Can't Work From Home: Pooled Nucleic Acid Testing of Laboratory Workers During the COVID-19 Pandemic.
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ABSTRACT:
SUBMITTER: Rawlings SA
PROVIDER: S-EPMC7989168 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND:Similar to other resource-limited settings, cost restricts availability of viral load monitoring for most patients receiving antiretroviral therapy in Tijuana, Mexico. We evaluated if a pooling method could improve efficiency and reduce costs while maintaining accuracy. METHODS:We evaluated 700 patient blood plasma specimens at a reference laboratory in Tijuana for detectable viremia, individually and in 10 × 10 matrix pools. Thresholds for virologic failure were set at ?500, ?1000 and ?1500 HIV RNA copies per milliliter. Detectable pools were deconvoluted using pre-set algorithms. Accuracy and efficiency of the pooling method were compared with individual testing. Quality assurance (QA) measures were evaluated after 1 matrix demonstrated low efficiency relative to individual testing. RESULTS:Twenty-two percent of the cohort had detectable HIV RNA (?50 copies/mL). Pooling methods saved approximately one third of viral load assays over individual testing, while maintaining negative predictive values of >90% to detect samples with virologic failure (?50 copies/mL). One matrix with low relative efficiency would have been detected earlier using the developed QA measures, but its exclusion would have only increased relative efficiency from 39% to 42%. These methods would have saved between $13,223 and $14,308 for monitoring this cohort. CONCLUSIONS:Despite limited clinical data, high prevalence of detectable viral loads and a contaminated matrix, pooling greatly improved efficiency of virologic monitoring while maintaining accuracy. By improving cost-effectiveness, these methods could provide sustainability of virologic monitoring in resource-limited settings, and incorporation of developed QA measures will most likely maximize pooling efficiency in future uses.
| S-EPMC3039117 | biostudies-literature
Project description:BACKGROUND:In resource-limited settings, viral load monitoring of HIV-infected patients receiving antiretroviral therapy (ART) is not readily available because of high costs. Here, we compared the accuracy and costs of quantitative and qualitative pooled methods with standard viral load testing. METHODS:Blood was collected prospectively from 461 patients receiving first-line ART in Mozambique who had not been evaluated previously with viral load testing. Screening for virologic failure of ART was performed quantitatively (ie, standard viral loads) and qualitatively [one and 2 rounds of polymerase chain reaction (PCR)]. Individual samples and minipools of 5 samples were then analyzed using both methods. The relative efficiency, accuracy, and costs of each method were calculated based on viral load thresholds for ART failure. RESULTS:Standard viral load testing of individual samples revealed a high rate of ART failure (19%-23%) across all virologic failure thresholds, and the majority of the patients (93%) with viral loads >1500 copies per milliliter had genotypic resistance to drugs in their ART regimen. Pooled quantitative screening and deconvolution testing had positive and negative predictive values exceeding 95% with cost savings of $11,250 compared with quantitative testing of each sample individually. Pooled qualitative screening and deconvolution testing had a higher cost savings of $30,147 for 1 PCR round and $25,535 for 2 PCR rounds compared with quantitative testing each sample individually. Both pooled qualitative PCR methods had positive and negative predictive values ?90%, but the pooled 1-round PCR method had a sensitivity of 64%. CONCLUSIONS:Given the high rate of undiagnosed ART failure and drug resistance in this cohort, it is clear that virologic monitoring is urgently needed in this population. Here, we compared alternative methods of virologic monitoring with standard viral load testing of individual samples and found these methods to be cost saving and accurate. The test characteristics of each method will likely need to be considered for each local population before it is adopted.
| S-EPMC4607635 | biostudies-literature
Project description:The coronavirus disease 2019 (COVID-19) has caused a large global outbreak. It is accordingly important to develop accurate and rapid diagnostic methods. The polymerase chain reaction (PCR)-based method including reverse transcription-polymerase chain reaction (RT-PCR) is the most widely used assay for the detection of SARS-CoV-2 RNA. Along with the RT-PCR method, digital PCR has emerged as a powerful tool to quantify nucleic acid of the virus with high accuracy and sensitivity. Non-PCR based techniques such as reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA) are considered to be rapid and simple nucleic acid detection methods and were reviewed in this paper. Non-conventional molecular diagnostic methods including next-generation sequencing (NGS), CRISPR-based assays and nanotechnology are improving the accuracy and sensitivity of COVID-19 diagnosis. In this review, we also focus on standardization of SARS-CoV-2 nucleic acid testing and the activity of the National Metrology Institutes (NMIs) and highlight resources such as reference materials (RM) that provide the values of specified properties. Finally, we summarize the useful resources for convenient COVID-19 molecular diagnostics.
