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Shofa M, Ohkawa A, Okabayashi T, Kaneko Y, Saito A. Development of a direct duplex real-time PCR assay for rapid detection of domestic cat hepadnavirus. J Vet Diagn Invest 2023; 35:139-144. [PMID: 36786316 PMCID: PMC9999387 DOI: 10.1177/10406387231154610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Domestic cat hepadnavirus (DCH) is a novel hepadnavirus, first identified in 2018. DCH is generally detected using conventional PCR assays, which include time-consuming agarose gel electrophoresis. We developed a rapid, sensitive, and specific real-time PCR (rtPCR) assay for the detection of the DCH genome. To streamline the procedure, our rtPCR assay was carried out using blood samples, without DNA extraction. A consensus primers/probe set was designed based on the nucleotide sequences of the surface/polymerase gene of all DCH strains available in GenBank. To exclude the possibility that the PCR reaction was blocked by anticoagulants, we also used a primers/probe set for amplifying the cat beta-actin gene as a reference gene. Our direct duplex rtPCR assay had high sensitivity, with a limit of detection of 10 copies/μL of blood for DCH. Our direct duplex rtPCR assay should be a useful tool for DCH detection and surveillance.
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Affiliation(s)
- Maya Shofa
- Department of Veterinary Science, University of Miyazaki, Miyazaki, Japan
- Faculty of Agriculture; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
| | - Akiho Ohkawa
- Department of Veterinary Science, University of Miyazaki, Miyazaki, Japan
| | - Tamaki Okabayashi
- Department of Veterinary Science, University of Miyazaki, Miyazaki, Japan
- Faculty of Agriculture; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Yasuyuki Kaneko
- Veterinary Teaching Hospital, University of Miyazaki, Miyazaki, Japan
| | - Akatsuki Saito
- Department of Veterinary Science, University of Miyazaki, Miyazaki, Japan
- Faculty of Agriculture; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
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Gutema G, Hailu H, W/semeyat B, Yilma A, Abdela S, Kidane E, Adane S, Yimer M, Tsegaye A. Effect of sample management on quantitative HIV-1 viral load measurement at Saint Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia. PLoS One 2022; 17:e0269943. [PMID: 35700178 PMCID: PMC9197020 DOI: 10.1371/journal.pone.0269943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 06/01/2022] [Indexed: 11/18/2022] Open
Abstract
Purpose This study was meant to determine the effect of time to plasma separation, storage duration, freeze-thawing cycle and dilution proportion on the HIV-1 viral load level. Methods Experimental study design was employed by collecting 10mL whole blood samples into two EDTA tubes from 88 eligible HIV infected patients at St Paul’s Hospital Millennium Medical College. The viral load test was done using Abbott m2000sp/rt analyzer. Data was entered into Microsoft excel and analyzed by SPSS version 20. Repeated measure analysis of variance was used to compare HIV RNA viral load mean difference between different time to plasma separation, storage, freeze-thawing cycles and dilution levels. Post-hoc analysis was employed to locate the place of significant differences. P value less than 0.05 was used to declare statistical significance while viral RNA level of 0.5 log copies/ml was used to determine clinical significance. Results There was significant HIV-1 RNA viral load log mean difference between plasma separation time at 6 hours (hrs) and 24hrs (p<0.001). There was also significant HIV-1 RNA viral load log mean difference between plasma tested within 6hrs and those stored at 2–8°C for 15 days (p = 0.006), and between plasma stored at 2–8°C for 6 days versus 15 days (p<0.001). There was significant log mean difference between plasma that was exposed to fourth cycle of freeze-thawing after storage at -20°C when compared with plasma tested within 6hrs (p = 0.013). Conclusion Plasma separated at 24hrs, stored at 2–8°C for 15 days or freeze-thawed for four cycles had significant effect on HIV viral load level. However, the differences were not clinically significant at a cut-off viral load level of 0.5 log copies/ml. Avoiding delays to plasma separation beyond 24 hrs, storing at 2–8°C for 15 days and freeze-thawing for no more than 4 cycles is recommended to improve the result quality.
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Affiliation(s)
- Gadissa Gutema
- HIV/AIDS Disease Research Team, TB and HIV/AIDS Disease Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- * E-mail:
| | - Habtyes Hailu
- TB Disease Research Team, TB and HIV/AIDS Disease Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Belete W/semeyat
- HIV/AIDS Disease Research Team, TB and HIV/AIDS Disease Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Amelework Yilma
- HIV/AIDS Disease Research Team, TB and HIV/AIDS Disease Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Saro Abdela
- HIV/AIDS Disease Research Team, TB and HIV/AIDS Disease Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Eleni Kidane
- HIV/AIDS Disease Research Team, TB and HIV/AIDS Disease Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Sisay Adane
- HIV/AIDS Disease Research Team, TB and HIV/AIDS Disease Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Mengistu Yimer
- HIV/AIDS Disease Research Team, TB and HIV/AIDS Disease Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Aster Tsegaye
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
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The Development of a Standardized Quality Assessment Material to Support Xpert ® HIV-1 Viral Load Testing for ART Monitoring in South Africa. Diagnostics (Basel) 2021; 11:diagnostics11020160. [PMID: 33499162 PMCID: PMC7911816 DOI: 10.3390/diagnostics11020160] [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: 11/30/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 11/17/2022] Open
Abstract
The tiered laboratory framework for human immunodeficiency virus (HIV) viral load monitoring accommodates a range of HIV viral load testing platforms, with quality assessment critical to ensure quality patient testing. HIV plasma viral load testing is challenged by the instability of viral RNA. An approach using an RNA stabilizing buffer is described for the Xpert® HIV-1 Viral Load (Cepheid) assay and was tested in remote laboratories in South Africa. Plasma panels with known HIV viral titres were prepared in PrimeStore molecular transport medium for per-module verification and per-instrument external quality assessment. The panels were transported at ambient temperatures to 13 testing laboratories during 2017 and 2018, tested according to standard procedures and uploaded to a web portal for analysis. A total of 275 quality assessment specimens (57 verification panels and two EQA cycles) were tested. All participating laboratories met study verification criteria (n = 171 specimens) with an overall concordance correlation coefficient (ρc) of 0.997 (95% confidence interval (CI): 0.996 to 0.998) and a mean bias of −0.019 log copies per milliliter (cp/mL) (95% CI: −0.044 to 0.063). The overall EQA ρc (n = 104 specimens) was 0.999 (95% CI: 0.998 to 0.999), with a mean bias of 0.03 log cp/mL (95% CI: 0.02 to 0.05). These panels are suitable for use in quality monitoring of Xpert® HIV-1 VL and are applicable to laboratories in remote settings.
