Digital PCR is a sensitive new technique for SARS-CoV-2 detection in clinical applications.

The global coronavirus disease 2019 (COVID-19) pandemic has posed great challenges in people's daily lives. Highly sensitive laboratory techniques played a critical role in clinical COVID-19 diagnosis and management. In this study the feasibility of using a new digital PCR-based detection assay for clinical COVID-19 diagnosis was investigated by comparing its performance with that of RT-PCR. Clinical patient samples and samples obtained from potentially contaminated environments were analyzed. The study included 10 patients with confirmed COVID-19 diagnoses, 32 validated samples of various types derived from different clinical timepoints and sites, and 148 environmentally derived samples. SARS-CoV-2 nucleic acids were more readily detected in respiratory tract samples (35.0%). In analyses of environmentally derived samples, the positivity rate of air samples was higher than that of surface samples, probably due to differences in virus concentrations. Digital PCR detected SARS-CoV-2 in several samples that had previously been deemed negative, including 3 patient-derived samples and 5 environmentally derived samples. In this study digital PCR exhibited higher sensitivity than conventional RT-PCR, suggesting that it may be a useful new method for clinical SARS-CoV-2 detection. Improvement of SARS-CoV-2 detection would substantially reduce the rates of false-negative COVID-19 test results, in particular those pertaining to asymptomatic carriers.

Diagnostic and Treatment Strategies for COVID-19.

The world is facing lockdown for the first time in decades due to the novel coronavirus COVID-19 (SARS-CoV-2) pandemic. This has led to massive global economic disruption, placed additional strain on local and global public health resources and, above all, threatened human health. We conducted a review of peer-reviewed and unpublished data, written in English, reporting on the current COVID-19 pandemic. This data includes previously used strategies against infectious disease, recent clinical trials and FDA-approved diagnostic and treatment strategies. The literature was obtained through a systematic search using PubMed, Web of Sciences, and FDA, NIH and WHO websites. Of the 98 references included in the review, the majority focused on pathogen and host targeting, symptomatic treatment and convalescent plasma utilization. Other sources investigated vaccinations in the pipeline for the possible prevention of COVID-19 infection. The results demonstrate various conventional as well as potentially advanced in vitro diagnostic approaches (IVD) for the diagnosis of COVID-19. Mixed results have been observed so far when utilising these approaches for the treatment of COVID-19 infection. Some treatments have been found highly effective in specific regions of the world while others have not altered the disease process. The responsiveness of currently available options is not conclusive. The novelty of this disease, the rapidity of its global outbreak and the unavailability of vaccines have contributed to the global public's fear. It is concluded that the exploration of a range of diagnostic and treatment strategies for the management of COVID-19 is the need of the hour.

Molecular Detection of Biological Agents in the Field: Then and Now.

Molecular detection of biological agents in the field has traditionally relied on the use of quantitative real-time PCR (qPCR), which now includes commercially available instruments that can be used in the laboratory or field. Adapting this technology for field-forward applications necessitated innovation to minimize size, weight, and power requirements. Rugged, portable instruments, efficient power sources, freeze-dried reagents, data communications, and standard operating procedures for minimally trained users are some examples of limitations that have been overcome to allow qPCR-based data to be generated at the point of need. Despite the high specificity and sensitivity of qPCR, the assays require a priori sequence-based knowledge of the etiological agent to design and produce specific targeted assays with primers and probes. However, in many cases the etiological agent may not be known and pathogen identification must rely on the use of an untargeted screening method. By extracting, preparing, and sequencing all of the genomic material in a particular sample at once, known as metagenomics, a less biased view of the biological entities in that sample can be ascertained. Using metagenomics methods in the field requires the development and optimization of straightforward sample preparation, sequencing, and bioinformatics workflows reminiscent of the challenges faced during the development of field-forward qPCR 15 years ago. To review the state of qPCR and sequencing in the field, we summarized a panel discussion from the 2019 ASM Biothreats Conference. Our discussion focused on the development, evolution, and comparison of molecular methods for biological agents and their utility in the field.

Identification of a novel, internal tRNA-derived RNA fragment as a new prognostic and screening biomarker in chronic lymphocytic leukemia, using an innovative quantitative real-time PCR assay.

