Acyclovir triphosphate inhibits the diagnostic polymerase chain reaction for cytomegalovirus

Development and validation of qPCR methods for nucleic acid biomarkers as a drug development tool: points to consider

Nucleic acid (NA) biomarkers play critical roles in drug development. However, the global regulatory guidelines for assessing quantification methods specific to NA biomarkers are limited. The validation of analytical methods is crucial for the use of biomarkers in clinical and post-marketing evaluations of drug efficacy and adverse reactions. Given that quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR (RT-qPCR) methods are the gold standards for the quantification of NA biomarkers, the Biomarker Analytical Method Validation Study Group in Japan has discussed considerations and made recommendations for the development and validation of qPCR- and RT-qPCR-based analytical methods for endogenous NA biomarkers as drug development tools. This white paper aims to contribute to the global harmonization of NA biomarker assay validation.

Taking a step back from testing: Preanalytical considerations in molecular infectious disease diagnostics

Recent studies evaluating the preanalytical factors that impact the outcome of nucleic-acid based methods for the confirmation of SARS-CoV-2 have illuminated the importance of identifying variables that promoted accurate testing, while using scarce resources efficiently. The majority of laboratory errors occur in the preanalytical phase. While there are many resources identifying and describing mechanisms for main laboratory testing on automated platforms, there are fewer comprehensive resources for understanding important preanalytical and environmental factors that affect accurate molecular diagnostic testing of infectious diseases. This review identifies evidence-based factors that have been documented to impact the outcome of nucleic acid-based molecular techniques for the diagnosis of infectious diseases.

Nucleic acid testing of SARS-CoV-2: A review of current methods, challenges, and prospects

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has brought a huge threat to public health and the global economy. Rapid identification and isolation of SARS-CoV-2-infected individuals are regarded as one of the most effective measures to control the pandemic. Because of its high sensitivity and specificity, nucleic acid testing has become the major method of SARS-CoV-2 detection. A deep understanding of different diagnosis methods for COVID-19 could help researchers make an optimal choice in detecting COVID-19 at different symptom stages. In this review, we summarize and evaluate the latest developments in current nucleic acid detection methods for SARS-CoV-2. In particular, we discuss biosensors and CRISPR-based diagnostic systems and their characteristics and challenges. Furthermore, the emerging COVID-19 variants and their impact on SARS-CoV-2 diagnosis are systematically introduced and discussed. Considering the disease dynamics, we also recommend optional diagnostic tests for different symptom stages. From sample preparation to results readout, we conclude by pointing out the pain points and future directions of COVID-19 detection.

Inclusion Body Disease and Columbid Alphaherpesvirus 1 Infection in a Eurasian Eagle-Owl (Bubo bubo) of Central Italy

Hepatosplenitis or inclusion body disease is a fatal disease in owls caused by Columbid alphaherpesvirus 1 (CoHV-1). A few old case reports describe it worldwide. In Italy, knowledge regarding virus circulation and disease development is lacking. Four Eurasian eagle-owls (Bubo bubo), two adults and two juveniles, were submitted for postmortem examination showing aspecific clinical signs a few hours before death. Grossly disseminated petechial hemorrhages on serosal surfaces (n = 4), hepatic and splenic necrosis (n = 3), bilateral and symmetric necrosis of pharyngeal tonsils (n = 2), and diffuse and bilateral dark-red discoloration and firmness in lungs (n = 2) were seen. Tissues were sampled for histology, bacteriology, molecular testing, and transmission electron microscopy (TEM). On histology, disseminated petechial hemorrhages (n = 4) and necrosis of liver (n = 3) and spleen (n = 3) were seen, as well as lympho-histiocytic interstitial pneumonia and meningoencephalitis (n = 2). Intranuclear inclusion bodies (INIBs) were detected in one case. A panherpesviral PCR led to positive results in one case, identified in sequencing as CoHV-1. On TEM, intranuclear and intracytoplasmic virions with herpesviral morphology were seen in the same case. For the other three birds, the lack of PCR positivity, INIBs, and TEM detection could be linked to a possible reduction of the virus to undetectable levels. Death possibly occurred secondarily to bacterial infections, supposedly established during the acute phase of CoHV-1 infection. This paper reports the presence of CoHV-1in Italy and the development of a fatal form of the disease in a Eurasian eagle-owl.