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Newman H, Hardie D. HIV-1 viral load testing in resource-limited settings: Challenges and solutions for specimen integrity. Rev Med Virol 2020; 31:e2165. [PMID: 32978882 DOI: 10.1002/rmv.2165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/20/2020] [Accepted: 08/22/2020] [Indexed: 11/07/2022]
Abstract
HIV-1 viral load (VL) testing is a crucial element in providing an antiretroviral treatment monitoring program. The success of these programs depends on the availability and quality of the VL testing services. There are several pre-analytic factors which can affect the quality of VL testing. Many of the challenges faced by resource-limited countries result in a compromise of specimen integrity, thus limiting widespread access to VL monitoring. The various logistic and financial challenges that exist are not insurmountable and several innovative solutions currently exist to overcome these barriers to providing widespread VL testing. This review summarizes the VL testing challenges in resource-limited settings and provides an overview of potential solutions including testing dried blood spots, dried plasma spots, plasma separation cards and the use of point of care tests.
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Affiliation(s)
- Howard Newman
- National Health Laboratory Service, South Africa.,Department of Pathology, Division of Medical Virology, Stellenbosch University, Stellenbosch, South Africa.,Faculty of Health Sciences, Nelson Mandela University, Port Elizabeth, South Africa
| | - Diana Hardie
- National Health Laboratory Service, South Africa.,Department of Pathology, Division of Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Singh D, Dhummakupt A, Siems L, Persaud D. Alternative Sample Types for HIV-1 Antiretroviral Drug Resistance Testing. J Infect Dis 2017; 216:S834-S837. [PMID: 29029130 DOI: 10.1093/infdis/jix386] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Monitoring human immunodeficiency virus type 1 (HIV-1) drug resistance is critical for assessing ART effectiveness and treatment outcomes for HIV-1-infected individuals, including children, worldwide. Traditionally, testing for HIV-1 drug resistance has primarily been performed on plasma samples, and with commercially available, clinically validated assays that are costly and difficult to access. While plasma is the preferred sample for HIV-1 drug resistance genotyping, plasma analysis requires sophisticated laboratory equipment, personnel, space, and stringent storage conditions for maintenance of sample integrity and transport. With the limitations in feasibility and affordability of providing these ideal conditions for plasma genotyping in resource-constrained settings, the field has gained substantial experience with the dried blood spot (DBS) technique as an alternative. Moreover, DBS analysis can be used to comprehensively monitor the spread of the epidemic with applications to more-sensitive and quantitative technologies to assess HIV-1 globally.
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Affiliation(s)
- Dolly Singh
- Department of Pediatrics, Johns Hopkins University School of Medicine
| | - Adit Dhummakupt
- Department of Pediatrics, Johns Hopkins University School of Medicine
| | - Lilly Siems
- Department of Pediatrics, Johns Hopkins University School of Medicine
| | - Deborah Persaud
- Department of Pediatrics, Johns Hopkins University School of Medicine
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Sefrioui D, Beaussire L, Clatot F, Delacour J, Perdrix A, Frebourg T, Michel P, Di Fiore F, Sarafan-Vasseur N. Heparinase enables reliable quantification of circulating tumor DNA from heparinized plasma samples by droplet digital PCR. Clin Chim Acta 2017; 472:75-79. [PMID: 28729136 DOI: 10.1016/j.cca.2017.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/15/2017] [Indexed: 01/26/2023]
Abstract
BACKGROUND Heparin is often used as a blood anticoagulant for tumor marker analysis but results in the inhibition of PCR detection of circulating tumor DNA (ctDNA), which has been deemed a potential "liquid biopsy". We aimed to evaluate the impact of heparinase addition on heparinized plasma samples to allow ctDNA analysis. METHODS Plasma samples were collected in heparinized (n=194) and EDTA (n=8) tubes from hormone receptor-positive metastatic breast cancer (HR+MBC) (n=144) and pancreatic adenocarcinoma (PA) patients (n=50). Circulating ESR1 and KRAS mutations were detected with or without heparinase by digital PCR in HR+MBC and PA patients, respectively. Patients were classified into 2 subgroups i) inhibition, I+ and ii) no inhibition, I- based on a threshold of 200copies/μL for PCR inhibition by heparin. RESULTS In the I+ subgroup (91/144 HR+MBC and 26/50 PA), heparinase treatment significantly improved PCR efficacy, enabling ctDNA detection in 22/91 and 13/26 patients. Moreover, comparable results for ctDNA detection (4/8) were obtained with heparinized and EDTA PA samples. In the I- subgroup, heparinase addition did not quantitatively and qualitatively alter ctDNA detection. CONCLUSION Heparinase addition removes the heparin inhibition and allows accurate ctDNA detection in heparinized samples. These findings could make the samples from heparinized blood suitable for ctDNA analysis.
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Affiliation(s)
- David Sefrioui
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Digestive Oncology Unit, F 76000 Rouen, France
| | - Ludivine Beaussire
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, F 76000 Rouen, France
| | - Florian Clatot
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Medical Oncology, Henri Becquerel Centre, F 76000 Rouen, France
| | - Julien Delacour
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, F 76000 Rouen, France
| | - Anne Perdrix
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Department of Biopathology, Henri Becquerel Centre, F 76000 Rouen, France
| | - Thierry Frebourg
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, F 76000 Rouen, France
| | - Pierre Michel
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine and Digestive Oncology Unit, F 76000 Rouen, France
| | - Frédéric Di Fiore
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, Digestive Oncology Unit and Department of Medical Oncology, Henri Becquerel Centre, F 76000 Rouen, France
| | - Nasrin Sarafan-Vasseur
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Rouen University Hospital, Normandy Centre for Genomic and Personalized Medicine, F 76000 Rouen, France.
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Oscorbin IP, Boyarskikh UA, Zakabunin AI, Khrapov EA, Filipenko ML. DNA-Binding Domain of DNA Ligase from the Thermophilic Archaeon Pyrococcus abyssi: Improving Long-Range PCR and Neutralization of Heparin's Inhibitory Effect. Appl Biochem Biotechnol 2015; 176:1859-69. [PMID: 26026263 DOI: 10.1007/s12010-015-1683-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 05/25/2015] [Indexed: 01/06/2023]
Abstract
The DNA-binding domain of the DNA ligase from Pyrococcus abyssi (PabDBD) was mapped and cloned into two expression vectors. The resulting 6X His-tagged proteins, with a predicted molecular mass of approximately 30 kDa, were overexpressed, purified using Ni-NTA resin, and biochemically characterized. Both PabDBD derivatives bound to double-stranded DNA fragments at the temperature range of 40-70 °C, and both were inactivated via heating at 95 °C for 15 min. Complexes of the PabDBD variants with either double- and single-stranded DNA fragments were less stable than the native DNA ligase of P. abyssi. Inclusion of the C-terminally 6X His-tagged PabDBD in the reaction mixture during long-range polymerase chain reaction (PCR) increased the efficacy of amplification and eliminated the inhibitory effect of heparin.
