A review of current effective COVID-19 testing methods and quality control.

COVID-19 is a highly infectious disease caused by the SARS-CoV-2 virus, which primarily affects the respiratory system and can lead to severe illness. The virus is extremely contagious, early and accurate diagnosis of SARS-CoV-2 is crucial to contain its spread, to provide prompt treatment, and to prevent complications. Currently, the reverse transcriptase polymerase chain reaction (RT-PCR) is considered to be the gold standard for detecting COVID-19 in its early stages. In addition, loop-mediated isothermal amplification (LMAP), clustering rule interval short palindromic repeats (CRISPR), colloidal gold immunochromatographic assay (GICA), computed tomography (CT), and electrochemical sensors are also common tests. However, these different methods vary greatly in terms of their detection efficiency, specificity, accuracy, sensitivity, cost, and throughput. Besides, most of the current detection methods are conducted in central hospitals and laboratories, which is a great challenge for remote and underdeveloped areas. Therefore, it is essential to review the advantages and disadvantages of different COVID-19 detection methods, as well as the technology that can enhance detection efficiency and improve detection quality in greater details.

Implementing QR codes in academia to improve sample tracking, data accessibility, and traceability in multicampus interdisciplinary collaborations.

The growing number of multicampus interdisciplinary projects in academic institutions expedites a necessity for tracking systems that provide instantly accessible data associated with devices, samples, and experimental results to all collaborators involved. This need has become particularly salient with the COVID pandemic when consequent travel restrictions have hampered in person meetings and laboratory visits. Minimizing post-pandemic travel can also help reduce carbon footprint of research activities. Here we developed a Quick Response (QR) code tracking system that integrates project management tools for seamless communication and tracking of materials and devices between multicampus collaborators: one school of medicine, two engineering laboratories, three manufacturing cleanroom sites, and three research laboratories. Here we aimed to use this system to track the design, fabrication, and quality control of bioelectronic devices, in vitro experimental results, and in vivo testing. Incorporating the tracking system into our project helped our multicampus teams accomplish milestones on a tight timeline via improved data traceability, manufacturing efficiency, and shared experimental results. This tracking system is particularly useful to track device issues and ensure engineering device consistency when working with expensive biological samples in vitro and animals in vivo to reduce waste of biological and animal resources associated with device failure.

Research Progress of Raman Spectroscopy and Raman Imaging in Pharmaceutical Analysis.

The analytical investigation of the pharmaceutical process monitors the critical process parameters of the drug, beginning from its development until marketing and post-marketing, and appropriate corrective action can be taken to change the pharmaceutical design at any stage of the process. Advanced analytical methods, such as Raman spectroscopy, are particularly suitable for use in the field of drug analysis, especially for qualitative and quantitative work, due to the advantages of simple sample preparation, fast, non-destructive analysis speed and effective avoidance of moisture interference. Advanced Raman imaging techniques have gradually become a powerful alternative method for monitoring changes in polymorph distribution and active pharmaceutical ingredient distribution in drug processing and pharmacokinetics. Surface-enhanced Raman spectroscopy (SERS) has also solved the inherent insensitivity and fluorescence problems of Raman, which has made good progress in the field of illegal drug analysis. This review summarizes the application of Raman spectroscopy and imaging technology, which are used in the qualitative and quantitative analysis of solid tablets, quality control of the production process, drug crystal analysis, illegal drug analysis, and monitoring of drug dissolution and release in the field of drug analysis in recent years.

IPVS policy statement on HPV nucleic acid testing guidance for those utilising/considering HPV as primary precancer screening: Quality assurance and quality control issues.

We advise that only clinically validated HPV assays which have fulfilled internationally accepted performance criteria be used for primary cervical screening. Further, assays should be demonstrated to be fit for purpose in the laboratory in which they will ultimately be performed, and quality materials manuals and frameworks will be helpful in this endeavor. Importantly, there is a fundamental shortage of well validated, low-cost, low complexity HPV tests that have demonstrated utility in a near-patient setting; representing a significant challenge and focus for future development in order to reach the WHO's goal of eliminating cervical cancer.

BIGwas: Single-command quality control and association testing for multi-cohort and biobank-scale GWAS/PheWAS data.

