assay in LMICs There will be no restriction regarding the language, date of publication, and publication status. We will include retrospective, cross-sectional and cohort observational studies will be included in the review. Selection of studies, data extraction and management, assessment of risk of bias, and quality of evidence will be performed by two independent reviewers (EB and BC). A third researcher (GM) will be consulted in case of discrepancies. Depending on the availability and quality of the data, a meta-analysis will be performed. Otherwise, findings will be qualitatively reported. Discussion: To our knowledge, this is the first systematic review and meta-analysis to assess the uptake of RT-PCR assay for SARS-CoV-2 detection from clinical samples in human in LMICs. This review will make available evidence on the uptake, accuracy, approach, and interpretation of results of this assay in the context of COVID-19 diagnosis which will meet an urgent need, considering the diagnostic challenges of RT-PCR assay for COVID-19 diagnosis in humans. Systematic review registration: PROSPERO CRD42021271894

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Analysis and validation of a highly sensitive one-step nested quantitative real-time polymerase chain reaction assay for specific detection of severe acute respiratory syndrome coronavirus 2

10.21203/rs.3.rs-74067/v1 ◽

2020 ◽

Author(s):

Yang Zhang ◽

Chunyang Dai ◽

Huiyan Wang ◽

Yong Gao ◽

Tuantuan Li ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Real Time ◽

Quantitative Polymerase Chain Reaction ◽

Clinical Samples ◽

Chain Reaction ◽

Pcr Assay ◽

Qrt Pcr ◽

Highly Sensitive ◽

One Step ◽

Polymerase Chain

Abstract Background Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, is posing a serious threat to global public health. Reverse transcriptase real-time quantitative polymerase chain reaction (qRT-PCR) is widely used as the gold standard for clinical detection of SARS-CoV-2. Due to technical limitations, the reported positive rates of qRT-PCR assay of throat swab samples vary from 30–60%. Therefore, the evaluation of alternative strategies to overcome the limitations of qRT-PCR is required. A previous study reported that one-step nested (OSN)-qRT-PCR revealed better suitability for detecting SARS-CoV-2. However, information on the analytical performance of OSN-qRT-PCR is insufficient. Method: In this study, we aimed to analyze OSN-qRT-PCR by comparing it with droplet digital PCR (ddPCR) and qRT-PCR by using a dilution series of SARS-CoV-2 pseudoviral RNA and a quality assessment panel. The clinical performance of OSN-qRT-PCR was also validated and compared with ddPCR and qRT-PCR using specimens from COVID-19 patients. Result The LoD (copies/ml) of qRT-PCR, ddPCR, and OSN-qRT-PCR were 520.1 (95% CI): 363.23–1145.69) for ORF1ab and 528.1 (95% CI: 347.7–1248.7) for N, 401.8 (95% CI: 284.8–938.3) for ORF1ab and 336.8 (95% CI: 244.6–792.5) for N, and 194.74 (95% CI: 139.7–430.9) for ORF1ab and 189.1 (95% CI: 130.9–433.9) for N, respectively. Of the 34 clinical samples from COVID-19 patients, the positive rates of OSN-qRT-PCR, ddPCR, and qRT-PCR were 82.35% (28/34), 67.65% (23/34), and 58.82% (20/34), respectively. Conclusion In conclusion, the highly sensitive and specific OSN-qRT-PCR assay is superior to ddPCR and qRT-PCR assays, showing great potential as a technique for detection of SARS-CoV-2 in patients with low viral loads.

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DETECTION OF RESPIRATORY SYNCITIAL VIRUS (RSV) IN LOWER ACUTE RESPIRATORY INFECTIONS BY NESTED REVERSE TRANSCRIPTION- POLYMERASE CHAIN REACTION

Journal of Medicine and Pharmacy ◽

10.34071/jmp.2011.3.2 ◽

2011 ◽

pp. 11-15

Author(s):

Keyword(s):

Polymerase Chain Reaction ◽

Reverse Transcription ◽

Respiratory Infections ◽

Clinical Samples ◽

Acute Respiratory Infections ◽

Rt Pcr ◽

Minimal Level ◽

Chain Reaction ◽

Pcr Assay ◽

Polymerase Chain

Objective: To develop and apply a nested reverse transcription- polymerase chain reaction (nested RT-PCR) for detection of RSV in lower acute respiratory infections. Materials and methods: A nested reverse transcription- polymerase chain reaction was used to amplify a sequence of the F gene in the RSV genomic RNA, optimized and compared the sensitivity and specificity of this assay with the control samples and then applied this procedure for diagnosing RSV from clinical samples. Results: This nested RT-PCR assay amplified the specific target fragment of RSV RNA and did not amplify any sequence of genomes of the tested common viruses and bacteria causing respiratory infections. The minimal level of detection of this procedure was 102 copies/ml. Results for detection of RSV on 109 samples of throat swabs or nasopharyngeal swabs from children with lower respiratory infections showed that twenty seven patients were positive with RSV ( 24.8%), among which six out of 30 (20%) were with bronchitis, seven out of 26 ( 27%) were with bronchiolitis and fourteen out of 53 (26.4%) were with pneumonia. Conclusion: This nested RT-PCR was found to be useful and reliable for detection of RSV in respiratory infections.

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A Comparison of Polymerase Chain Reaction with and without RNA Extraction and Virus Isolation for Detection of Bovine Viral Diarrhea Virus in Young Calves

Journal of Veterinary Diagnostic Investigation ◽

10.1177/104063870201400516 ◽

2002 ◽

Vol 14 (5) ◽

pp. 433-437 ◽

Cited By ~ 16

Author(s):

D. Deregt ◽

P. S. Carman ◽

R. M. Clark ◽

K. M. Burton ◽

W. O. Olson ◽

...

Keyword(s):

Virus Isolation ◽

Rna Extraction ◽

Bovine Viral Diarrhea ◽

Chain Reaction ◽

Pcr Assay ◽

Diarrhea Virus ◽

Viral Diarrhea ◽

Polymerase Chain ◽

Pcr Assays ◽

Viral Diarrhea Virus

Previously, the authors described a multiplex reverse transcriptase–polymerase chain reaction (PCR) assay for detection and typing of bovine viral diarrhea virus (BVDV) from blood of persistently infected (PI) cattle that could be used with or without RNA extraction. In the present study, the PCR assay was evaluated for its ability to detect BVDV in young calves as a screening tool for detection of persistent infections. Both methods, PCR after RNA extraction (rPCR) and the direct method without RNA extraction (dPCR) were applied and compared with virus isolation (VI) with diagnostic specimens. From 450 whole blood samples from Ontario calves, 47 and 39 samples were positive by rPCR and VI, respectively. From the 47 samples positive by rPCR, 45 (96%) also were positive by dPCR when samples were tested both undiluted and diluted 1:10. In comparison to VI, the relative sensitivities of both PCR assays were 100%. Examination of the results indicates that both PCR assays can be used for screening calves for persistent infection with BVDV.

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