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Affiliation(s)
- Igor P Oscorbin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation,
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Associations of common variants in the BST2 region with HIV-1 acquisition in African American and European American people who inject drugs. AIDS 2015; 29:767-77. [PMID: 25985399 DOI: 10.1097/qad.0000000000000604] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
OBJECTIVE The bone marrow stromal cell antigen 2 (BST2) gene encodes a host restriction factor that acts as an innate immune sensor of HIV-1 exposure and suppresses release of HIV-1 particles. We aimed to identify associations of variants in the BST2 gene region with HIV-1 acquisition and disease progression. DESIGN/METHODS Using HIV+ cases and HIV- controls from the Urban Health Study (n=3136 African Americans and European Americans who inject drugs), we tested 470 variants in BST2 and its flanking regions for association with HIV-1 acquisition and log-transformed viral load. RESULTS We found that the single nucleotide polymorphism (SNP) rs113189798 surpassed the P value threshold corrected for multiple testing. The rs113189798-G allele (frequency=16% in African Americans, 4% in European Americans) was associated with increased HIV-1 acquisition risk (meta-analysis P=1.43 × 10): odds ratio (95% confidence interval) of 1.22 (1.01-1.49) in African Americans and 2.17 (1.43-3.33) in European Americans. We also found that the previously reported rs12609479-A allele (frequency=35% in African Americans, 81% in European Americans) was nominally associated with decreased risk of acquiring HIV-1 in our study (meta-analysis P=0.036). Rs12609479-A is predicted to increase BST2 expression and thereby decrease risk of acquiring HIV-1. Rs113189798 and rs12609479 were only weakly correlated [square of the correlation coefficient (r)=0.2-0.4] and represented distinct association signals. None of our tested variants were significantly associated with log-transformed viral load among the HIV-infected cases. CONCLUSION Our findings support BST2 as a genetic susceptibility factor for HIV-1 acquisition: identifying a novel SNP association for rs13189798 and linking the previously reported regulatory SNP rs12609479 to HIV-1 acquisition.
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Expanding access to HIV viral load testing: a systematic review of RNA stability in EDTA tubes and PPT beyond current time and temperature thresholds. PLoS One 2014; 9:e113813. [PMID: 25437009 PMCID: PMC4249975 DOI: 10.1371/journal.pone.0113813] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 10/30/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND HIV viral load (VL) testing is the gold standard for antiretroviral treatment monitoring, but many barriers exist to VL testing in resource-limited settings, including storage and transport limitations for whole blood and plasma. Data from various studies indicate that HIV RNA is stable beyond current recommendations. We conducted a systematic review to assess stability data of HIV RNA in whole blood and plasma across times and temperatures. METHODS AND FINDINGS Using a pre-defined protocol, five databases were searched for studies where blood samples from HIV patients were stored at time and temperature points that exceeded manufacturer recommendations. RNA stability, the primary outcome, was measured by the difference in means compared to samples stored within established thresholds. RNA stability was defined as ≤0.5 log degradation. The search identified 10,716 titles, of which nine full-text articles were included for review. HIV RNA maintained stability in EDTA whole blood and plasma at all measured time points up to 168 hours when stored at 4°C, while stability was detected at 72 hours (95% confidence) in whole blood at 25°C, with data points before and beyond 72 hours suggesting stability but not reaching statistical significance. For EDTA plasma stored at 30°C, stability was maintained up to 48 hours (95% confidence), with OLS linear regression estimates up to 127 hours, suggesting stability. Overall, quality of studies was moderate. Limitations included small sample sizes, few studies meeting inclusion criteria, and no studies examining RNA stability in low viremia (<3,000 copies/mL) environments. CONCLUSIONS Whole blood and plasma samples in EDTA may remain stable under conditions exceeding current manufacturer recommendations for HIV VL testing. However, given the limited number of studies addressing this question, especially at low levels of viremia, additional evaluations on HIV RNA stability in EDTA tubes and PPT in field conditions are needed.
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Chiu YJ, Cho SH, Mei Z, Lien V, Wu TF, Lo YH. Universally applicable three-dimensional hydrodynamic microfluidic flow focusing. LAB ON A CHIP 2013; 13:1803-9. [PMID: 23493956 PMCID: PMC3654829 DOI: 10.1039/c3lc41202d] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We have demonstrated a microfluidic device that can not only achieve three-dimensional flow focusing but also confine particles to the center stream along the channel. The device has a sample channel of smaller height and two sheath flow channels of greater height, merged into the downstream main channel where 3D focusing effects occur. We have demonstrated that both beads and cells in our device display significantly lower CVs in velocity and position distributions as well as reduced probability of coincidental events than they do in conventional 2D-confined microfluidic channels. The improved particle confinement in the microfluidic channel is highly desirable for microfluidic flow cytometers and in fluorescence-activated cell sorting (FACS). We have also reported a novel method to measure the velocity of each individual particle in the microfluidic channel. The method is compatible with the flow cytometer setup and requires no sophisticated visualization equipment. The principles and methods of device design and characterization can be applicable to many types of microfluidic systems.
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Affiliation(s)
- Yu-Jui Chiu
- Materials Science Program, University of California at San Diego, La Jolla, California 92093-0418, USA.
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Evaluation of the use of plasma preparation tubes for HIV viral load testing on the COBAS AmpliPrep/COBAS TaqMan HIV-1 version 2.0. J Virol Methods 2012. [PMID: 23178587 DOI: 10.1016/j.jviromet.2012.11.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
HIV viral load monitoring forms an essential part of the management of patients receiving antiretroviral therapy, but transport of samples without loss of RNA integrity may be problematic in resource limited settings. The use of plasma preparation tubes (PPT) which can be centrifuged to separate cellular components before transport may provide a simple and cost-effective alternative to standard EDTA samples. We investigated whether PPT generated reliable results using the COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HIV-1 test version 2.0 (CAP/CTM HIV-1 v2.0). The mean difference between EDTA and PPT prepared samples (n=261) was acceptable (log 0.04 copies/ml, percentage similarity CV 3.53%). PPT can be used for viral load testing on the CAP/CTM HIV-1 v2.0.
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Efficient Quantification of HIV-1 in Heparin Plasma Spiked with Cultured HIV-1 by the Roche Cobas TaqMan and Abbott RealTime HIV-1 Tests. J Clin Microbiol 2012; 50:2804-6. [DOI: 10.1128/jcm.00706-12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
The current automated real-time HIV-1 viral load assays, the Roche Cobas AmpliPrep/Cobas TaqMan test and the Abbott RealTime test, are FDA cleared for use with EDTA plasma. We show that both real-time reverse transcription-PCR (RT-PCR) tests reliably quantify HIV-1 RNA in heparin plasma specimens spiked with HIV-1 isolate MN.
