Automated procedure for improving the RNA isolation step in viral load testing for human immunodeficiency virus.
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ABSTRACT:
SUBMITTER: Xu M
PROVIDER: S-EPMC321698 | biostudies-other | 2004 Jan
REPOSITORIES: biostudies-other
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Project description:BackgroundViral load (VL) testing coverage remains low particularly in resource limited countries despite recommendation by World Health Organization, and Malawi is no exception. A quality improvement (QI) approach was used to improve VL testing coverage from 27% to a target of 80% at an urban health facility in Malawi.MethodsA QI study employing a time-series quasi-experimental design with no comparison group was conducted at Chilomoni health centre in Blantyre from April 2020 to July 2020. A retrospective record review of all patient records (257) from 8 weeks before the study was conducted to determine baseline VL testing coverage. Root cause analysis of low VL testing coverage was done using fish-bone tool and factors prioritized using a Pareto-chart. Priority factors included inadequate capacity to update electronic medical records and competing tasks. Change ideas were identified and prioritized using an effort-impact matrix. Two change ideas; re-orienting ART providers on VL test order in EMR and dedicated ART provider to serve VL tested patients were implemented and tested in 5 Plan-Do-Study-Act (PDSA) cycles from the Model for Improvement (MFI), each lasting one week. The latter was tested, and adapted in 3 cycles, and eventually adopted for monitoring for another 5 weeks. VL testing coverage was tracked throughout the study using run charts and p-charts.ResultsVL testing coverage increased from 27% to 71% by the end of the study, with children aged 0 to 14 years having the lowest coverage throughout the study.ConclusionThe MFI as a QI approach improved VL testing coverage through implementation of contextualized change ideas. A reliable data system, leadership buy-in and commitment are important for sustained improvement. Future research should focus on evaluating sustainability of improved VL testing coverage at the health facility and assessing barriers to VL testing among the paediatric population.
| S-EPMC9176770 | biostudies-literature
Project description:BackgroundSince 2014, the recommended algorithm for laboratory diagnosis of HIV infection in the United States has consisted of an HIV-1/2 antigen/antibody (Ag/Ab) test followed by an HIV-1/2 antibody (Ab) differentiation test and, if necessary, a diagnostic HIV-1 nucleic acid test to resolve discordant or indeterminate results.MethodsUsing stored specimens from persons seeking HIV testing who had not received a previous diagnosis or treatment, we compared the performance of a 3-step alternative algorithm consisting of an Ag/Ab test followed by a quantitative HIV-1 RNA viral load assay and, if viral load is not detected, an Ab differentiation test, to that of the recommended algorithm. We calculated the sensitivity and specificity of 5 Ag/Ab tests and the proportion of specimens correctly classified by the alternative algorithm compared with the recommended algorithm. Results were examined separately for specimens classified as early infection, established infection, and false-reactive screening.ResultsSensitivity and specificity were similar among all Ag/Ab tests. Viral load quantification correctly classified all specimens from early infection, all false-reactive screening specimens, and the majority of specimens from established infection.ConclusionsAlthough cost, regulatory barriers, test availability, and the ability to differentiate early from established infection must be considered, this alternative algorithm can potentially decrease the total number of tests performed and reduce turnaround time, thereby streamlining HIV diagnosis and initiation of treatment.
| S-EPMC7246040 | biostudies-literature
Project description:BackgroundViral load (VL) scale-up efforts have largely focused on laboratory systems, with less attention on facility-level strengthening of staff who facilitate VL testing. To address this gap we implemented a quality improvement (QI) program at 13 health facilities in central and southern Malawi.MethodsQI program tools focused on patient and provider VL knowledge and clarification of site-level roles and responsibilities, including the designation of a VL 'focal person' to oversee all VL activities. T-tests were used to compare differences in VL testing before (November 2016-April 2017) and after (May 2017-November 2017) the intervention.ResultsThe mean number of VL tests performed significantly increased after implementation of the QI program. Overall there was a 164% increase in the mean number of routine VL tests performed per month (p<0.001). Increased VL testing was sustained during the 6 months of follow-up.ConclusionsA simple QI program focused on improving VL knowledge among patients and providers, and clarifying staff roles at a facility level increased VL testing over a 6-month period. Further investigation is needed on whether this program can be scaled in different settings across sub-Saharan Africa and on the duration of follow-up required for sustained improvements in VL testing.