Progress of Research into Novel Drugs and Potential Drug Targets against Porcine Pseudorabies Virus

Pseudorabies virus (PRV) is the causative agent of pseudorabies (PR), infecting most mammals and some birds. It has been prevalent around the world and caused huge economic losses to the swine industry since its discovery. At present, the prevention of PRV is mainly through vaccination; there are few specific antivirals against PRV, but it is possible to treat PRV infection effectively with drugs. In recent years, some drugs have been reported to treat PR; however, the variety of anti-pseudorabies drugs is limited, and the underlying mechanism of the antiviral effect of some drugs is unclear. Therefore, it is necessary to explore new drug targets for PRV and develop economic and efficient drug resources for prevention and control of PRV. This review will focus on the research progress in drugs and drug targets against PRV in recent years, and discuss the future research prospects of anti-PRV drugs.

Whole blood samples for faster real-time PCR analysis of thrombophilic mutations in SARS-CoV-2 virus positive patients

High incidence of thrombosis and venous thromboembolism was reported in patients with COVID-19. In this study, we focused on analysis of thrombophilic mutations performed without a standard DNA extraction step. In one hundred of COVID-19 positive outpatients, real-time PCR for Leiden mutation in the FV gene and G20210A mutation in the FII gene was carried out from DNA extracts and modified whole blood samples, and their cycle threshold (Ct) values were evaluated. In the extracts, healthy homozygotes (wt/wt), heterozygotes (M/wt), and homozygous carriers of Leiden mutation (M/M) provided median Ct values of 18.5, 19.4/22.0, and 20.9. In the whole blood, Ct values were 25.3 (wt/wt), 24.8/27.2 (M/wt), and 26.9 (M/M). Median Ct values for G20210A in the extracts were 19.6 for homozygotes (wt/wt), and 19.7/20.4 for heterozygous carriers. The whole blood samples provided Ct values of 23.9 in healthy homozygotes and 26.3/27.2 in heterozygotes for G20210A mutation. No homozygous subjects for G20210A and no double heterozygotes (for Leiden and G20210A mutations) were found. Despite significant differences in the Ct values, genotyping showed complete result concordance of the DNA extracts and the whole blood samples. The integrity and amplificability of DNA molecules in the whole blood samples during 28 days of deep freezing, interrupted by four cycles of thawing, did not significantly change. In conclusion, we demonstrated a new protocol for the detection of the thrombophilic mutations via real time PCR on the modified whole blood of COVID-19 positive patients. The blood modification was reliable, easy, cheap, and saving costs and turnaround time of the whole laboratory process.

Accurate nucleic acid quantification in a single sample tube without the need for calibration

Convenient and accurate nucleic acid quantification (NAQ) is crucial to clinical diagnosis, forensic medicine, veterinary medicine and food analysis. However, traditional NAQ relies on the preparation of a laborious, time-consuming and expensive calibration curve, which would also propagate pipette errors through serially dilutions. Besides, traditional NAQ is run in different tubes, which introduces bias from random tube-to-tube variations and is unable to detect inhibitors from biological samples. To solve these problems, a single-tube quantitative PCR (stqPCR) technique is proposed which enables accurate quantification without the need for a calibration curve. In this method, an internal quantitative standard DNA (IQS-DNA) for quantification was screened out by co-amplification with the target DNA. Then the difference between the quantification cycle value (ΔCq) of the IQS-DNA and the target DNA was used for NAQ. The method permitted high accuracy quantification with reliable data for concentrations in plasmid, serum standard, and clinical samples being confirmed (R² values of 0.9951, 0.9889, and 0.9727, slope values of 1.011, 1.028, and 0.9327, and intercept values of -0.06037, -0.1486, and 0.3325, respectively). Accurate NAQ could also be achieved by stqPCR even though inhibitors were present in a sample; however, in the case of using a commercial assay kit, satisfactory performance was only attained after the same sample was diluted some 32-fold. Moreover, integration of the present method into a microfluidic system could achieve super-fast NAQ in less than 30 min and achieve super-fast "sample in, quantitative answer out" testing in less than 40 min. Thus, the stqPCR method present here would promote the development of NAQ in the laboratory and on site.