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Hosseini-Moghaddam SM, Iran-Pour E, Rotstein C, Husain S, Lilly L, Renner E, Mazzulli T. Hepatitis C core Ag and its clinical applicability: Potential advantages and disadvantages for diagnosis and follow-up? Rev Med Virol 2011; 22:156-65. [DOI: 10.1002/rmv.717] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 09/18/2011] [Accepted: 09/19/2011] [Indexed: 12/20/2022]
Affiliation(s)
- SM Hosseini-Moghaddam
- Division of Infectious Diseases; University of Toronto, University Health Network, Transplant Infectious Diseases, Toronto General Hospital; Toronto ON Canada
- Urology and Nephrology Research Center (UNRC); Shahid Beheshti University of Medical Sciences; Tehran IR Iran
| | - E. Iran-Pour
- Islamic Azad University; Tehran Medical Branch; Tehran IR Iran
| | - C. Rotstein
- Division of Infectious Diseases; University of Toronto, University Health Network, Transplant Infectious Diseases, Toronto General Hospital; Toronto ON Canada
| | - S. Husain
- Division of Infectious Diseases; University of Toronto, University Health Network, Transplant Infectious Diseases, Toronto General Hospital; Toronto ON Canada
| | - L. Lilly
- Hepatology; University of Toronto, University Health Network, Transplant Hepatology, Toronto General Hospital; Toronto ON Canada
| | - E. Renner
- Hepatology; University of Toronto, University Health Network, Transplant Hepatology, Toronto General Hospital; Toronto ON Canada
| | - T. Mazzulli
- Virology, Department of Microbiology; University of Toronto, University Health Network, Mount Sinai Hospital; Toronto ON Canada
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Molecular Detection and Characterization of HIV‐1. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch35] [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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Cho SH, Godin JM, Chen CH, Qiao W, Lee H, Lo YH. Review Article: Recent advancements in optofluidic flow cytometer. BIOMICROFLUIDICS 2010; 4:43001. [PMID: 21267434 PMCID: PMC3026024 DOI: 10.1063/1.3511706] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 10/14/2010] [Indexed: 05/05/2023]
Abstract
There is an increasing need to develop optofluidic flow cytometers. Optofluidics, where optics and microfluidics work together to create novel functionalities on a small chip, holds great promise for lab-on-a-chip flow cytometry. The development of a low-cost, compact, handheld flow cytometer and microfluorescence-activated cell sorter system could have a significant impact on the field of point-of-care diagnostics, improving health care in, for example, underserved areas of Africa and Asia, that struggle with epidemics such as HIV∕AIDS. In this paper, we review recent advancements in microfluidics, on-chip optics, novel detection architectures, and integrated sorting mechanisms.
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Schulze TJ, Weiß C, Luhm J, Brockmann C, Görg S, Hennig H. Preanalytical stability of HIV-1 and HCV RNA: impact of storage and plasma separation from cells on blood donation testing by NAT. Transfus Med 2010; 21:99-106. [DOI: 10.1111/j.1365-3148.2010.01051.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Overestimation of human immunodeficiency virus type 1 load caused by the presence of cells in plasma from plasma preparation tubes. J Clin Microbiol 2009; 47:2170-4. [PMID: 19420166 DOI: 10.1128/jcm.00519-09] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) load is an important marker of disease progression and treatment efficacy in patients with HIV-1 infection. In recent years, an increase in the number of samples with detectable HIV-1 RNA has been reported among patients with previously suppressed viral loads, affecting clinical patient care and leading to repeat measurements of viral load and drug resistance. This rise seems to have coincided with the increased use of plasma preparation tubes (PPTs) for sample collection, and we have aimed to explain why PPTs might yield elevated HIV-1 RNA levels. The impacts of different sample-processing procedures on HIV-1 RNA levels were compared retrospectively. Prospectively, the presence of different cells and cell-associated HIV-1 nucleic acids in paired plasma samples from PPTs centrifuged before (PPT1) and after (PPT2) transportation to the laboratory was compared. A retrospective analysis of 4,049 patient samples with <1,000 HIV-1 RNA copies/ml showed elevated HIV-1 RNA levels in plasma from PPT1 compared with the levels from PPT2 and standard EDTA-containing tubes. Prospective data revealed cell-associated HIV-1 nucleic acids and abundant blood cells in plasma from PPT1 but not from the corresponding PPT2. The levels of HIV-1 RNA correlated with the lymphocyte counts in plasma in PPT1. Cells could be removed by the recentrifugation of PPT1 before analysis. In conclusion, the transportation of PPTs after centrifugation may render cells in the plasma fraction containing cell-associated HIV-1 nucleic acids that contribute significantly to the HIV-1 RNA copy numbers in patients with low viral loads.
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Dineva MA, MahiLum-Tapay L, Lee H. Sample preparation: a challenge in the development of point-of-care nucleic acid-based assays for resource-limited settings. Analyst 2008; 132:1193-9. [PMID: 18318279 DOI: 10.1039/b705672a] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Currently available nucleic acid testing (NAT)-based assays are complex and time-consuming, and they require expensive instrumentation and dedicated laboratory spaces for sample preparation as well as for amplification and detection of the nucleic acid target. Reagents required for these tests are also expensive and must be transported and stored refrigerated or frozen. These characteristics have limited the use of such assays for point-of-care (POC) testing, especially in resource-poor settings. Efforts to develop simple and rapid NAT-based assays have focused predominantly on the amplification and detection steps, with sample preparation and nucleic acid extraction remaining the bottleneck in the development of NAT systems suitable for POC applications or resource-limited settings. A review of NAT platforms and technologies currently under development and validation for rapid field testing revealed that, in addition to requiring expensive and complex instrumentation, many of these systems also require off-line sample preparation and reagent handling. In their current format, they are therefore not appropriate for POC testing in resource-limited settings. We evaluated several commercially available technologies and procedures for the isolation of nucleic acid with the extraction of HIV-1 RNA from human plasma as a model system. Our results indicate that solid-phase extraction with silica or glass in the presence of a chaotropic salt provides the highest extraction efficiency. However, none of the existing methods and technologies is readily adaptable to a POC system. The integration of sample preparation procedures well suited to NAT-based assays in resource-limited settings therefore remains a challenge.
