SARS-CoV-2/COVID-19 laboratory biosafety practices and current molecular diagnostic tools

Development and evaluation of the automated multipurpose molecular testing system PCRpack for high-throughput SARS-CoV-2 testing

IMPORTANCE

Accurate and fast molecular testing is important for the diagnosis and control of COVID-19. During patient surges in the COVID-19 pandemic, laboratories were challenged by a higher demand for molecular testing under skilled staff shortages. We developed an automated multipurpose molecular testing system, named PCRpack, for the rapid, high-throughput testing of infectious pathogens, including SARS-CoV-2. The system is provided in an all-in-one package, including a liquid handling instrument, a laboratory information management system, and other materials needed for testing operation; is highly customizable; and is easily implemented. PCRpack showed robust liquid handling performance, high clinical diagnostic performance, a shorter turn-around time with minimal hands-on time, and a high testing capacity. These features contribute to the rapid implementation of the high-performance and high-throughput molecular testing environment at any phase of the pandemic caused by SARS-CoV-2 or future emerging pathogens.

Performance Evaluation of a BZ COVID-19 NALF Assay for Rapid Diagnosis of SARS-CoV-2

Coronavirus disease (COVID-19) caused by SARS-CoV-2 infection has been a global pandemic for more than two years, and it is important to quickly and accurately diagnose and isolate patients with SARS-CoV-2 infection. The BZ COVID-19 NALF Assay could sensitively detect SARS-CoV-2 from a nasopharyngeal swab because it adopts both a loop-mediated isothermal amplification and lateral flow immunochromatography technology. In this study, a total of 389 nasopharyngeal swab samples, of which 182 were SARS-CoV-2 PCR positive and 207 were negative samples, were recruited. Compared to the Allplex™ SARS-CoV-2 Assay, the BZ COVID-19 NALF Assay showed 95.05% sensitivity and 99.03% specificity for detecting SARS-CoV-2. The concordance rate between the BZ COVID-19 NALF Assay and Allplex™ SARS-CoV-2 Assay was 97.69%. The turnaround time of the BZ COVID-19 NALF Assay is only about 40~55 min. The BZ COVID-19 NALF Assay is an accurate, easy, and quick molecular diagnostic test compared to the conventional PCR test for detection of SARS-CoV-2. In addition, the BZ COVID-19 NALF Assay is thought to be very useful in small size medical facilities or developing countries where it is difficult to operate a clinical laboratory.

Current Technologies for Detection of COVID-19: Biosensors, Artificial Intelligence and Internet of Medical Things (IoMT): Review

Despite the fact that COVID-19 is no longer a global pandemic due to development and integration of different technologies for the diagnosis and treatment of the disease, technological advancement in the field of molecular biology, electronics, computer science, artificial intelligence, Internet of Things, nanotechnology, etc. has led to the development of molecular approaches and computer aided diagnosis for the detection of COVID-19. This study provides a holistic approach on COVID-19 detection based on (1) molecular diagnosis which includes RT-PCR, antigen-antibody, and CRISPR-based biosensors and (2) computer aided detection based on AI-driven models which include deep learning and transfer learning approach. The review also provide comparison between these two emerging technologies and open research issues for the development of smart-IoMT-enabled platforms for the detection of COVID-19.

Resilience and Protection of Health Care and Research Laboratory Workers During the SARS-CoV-2 Pandemic: Analysis and Case Study From an Austrian High Security Laboratory

The SARS-CoV-2 pandemic has highlighted the interdependency of healthcare systems and research organizations on manufacturers and suppliers of personnel protective equipment (PPE) and the need for well-trained personnel who can react quickly to changing working conditions. Reports on challenges faced by research laboratory workers (RLWs) are rare in contrast to the lived experience of hospital health care workers. We report on experiences gained by RLWs (e.g., molecular scientists, pathologists, autopsy assistants) who significantly contributed to combating the pandemic under particularly challenging conditions due to increased workload, sickness and interrupted PPE supply chains. RLWs perform a broad spectrum of work with SARS-CoV-2 such as autopsies, establishment of virus cultures and infection models, development and verification of diagnostics, performance of virus inactivation assays to investigate various antiviral agents including vaccines and evaluation of decontamination technologies in high containment biological laboratories (HCBL). Performance of autopsies and laboratory work increased substantially during the pandemic and thus led to highly demanding working conditions with working shifts of more than eight hours working in PPE that stressed individual limits and also the ergonomic and safety limits of PPE. We provide detailed insights into the challenges of the stressful daily laboratory routine since the pandemic began, lessons learned, and suggest solutions for better safety based on a case study of a newly established HCBL (i.e., BSL-3 laboratory) designed for autopsies and research laboratory work. Reduced personal risk, increased resilience, and stress resistance can be achieved by improved PPE components, better training, redundant safety measures, inculcating a culture of safety, and excellent teamwork.

Long-Term Preservation of SARS-CoV-2 RNA in Silk for Downstream RT-PCR Tests

Positive controls made of viral gene components are essential to validate the performance of diagnostic assays for pathogens like severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, most of them are target-specific, limiting their application spectrum when validating assays beyond their specified targets. The use of an inactivated whole-virus RNA reference standard could be ideal, but RNA is a labile molecule that needs cold chain storage and transportation to preserve its integrity and activity. The cold chain process stretches the already dwindling storage capacities, incurs huge costs, and limits the distribution of reference materials to low-resource settings. To circumvent these issues, we developed an inactivated whole-virus SARS-CoV-2 RNA reference standard and studied its stability in silk fibroin matrices, i.e., silk solution (SS) and silk film (SF). Compared to preservation in nuclease-free water (ddH2O) and SS, SF was more stable and could preserve the SARS-CoV-2 RNA reference standard at room temperature for over 21 weeks (∼6 months) as determined by reverse transcription polymerase chain reaction (RT-PCR). The preserved RNA reference standard in SF was able to assess the limits of detection of four commercial SARS-CoV-2 RT-PCR assays. In addition, SF is compatible with RT-PCR reactions and can be used to preserve a reaction-ready primer and probe mix for RT-PCR at ambient temperatures without affecting their activity. Taken together, these results offer extensive flexibility and a simpler mechanism of preserving RNA reference materials for a long time at ambient temperatures of ≥25 °C, with the possibility of eliminating cold chains during storage and transportation.

Digital PCR Applications in the SARS-CoV-2/COVID-19 Era: a Roadmap for Future Outbreaks

The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global public health disaster. The current gold standard for the diagnosis of infected patients is real-time reverse transcription-quantitative PCR (RT-qPCR). As effective as this method may be, it is subject to false-negative and -positive results, affecting its precision, especially for the detection of low viral loads in samples. In contrast, digital PCR (dPCR), the third generation of PCR, has been shown to be more effective than the gold standard, RT-qPCR, in detecting low viral loads in samples. In this review article, we selected publications to show the broad-spectrum applications of dPCR, including the development of assays and reference standards, environmental monitoring, mutation detection, and clinical diagnosis of SARS-CoV-2, while comparing it analytically to the gold standard, RT-qPCR. In summary, it is evident that the specificity, sensitivity, reproducibility, and detection limits of RT-dPCR are generally unaffected by common factors that may affect RT-qPCR. As this is the first time that dPCR is being tested in an outbreak of such a magnitude, knowledge of its applications will help chart a course for future diagnosis and monitoring of infectious disease outbreaks.