Nucleic Acid and Immunological Diagnostics for SARS-CoV-2: Processes, Platforms and Pitfalls

Accurate diagnosis at an early stage of infection is essential for the successful management of any contagious disease. The coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus is a pandemic that has affected 214 countries affecting more than 37.4 million people causing 1.07 million deaths as of the second week of October 2020. The primary diagnosis of the infection is done either by the molecular technique of RT-qPCR by detecting portions of the RNA of the viral genome or through immunodiagnostic tests by detecting the viral proteins or the antibodies produced by the host. As the demand for the test increased rapidly many naive manufacturers entered the market with novel kits and more and more laboratories also entered the diagnostic arena making the test result more error-prone. There are serious debates globally and regionally on the sensitivity and specificity of these tests and about the overall accuracy and reliability of the tests for decision making on control strategies. The significance of the test is also complexed by the presence of asymptomatic carriers, re-occurrence of infection in cured patients as well as by the varied incubation periods of the infection and shifting of the viral location in the host tissues. In this paper, we review the techniques available for SARS-CoV-2 diagnosis and probable factors that can reduce the sensitivity and specificity of the different test methods currently in vogue. We also provide a checklist of factors to be considered to avoid fallacious practices to reduce false positive and false negative results by the clinical laboratories.

Overcoming inhibition in real-time diagnostic PCR

PCR is an important and powerful tool in several fields, including clinical diagnostics, food analysis, and forensic analysis. In theory, PCR enables the detection of one single cell or DNA molecule. However, the presence of PCR inhibitors in the sample affects the amplification efficiency of PCR, thus lowering the detection limit, as well as the precision of sequence-specific nucleic acid quantification in real-time PCR. In order to overcome the problems caused by PCR inhibitors, all the steps leading up to DNA amplification must be optimized for the sample type in question. Sampling and sample treatment are key steps, but most of the methods currently in use were developed for conventional diagnostic methods and not for PCR. Therefore, there is a need for fast, simple, and robust sample preparation methods that take advantage of the accuracy of PCR. In addition, the thermostable DNA polymerases and buffer systems used in PCR are affected differently by inhibitors. During recent years, real-time PCR has developed considerably and is now widely used as a diagnostic tool. This technique has greatly improved the degree of automation and reduced the analysis time, but has also introduced a new set of PCR inhibitors, namely those affecting the fluorescence signal. The purpose of this chapter is to view the complexity of PCR inhibition from different angles, presenting both molecular explanations and practical ways of dealing with the problem. Although diagnostic PCR brings together scientists from different diagnostic fields, end-users have not fully exploited the potential of learning from each other. Here, we have collected knowledge from archeological analysis, clinical diagnostics, environmental analysis, food analysis, and forensic analysis. The concept of integrating sampling, sample treatment, and the chemistry of PCR, i.e., pre-PCR processing, will be addressed as a general approach to overcoming real-time PCR inhibition and producing samples optimal for PCR analysis.

PCR inhibitors - occurrence, properties and removal

The polymerase chain reaction (PCR) is increasingly used as the standard method for detection and characterization of microorganisms and genetic markers in a variety of sample types. However, the method is prone to inhibiting substances, which may be present in the analysed sample and which may affect the sensitivity of the assay or even lead to false-negative results. The PCR inhibitors represent a diverse group of substances with different properties and mechanisms of action. Some of them are predominantly found in specific types of samples thus necessitating matrix-specific protocols for preparation of nucleic acids before PCR. A variety of protocols have been developed to remove the PCR inhibitors. This review focuses on the general properties of PCR inhibitors and their occurrence in specific matrices. Strategies for their removal from the sample and for quality control by assessing their influence on the individual PCR test are presented and discussed.

Real-time PCR method with statistical analysis to compare the potential of DNA isolation methods to remove PCR inhibitors from samples for diagnostic PCR

A real-time PCR method for fast comparison of different DNA isolation methods to remove PCR inhibitors from samples is presented. A fixed amount of target-200 copies of a 79-bp region of the COCH gene of the zebrafish (Danio rerio)-was added to each PCR reaction together with isolated DNA from different types of samples including chicken feces. Four commercial DNA isolation kits and a chelex-based technique were compared using this method. The copy numbers calculated and the endpoint fluorescence were statistically compared to the values of 22 control samples containing the control target and water instead of isolated DNA, processed together in the same PCR run. The level of the endpoint fluorescence was more often negatively influenced by inhibitors than the copy number calculated, suggesting a more pronounced effect on the plateau phase of the reaction by limiting one or more compounds in the PCR reaction.