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Banfi G, Salvagno GL, Lippi G. The role of ethylenediamine tetraacetic acid (EDTA) as in vitro anticoagulant for diagnostic purposes. Clin Chem Lab Med 2007; 45:565-76. [PMID: 17484616 DOI: 10.1515/cclm.2007.110] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Anticoagulants are used to prevent clot formation both in vitro and in vivo. In the specific field of in vitro diagnostics, anticoagulants are commonly added to collection tubes either to maintain blood in the fluid state for hematological testing or to obtain suitable plasma for coagulation and clinical chemistry analyses. Unfortunately, no universal anticoagulant that could be used for evaluation of several laboratory parameters in a sample from a single test tube is available so far. Ethylenediamine tetraacetic acid (EDTA) is a polyprotic acid containing four carboxylic acid groups and two amine groups with lone-pair electrons that chelate calcium and several other metal ions. Calcium is necessary for a wide range of enzyme reactions of the coagulation cascade and its removal irreversibly prevents blood clotting within the collection tube. Historically, EDTA has been recommended as the anticoagulant of choice for hematological testing because it allows the best preservation of cellular components and morphology of blood cells. The remarkable expansion in laboratory test volume and complexity over recent decades has amplified the potential spectrum of applications for this anticoagulant, which can be used to stabilize blood for a variety of traditional and innovative tests. Specific data on the behavior of EDTA as an anticoagulant in hematology, including possible pitfalls, are presented. The use of EDTA for measuring cytokines, protein and peptides, and cardiac markers is described, with an outline of the protection of labile molecules provided by this anticoagulant. The use of EDTA in proteomics and in general clinical chemistry is also described in comparison with other anticoagulants and with serum samples. Finally, the possible uses of alternative anticoagulants instead of EDTA and the potential use of a universal anticoagulant are illustrated.
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Affiliation(s)
- Giuseppe Banfi
- IRCCS Galeazzi and Chair of Clinical Biochemistry, School of Medicine, University of Milan, Milano, Italy.
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Niedrig M, Meyer H, Panning M, Drosten C. Follow-up on diagnostic proficiency of laboratories equipped to perform orthopoxvirus detection and quantification by PCR: the second international external quality assurance study. J Clin Microbiol 2006; 44:1283-7. [PMID: 16597852 PMCID: PMC1448685 DOI: 10.1128/jcm.44.4.1283-1287.2006] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two years after the first external quality assurance study on bioterrorism-relevant viruses, we have conducted a follow-up study on orthopoxvirus detection by PCR. Thirty-three laboratories (27 European, 4 Austral-Asian, and 2 American) participated. Samples contained 0 to 40,000,000 DNA copies of lyophilized monkeypox, cowpox, and vaccinia virus per ml. Laboratories achieved a >80% detection chance above 56,234 copies per ml. Global sensitivity was not significantly improved over that of the first study. Twenty-seven and 9 participants, respectively, were able to genotype and quantify virus. Four of 27 genotyping results were incorrect. Quantification accuracy was significantly better for vaccinia virus than for the other viruses. False-positive results occurred in 22 (11.8%) of all 186 tests on negative samples, but 18 of these were contributed by only five laboratories. Fifty-five percent of laboratories could appropriately detect PCR inhibition. The use of either real-time PCR or commercial diagnostic kits had significant positive influence on laboratory performance.
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Affiliation(s)
- Matthias Niedrig
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht Str. 74, 20359 Hamburg, Germany.
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Coelho SM, Vaisman M, de Carvalho DP. [Thyroglobulin mRNA amplification in peripheral blood of patients with differentiated thyroid carcinoma: what does it really mean?]. ARQUIVOS BRASILEIROS DE ENDOCRINOLOGIA E METABOLOGIA 2006; 50:427-35. [PMID: 16936982 DOI: 10.1590/s0004-27302006000300004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2005] [Accepted: 03/23/2006] [Indexed: 11/21/2022]
Abstract
Despite the excellent prognosis, differentiated thyroid carcinoma (DTC) may recur in 20-40%, and prognosis is particularly related to early detection of recurrent disease. Therefore, long-term follow-up with sensitive tests is need. Serum thyroglobulin (Tg) has an established role as a tumor marker of relapse. However, there are technical limitations of Tg immunoassays, in special, the interference of anti-Tg antibodies and the method sensitivity is dependent on TSH stimulation. Detection of circulating malignant cells by amplification of tumor-specific mRNA showed initial promising results. However, almost one decade of studies of Tg mRNA detection in peripheral blood, its real contribution for DTC follow-up had not yet been established. After a critical analysis of published data, it is clear that there are many protocol differences and conflicting results. Therefore, it seems that amplification of thyroid-specific mRNAs is not superior to sensitive Tg assays and illegitimate transcription and alternative splicing of Tg are factors that may influence mRNA test specificity.
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Affiliation(s)
- Sabrina Mendes Coelho
- Serviço de Endocrinologia, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rua Potiguara 325/104, 22750-290 Rio de Janeiro, RJ.
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Stewart M, Desport M, Hartaningsih N, Wilcox G. TaqMan real-time reverse transcription-PCR and JDVp26 antigen capture enzyme-linked immunosorbent assay to quantify Jembrana disease virus load during the acute phase of in vivo infection. J Clin Microbiol 2005; 43:5574-80. [PMID: 16272489 PMCID: PMC1287780 DOI: 10.1128/jcm.43.11.5574-5580.2005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Jembrana disease virus (JDV) is an acutely pathogenic lentivirus that affects Bali cattle in Indonesia. The inability to propagate the virus in vitro has made it difficult to quantitate JDV and determine the kinetics of virus replication during the acute phase of the disease process. We report for the first time two techniques that enable quantification of the virus and the use of these techniques to quantify the virus load during the acute phase of the disease process. A one-step JDV gag [corrected] TaqMan real-time reverse transcription-PCR (RT-PCR) assay was developed for the detection and quantification of JDV RNA in plasma. The limit of detection was 9.8 x 10(2) JDV viral RNA copies over 35 cycles, equivalent to 4.2 x 10(4) JDV genome copies/ml, and a peak virus load of 1.6 x 10(12) during the acute febrile period. An antigen capture enzyme-linked immunosorbent assay (ELISA) was also developed to quantify the levels of JDV capsid (JDVp26) over a linear range of 10 to 200 ng/ml. Viral RNA and JDVp26 levels were correlated in 48 plasma samples obtained from experimentally infected cattle. A significant positive correlation (R = 0.860 and r(2) = 0.740) was observed between the two techniques within the range of their detection limits. The relatively insensitive capture ELISA provides an economical and feasible method for monitoring of virus in the absence of more sensitive techniques.
