Discrepancy of SARS-CoV-2 PCR results due to the sample collection sites and possible improper sampling.
Ontology highlight
ABSTRACT:
SUBMITTER: Irifune S
PROVIDER: S-EPMC8282446 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Background.:Variable adherence to standardized case definitions, clinical procedures, specimen collection techniques, and laboratory methods has complicated the interpretation of previous multicenter pneumonia etiology studies. To circumvent these problems, a program of clinical standardization was embedded in the Pneumonia Etiology Research for Child Health (PERCH) study. Methods.:Between March 2011 and August 2013, standardized training on the PERCH case definition, clinical procedures, and collection of laboratory specimens was delivered to 331 clinical staff at 9 study sites in 7 countries (The Gambia, Kenya, Mali, South Africa, Zambia, Thailand, and Bangladesh), through 32 on-site courses and a training website. Staff competency was assessed throughout 24 months of enrollment with multiple-choice question (MCQ) examinations, a video quiz, and checklist evaluations of practical skills. Results.:MCQ evaluation was confined to 158 clinical staff members who enrolled PERCH cases and controls, with scores obtained for >86% of eligible staff at each time-point. Median scores after baseline training were ?80%, and improved by 10 percentage points with refresher training, with no significant intersite differences. Percentage agreement with the clinical trainer on the presence or absence of clinical signs on video clips was high (?89%), with interobserver concordance being substantial to high (AC1 statistic, 0.62-0.82) for 5 of 6 signs assessed. Staff attained median scores of >90% in checklist evaluations of practical skills. Conclusions.:Satisfactory clinical standardization was achieved within and across all PERCH sites, providing reassurance that any etiological or clinical differences observed across the study sites are true differences, and not attributable to differences in application of the clinical case definition, interpretation of clinical signs, or in techniques used for clinical measurements or specimen collection.
| S-EPMC5447838 | biostudies-literature
Project description:Iatrogenic peripheral nerve injuries are a common source of postprocedural morbidity. The authors present a case report of a patient who developed brachial plexopathy from positioning during radiofrequency ablation of a renal mass. Though incidence data on the majority of iatrogenic peripheral nerve injury is scarce, there is more concrete data on iatrogenic brachial plexopathy. The incidence of brachial plexopathies is ~0.2% of all patients who receive general anesthesia, with between 7 and 10% of brachial plexopathies being iatrogenic in nature. The mechanism of injury in the majority of cases is due to stretching or compression of the nerve tissue. Treatment is largely supportive. Prevention is key in minimizing this form of patient morbidity. It is the operator's responsibility to mitigate this risk by employing proper positioning techniques and communicating closely with the anesthesia staff when applicable.
| S-EPMC3193318 | biostudies-other
Project description:Evaluating fungal contamination indoors is complicated because of the many different sampling methods utilized. In this study, fungal contamination was evaluated using five sampling methods and four matrices for results. The five sampling methods were a 48 hour indoor air sample collected with a Button™ inhalable aerosol sampler and four types of dust samples: a vacuumed floor dust sample, newly settled dust collected for four weeks onto two types of electrostatic dust cloths (EDCs) in trays, and a wipe sample of dust from above floor surfaces. The samples were obtained in the bedrooms of asthmatic children (n = 14). Quantitative polymerase chain reaction (qPCR) was used to analyze the dust and air samples for the 36 fungal species that make up the Environmental Relative Moldiness Index (ERMI). The results from the samples were compared by four matrices: total concentration of fungal cells, concentration of fungal species associated with indoor environments, concentration of fungal species associated with outdoor environments, and ERMI values (or ERMI-like values for air samples). The ERMI values for the dust samples and the ERMI-like values for the 48 hour air samples were not significantly different. The total cell concentrations of the 36 species obtained with the four dust collection methods correlated significantly (r = 0.64-0.79, p < 0.05), with the exception of the vacuumed floor dust and newly settled dust. In addition, fungal cell concentrations of indoor associated species correlated well between all four dust sampling methods (r = 0.68-0.86, p < 0.01). No correlation was found between the fungal concentrations in the air and dust samples primarily because of differences in concentrations of Cladosporium cladosporioides Type 1 and Epicoccum nigrum. A representative type of dust sample and a 48 hour air sample might both provide useful information about fungal exposures.
