HIV-1 low-level viraemia assessed with 3 commercial real-time PCR assays show high variability

Background. Several studies have compared the use of dried blot spot (DBS) as an alternative to plasma specimens, mainly using Whatman 903 cards as filter paper. The aim of this study was to evaluate the use of Whatman FTA card (FTA card) specimens for HIV-1 viral load testing compared to plasma specimens using two real-time PCR assays manufactured by Roche and Abbott. Methodology. A cross-sectional study was conducted between April 2017 and September 2017 on HIV-1 patients admitted to Yalgado Ouédraogo Teaching Hospital. Paired FTA cards and plasma specimens were collected and analysed using the Abbott Real-Time HIV-1 assay (Abbott) and COBAS AmpliPrep/COBAS TaqMan v2.0 (Roche). Results. In total, 107 patients were included. No statistical differences (P>0.05) were observed between the mean viral loads obtained from the FTA cards and those of the plasma specimens using the Roche and Abbott assays. In total, 29 samples with Roche and 15 samples with Abbott assay showed discrepant results. At viral loads of ≤1000 copies ml−1, the sensitivity and specificity of the FTA cards were 78.6 and 100% with Roche, and 92.3 and 95.9% with Abbott, respectively. Both the Roche and Abbott assays showed good correlation and agreement between the FTA cards and plasma values. Conclusion. Our study demonstrates the feasibility of using FTA card filter paper for HIV-1 viral load testing. However, further studies will be required for the validation of the use of FTA card filter paper in HIV-1 treatment monitoring.

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Analytical sensitivity of three real-time PCR assays for measuring subtype B HIV-1 RNA

Journal of Clinical Virology ◽

10.1016/j.jcv.2012.12.017 ◽

2013 ◽

Vol 57 (1) ◽

pp. 80-83 ◽

Cited By ~ 9

Author(s):

K. Sauné ◽

C. Delaugerre ◽

S. Raymond ◽

F. Nicot ◽

J. Boineau ◽

...

Keyword(s):

Real Time ◽

Real Time Pcr ◽

Analytical Sensitivity ◽

Subtype B ◽

Pcr Assays ◽

Hiv 1

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Reproducibility of Roche cobas HIV-1, HBV and HCV real-time PCR assays on cobas 4800 in comparison with COBAS AmpliPrep/COBAS TaqMan assay equivalents

International Journal of Infectious Diseases ◽

10.1016/j.ijid.2020.09.527 ◽

2020 ◽

Vol 101 ◽

pp. 197

Author(s):

M.N. Abdul Samat ◽

Z. Zainol Rashid ◽

A. Noordin ◽

N.H. Ghulam ◽

N. Ismail

Keyword(s):

Real Time ◽

Real Time Pcr ◽

Taqman Assay ◽

Cobas Taqman ◽

Pcr Assays ◽

Hiv 1 ◽

Roche Cobas

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DEVELOPMENT OF MULTIPLEX REAL-TIME PCR ASSAY FOR SIX PATHOGENS: RAPID TOOL FOR DIAGNOSIS OF BACTERIAL MENINGITIS

Journal of Medicine and Pharmacy ◽

10.34071/jmp.2019.3.8 ◽

2019 ◽

pp. 60-66

Author(s):

Viet Quynh Tram Ngo ◽

Thi Ti Na Nguyen ◽

Hoang Bach Nguyen ◽

Thi Tuyet Ngoc Tran ◽

Thi Nam Lien Nguyen ◽

...

Keyword(s):

Bacterial Meningitis ◽

Real Time ◽

Real Time Pcr ◽

Diagnostic Methods ◽

Type B ◽

E Coli ◽

Pcr Assays ◽

Set Up ◽

Etiological Agents ◽

Suis Serotype

Introduction: Bacterial meningitis is an acute central nervous infection with high mortality or permanent neurological sequelae if remained undiagnosed. However, traditional diagnostic methods for bacterial meningitis pose challenge in prompt and precise identification of causative agents. Aims: The present study will therefore aim to set up in-house PCR assays for diagnosis of six pathogens causing the disease including H. influenzae type b, S. pneumoniae, N. meningitidis, S. suis serotype 2, E. coli and S. aureus. Methods: inhouse PCR assays for detecting six above-mentioned bacteria were optimized after specific pairs of primers and probes collected from the reliable literature resources and then were performed for cerebrospinal fluid (CSF) samples from patients with suspected meningitis in Hue Hospitals. Results: The set of four PCR assays was developed including a multiplex real-time PCR for S. suis serotype 2, H. influenzae type b and N. meningitides; three monoplex real-time PCRs for E. coli, S. aureus and S. pneumoniae. Application of the in-house PCRs for 116 CSF samples, the results indicated that 48 (39.7%) cases were positive with S. suis serotype 2; one case was positive with H. influenzae type b; 4 cases were positive with E. coli; pneumococcal meningitis were 19 (16.4%) cases, meningitis with S. aureus and N. meningitidis were not observed in any CSF samples in this study. Conclusion: our in-house real-time PCR assays are rapid, sensitive and specific tools for routine diagnosis to detect six mentioned above meningitis etiological agents. Key words: Bacterial meningitis, etiological agents, multiplex real-time PCR

