Clinical Applications of Quantitative Real-Time PCR in Virology

Multiplex one-step RT-qPCR assays for simultaneous detection of BRV, BCoV, Escherichia coli K99+ and Cryptosporidium parvum

Introduction

Bovine rotavirus (BRV), bovine coronavirus (BCoV), Escherichia coli K99+ (E. coli K99+), and Cryptosporidium parvum (C. parvum) are the most common pathogens involved in calf production. These pathogens can cause calf diarrhea, leading to significant economic losses in the cattle farming industry. These four pathogens have similar clinical symptoms, making them difficult to distinguish. Therefore, we established a one-step quadruple TaqMan fluorescence quantitative PCR method capable of simultaneously and rapidly detecting BRV, BCoV, E. coli K99+, and C. parvum.

Methods

Specific primers and TaqMan probes were designed for the BRV VP-6 gene, BCoV N gene, E. coli K99+ K99 gene, and C. parvum 18S rRNA gene. Standard positive plasmids were constructed, and the reaction conditions of the method were optimized. The sensitivity, specificity, and repeatability of the method were validated, and clinical samples were tested.

Results

The minimum detection limits of this method for BRV, BCoV, E. coli K99+, and C. parvum were 5.8 × 101, 2.3 × 101, 4.5 × 102, and 2.6 × 101 copies/μL, respectively. The intra- and intergroup coefficients of variation were all less than 1.2%. This method has the advantages of strong specificity, reproducibility, low cost, and no cross-reaction with other bovine pathogens. Compared with the commercial reagent kit method were used to analyze clinical samples, and both the diagnostic sensitivity (DSe) and diagnostic specificity (DSp) were above 90%, with kappa values greater than 0.9.

Discussion

The one-step multiplex RT-qPCR method developed in this study for detecting BRV, BCoV, E. coli K99+, and C. parvum is expected to be an effective tool for the rapid and economical diagnosis and monitoring of diarrhoeal diseases in calves.

Strengthening molecular testing capacity in Colombia: Challenges and opportunities

The COVID-19 pandemic has accelerated efforts to enhance pathogen detection using molecular biology techniques. This study examines the expansion of molecular testing capacity in Colombia, identifying strengths and areas for improvement in the existing infrastructure. The study began with the creation of a database inventorying laboratories based on publicly available data from government entities and active web searches. Ten laboratories were selected for detailed characterization. Structured surveys assessed their testing capacity and progress in implementing molecular-based diagnostic tests for various infectious diseases. The strategy for identifying laboratories showed a total of 311 laboratories. Of these, 65 % (n = 202) are private and 21 % (n = 65) are state-owned, mainly public health laboratories, and the remaining 14 % (n = 44) are affiliated with academic institutions. The highest concentration of these labs is in Bogotá, Antioquia, and Valle del Cauca, primarily in urban areas. Key limitations affecting testing laboratories in Colombia include: i) infrastructure (26.2 %), highlighting the need for standardized facility guidelines; ii) quality and documentation (16.7 %), requiring stronger quality management systems; iii) biosafety (14.3 %), emphasizing the need for continuous waste management, especially in public labs; and iv) human talent (10.7 %), needing better policies for staff retention, particularly in government institutions. Strengthening laboratories can establish a comprehensive national molecular testing system. Integrating molecular tests into health system diagnostic algorithms and implementing sustainable laboratory strategies will address human health challenges and support the "One Health" approach for animal and environmental health.

Effectiveness and user experience of nose and throat swabbing techniques for SARS-CoV-2 detection: results from the UK COVID-19 National Testing Programme

BACKGROUND

The UK's National Health Service Test and Trace (NHSTT) program aimed to provide the most effective and accessible SARS-CoV-2 testing approach possible. Early user feedback indicated that there were accessibility issues associated with throat swabbing. We report the results of service evaluations performed by NHSTT to assess the effectiveness and user acceptance of swabbing approaches, as well as qualitative findings of user experiences from research reports, surveys, and incident reports. Our intent is to present and summarize our findings about the application of alternative swabbing approaches during the COVID-19 pandemic in the UK.

METHODS

From May 2020 to December 2021, NHSTT conducted a series of service evaluations assessing self-swabbing and assisted swabbing of the nose and throat, and nose only (anterior nares/mid-turbinate) using polymerase chain reaction (PCR) and lateral flow devices (LFDs), for diagnostic suitability within the COVID-19 National Testing Programme. Outcomes included observational user feedback on swabbing approaches and quantitative testing performance (concordance, sensitivity, and specificity). A post-hoc indirect comparison of swabbing approaches was also performed. Additionally, an analysis of existing cross-service research was conducted in April 2021 to determine user feedback regarding swabbing approaches.

RESULTS

Observational data from cross-service research indicated a user preference for nose swabbing over throat swabbing. Significantly more users reported that nose swabbing was easier to perform than throat swabbing (50% vs. 12%) and there were significantly fewer reported incidents. In the service evaluations, while there was reduced sensitivity for nose-only swabbing for PCR (88%) compared with nose and throat swabbing, similar sensitivities were observed for nose-only and nose and throat swabbing for LFDs. The sensitivity of nose-only swabbing for LFDs was higher for individuals with higher viral concentrations.