Quantitative assay of hepatitis C virus RNA using an automated extraction system for specific capture with probes and paramagnetic particle separation

A commercially available automated specimen preparation instrument for specific probe capture and paramagnetic separation has been developed (AmpliCap/GT-12; Roche Molecular Systems). We evaluated assay performance of the AmpliCap/GT-12 in the quantitative assay for hepatitis C virus (HCV) RNA with the AMPLICOR HCV MONITOR Test (version 2.0). Assay linearity using serial dilutions from a serum panel was observed in the range of 500 to 850000 IU/ml, with a slightly compromised slope in the higher viral titers. The overall within-run and between-run reproducibility of the entire detection process for 3 and 5 log(10) (IU/ml) of HCV RNA in samples had a standard deviation of <0.2, which was comparable to a manual method based on organic extraction and isopropanol precipitation (Roche Molecular Systems). Comparison of the test results with those obtained by the manual method showed a good correlation (R(2) = 0.972, n = 86). Using heparin (3, 6.5, and 13 U/ml), dextran sulfate (0.1, 1, and 5 mM), hemoglobin (1.13, 2.25, and 4.5 g/liter), conjugated or unconjugated bilirubin (7.5, 15, and 30 mg/dl), and ATP (1.25, 2.5, and 5.0 mM) as known inhibitors, inhibition was only detected at a dextran sulfate concentration of 1 mM with the manual method but not with the AmpliCap/GT-12 extraction. In summary, the AmpliCap/GT-12 system was shown to permit a stable extraction process and accurate results for the quantitative assay of HCV RNA, successfully eliminating the inhibitory effect of dextran sulfate. This automated extraction system provides reliable and reproducible test results and saves labor; thus, it is suitable for routine diagnostic PCR.

Techniques for the evaluation of nucleic acid amplification technology performance with specimens containing interfering substances: efficacy of boom methodology for extraction of HIV-1 RNA

Accurate HIV-1 RNA quantitation with nucleic acid amplification assays (NAAA) is partly dependent on overall assay design to ensure proper and reproducible functioning in the presence of endogenous interfering substances present in a clinical specimen, or exogenous interfering substances introduced as a result of specimen collection or handling. This study tested various methods of evaluating interfering substances that could potentially affect the outcome of HIV-1 RNA amplification in a NAAA. Clinical specimens from HIV-1 seronegative subjects containing various endogenous interferents were evaluated with and without an HIV-1 RNA spike to assess recovery and specificity, respectively, with a non-PCR NAAA (NASBA HIV-1 RNA QT, Organon Teknika) that incorporates Boom methodology for nucleic acid extraction. Additional specimens were prepared to simulate various circumstances that might occur during specimen preparation to result in the introduction of exogenous interferents. A retrovirus reverse transcriptase inhibitor, zidovudine (AZT), was added to plasma specimens prior to testing. NAAA results obtained with 127 total clinical specimens, 10 bacterially contaminated specimens, 5 platelet enriched specimens, 5 AZT specimens, and 30 anticoagulated specimens were consistent with the expected outcomes in the presence and absence of the HIV-1 RNA spike, giving an assay specificity of 100%. The spiked HIV-1 RNA copies in the clinical specimens reported by the assay were 99% of the copies reported for a positive index control (normal plasma plus HIV-1 RNA spike). Compared to the amplification levels of the three internal assay calibrators obtained for normal plasma controls, no differences in the amplification levels of the calibrators for each type of specimen were observed. This result indicated that the interferents examined did not affect adversely assay function. Addition of known PCR interferents (hemoglobin and heparin) and AZT to isolated HIV-1 RNA resulted in a substantial reduction of amplification and invalid results, whereas no inhibition was observed when these interferents were added to the test system prior to isolation; these results directly demonstrate the efficient removal of such interferents during the NASBA HIV-1 RNA QT isolation procedure. The several approaches to investigate interference described in this study may be utilized for the evaluation of other assays using nucleic acid amplification technology.