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Affiliation(s)
- Meredith Stewart
- School of Veterinary and Biomedical Science, Murdoch University, South St., Murdoch, WA 6150, Australia
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Marteau JB, Mohr S, Pfister M, Visvikis-Siest S. Collection and Storage of Human Blood Cells for mRNA Expression Profiling: A 15-Month Stability Study. Clin Chem 2005; 51:1250-2. [PMID: 15976103 DOI: 10.1373/clinchem.2005.048546] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jean-Brice Marteau
- Institut National de la Santé et de la Recherche Médicale, U525 Equipe 4, Faculté de Pharmacie, Nancy, France
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Gessoni G, Barin P, Valverde S, Giacomini A, Di Natale C, Orlandini E, Arreghini N, De Fusco G, Frigato A, Fezzi M, Antico F, Marchiori G. Biological qualification of blood units: considerations about the effects of sample's handling and storage on stability of nucleic acids. Transfus Apher Sci 2005; 30:197-203. [PMID: 15172624 DOI: 10.1016/j.transci.2003.11.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2003] [Revised: 11/01/2003] [Accepted: 11/01/2003] [Indexed: 10/26/2022]
Abstract
BACKGROUND In transfusional setting introduction of nucleic amplification technique (NAT) for HBV-DNA, HCV-RNA and HIV-RNA in biological qualification of blood units suggest some problems. At first the opportunity to operate on mini-pool, at second the need to store the samples at +4 degrees C. The authors therefore have tried to estimate the impact of these conditions on the operativity of NAT testing in the transfusional setting. METHODS The following parameters has been estimated: distribution of viral-load in untreated subjects, stability of nucleic acids during storage at +4 degrees C, stability of nucleic acids after repeated cycles of freezing and defrosting, robustness of the test to the cross-contamination, definition of the detection-limit (95%). Quantitative tests has been performed by using the following kits: Cobas Amplicor HBV Monitor, Cobas Amplicor HCV Monitor, Cobas Amplicor HIV Monitor; the qualitative tests has been performed by using the following kits: Ampliscreen HBV, Ampliscreen HCV 2,0, Ampliscreen HIV 1,5 all supplied by Roche Molecular System (Brancburg, NJ). RESULTS Viral load in untreated subjects showed wide variation for HBV, HCV and HIV. HBV has been demonstrated much stable to the conservation +4 degrees C also until 168 h while for HCV and HIV a greater decrease of the viral-load was observed. For all and three virus the conservation to +4 degrees C until 72 h does not seem to involve meaningful fall in the viral-load. A remarkable reduction of the viral-load has been observed after five cycles of freezing and defrosting. All the tests showed a good robustness to cross-contamination. The detection-limit (95%) was 8 U/ml for HBV, 21 U/ml for HCV and 27 copy/ml for HIV. CONCLUSIONS Samples for NAT testing, can be stored until 72 h to +4 degrees C without appreciable lowering of the viral-load. Repeated cycles of changes of state should be avoided. The tests showed a good robustness to cross-contamination. NAT tests for biological qualification of blood units had a minimal sensibility around 50 (copy/unit/ml). In our experience the detection-limit (95%) was 21 U/ml for HCV, 27 copies/ml for HIV, 8 U/ml for HBV. The availability of NAT test for HBV-DNA, HCV-RNA e HIV-RNA, sensitive and reliable, together with epidemiological data, suggest the opportunity to place side by side, in the biological qualification of the blood units, to add the tests for HBV-DNA and HIV-RNA to the test for HCV-RNA mandatory by low, in Italy in the biological qualification of blood units.
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Affiliation(s)
- G Gessoni
- Regione Veneto, A-ULS 14 Chioggia Clinical Pathology Department, Ospedale Civile, Via Madonna Marina 500, 30015 Chioggia VE, Italy.
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Sabino EC, Gaburo N, Leite JP, Viecili M, Rosenfeld LG. Platelets May Affect Detection and Quantitation of HIV RNA in Plasma Samples With Low Viral Loads. J Acquir Immune Defic Syndr 2004; 37:1432-3. [PMID: 15483474 DOI: 10.1097/00126334-200411010-00013] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ghosh MK, Kuhn L, West J, Semrau K, Decker D, Thea DM, Aldrovandi GM. Quantitation of human immunodeficiency virus type 1 in breast milk. J Clin Microbiol 2003; 41:2465-70. [PMID: 12791866 PMCID: PMC156553 DOI: 10.1128/jcm.41.6.2465-2470.2003] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2002] [Revised: 01/31/2003] [Accepted: 03/24/2003] [Indexed: 11/20/2022] Open
Abstract
The distribution and stability of human immunodeficiency virus type 1 (HIV-1) in breast milk (BM) components remain largely unknown. Inhibitory effects, if any, of BM on HIV RNA and DNA PCR amplification are poorly understood. We have addressed these issues by using virus-spiked BM samples from HIV-negative women. BM samples from HIV-negative women were spiked with HIV-1 virions or cells containing a single integrated copy of HIV DNA (8E5/LAV). After incubation under different experimental conditions, viral RNA was detected by the Roche Amplicor UltraSensitive assay in whole-milk, skim milk, and lipid fractions. We found excellent correlation between HIV-1 input copy and recovery in whole milk (r = 0.965, P < 0.0001), skim milk (r = 0.972, P < 0.0001), and the lipid fraction (r = 0.905, P < 0.001). PCR inhibition was observed in less than 10% of the spiked samples. Similar levels of inhibition were noted in BM samples collected from HIV-infected women. HIV proviral DNA was detected in BM samples using real-time PCR (linear correlation between the threshold cycle versus log DNA copy number, >0.982). The effects of incubation duration and temperature and repeated freeze-thaw cycles on HIV RNA recovery were analyzed. HIV RNA levels were remarkably stable in whole milk after three freeze-thaw cycles and for up to 30 h at room temperature. Our findings improve the understanding of the dynamics of HIV detection in BM and the conditions for BM sample collection, storage, and processing.
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Affiliation(s)
- M K Ghosh
- Department of Pediatrics. Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35249, USA
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Kuritzkes DR, Grant RM, Feorino P, Griswold M, Hoover M, Young R, Day S, Lloyd RM, Reid C, Morgan GF, Winslow DL. Performance characteristics of the TRUGENE HIV-1 Genotyping Kit and the Opengene DNA Sequencing System. J Clin Microbiol 2003; 41:1594-9. [PMID: 12682150 PMCID: PMC153857 DOI: 10.1128/jcm.41.4.1594-1599.2003] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The TRUGENE HIV-1 Genotyping Kit and OpenGene DNA Sequencing System are designed to sequence the protease (PR)- and reverse transcriptase (RT)-coding regions of human immunodeficiency virus type 1 (HIV-1) pol. Studies were undertaken to determine the accuracy of this assay system in detecting resistance-associated mutations and to determine the effects of RNA extraction methods, anticoagulants, specimen handling, and potentially interfering substances. Samples were plasma obtained from HIV-infected subjects or seronegative plasma to which viruses derived from wild-type and mutant infectious molecular clones (IMC) of HIV-1 were added. Extraction methods tested included standard and UltraSensitive AMPLICOR HIV-1 MONITOR, QIAGEN viral RNA extraction mini kit, and QIAGEN Ultra HIV extraction kit, and NASBA manual HIV-1 quantitative NucliSens. Sequence data from test sites were compared to a "gold standard" reference sequence to determine the percent agreement. Comparisons between test and reference sequences at the nucleotide level showed 97.5 to 100% agreement. Similar results were obtained regardless of extraction method, regardless of use of EDTA or acid citrate dextrose as anticoagulant, and despite the presence of triglycerides, bilirubin, hemoglobin, antiretroviral drugs, HIV-2, hepatitis C virus (HCV), HBV, cytomegalovirus, human T-cell leukemia virus type 1 (HTLV-1), or HTLV-2. Samples with HIV-1 RNA titers of >or=1,000 copies/ml gave consistent results. The TRUGENE HIV-1 Genotyping Kit and OpenGene DNA Sequencing System consistently generate highly accurate sequence data when tested with IMC-derived HIV and patient samples.