BACKGROUND: Genome-wide association studies (GWAS) and phenome-wide association studies (PheWAS) involving 1 million GWAS samples from dozens of population-based biobanks present a considerable computational challenge and are carried out by large scientific groups under great expenditure of time and personnel. Automating these processes requires highly efficient and scalable methods and software, but so far there is no workflow solution to easily process 1 million GWAS samples. RESULTS: Here we present BIGwas, a portable, fully automated quality control and association testing pipeline for large-scale binary and quantitative trait GWAS data provided by biobank resources. By using Nextflow workflow and Singularity software container technology, BIGwas performs resource-efficient and reproducible analyses on a local computer or any high-performance compute (HPC) system with just 1 command, with no need to manually install a software execution environment or various software packages. For a single-command GWAS analysis with 974,818 individuals and 92 million genetic markers, BIGwas takes ∼16 days on a small HPC system with only 7 compute nodes to perform a complete GWAS QC and association analysis protocol. Our dynamic parallelization approach enables shorter runtimes for large HPCs. CONCLUSIONS: Researchers without extensive bioinformatics knowledge and with few computer resources can use BIGwas to perform multi-cohort GWAS with 1 million GWAS samples and, if desired, use it to build their own (genome-wide) PheWAS resource. BIGwas is freely available for download from http://github.com/ikmb/gwas-qc and http://github.com/ikmb/gwas-assoc.

Phytest: quality control for phylogenetic analyses.

MOTIVATION: The ability to automatically conduct quality control checks on phylogenetic analyses is becoming more important with the increase in genetic sequencing and the use of real-time pipelines e.g. in the SARS-CoV-2 era. Implementations of real-time phylogenetic analyses require automated testing to make sure that problems in the data are caught automatically within analysis pipelines and in a timely manner. Here, we present Phytest (version 1.1) a tool for automating quality control checks on sequences, trees and metadata during phylogenetic analyses. RESULTS: Phytest is a phylogenetic analysis testing program that easily integrates into existing phylogenetic pipelines. We demonstrate the utility of Phytest with real-world examples. AVAILABILITY AND IMPLEMENTATION: Phytest source code is available on GitHub (https://github.com/phytest-devs/phytest) and can be installed via PyPI with the command 'pip install phytest'. Extensive documentation can be found at https://phytest-devs.github.io/phytest/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Quality metrics and outcomes among critically ill patients in China: results of the national clinical quality control indicators for critical care medicine survey 2015-2019.

BACKGROUND: It is crucial to improve the quality of care provided to ICU patient, therefore a national survey of the medical quality of intensive care units (ICUs) was conducted to analyze adherence to quality metrics and outcomes among critically ill patients in China from 2015 to 2019. METHODS: This was an ICU-level study based on a 15-indicator online survey conducted in China. Considering that ICU care quality may vary between secondary and tertiary hospitals, direct standardization was adopted to compare the rates of ICU quality indicators among provinces/regions. Multivariate analysis was performed to identify potential factors for in-hospital mortality and factors related to ventilator-associated pneumonia (VAP), catheter-related bloodstream infections (CRBSIs), and catheter-associated urinary tract infections (CAUTIs). RESULTS: From the survey, the proportions of structural indicators were 1.83% for the number of ICU inpatients relative to the total number of inpatients, 1.44% for ICU bed occupancy relative to the total inpatient bed occupancy, and 51.08% for inpatients with Acute Physiology and Chronic Health Evaluation II scores ≥15. The proportions of procedural indicators were 74.37% and 76.60% for 3-hour and 6-hour surviving sepsis campaign bundle compliance, respectively, 62.93% for microbiology detection, 58.24% for deep vein thrombosis prophylaxis, 1.49% for unplanned endotracheal extubations, 1.99% for extubated inpatients reintubated within 48 hours, 6.38% for unplanned transfer to the ICU, and 1.20% for 48-hour ICU readmission. The proportions of outcome indicators were 1.28‰ for VAP, 3.06‰ for CRBSI, 3.65‰ for CAUTI, and 10.19% for in-hospital mortality. Although the indicators varied greatly across provinces and regions, the treatment level of ICUs in China has been stable and improved based on various quality control indicators in the past 5 years. The overall mortality rate has dropped from 10.19% to approximately 8%. CONCLUSIONS: The quality indicators of medical care in China's ICUs are heterogeneous, which is reflected in geographic disparities and grades of hospitals. This study is of great significance for improving the homogeneity of ICUs in China.

Transformation of Biopharmaceutical Manufacturing Through Single-Use Technologies: Current State, Remaining Challenges, and Future Development.

Single-use technologies have transformed conventional biopharmaceutical manufacturing, and their adoption is increasing rapidly for emerging applications like antibody-drug conjugates and cell and gene therapy products. These disruptive technologies have also had a significant impact during the coronavirus disease 2019 pandemic, helping to advance process development to enable the manufacturing of new monoclonal antibody therapies and vaccines. Single-use systems provide closed plug-and-play solutions and enable process intensification and continuous processing. Several challenges remain, providing opportunities to advance single-use sensors and their integration with single-use systems, to develop novel plastic materials, and to standardize design for interchangeability. Because the industry is changing rapidly, a holistic analysis of the current single-use technologies is required, with a summary of the latest advancements in materials science and the implementation of these technologies in end-to-end bioprocesses.