| S-EPMC6676971 | biostudies-literature
Project description:BackgroundWorld Health Organization guidelines now recommend routine use of viral load testing, where available, for patients receiving antiretroviral treatment (ART). However, its use has not been routinely implemented in many resource-limited settings due to cost, availability and accessibility. Viral load testing is complex, making its application in resource-limited settings challenging. We describe the issues encountered by Médecins Sans Frontières (MSF) when using routine viral load testing in a large HIV programme in sub-Saharan Africa.MethodsBetween October 2005 and August 2006, more than 1200 patients on ART had viral load tests at baseline and at three-month intervals performed by a local reference laboratory that was quality assured by an experienced international institution. Concerns with reliability of results halted testing. The quality control measures instituted with a second laboratory and outcomes of these were documented.ResultsIn 2005 and 2006, only 178 of 334 (53%) previously ART-naïve patients tested after six to 12 months of treatment had viral loads of less than 1000 copies/mL. Similar MSF programmes elsewhere demonstrated virological suppression rates of more than 85%, and duplicate testing showed unacceptable discordance. Laboratory problems encountered included: disregarded quality control; time delays; requirement for retesting; and duplicate sample variations. Potentially harmful clinical outcomes of inaccurate viral load results include: unnecessary ART regimen changes; unnecessary enhanced adherence counselling after "false failures"; and undetected virological failure.ConclusionsViral load testing performed without rigorous quality control carries the risk of erroneous and potentially damaging results. Viral load testing should be utilized only if robust quality assurance has been implemented. Our experience in this and other settings led to the development of a guide for assessing the suitability of a laboratory for viral load testing that can be used to help achieve reliable results.
| S-EPMC3116452 | biostudies-literature
Project description:BACKGROUND:Persistent high-risk (HR) human papillomavirus (HPV) infection and increased HR-HPV viral load are associated with the development of cancer. This study investigated the effect of human immunodeficiency virus (HIV) co-infection, HIV viral load and CD4 count on the HR-HPV viral load; and also investigated the predictors of cervical abnormalities. METHODS:Participants were 292 HIV-negative and 258 HIV-positive women. HR-HPV viral loads in cervical cells were determined by the real-time polymerase chain reaction. RESULTS:HIV-positive women had a significantly higher viral load for combined alpha-9 HPV species compared to HIV-negative women (median 3.9 copies per cell compared to 0.63 copies per cell, P = 0.022). This was not observed for individual HPV types. HIV-positive women with CD4 counts >350/?l had significantly lower viral loads for alpha-7 HPV species (median 0.12 copies per cell) than HIV-positive women with CD4 ?350/?l (median 1.52 copies per cell, P = 0.008), but low CD4 count was not significantly associated with increased viral load for other HPV species. High viral loads for alpha-6, alpha-7 and alpha-9 HPV species were significant predictors of abnormal cytology in women. CONCLUSION:HIV co-infection significantly increased the combined alpha-9 HPV viral load in women but not viral loads for individual HPV types. High HR-HPV viral load was associated with cervical abnormal cytology.
| S-EPMC3922074 | biostudies-literature
Project description:Background:Existing respiratory mucosal sampling methods are flawed, particularly in a pediatric bronchiolitis setting. Methods:Twenty-four infants with bronchiolitis were recruited: 12 were respiratory syncytial virus (RSV)-positive, 12 were RSV-negative. Infants were sampled by nasosorption and nasopharyngeal aspiration (NPA). Results:Nasosorption was well tolerated and identified all RSV+ samples. RSV load measured by nasosorption (but not NPA) correlated with length of hospital stay (P = .04) and requirement for mechanical ventilation (P = .03). Nasosorption (but not NPA) levels of interferon ?, interleukin 1?, CCL5/RANTES, and interleukin 10 (IL-10) were elevated in RSV+ bronchiolitis (all P < .05), furthermore CCL5 and IL-10 correlated with RSV load (P < .05). Conclusions:Nasosorption allowed measurement of RSV load and the mucosal inflammatory response in infants.