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Affiliation(s)
- Daniel R Kuritzkes
- Division of Infectious Diseases, University of Colorado Health Sciences Center, Denver, Colorado, USA.
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Abstract
This review addresses the diagnostics of viral hemorrhagic fevers (VHFs). In the first part, an overview is given on classical methods of VHF diagnostics as well as novel molecular diagnostic tools. Currently available polymerase chain reaction (PCR) assays for diagnosis of VHF are summarized and discussed. In the second part, VHF diagnostics are described in particular for Lassa fever, yellow fever, and Crimean-Congo hemorrhagic fever, based on cases that were imported into or occurred within Europe. The third part is focussed on important differential diagnoses of VHF.
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Affiliation(s)
- Christian Drosten
- Department of Virology, Bernhard-Nocht-Institute of Tropical Medicine, Bernhard-Nocht Strasse 74, 20359 Hamburg, Germany
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Singer EJ, Aronow HA, Lee SY, Hinkin CH, Lazarus T. Stability of human immunodeficiency virus type 1 RNA in cerebrospinal fluid determined with the AMPLICOR HIV-1 MONITOR test, version 1.5 (ultrasensitive). J Clin Microbiol 2002; 40:3863-4. [PMID: 12354902 PMCID: PMC130842 DOI: 10.1128/jcm.40.10.3863-3864.2002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We evaluated the effects of time, temperature, freezing, and thawing on the cerebrospinal fluid viral load by using the Roche AMPLICOR HIV-1 MONITOR test, version 1.5 (ultrasensitive). While a statistically significant decrease from the baseline was observed at 24 h, but not at 6 or 12 h, and with one freeze-thaw cycle, all changes were within the range of intra-assay variability.
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Affiliation(s)
- Elyse J Singer
- Department of Neurology, School of Medicine, University of California at Los Angeles, 11645 Wilshire Boulevard, Suite 770, Los Angeles, CA 90025, USA.
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García ME, Blanco JL, Caballero J, Gargallo-Viola D. Anticoagulants interfere with PCR used to diagnose invasive aspergillosis. J Clin Microbiol 2002; 40:1567-8. [PMID: 11923400 PMCID: PMC140326 DOI: 10.1128/jcm.40.4.1567-1568.2002] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Kellogg JA, Atria PV, Sanders JC, Eyster ME. Intra- and interlaboratory variabilities of results obtained with the Quantiplex human immunodeficiency virus type 1 RNA bDNA assay, version 3.0. CLINICAL AND DIAGNOSTIC LABORATORY IMMUNOLOGY 2001; 8:560-3. [PMID: 11329458 PMCID: PMC96101 DOI: 10.1128/cdli.8.3.560-563.2001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Normal assay variation associated with bDNA tests for human immunodeficiency virus type 1 (HIV-1) RNA performed at two laboratories with different levels of test experience was investigated. Two 5-ml aliquots of blood in EDTA tubes were collected from each patient for whom the HIV-1 bDNA test was ordered. Blood was stored for no more than 4 h at room temperature prior to plasma separation. Plasma was stored at -70 degrees C until transported to the Central Pennsylvania Alliance Laboratory (CPAL; York, Pa.) and to the Hershey Medical Center (Hershey, Pa.) on dry ice. Samples were stored at < or =-70 degrees C at both laboratories prior to testing. Pools of negative (donor), low-HIV-1-RNA-positive, and high-HIV-1-RNA-positive plasma samples were also repeatedly tested at CPAL to determine both intra- and interrun variation. From 11 August 1999 until 14 September 2000, 448 patient specimens were analyzed in parallel at CPAL and Hershey. From 206 samples with results of > or =1,000 copies/ml at CPAL, 148 (72%) of the results varied by < or =0.20 log(10) when tested at Hershey and none varied by >0.50 log(10). However, of 242 specimens with results of <1,000 copies/ml at CPAL, 11 (5%) of the results varied by >0.50 log(10) when tested at Hershey. Of 38 aliquots of HIV-1 RNA pool negative samples included in 13 CPAL bDNA runs, 37 (97%) gave results of <50 copies/ml and 1 (3%) gave a result of 114 copies/ml. Low-positive HIV-1 RNA pool intrarun variation ranged from 0.06 to 0.26 log(10) while the maximum interrun variation was 0.52 log(10). High-positive HIV-1 RNA pool intrarun variation ranged from 0.04 to 0.32 log(10), while the maximum interrun variation was 0.55 log(10). In our patient population, a change in bDNA HIV-1 RNA results of < or =0.50 log(10) over time most likely represents normal laboratory test variation. However, a change of >0.50 log(10), especially if the results are >1,000 copies/ml, is likely to be significant.
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Affiliation(s)
- J A Kellogg
- Central Pennsylvania Alliance Laboratory, York, Pennsylvania, USA.
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Jennings C, Bremer JW, Brambilla DJ. Investigation of effects of acid citrate dextrose and EDTA on ability to quantitatively culture human immunodeficiency virus. J Clin Microbiol 2000; 38:3522. [PMID: 11203333 PMCID: PMC87427 DOI: 10.1128/jcm.38.9.3522-3522.2000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Anastos K, Gange SJ, Lau B, Weiser B, Detels R, Giorgi JV, Margolick JB, Cohen M, Phair J, Melnick S, Rinaldo CR, Kovacs A, Levine A, Landesman S, Young M, Muñoz A, Greenblatt RM. Association of race and gender with HIV-1 RNA levels and immunologic progression. J Acquir Immune Defic Syndr 2000; 24:218-26. [PMID: 10969345 DOI: 10.1097/00126334-200007010-00004] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
CONTEXT HIV-1 RNA and lymphocyte subset levels are the principal indications for antiretroviral treatment. Past reports have differed with regard to the effect of gender and race on these measures and in measures of disease progression. OBJECTIVE To assess racial and gender differences in HIV-1 RNA levels and CD4+ lymphocyte decline. DESIGN A longitudinal study based in the two largest HIV natural history cohort studies conducted in 7 metropolitan areas of the United States. RESULTS In all, 1256 adult women and 1603 adult men for whom multiple data points were available prior to initiation of antiretroviral therapy were included. Women were more likely to be nonwhite, to have a history of injection drug use, and to have HIV-associated symptoms. After adjustment for differences in measurement method, baseline CD4+ cell count, age, and clinical symptoms, HIV-1 RNA levels were 32% to 50% lower in women than in men at CD4+ counts >200 cells/mm3 (p <.001) but not at CD4+ cell counts <200 cells/mm3. HIV-1 RNA levels were also 41% lower in nonwhites than in whites (p <.001) and 21% lower in persons reporting a prior history of injection drug use (p <.001). Women had more rapid declines in CD4+ cell counts over time than men (difference in slope of 46 cells/year) and nonwhite individuals had slower decline in CD4 cell counts than whites (difference of 39 cells/year). CONCLUSIONS Both race and gender influence the values of HIV-1 RNA and the rate of HIV-1 disease progression as indicated by decline in CD4 cell counts over time. These effects could provide clues regarding the factors that influence HIV-disease progression and may indicate that guidelines for therapy should be adjusted for demographic characteristics.