| S-EPMC5884110 | biostudies-literature
Project description:The outbreak of the SARS-CoV-2 pandemic created an unprecedented requirement for diagnostic testing, challenging not only healthcare workers and laboratories, but also providers. Quantitative RT-PCR of various specimen types is considered the diagnostic gold standard for the detection of SARS-CoV-2, both in terms of sensitivity and specificity. The pre-analytical handling of patient specimens is a critical factor to ensure reliable and valid test results. Therefore, the effect of storage duration and temperature on SARS-CoV-2 RNA copy number stability was examined in various commercially available specimen collection, transport and storage devices for naso/oropharyngeal swabs and saliva. The swab specimen transport and storage devices tested showed no significant alteration of viral RNA copy numbers when stored at room temperature, except for one system when stored for up to 96 h. However, at 37 °C a significant reduction of detectable RNA was found in 3 out of 4 of the swab solutions tested. It was also found that detectability of viral RNA remained unchanged in all 7 saliva devices as well as in unstabilized saliva when stored for 96 h at room temperature, but one device showed marked RNA copy number loss at 37 °C. All tested saliva collection devices inhibited SARS-CoV-2 infectivity immediately, whereas SARS-CoV-2 remained infectious in the swab transport systems examined, which are designed to be used for viral or bacterial growth in cell culture systems.
| S-EPMC8990442 | biostudies-literature
Project description:The major aquatic interface between host and environment in teleost finfish species is the gill. The diversity of this infraclass, high complexity of the organ, and its direct exposure to the surrounding environment make it an ideal candidate for furthering our understanding of the intertwined relationships between host and microbiome. Capturing the structure and diversity of bacterial communities from this low-biomass, inhibitor-rich tissue can, however, prove challenging. Lessons learned in doing so are directly applicable to similar sample types in other areas of microbiology. Through the development of a quantitative PCR assay for both host material and 16S rRNA genes, we tested and developed a robust method for low-biomass sample collection which minimized host DNA contamination. Quantification of 16S rRNA facilitated not only the screening of samples prior to costly library construction and sequencing but also the production of equicopy libraries based on 16S rRNA gene copies. A significant increase in diversity of bacteria captured was achieved, providing greater information on the true structure of the microbial community. Such findings offer important information for determining functional processes. Results were confirmed across fresh, brackish, and marine environs with four different fish species, with results showing broad homology between samples, demonstrating the robustness of the approach. Evidence presented is widely applicable to samples similar in composition, such as sputum or mucus, or those that are challenging due to the inherent inclusion of inhibitors. IMPORTANCE The interaction between the fish gill and surrounding bacteria-rich water provides an intriguing model for examining the interaction between the fish, free-floating bacteria, and the bacterial microbiome on the gill surface. Samples that are inherently low in bacteria, or that have components that inhibit the ability to produce libraries that identify the components of microbial communities, present significant challenges. Gill samples present both of these types of challenges. We developed methods for quantifying both the bacterial and host DNA material and established a sampling method which both reduced inhibitor content and maximized bacterial diversity. By quantifying and normalizing bacteria prior to library construction, we showed significant improvements with regards to the fidelity of the final data. Our results support wide-ranging applications for analyzing samples of similar composition, such as mucus and sputum, in other microbiological spheres.