| S-EPMC8201071 | biostudies-literature
Project description:The rapid development of global COVID-19 pandemic poses an unprecedented challenge to the safety and quality of laboratory diagnostic testing. Little is known about the laboratory surface areas and operation behaviors that may cause potential contamination in SARS-CoV-2 nucleic acid testing. This study aims to provide reference basis for the improvement of laboratory disinfection programs and personal operating protocols. In this study, we compared the qRT-PCR and ddPCR in detecting of residual virus that existed on the object surfaces from sample transportation and reception related facilities, testing related instruments, personal protective equipment and other facilities in nucleic acid testing laboratory. All samples were negative by qRT-PCR, in contrast, 13 of 61 samples were positive for SARS-CoV-2 by ddPCR. The areas with highest density of SARS-CoV-2 nucleic acid were the outer gloves of operator A (37.4 copies/cm2), followed by door handle of 4 °C refrigerator (26.25 copies/cm2), goggles of operator A (22.16 copies/cm2), outer cover of high speed centrifuge (19.95 copies/cm2), inner wall of high speed centrifuge (14.70 copies/cm2) and others. We found that all the positive objects were directly or indirectly contacted by the operator's gloved hands, suggesting that hands contact was the main transmission pathway that led to laboratory environmental contamination. In summary, ddPCR has an advantage over qRT-PCR in tracing laboratory contamination. We evaluated the risk areas and operation behaviors that may easily cause contamination, and provided recommendation for improving the laboratory disinfection programs and personal operating specifications.
| S-EPMC7303629 | biostudies-literature
Project description:The coronavirus disease 2019 (COVID-19) pandemic has drastically changed work styles and environments. Given the coexistence of work in the office and work from home (WFH) in the future, studies are needed to identify ways to increase productivity when working in both places. We conducted a questionnaire survey and environment measurements of 916 workers in 22 offices across 2 weeks in November-December 2020 in Japan. While average workdays at the offices decreased from 4.9 to 3.9 days/week, those at homes increased from 0.1 to 1.1 days/week due to COVID-19, indicating an increase in the relative importance of WFH. Compared to the office, the satisfaction rate was lower for lighting, spatial, and information technology (IT) environments, but higher for thermal, air, and sound environments at home. Although it was easier to concentrate on work and to refresh at home, workers experienced challenges associated with business communication from home. Meanwhile, in the office, satisfaction with COVID-19 countermeasures was significantly associated with work productivity. Furthermore, lower PM2.5 concentration was associated with greater satisfaction with COVID-19 countermeasures, indicating that reducing PM2.5 may increase satisfaction with COVID-19 countermeasures and work productivity. We expect these findings will help improve work productivity in the New Normal era.
| S-EPMC8446952 | biostudies-literature
Project description:To estimate the proportion of healthcare workers (HCWs) willing to work during an influenza pandemic and identify associated risk factors, we undertook a systematic review and meta-analysis compliant with PRISMA guidance. Databases and grey literature were searched to April 2013, and records were screened against protocol eligibility criteria. Data extraction and risk of bias assessments were undertaken using a piloted form. Random-effects meta-analyses estimated (i) pooled proportion of HCWs willing to work and (ii) pooled odds ratios of risk factors associated with willingness to work. Heterogeneity was quantified using the I(2) statistic, and publication bias was assessed using funnel plots and Egger's test. Data were synthesized narratively where meta-analyses were not possible. Forty-three studies met our inclusion criteria. Meta-analysis of the proportion of HCWs willing to work was abandoned due to excessive heterogeneity (I(2) = 99.2%). Narrative synthesis showed study estimates ranged from 23.1% to 95.8% willingness to work, depending on context. Meta-analyses of specific factors showed that male HCWs, physicians and nurses, full-time employment, perceived personal safety, awareness of pandemic risk and clinical knowledge of influenza pandemics, role-specific knowledge, pandemic response training, and confidence in personal skills were statistically significantly associated with increased willingness. Childcare obligations were significantly associated with decreased willingness. HCWs' willingness to work during an influenza pandemic was moderately high, albeit highly variable. Numerous risk factors showed a statistically significant association with willingness to work despite significant heterogeneity between studies. None of the included studies were based on appropriate theoretical constructs of population behaviour.
| S-EPMC4415696 | biostudies-other
Project description:Although nucleic acid amplification testing (NAAT) has become the cornerstone for molecular diagnosis of diseases, expanding the multiplexed detection capacity of NAAT remains an important objective. To this end, encoding each nucleic acid target with a specific fluorescently labeled probe has been the most mature approach for multiplexed detection. Unfortunately, the number of targets that can be differentiated via this one-target-one-fluorophore multiplexed detection approach is restricted by spectral overlaps between fluorophores. In response, we present herein a new multiplexed detection approach termed ratiometric fluorescence coding, in which we encode each nucleic acid target with a specific ratio between two standard fluorophores. In ratiometric fluorescence coding, we employ the padlock probe chemistry to encode each nucleic acid target with a specific number of binding sites for two probes labeled with different fluorophores. Coupling the padlock probes with either rolling circle amplification (RCA) or hyperbranched rolling circle amplification (HRCA), we transform each nucleic acid target into a specific template that allows hybridization with the fluorescently labeled probes at predesigned ratios, thereby achieving multiplexed detection. For demonstration, we detected DNA targets from six infectious diseases and demonstrated the potential for further expanding the multiplexing capability of our approach. With further development, ratiometric fluorescence coding has the potential to enable highly multiplexed detection of nucleic acid targets and facilitate molecular diagnosis of diseases.