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Affiliation(s)
- K Anastos
- Montefiore Medical Center, Bronx, New York 10467, USA.
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Fiscus SA, Chakraborty H, Shepard R, Goodman M. Comparison of blood collected in acid-citrate-dextrose and EDTA for use in human immunodeficiency virus peripheral blood mononuclear cell cultures. J Clin Microbiol 2000; 38:858-60. [PMID: 10655398 PMCID: PMC86223 DOI: 10.1128/jcm.38.2.858-860.2000] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Paired blood samples collected in acid-citrate-dextrose and EDTA were compared for human immunodeficiency virus (HIV) infectivity on the day of collection or after 1 day of storage at room temperature. No significant differences between the anticoagulants were observed. Culture positivity was significantly associated with HIV RNA viral loads for both anticoagulants.
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Affiliation(s)
- S A Fiscus
- Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7140, USA.
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Holodniy M, Rainen L, Herman S, Yen-Lieberman B. Stability of plasma human immunodeficiency virus load in VACUTAINER PPT plasma preparation tubes during overnight shipment. J Clin Microbiol 2000; 38:323-6. [PMID: 10618109 PMCID: PMC88717 DOI: 10.1128/jcm.38.1.323-326.2000] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/1999] [Accepted: 09/29/1999] [Indexed: 12/28/2022] Open
Abstract
VACUTAINER PPT plasma preparation tubes were evaluated to determine the effects of various handling and shipping conditions on plasma human immunodeficiency virus (HIV) load determinations. Plasmas obtained from PPT tubes stored and shipped under nine different conditions were compared to conventional EDTA tube plasmas stored at -70 degrees C within 2 h after phlebotomy. Compared to viral loads in frozen EDTA plasma, those in PPT tube plasma that was frozen immediately and either separated or shipped in situ were not significantly different. Viral loads in PPT tube plasma after storage for 6 h at either room temperature or 4 degrees C, followed by shipment at ambient temperature or on wet or dry ice, were not significantly different from baseline viral loads in EDTA or PPT plasma. The results of this study indicate that the HIV load in PPT tube plasma is equivalent to that in standard EDTA plasma. Plasma viral load is not affected by storage or shipment temperature when plasma is collected in PPT tubes. Furthermore, plasmas can be shipped in spun PPT tubes, and the tubes provide a safer and more convenient method for sample collection and transport than regular EDTA tubes.
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Affiliation(s)
- M Holodniy
- AIDS Research Center, VA Palo Alto Health Care System, Palo Alto, California, USA
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Kirstein LM, Mellors JW, Rinaldo CR, Margolick JB, Giorgi JV, Phair JP, Dietz E, Gupta P, Sherlock CH, Hogg R, Montaner JS, Muñoz A. Effects of anticoagulant, processing delay, and assay method (branched DNA versus reverse transcriptase PCR) on measurement of human immunodeficiency virus type 1 RNA levels in plasma. J Clin Microbiol 1999; 37:2428-33. [PMID: 10405379 PMCID: PMC85245 DOI: 10.1128/jcm.37.8.2428-2433.1999] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/1999] [Accepted: 04/29/1999] [Indexed: 11/20/2022] Open
Abstract
We conducted two studies to determine the potential influence of delays in blood processing, type of anticoagulant, and assay method on human immunodeficiency virus type 1 (HIV-1) RNA levels in plasma. The first was an experimental study in which heparin- and EDTA-anticoagulated blood samples were collected from 101 HIV-positive individuals and processed to plasma after delays of 2, 6, and 18 h. HIV-1 RNA levels in each sample were then measured by both branched-DNA (bDNA) and reverse transcriptase PCR (RT-PCR) assays. Compared to samples processed within 2 h, the loss (decay) of HIV-1 RNA in heparinized blood was significant (P < 0.05) but small after 6 h (bDNA assay, -0.12 log(10) copies/ml; RT-PCR, -0.05 log(10) copies/ml) and after 18 h (bDNA assay, -0.27 log(10) copies/ml; RT-PCR, -0.15 log(10) copies/ml). Decay in EDTA-anticoagulated blood was not significant after 6 h (bDNA assay, -0.002 log(10) copies/ml; RT-PCR, -0.02 log(10) copies/ml), but it was after 18 h (bDNA assay, -0.09 log(10) copies/ml; RT-PCR, -0.09 log(10) copies/ml). Only 4% of samples processed after 6 h lost more than 50% (>/=0.3 log(10) copies/ml) of the HIV-1 RNA, regardless of the anticoagulant or the assay that was used. The second study compared HIV-1 RNA levels in samples from the Multicenter AIDS Cohort Study (MACS; samples were collected in heparin-containing tubes in 1985, had a 6-h average processing delay, and were assayed by bDNA assay) and the British Columbia Drug Treatment Program (BCDTP) (collected in EDTA- or acid citrate dextrose-containing tubes in 1996 and 1997, had a 2-h maximum processing delay, and were assayed by RT-PCR). HIV-1 RNA levels in samples from the two cohorts were not significantly different after adjusting for CD4(+)-cell count and converting bDNA assay values to those corresponding to the RT-PCR results. In summary, the decay of HIV-1 RNA measured in heparinized blood after 6 h was small (-0.05 to -0.12 log(10) copies/ml), and the minor impact of this decay on HIV-1 RNA concentrations in archived plasma samples of the MACS was confirmed by the similarity of CD4(+)-cell counts and assay-adjusted HIV-1 RNA concentrations in the MACS and BCDTP.
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Affiliation(s)
- L M Kirstein
- Department of Epidemiology, Johns Hopkins School of Hygiene and Public Health, Baltimore, Maryland, USA.
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Lew J, Reichelderfer P, Fowler M, Bremer J, Carrol R, Cassol S, Chernoff D, Coombs R, Cronin M, Dickover R, Fiscus S, Herman S, Jackson B, Kornegay J, Kovacs A, McIntosh K, Meyer W, Michael N, Mofenson L, Moye J, Quinn T, Robb M, Vahey M, Weiser B, Yeghiazarian T. Determinations of levels of human immunodeficiency virus type 1 RNA in plasma: reassessment of parameters affecting assay outcome. TUBE Meeting Workshop Attendees. Technology Utilization for HIV-1 Blood Evaluation and Standardization in Pediatrics. J Clin Microbiol 1998; 36:1471-9. [PMID: 9620364 PMCID: PMC104860 DOI: 10.1128/jcm.36.6.1471-1479.1998] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- J Lew
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA.
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