Chronic lymphocytic leukemia (CLL) is one of the most common types of leukemia in adults. Several studies have identified various prognostic biomarkers in CLL. In this study, we investigated the potential value of an internal fragment of the tRNAs bearing the Glycine anticodon CCC (i-tRF-GlyCCC), which is a small non-coding RNA, as a prognostic and screening biomarker in CLL. For this purpose, blood samples were collected from 90 CLL patients and 43 non-leukemic blood donors. Peripheral blood mononuclear cells (PBMCs) were isolated, total RNA was extracted and in-vitro polyadenylated, and first-strand cDNA was synthesized using an oligo-dT-adaptor primer. A real-time quantitative PCR assay was developed and applied for the quantification of i-tRF-GlyCCC in our samples. The biostatistical analysis revealed that i-tRF-GlyCCC levels are significantly lower in PBMCs of CLL patients, compared to PBMCs of non-leukemic controls, and that i-tRF-GlyCCC could be considered as a screening biomarker. Kaplan-Meier overall survival (OS) analysis revealed reduced OS for CLL patients with positive i-tRF-GlyCCC expression (P = 0.001). Multivariate Cox regression confirmed its independent unfavorable prognostic power with regard to OS. In conclusion, i-tRF-GlyCCC may constitute a promising molecular biomarker in CLL, for screening and prognostic purposes.

Estandarización de la técnica Real Time PCR para la detección molecular de la mutación V617F en el gen de JAK-2 en neoplasias mieloproliferativas crónicas / Standardization of the Real Time PCR technique for the molecular detection of the V617F mutation in the JAK-2 gene in chronic myeloproliferative neoplasms

V617F mutation in exon 14 of Janus Kinase 2 gene (jak-2) is used as a molecular marker for the diagnosis of Philadelphia negative myeloproliferative neoplasms (Phi-) such as Polycythemia Vera (PV), Essential Thrombocythemia (ET) and Primary Myelofibrosis (MFP). To detect this mutation, we used conventional polymerase chain reaction technique (PCR), a simple and inexpensive technique, however, has some drawbacks that current technology allows to solve. During the last years, more sensitive molecular techniques have been incorporated in clinical practice to support the diagnosis, prognosis and follow-up of hematological patients. For its implementation in the clinical routine should be considered technical and economic aspects, so in this work, we evaluate the Real Time PCR technique as a diagnostic method for the detection of the Jak-2-V617F mutation, using in house primers design. Our result show that the technique implemented has a concordance index of 0.87 with the conventional PCR used in the molecular diagnosis of myeloproliferative neoplasms. In addition, it has the same specificity, greater sensitivity and, shorter execution time in relation to conventional PCR. The implementation of this diagnostic method in our Hospital is technically possible and commercially convenient. (AU)

An Overview of Digital PCR.

Digital polymerase chain reaction (dPCR) is a new method for absolute quantification of nucleic acids. The dPCR reaction solution is divided into numerous partitions followed by independent amplification. Target copy number is counted using statistical analyses of positive signals. in contrast to quantitative PCR, a standard curve is not necessary for dPCR. Here, we reviewed the development, principles, and applications of dPCR.

Development of Lyophilized Loop-Mediated Isothermal Amplification Reagents for the Detection of Leptospira.

Leptospirosis is considered to be the most widespread zoonosis. This worldwide emerging infectious disease is caused by the pathogenic species belonging to the genus Leptospira. Polymerase chain reaction (PCR)-based diagnostic assays have been developed for detecting Leptospira DNA in cell cultures and clinical samples. Because PCR requires specialized equipment and extensive end-user training, it is not suitable for routine work in resource-limited areas. We have developed a loop-mediated isothermal amplification (LAMP) assay to detect the presence of Leptospira in patient, animal and environmental samples using lyophilized reagents at a single temperature of around 63°C with a heating block. The sensitivity of this LAMP assay is very similar to the PCR method. The amplified DNA products can be visualized with the naked eyes using hydroxy naphthol blue or detected by the fluorescence signal of SYBR green dye in the reaction when an ultraviolet lamp or compact fluorescence tube scanner is used. This LAMP assay is simple, rapid, and can be performed with a water bath or heating block. The lyophilized LAMP reagents are stable for 3 months when stored at 4°C and 1 month when stored at 25°C, respectively. It is ideal for resource-limited settings where leptospirosis is endemic.

Quality Control of Widely Used Therapeutic Recombinant Proteins by a Novel Real-Time PCR Approach.