A nested-PCR assay for the simultaneous amplification of HSV-1, HSV-2, and HCMV genomes in patients with presumed herpetic CNS infections

To facilitate early diagnosis of herpes virus infection of the central nervous system (CNS), a nested polymerase chain reaction (nPCR) assay was developed to test simultaneously for the presence of HSV-1, HSV-2, and HCMV DNA in the cerebrospinal fluid (CSF) of patients with herpetic CNS disease suspected on clinical grounds. The virus type-specific PCR products were differentiated either by agarose gel electrophoresis or by DNA enzyme immunoassay. Using titrated viral stocks as standards, a sensitivity of at least 0.03 infectious units was obtained for HSV-1, HSV-2 and HCMV and no cross-reactions were recorded. Among 178 CSF specimens (171 patients), which were tested under routine conditions, three contained HSV-1 DNA, one contained HSV-2 DNA and one contained HCMV DNA. No double or triple infection was diagnosed. The presence of inhibitors of the Taq DNA polymerase was monitored by spiking aliquots of the above CSF samples with 3 infectious units each of HSV-1 and HSV-2 or HCMV. Whereas none of 93 samples spiked with HSV-1 and HSV-2 contained inhibitors, the PCR reaction was inhibited in three out of 175 samples (1.7%) spiked with HCMV. The complete procedure which requires only 150 microl of CSF is easily completed within 8 h. Through its speed, reliability and sensitivity, this nPCR assay has met the specific criteria of the diagnostic laboratory.

A system for the quantitation of DNA using a microtiter plate-based hybridization and enzyme amplification technology

A quantitative hybridization technique for the detection of plasmid DNA by the action of a nuclease enzyme is described. The process utilizes the specific capture and detection of a sandwich hybridization, in a microtiter plate, that occurs in a single step. The detector probe is labeled with nuclease P1. The pH-dependent specificity of this enzyme for 3'-dinucleotides is used to generate a measurable signal by activating apo-glucose oxidase, which triggers an enzyme amplification cascade in the same microtiter plate. The sensitivity of the assay system is demonstrated in an assay of a mutated form of the human pancreatic ribonuclease gene inserted into the plasmid pUC 18. The system was able to detect 35 amol of target DNA in an assay composed of a 60-min hybridization and 20 min of signal generation. This use of nuclease P1 as the enzyme label and apo-glucose oxidase as the trigger for the amplification cascade results in an assay that is more sensitive than previously described enzyme amplification systems using colorimetric detection.

The role of PCR in the diagnosis and management of CMV in solid organ recipients: what is the predictive value for the development of disease and should PCR be used to guide antiviral therapy?

Cytomegalovirus remains a significant source of morbidity and mortality in immunocompromised hosts. The increased sensitivity of molecular diagnostic techniques (PCR, antigenemia) has resulted in our ability to detect viral replication earlier in the posttransplant period, before the onset of symptoms. With the advent of effective antiviral therapy, "preemptive therapy," guided by sensitive, early and specific predictors of CMV disease, has become a realistic objective. Although multiple studies have analyzed the sensitivity and specificity of these tests, their predictive value for the development of disease has not been defined. The purpose of this study was to evaluate the predictive value of a positive CMV PCR in the setting of solid abdominal organ transplantation. A total of 476 PCR assays were performed on 134 transplant recipients (102 kidney, 19 kidney/pancreas, 11 liver, 2 other) either as protocol serial samples or as dictated by clinical events. All samples were concomitantly analyzed using standard virological assays for CMV including culture, shell vial, and serology. Patients with any CMV seropositive donor/recipient (D/R) combination received ganciclovir prophylaxis in conjunction with antilymphocyte induction for 14 days. No subsequent CMV prophylaxis was used. The positive predictive value was 55% in all seropositive donor/recipient combinations. The highest risk group (seronegative recipient of seropositive donor) showed the highest positive predictive value, whereas seropositive recipients of either seropositive or seronegative donors showed positive predictive values of 45% and 25%, respectively. Negative predictive value was 100% for all groups. Early detection of CMV infection has important implications for patient management, including preemptive therapy, which can be guided by PCR, especially in high risk (D+/R-) patients.