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:BackgroundFarm work entails a heterogeneous mixture of exposures that vary considerably across farms and farmers. Farm work is associated with various health outcomes, both adverse and beneficial. One mechanism by which farming exposures can impact health is through the microbiome, including the indoor built environment microbiome. It is unknown how individual occupational exposures shape the microbial composition in workers' homes.ObjectivesWe investigated associations between farm work activities, including specific tasks and pesticide use, and the indoor microbiome in the homes of 468 male farmers.MethodsParticipants were licensed pesticide applicators, mostly farmers, enrolled in the Agricultural Lung Health Study from 2008-2011. Vacuumed dust from participants' bedrooms underwent whole-genome shotgun sequencing for indoor microbiome assessment. Using questionnaire data, we evaluated 6 farm work tasks (processing of either hay, silage, animal feed, fertilizer, or soy/grains, and cleaning grain bins) and 19 pesticide ingredients currently used in the past year, plus 7 persistent banned pesticide ingredients ever used.ResultsAll 6 work tasks were associated with increased within-sample microbial diversity, with a positive dose-response for the sum of tasks (p=0.001). All tasks were associated with altered overall microbial compositions (weighted UniFrac p=0.001) and with higher abundance of specific microbes, including soil-based microbes such as Haloterrigena . Among the 19 pesticides, only current use of glyphosate and past use of lindane were associated with increased within-sample diversity (p=0.02-0.04). Ten currently used pesticides and all 7 banned pesticides were associated with altered microbial composition (p=0.001-0.04). Six pesticides were associated with differential abundance of certain microbes.DiscussionSpecific farm activities and exposures can impact the dust microbiome inside homes. Our work suggests that occupational farm exposures could impact the health of workers and their families through modifying the indoor environment, specifically the microbial composition of house dust, offering possible future intervention targets.
| S-EPMC10473816 | biostudies-literature
Project description:Molecular detection of pathogenic nucleic acids from patient samples requires incubating biochemical reactions at specific temperatures to amplify DNA. This incubation is typically carried out with an electrical heater and a temperature controller. To reduce test cost, to eliminate the need for manufacturing incubators, which may require significant time, and to enable electricity-free operation, we use energetic compounds such as an Mg(Fe) alloy mixed with a phase-change material (PCM) that undergoes phase transformation at the desired incubation temperature. We dubbed this composite Energetic Phase Change Material (EPCM). When the EPCM is brought into contact with water, the magnesium alloy interacts with the water to produce heat. The EPCM heats up to its phase transition temperature. Any excess heat is absorbed as latent heat and the system is maintained at its desired incubation temperature, independent of ambient temperatures, long enough to facilitate enzymatic amplification. The EPCM together with colorimetric amplicon detection facilitates an inexpensive, disposable, point-of-need diagnostic test that does not require any electric power. We demonstrate the feasibility of our approach by detecting SARS-Cov-2 in saliva samples either without any instrumentation or with a palm-size CCD camera that enables us to follow the amplification process in real time.
| S-EPMC8238897 | 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: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:Frequent working from home (WFH) may stay as a new work norm after the COVID-19 pandemic. Prior observational studies on WFH and work outcomes under non-pandemic circumstances are mostly cross-sectional and often studied employees who worked from home in limited capacity. To provide additional insights that might inform post-pandemic work policies, using longitudinal data collected before the COVID-19 pandemic (June 2018 to July 2019), this study aims to examine the associations between WFH and multiple subsequent work-related outcomes, as well as potential modifiers of these associations, in a sample of employees among whom frequent or even full-time WFH was common (N = 1,123, Meanage = 43.37 years). In linear regression models, each subsequent work outcome (standardized score was used) was regressed on frequencies of WFH, adjusting for baseline values of the outcome variables and other covariates. The results suggested that WFH for 5 days/week versus never WFH was associated with subsequently less work distraction (ß = -0.24, 95% CI = -0.38, -0.11), greater perceived productivity/engagement (ß = 0.23, 95% CI = 0.11, 0.36), and greater job satisfaction (ß = 0.15, 95% CI = 0.02, 0.27), and was associated with subsequent work-family conflicts to a lesser extent (ß = -0.13, 95% CI = -0.26, 0.004). There was also evidence suggesting that long work hours, caregiving responsibilities, and a greater sense of meaningful work can all potentially attenuate the benefits of WFH. As we move towards the post-pandemic era, further research will be needed to understand the impacts of WFH and resources for supporting employees who work from home.
| S-EPMC10072379 | 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:PurposeLaboratory animal workers (LAW) working with laboratory mice are exposed to mouse allergens (MA). If MA are spread to home environments, this might increase the risk for allergies in LAW and their families. This study aimed to assess 1. whether spreading of MA from workplace to home environment takes place; 2. which factors increase spreading of MA.MethodsIn a cross-sectional study, dust samples were taken on the mattress and seating in homes of LAW (n = 105) and an unexposed comparison group (n = 13). From 89 LAW, additional dust samples were taken from their workplaces. Samples were analysed using Mus m1 ELISA kits [detection limit (DL) 0.2 ng mus m1/ml]. Sociodemographic data, personal history of allergies and cleaning habits, as well as work-related characteristics (LAW only) were assessed by questionnaire. Latent factors were assessed via factor analysis. Tobit models were fitted to analyse the latent factors' contribution to MA spreading.ResultsMA concentration on the seating was significantly higher in home environments of LAW (median = 1.28 ng mus m1/m2) than in the comparison group (median < DL, p = 0.019). The highest workplace MA concentration was found on the floor of the scullery (median = 140,000.00 ng mus m1/m2), followed by hair-covering caps (median = 76.02 ng mus m1/m2). Cage and mouse facility cleaning tasks and infrequent changing of bed linen at home were statistically significantly associated with higher MA concentrations at home.ConclusionsSpreading of MA from LAW's workplace to their home environment takes place, especially among LAWs involved in cleaning tasks.
| S-EPMC8068679 | biostudies-literature