| S-EPMC6363117 | biostudies-literature
Project description:BackgroundThe Covid-19 pandemic necessitated social distancing restrictions, which placed limitations on access to ophthalmic care to only those who had an imminent risk of sight loss. All other face-to-face consultations were converted to telephone consultations or were postponed. We investigated whether parents were able to test their child's vision using available home vision testing applications, with an aim to aid decision making during a telephone consultation.MethodsFamilies with follow-up consultations at Birmingham Children's Hospital were asked to test their child's vision at home. Instructions for the use of Peek acuity, or iSight Pro, were emailed to a parent. Parents chose to use a particular app based on available devices at home. Parents were asked to test uniocular visual acuity twice. Home versus hospital acuity was correlated. Home acuity test-retest reliability was acquired. Parental feedback was obtained through questionnaires.ResultsOne hundred and three families were contacted, 15 families completed home vision testing. Ten families used Peek acuity, five families used iSight Pro. Uniocular visual acuity test-retest reliability was 0.03 LogMAR. Home-hospital acuity testing had a bias of 0.14 LogMAR, hospital acuity yielding a lower LogMAR score. Most families who completed testing found it easy to do; however, some struggled, and 81 families did not undertake home vision testing.ConclusionsUptake of home vision testing was limited by parental engagement, most likely influenced by the current pandemic. Most families who undertook home vision testing were able to generate results that could be used for clinical decision making. Extending the impact of parental vision testing will require education by clinicians and further study to increase sample sizes and to improve confidence.
| S-EPMC8269789 | biostudies-literature
Project description:BackgroundEmerging cross-sectional reports find that the COVID-19 pandemic and related social restrictions negatively affect lifestyle behaviours and mental health in general populations.AimsTo study the longitudinal impact of COVID-19 on work practices, lifestyle and well-being among desk workers during shelter-at-home restrictions.MethodsWe added follow-up after completion of a clinical trial among desk workers to longitudinally measure sedentary behaviour, physical activity, sleep, diet, mood, quality of life and work-related health using validated questionnaires and surveys. We compared outcomes assessed before and during COVID-19 shelter-at-home restrictions. We assessed whether changes in outcomes differed by remote working status (always, changed to or never remote) using analysis of covariance (ANCOVA).ResultsParticipants (N = 112; 69% female; mean (SD) age = 45.4 (12.3) years; follow-up = 13.5 (6.8) months) had substantial changes to work practices, including 72% changing to remote work. Deleterious changes from before to during shelter-at-home included: 1.3 (3.5)-h increase in non-workday sedentary behaviour; 0.7 (2.8)-point worsening of sleep quality; 8.5 (21.2)-point increase in mood disturbance; reductions in five of eight quality of life subscales; 0.5 (1.1)-point decrease in work-related health (P < 0.05). Other outcomes, including diet, physical activity and workday sedentary behaviour, remained stable (P ≥ 0.05). Workers who were remote before and during the pandemic had greater increases in non-workday sedentary behaviour and stress, with greater declines in physical functioning. Wake time was delayed overall by 41 (61) min, and more so in workers who changed to remote.ConclusionsEmployers should consider supporting healthy lifestyle and well-being among desk workers during pandemic-related social restrictions, regardless of remote working status.
| S-EPMC7928687 | biostudies-literature
Project description:ObjectivesRT-PCR testing is indispensable in Covid-19 pandemic management. With the spread of the pandemic with emerging variants, the RT-PCR capacity is overburdened and new strategies and capabilities need to be established. One option is the pooled RT-PCR testing.DesignWe conducted an experiment with various mixtures of Covid-19 samples known to be negative and positive, and investigated the impact of pool size and mixture level on final cycle threshold (CT)- measures. More specifically, 5, 10, and 20 Covid-19 negative samples are combined with 1, 2 or 3 low-CT or high-CT Covid-19 positive samples.ResultsWe have shown that average input CT and number of high and low CT samples in the pool are the main drivers of the final CT assessment, making the detectability easier. Pool size was not significantly associated with Final CT albeit suggestive.ConclusionsWe conclude that pooled RT-PCR testing strategy does not reduce the sensitivity of RT-PCR and thus provides a practical way to expand the RT-PCR screening capacity in pandemic management. The pool size not being significnat, we recommend that the pool size of 20 would be a practical level reducing the time to obtain the results and the cost of RT-PCR testing needs.
| S-EPMC8673736 | biostudies-literature