CONCLUSIONS

User experience analyses supported a preference for nose-only swabbing. Nose-only swabbing for LFDs provided sufficient diagnostic accuracy, supporting its use as a viable option in the COVID-19 National Testing Programme. Less invasive swabbing approaches are important to maximize testing accessibility and alongside other behavioral interventions, increase user uptake.

Digital PCR in Virology: Current Applications and Future Perspectives

Digital PCR (dPCR) has been used in the field of virology since its inception. Technological innovations in microfluidics more than a decade ago caused a sharp increase in its use. There is an emerging consensus that dPCR now outperforms quantitative PCR (qPCR) in the basic parameters such as precision, sensitivity, accuracy, repeatability and resistance to inhibitors. These strengths have led to several current applications in quantification, mutation detection and environmental DNA and RNA samples. In high throughput scenarios, such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, the cost and throughput still significantly hampered the adaption of dPCR. There is much unexplored potential within the multiplexing capabilities of dPCR. This will allow simultaneous multi-target quantification and can also partially alleviate the throughput and cost drawback. In this review, we discuss the strengths and weaknesses of dPCR with a focus on virology applications and we discuss future applications. Finally, we discuss recent evolutions of the technology in the form of real-time dPCR and digital high-resolution melting.

RNA biomarkers in cancer therapeutics: The promise of personalized oncology

Cancer therapy is a rapidly evolving and constantly expanding field. Current approaches include surgery, conventional chemotherapy and novel biologic agents as in immunotherapy, that together compose a wide armamentarium. The plethora of choices can, however, be clinically challenging in prescribing the most suitable treatment for any given patient. Fortunately, biomarkers can greatly facilitate the most appropriate selection. In recent years, RNA-based biomarkers have proven most promising. These molecules that range from small noncoding RNAs to protein coding gene transcripts can be valuable in cancer management and especially in cancer therapeutics. Compared to their DNA counterparts which are stable throughout treatment, RNA-biomarkers are dynamic. This allows prediction of success prior to treatment start and can identify alterations in expression that could reflect response. Moreover, improved nucleic acid technology allows RNA to be extracted from practically every biofluid/matrix and evaluated with exceedingly high analytic sensitivity. In addition, samples are largely obtained by minimally invasive procedures and as such can be used serially to assess treatment response real-time. This chapter provides the reader insight on currently known RNA biomarkers, the latest research employing Artificial Intelligence in the identification of such molecules and in clinical decisions driving forward the era of personalized oncology.

The development, evaluation, performance, and validation of micro-PCR and extractor for the quantification of HIV-1 &-2 RNA

HIV infection has been a global public health threat and overall reported ~ 40 million deaths. Acquired immunodeficiency syndrome (AIDS) is attributed to the retroviruses (HIV-1/2), disseminated through various body fluids. The temporal progression of AIDS is in context to the rate of HIV-1 infection, which is twice as protracted in HIV-2 transmission. Q-PCR is the only available method that requires a well-developed lab infrastructure and trained personnel. Micro-PCR, a portable Q-PCR device, was developed by Bigtec Labs, Bangalore, India. It is simple, accurate, fast, and operationalised in remote places where diagnostic services are inaccessible in developing countries. This novel micro-PCR determines HIV-1 and HIV-2 viral load using a TruePrep™ extractor device for RNA isolation. Five ml blood samples were collected at the blood collection centre at AIIMS, New Delhi, India. Samples were screened for serology, and a comparison of HIV-1/2 RNA was done between qPCR and micro-PCR in the samples. The micro-PCR assay of HIV-RNA has compared well with those from real-time PCR (r = 0.99, i < 0.002). Micro-PCR has good inter and intra-assay reproducibility over a wide dynamic range (1.0 × 102-1.0 × 108 IU/ml). The linear dynamic range was 102-108 IU/ml. The clinical and analytical specificity of the assay was comparable, i.e., 100%. Intra-assay and inter-assay coefficients of variation ranged from 1.17% to 3.15% and from 0.02% to 0.46%, respectively. Moreover, due to the robust, simple, and empirical method, the Probit analysis has also been done for qPCR LODs to avoid uncertainties in target recoveries. The micro-PCR is reliable, accurate, and reproducible for early detection of HIV-1 and HIV-2 viral loads simultaneously. Thus, it can easily be used in the field and in remote places where quantification of both HIV-1/2 is not reachable.

A guide to the use of bioassays in exploration of natural resources

Bioassays are the main tool to decipher bioactivities from natural resources thus their selection and quality are critical for optimal bioprospecting. They are used both in the early stages of compounds isolation/purification/identification, and in later stages to evaluate their safety and efficacy. In this review, we provide a comprehensive overview of the most common bioassays used in the discovery and development of new bioactive compounds with a focus on marine bioresources. We present a comprehensive list of practical considerations for selecting appropriate bioassays and discuss in detail the bioassays typically used to explore antimicrobial, antibiofilm, cytotoxic, antiviral, antioxidant, and anti-ageing potential. The concept of quality control and bioassay validation are introduced, followed by safety considerations, which are critical to advancing bioactive compounds to a higher stage of development. We conclude by providing an application-oriented view focused on the development of pharmaceuticals, food supplements, and cosmetics, the industrial pipelines where currently known marine natural products hold most potential. We highlight the importance of gaining reliable bioassay results, as these serve as a starting point for application-based development and further testing, as well as for consideration by regulatory authorities.