| S-EPMC9769501 | biostudies-literature
Project description:Molecular diagnostics has drastically improved the survival rate of patients diagnosed with non-small cell lung cancer (NSCLC) over the last 10 years. Despite advancements in molecular testing, targeted therapies, and national guideline recommendations, more than half of NSCLC patients in the United States either never receive testing or patient care is not informed via molecular testing. Here, we sought to explore the relationship between DNA/RNA input, the molecular testing method, and test success rates. On a shared set of low-input reference test materials (n = 3), we ran both a hybrid capture-based, next-generation sequencing (NGS) assay and a multiplexed digital PCR (dPCR) panel. The dPCR panel was highly sensitive and specific for low-input samples in dilution studies ranging from 40 to 1 ng DNA and from 20 to 2.5 ng RNA, while NGS had up to an 86% loss in sensitivity as contrived sample inputs were serially diluted. The dPCR panel also demonstrated a high PPA (>95%) at diluted inputs as low as 15/7.5 ng DNA/RNA on 23 banked clinical samples with the same NGS hybrid capture assay at a high input. These data suggest that digital PCR is an accurate and effective way of identifying clinically relevant NSCLC mutations at low nucleotide input and quality.
| S-EPMC10854965 | biostudies-literature
Project description:ObjectiveTo investigate the effect of somatic, postzygotic, gain-of-function mutation of Endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1) encoding hypoxia-inducible factor-2α (HIF-2α) on posterior fossa development and spinal dysraphism in EPAS1 gain-of-function syndrome, which consists of multiple paragangliomas, somatostatinoma, and polycythemia.MethodsPatients referred to our institution for evaluation of new, recurrent, and/or metastatic paragangliomas/pheochromocytoma were confirmed for EPAS1 gain-of-function syndrome by identification of the EPAS1 gain-of-function mutation in resected tumors and/or circulating leukocytes. The posterior fossa, its contents, and the spine were evaluated retrospectively on available MRI and CT images of the head and neck performed for tumor staging and restaging. The transgenic mouse model underwent Microfil vascular perfusion and subsequent intact ex vivo 14T MRI and micro-CT as well as gross dissection, histology, and immunohistochemistry to assess the role of EPAS1 in identified malformations.ResultsAll 8 patients with EPAS1 gain-of-function syndrome demonstrated incidental posterior fossa malformations-one Dandy-Walker variant and 7 Chiari malformations without syringomyelia. These findings were not associated with a small posterior fossa; rather, the posterior fossa volume exceeded that of its neural contents. Seven of 8 patients demonstrated spinal dysraphism; 4 of 8 demonstrated abnormal vertebral segmentation. The mouse model similarly demonstrated features of neuraxial dysraphism, including cervical myelomeningocele and spinal dysraphism, and cerebellar tonsil displacement through the foramen magnum. Histology and immunohistochemistry demonstrated incomplete mesenchymal transition in the mutant but not the control mouse.ConclusionsThis study characterized posterior fossa and spinal malformations seen in EPAS1 gain-of-function syndrome and suggests that gain-of-function mutation in HIF-2α results in improper mesenchymal transition.
| S-EPMC7164966 | biostudies-literature
Project description:Introduction. Non-invasive sample collection and viral sterilizing buffers have independently enabled workflows for more widespread COVID-19 testing by reverse-transcriptase polymerase chain reaction (RT-PCR).Gap statement. The combined use of sterilizing buffers across non-invasive sample types to optimize sensitive, accessible, and biosafe sampling methods has not been directly and systematically compared.Aim. We aimed to evaluate diagnostic yield across different non-invasive samples with standard viral transport media (VTM) versus a sterilizing buffer eNAT- (Copan diagnostics Murrieta, CA) in a point-of-care diagnostic assay system.Methods. We prospectively collected 84 sets of nasal swabs, oral swabs, and saliva, from 52 COVID-19 RT-PCR-confirmed patients, and nasopharyngeal (NP) swabs from 37 patients. Nasal swabs, oral swabs, and saliva were placed in either VTM or eNAT, prior to testing with the Xpert Xpress SARS-CoV-2 (Xpert). The sensitivity of each sampling strategy was compared using a composite positive standard.Results. Swab specimens collected in eNAT showed an overall superior sensitivity compared to swabs in VTM (70 % vs 57 %, P=0.0022). Direct saliva 90.5 %, (95 % CI: 82 %, 95 %), followed by NP swabs in VTM and saliva in eNAT, was significantly more sensitive than nasal swabs in VTM (50 %, P<0.001) or eNAT (67.8 %, P=0.0012) and oral swabs in VTM (50 %, P<0.0001) or eNAT (58 %, P<0.0001). Saliva and use of eNAT buffer each increased detection of SARS-CoV-2 with the Xpert; however, no single sample matrix identified all positive cases.Conclusion. Saliva and eNAT sterilizing buffer can enhance safe and sensitive detection of COVID-19 using point-of-care GeneXpert instruments.