Presence of unsafe chemical impurities, accelerated evaporation of alcohol, and lack of key labeling requirements are risks and concerns for some alcohol-based hand sanitizers and dispenser practices during the COVID-19 pandemic.

Alcohol-based hand sanitizers (ABHS) have been an important hand hygiene tool during the COVID-19 pandemic. Recently, ABHS from non-traditional drug manufacturers have entered the market, triggered by a lack of ABHS availability. Some of these ABHS contain high levels of chemical impurities that may be harmful with frequent exposure. Additionally, the use of refillable dispensers designed to accept ABHS from bulk containers allows for mixing and evaporation that may compromise ABHS integrity. To understand the risks associated with low quality ABHS and bulk refilling practices, we collected 77 ABHS samples sourced from community settings (restaurants, grocery stores, etc.) and 40 samples from a single school district. All samples were obtained from bulk refillable dispensers that were in use. Samples were analyzed for alcohol content, chemical impurities, aesthetic qualities, and presence of drug labeling information. Additionally, we performed laboratory-based experiments to determine the impact of dispenser design on alcohol evaporation rates. Over 70% of samples for which photos were available showed lack of essential labeling information, including missing "Drug Facts Labels". For ABHS samples acquired from community settings, nearly 14% of samples had visible impurities, and over 30% of samples had concentrations of acetal and acetaldehyde in excess of FDA interim limits. Subpotent ethanol concentrations were observed in 9.09% and 82.05% of samples from community settings and the school district, respectively, with the school district sample results being associated with dispenser misuse. Laboratory-based experiments show dispenser design significantly impacts the rate of ethanol evaporation of ABHS products, especially if stored in open refillable dispensers without an internal reservoir. This study demonstrates risks associated with use of inferior ABHS and bulk refilling practices. Regulatory agencies should issue guidance on best practices in community settings to ensure the integrity of ABHS as an essential public health tool to prevent the spread of COVID-19 and other transmissible diseases.

Assessment of quality of alcohol-based hand sanitizers used in Johannesburg area during the CoViD-19 pandemic.

Since the outbreak of the Coronavirus Disease 2019 (CoViD-19), the World Health Organization has recommended that, in absence of soap and water, alcohol-based hand sanitizer can be used to prevent the transmission of coronaviruses. Unfortunately, many media and anecdotal reports indicate that many alcohol-based hand sanitizers sold in South Africa are substandard and some contain potentially toxic ingredients. The study aimed to identify hand sanitizers used in the Johannesburg area during the CoViD-19 pandemic that do not contain the recommended alcohol concentration of at least 70% propanol or 60% ethanol, and contain traces of toxic ingredients. Hand sanitizers randomly collected from various traders around Johannesburg were analyzed using Agilent auto sampler coupled to a gas chromatograph utilizing flame ionisation detection. Of the 94 hand sanitizer samples collected, three preparations contained no alcohol, whereas the rest contained either ethanol, 2-propanol or 1-propanol or a combination of two alcohols. Of the alcohol-containing hand sanitizers, 37 (41%) contained less than 60% alcohol. Ethyl acetate, isobutanol and other non-recommended alcohols (methanol and 3-methyl-butanol) were also identified. Consumers are therefore warned that among the many brands of hand sanitizers found around Johannesburg, there are some substandard preparations and some that contain traces of toxic ingredients.

Quality Assurance Through Standard Operating Procedures Development and Deviation: A Medicolegal Death Investigation Systems Response to the COVID-19 Pandemic.

ABSTRACT: Standard operating procedures drive everyday practice within any organization, including those within a forensic setting. In the event of unusual circumstances, organizations must respond rapidly to address the impact on operations while ensuring that the quality and safety outcomes of routine services are not affected. This case study illustrates how standard operating procedures can be newly developed or modified, and rapidly deployed and quickly revised, to address unusual circumstances. The response to the COVID-19 pandemic is used as an example in this case report.

AutoPlate: Rapid Dose-Response Curve Analysis for Biological Assays.

The emergence of COVID-19 has emphasised that biological assay data must be analysed quickly to develop safe, effective and timely vaccines/therapeutics. For viruses such as SARS-CoV-2, the primary way of measuring immune correlates of protection is through assays such as the pseudotype microneutralisation (pMN) assay, thanks to its safety and versatility. However, despite the presence of existing tools for data analysis such as PRISM and R the analysis of these assays remains cumbersome and time-consuming. We introduce an open-source R Shiny web application and R library (AutoPlate) to accelerate data analysis of dose-response curve immunoassays. Using example data from influenza studies, we show that AutoPlate improves on available analysis software in terms of ease of use, flexibility and speed. AutoPlate (https://philpalmer.shinyapps.io/AutoPlate/) is a tool for the use of laboratories and wider scientific community to accelerate the analysis of biological assays in the development of viral vaccines and therapeutics.