BACKGROUND: Existence of bacterial host-cell DNA contamination in biopharmaceutical products is a potential risk factor for patients receiving these drugs. Hence, the quantity of contamination must be controlled under the regulatory standards. Although different methods such as hybridization assays have been employed to determine DNA impurities, these methods are labor intensive and rather expensive. In this study, a rapid real-time PCR test was served as a method of choice to quantify the E. coli host- cell DNA contamination in widely used recombinant streptokinase (rSK) , and alpha interferon (IFN-α) preparations. METHODS: A specific primer pair was designed to amplify a sequence inside the E. coli 16S rRNA gene. Serial dilutions of DNA extracted from E. coli host cells, along with DNA extracted from Active Pharmaceutical Ingredients of rSK, and IFN-α samples were subjected to an optimized real-time PCR assay based on SYBR Green chemistry. RESULTS: The test enabled us to detect a small quantity of genomic DNA contamination as low as 0.0002 pg in recombinant protein-based drugs. For the first time, this study showed that DNA contamination in rSK and IFN-α preparation manufactured in Pasteur Institute of Iran is much lower than the safety limit suggested by the US FDA. CONCLUSION: Real-time PCR is a reliable test for rapid detection of host-cell DNA contamination, which is a major impurity of therapeutic recombinant proteins to keep manufacturers' minds on refining drugs, and provides consumers with safer biopharmaceuticals.

Recent advances in molecular diagnostics of hepatitis B virus.

Hepatitis B virus (HBV) is one of the important global health problems today. Infection with HBV can lead to a variety of clinical manifestations including severe hepatic complications like liver cirrhosis and hepatocellular carcinoma. Presently, routine HBV screening and diagnosis is primarily based on the immuno-detection of HBV surface antigen (HBsAg). However, identification of HBV DNA positive cases, who do not have detectable HBsAg has greatly encouraged the use of nucleic acid amplification based assays, that are highly sensitive, specific and are to some extent tolerant to sequence variation. In the last few years, the field of HBV molecular diagnostics has evolved rapidly with advancements in the molecular biology tools, such as polymerase chain reaction (PCR) and real-time PCR. Recently, apart of PCR based amplification methods, a number of isothermal amplification assays, such as loop mediated isothermal amplification, transcription mediated amplification, ligase chain reaction, and rolling circle amplification have been utilized for HBV diagnosis. These assays also offer options for real time detection and integration into biosensing devices. In this manuscript, we review the molecular technologies that are presently available for HBV diagnostics, with special emphasis on isothermal amplification based technologies. We have also included the recent trends in the development of biosensors and use of next generation sequencing technologies for HBV.

New Developments in Quantitative Real-time Polymerase Chain Reaction Technology.

Real time-quantitative PCR (RT-qPCR) technology has revolutionized the detection landscape in every area of molecular biology. The fundamental basis of this technology has remained unchanged since its inception, however various modifications have enhanced the overall performance of this highly versatile technology. These improvements have ranged from changes in the individual components of the enzymatic reaction cocktail (polymerizing enzymes, reaction buffers, probes, etc.) to the detection system itself (instrumentation, software, etc.). The RT-qPCR technology currently available to researchers is more sensitive, faster and affordable than when this technology was first introduced. In this article, we summarize the developments of the last few years in RT-qPCR technology and nucleic acid amplification.

[Current advancement of the PCR-based molecular diagnosis for tuberculous meningitis].

Central nervous system (CNS) tuberculosis, particularly tuberculous meningitis (TBM), is one of the severest forms of tuberculosis. At present, the diagnosis of CNS tuberculosis remains a complex issue because the most widely used conventional "gold standard" based on bacteriological detection methods, such as direct smear and culture identification, cannot rapidly detect Mycobacterium tuberculosis (M.Tb) bacilli in CSF specimens with sufficient sensitivity in the acute phase of TBM. Recently, instead of the conventional "gold standard", the various molecular-based methods, such as polymerase chain reaction (PCR) assay, has emerged as a promising new method for the diagnosis of TBM. Moreover, nested PCR assay has been reported as a key method that drastically increases the sensitivity and specificity of DNA amplification compared with conventional single-step PCR. Currently, a novel assay technique, which is internally controlled and combines the high sensitivity of nested PCR with the accurate quantification of real-time PCR, namely, Wide Range Quantitative Nested Real-time PCR (WR-QNRT-PCR) assay, has been developed. This novel assay technique is useful for the rapid diagnosis and the assessment of anti-tuberculosis treatment during clinical course of TBM. Therefore, in actual clinical practice, its wider use for diagnosis of TBM is expected in the future.

[Research progress of real-time quantitative PCR method for group A rotavirus detection].

Group A rotavirus is one of the most significant etiological agents which causes acute gastroenteritis among infants and young children worldwide. So far, several method which includes electron microscopy (EM), enzyme immunoassay (EIA), reverse transcription-polymerase chain reaction (RT-PCR)and Real-time Quantitative PCR has been established for the detection of rotavirus. Compared with other methods, Real-time quantitative PCR have advantages in specificity, sensitivity, genotyping and quantitative accuracy. This article shows a overview of the application of real-time quantitative PCR technique to detecte group A rotavirus.