| S-EPMC8697510 | biostudies-literature
Project description:BackgroundPlant performance is affected by the level of expression of PsbS, a key photoprotective protein involved in the process of feedback de-excitation (FDE), or the qE component of non-photochemical quenching, NPQ.ResultsIn studies presented here, under constant laboratory conditions the metabolite profiles of leaves of wild-type Arabidopsis thaliana and plants lacking or overexpressing PsbS were very similar, but under natural conditions their differences in levels of PsbS expression were associated with major changes in metabolite profiles. Some carbohydrates and amino acids differed ten-fold in abundance between PsbS-lacking mutants and over-expressers, with wild-type plants having intermediate amounts, showing that a metabolic shift had occurred. The transcriptomes of the genotypes also varied under field conditions, and the genes induced in plants lacking PsbS were similar to those reportedly induced in plants exposed to ozone stress or treated with methyl jasmonate (MeJA). Genes involved in the biosynthesis of JA were up-regulated, and enzymes involved in this pathway accumulated. JA levels in the undamaged leaves of field-grown plants did not differ between wild-type and PsbS-lacking mutants, but they were higher in the mutants when they were exposed to herbivory.ConclusionThese findings suggest that lack of FDE results in increased photooxidative stress in the chloroplasts of Arabidopsis plants grown in the field, which elicits a response at the transcriptome level, causing a redirection of metabolism from growth towards defence that resembles a MeJA/JA response.
| S-EPMC2656510 | biostudies-literature
Project description:BackgroundReadily available testing for SARS-CoV-2 is necessary to mitigate COVID-19 disease outbreaks. At-home collection kits, in which samples are self-collected without requiring a laboratory or clinic visit and sent to an external laboratory for testing, can provide convenient testing to those with barriers to access. They can prevent unnecessary exposure between patient and clinical staff, increase access for patients with disabilities or remote workers, and decrease burdens on health care resources, such as provider time and personal protective equipment. Exact Sciences developed an at-home collection kit for samples to be tested to detect SARS-CoV-2 that includes an Instructions for Use (IFU) document, which guides people without prior experience on collecting a nasal swab sample. Demonstrating successful sample collection and usability is critical to ensure that these samples meet the same high-quality sample collection standards as samples collected in clinics.ObjectiveThe aim of this study was to determine the usability of a SARS-CoV-2 at-home nasal swab sample collection kit.MethodsA human factors usability study was conducted with 30 subjects without prior medical, laboratory, or health care training and without COVID-19 sample self-collection experience. Subjects were observed while they followed the IFU for the at-home sample collection portion of the SARS-CoV-2 test in a setting that simulated a home environment. IFU usability was further evaluated by requiring the subjects to complete a survey, answer comprehension questions, provide written feedback, and respond to questions from the observer about problems during use.ResultsAll 30 subjects successfully completed the sample collection process, and all 30 samples were determined by reverse transcription-polymerase chain reaction (RT-PCR) testing to meet quality standards for SARS-CoV-2 testing. The subjects' written feedback and comments revealed several recommendations to improve the IFU.ConclusionsThe study demonstrated the overall usability of an at-home SARS-CoV-2 collection kit. Various feedback mechanisms provided opportunities to improve the wording and graphics for some critical tasks, including placing the label correctly on the tube. A modified IFU was prepared based on study outcomes.
| S-EPMC8673714 | biostudies-literature