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Faculty Opinions recommendation of Evaluation of conventional and real-time PCR assays using two targets for confirmation of results of the COBAS AMPLICOR Chlamydia trachomatis/Neisseria gonorrhoeae test for detection of Neisseria gonorrhoeae in clinical samples.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1025709.374387 ◽

2006 ◽

Author(s):

David Persing

Keyword(s):

Chlamydia Trachomatis ◽

Neisseria Gonorrhoeae ◽

Real Time ◽

Real Time Pcr ◽

Clinical Samples ◽

Pcr Assays

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Faculty Opinions recommendation of Comparison of real-time PCR assays for monitoring serum hepatitis B virus DNA levels during antiviral therapy.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1040569.489566 ◽

2006 ◽

Author(s):

David Persing

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Antiviral Therapy ◽

Real Time ◽

Real Time Pcr ◽

Serum Hepatitis ◽

Hepatitis B Virus Dna ◽

B Virus ◽

Pcr Assays

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Differing Effects of Standard and Harsh Nucleic Acid Extraction Procedures on Diagnostic Helminth Real-Time PCRs Applied to Human Stool Samples

Pathogens ◽

10.3390/pathogens10020188 ◽

2021 ◽

Vol 10 (2) ◽

pp. 188

Author(s):

Tanja Hoffmann ◽

Andreas Hahn ◽

Jaco J. Verweij ◽

Gérard Leboulle ◽

Olfert Landt ◽

...

Keyword(s):

Nucleic Acid ◽

Real Time ◽

Real Time Pcr ◽

Acid Extraction ◽

Nucleic Acid Extraction ◽

Pcr Assay ◽

Bead Beating ◽

Stool Samples ◽

Pcr Assays ◽

Human Stool

This study aimed to assess standard and harsher nucleic acid extraction schemes for diagnostic helminth real-time PCR approaches from stool samples. A standard procedure for nucleic acid extraction from stool and a procedure including bead-beating as well as proteinase K digestion were compared with group-, genus-, and species-specific real-time PCR assays targeting helminths and nonhelminth pathogens in human stool samples. From 25 different in-house and commercial helminth real-time PCR assays applied to 77 stool samples comprising 67 historic samples and 10 external quality assessment scheme samples positively tested for helminths, higher numbers of positive test results were observed after bead-beating-based nucleic acid extraction for 5/25 (20%) real-time PCR assays irrespective of specificity issues. Lower cycle threshold values were observed for one real-time PCR assay after the standard extraction scheme, and for four assays after the bead-beating-based scheme. Agreement between real-time PCR results after both nucleic acid extraction strategies according to Cohen’s kappa ranged from poor to almost perfect for the different assays. Varying agreement was observed in eight nonhelminth real-time PCR assays applied to 67 historic stool samples. The study indicates highly variable effects of harsh nucleic acid extraction approaches depending on the real-time PCR assay used.

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Comparative Assessment of In-House Real-Time PCRs Targeting Enteric Disease-Associated Microsporidia in Human Stool Samples

Pathogens ◽

10.3390/pathogens10060656 ◽

2021 ◽

Vol 10 (6) ◽

pp. 656

Author(s):

Konstantin Tanida ◽

Andreas Hahn ◽

Kirsten Alexandra Eberhardt ◽

Egbert Tannich ◽

Olfert Landt ◽

...

Keyword(s):

Real Time ◽

Indigenous People ◽

Real Time Pcr ◽

Latent Class ◽

Enterocytozoon Bieneusi ◽

Enteric Disease ◽

Immunosuppressed Patients ◽

Study Population ◽

Stool Samples ◽

Pcr Assays

Microsporidiosis is an infection predominantly occurring in immunosuppressed patients and infrequently also in travelers. This study was performed to comparatively evaluate the diagnostic accuracy of real-time PCR assays targeting microsporidia with etiological relevance in the stool of human patients in a latent class analysis-based test comparison without a reference standard with perfect accuracy. Thereby, two one-tube real-time PCR assays and two two-tube real-time PCR assays targeting Enterocytozoon bieneusi and Encephalocytozoon spp. were included in the assessment with reference stool material (20), stool samples from Ghanaian HIV-positive patients (903), and from travelers, migrants and Colombian indigenous people (416). Sensitivity of the assays ranged from 60.4% to 97.4% and specificity from 99.1% to 100% with substantial agreement according to Cohen’s kappa of 79.6%. Microsporidia DNA was detected in the reference material and the stool of the HIV patients but not in the stool of the travelers, migrants, and the Colombian indigenous people. Accuracy-adjusted prevalence was 5.8% (n = 78) for the study population as a whole. In conclusion, reliable detection of enteric disease-associated microsporidia in stool samples by real-time PCR could be demonstrated, but sensitivity between the compared microsporidia-specific real-time PCR assays varied.

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