| S-EPMC5441107 | biostudies-literature
Project description:BACKGROUND: Strand specific RNA sequencing is rapidly replacing conventional cDNA sequencing as an approach for assessing information about the transcriptome. Alongside improved laboratory protocols the development of bioinformatical tools is steadily progressing. In the current procedure the Illumina TruSeq library preparation kit is used, along with additional reagents, to make stranded libraries in an automated fashion which are then sequenced on Illumina HiSeq 2000. By the use of freely available bioinformatical tools we show, through quality metrics, that the protocol is robust and reproducible. We further highlight the practicality of strand specific libraries by comparing expression of strand specific libraries to non-stranded libraries, by looking at known antisense transcription of pseudogenes and by identifying novel transcription. Furthermore, two ribosomal depletion kits, RiboMinus and RiboZero, are compared and two sequence aligners, Tophat2 and STAR, are also compared. RESULTS: The, non-stranded, Illumina TruSeq kit can be adapted to generate strand specific libraries and can be used to access detailed information on the transcriptome. The RiboZero kit is very effective in removing ribosomal RNA from total RNA and the STAR aligner produces high mapping yield in a short time. Strand specific data gives more detailed and correct results than does non-stranded data as we show when estimating expression values and in assembling transcripts. Even well annotated genomes need improvements and corrections which can be achieved using strand specific data. CONCLUSIONS: Researchers in the field should strive to use strand specific data; it allows for more confidence in the data analysis and is less likely to lead to false conclusions. If faced with analysing non-stranded data, researchers should be well aware of the caveats of that approach.
| S-EPMC4247151 | biostudies-literature
Project description:A key challenge during the transition from laboratory/small batch to continuous manufacturing is the development of a process strategy that can easily be adopted for a larger batch/continuous process. Industrial practice is to develop the isolation strategy for a new drug/process in batch using the design of experiment (DoE) approach to determine the best isolation conditions and then transfer the isolation parameters selected to a large batch equipment/continuous isolation process. This stage requires a series of extra investigations to evaluate the effect of different equipment geometry or even the adaptation of the parameters selected to a different isolation mechanism (e.g., from dead end to cross flow filtration) with a consequent increase of R&D cost and time along with an increase in material consumption. The CFD25 is an isolation device used in the first instance to develop an isolation strategy in batch (optimization mode) using a screening DoE approach and to then verify the transferability of the strategy to a semicontinuous process (production mode). A d-optimal screening DoE was used to determine the effect of varying the input slurry. Properties such as solid loading, particle size distribution, and crystallization solvent were investigated to determine their impact on the filtration and washing performance and the characteristics of the dry isolated product. A series of crystallization (ethanol, isopropanol, and 3-methylbutan-1-ol) and wash solvents (n-heptane, isopropyl acetate and n-dodcane) were used for the process. To mimic a real isolation process, paracetamol-related impurities, acetanilide and metacetamol, were dissolved in the mother liquor. The selected batch isolation strategy was used for the semicontinuous isolation run. Throughput and filtration parameters, such as cake resistance and flow rate, cake residual liquid content and composition, cake purity, particle-particle aggregation, and extent and strength of agglomerates, were measured to evaluate the consistency of the isolated product produced during a continuous experiment and compared with the isolated product properties obtained during the batch process development. Overall, the CFD25 is a versatile tool which allows both new chemical entity process development in batch and the production of the active pharmaceutical ingredient in semicontinuous mode using the same process parameters without changing equipment. The isolated product properties gained during the semicontinuous run are overall comparable between samples. The residual solvent content and composition differs between some samples due to filter plate blockage. In general, the mean properties obtained during semicontinuous running are comparable with the product properties simulated using the DoE.
| S-EPMC7171873 | biostudies-literature
Project description:Point-of-care viral load tests are being developed to monitor patients on antiretroviral therapy (ART) in sub-Saharan Africa. Test design involves trade-offs between test attributes, including accuracy, complexity, robustness, and cost. We used a model of the human immunodeficiency virus epidemic and ART program in Zimbabwe and found that the attributes of a viral load testing approach that are most influential for cost effectiveness are avoidance of a high proportion of failed tests or results not received, use of an approach that best facilitates retention on ART, and the ability to facilitate greater use of differentiated care, including through expanding coverage of testing availability.
| S-EPMC5047406 | biostudies-other
Project description:We investigated the in vitro RNA dimerization properties of the untranslated leader RNA derived from human immunodeficiency virus type 1 variants circulating in an individual with a low viral load and slow disease progression. The leader sequences of these viruses contain highly unusual polymorphisms within the dimerization initiation site (DIS): an insert that abolishes dimerization and a compensatory substitution. The dimerization of leader RNA from late stages of infection is further improved by additional mutations outside the DIS motif that facilitate a secondary structure switch from a dimerization-incompetent to a dimerization-competent RNA conformation.
| S-EPMC387700 | biostudies-literature