Getting rid of ‘rain’ and ‘stars’: Mitigating inhibition effects on ddPCR data analysis, the case study of the invasive crayfish Pacifastacus leniusculus in the streams of Luxembourg

A Highly Precise Method for the Quantitation of rAAV Cellular Uptake by ddPCR

Recombinant adeno-associated virus (rAAV) has emerged as a leading vehicle for human gene therapy. An accurate and precise infectious titer assay is critical for assessing rAAV quality, potency, and product stability. The current gold standard for measuring rAAV infectivity is the median tissue culture infectivity dose (TCID50) method, which is laborious and highly variable. In the past several years, the droplet digital PCR (ddPCR) technology has made profound impacts on gene therapy analytics as it provides absolute DNA copy quantitation and is more accurate and precise than qPCR. In this article, we leveraged the ddPCR technology and developed a method to quantify rAAV cellular uptake in vitro. The results demonstrated that our method is consistent with TCID50 but is significantly more precise. Utilizing a stable AAV receptor (AAVR) cell line, this method can be implemented as a platform approach for various AAV serotypes and target genes. Moreover, the method is stability indicating, as desired for a potency assay. In conclusion, a novel rAAV uptake assay has been developed which reflects the mechanism of action of rAAV, and is accurate, precise and sensitive to product quality; thus overcoming many of the challenges of the traditional TCID50 method. It is particularly useful for initial rAAV product quality assessment and can contribute to a robust assay matrix with other product-specific potency assays for late-stage programs.

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.

Development of two step reverse transcription droplet digital PCR (RT-ddPCR) for simultaneous identification of saliva and semen

Determination of the type of body fluids is essential for crime scene reconstruction and for improving the reliability of expert testimonies. Messenger RNA (mRNA) analysis by reverse transcription quantitative PCR (RT-qPCR) has been used in forensic genetics, particularly for body fluid identification. It is a relative quantification method that compares the Ct values of target and reference gene. Thus, the method is unsuitable for determining exact copy numbers of the target gene. To address this limitation, this study performed body fluid-specific mRNA analysis using two-step reverse transcription droplet digital PCR (RT-ddPCR), which is capable of absolute quantification. We found that RT-ddPCR was accurate and sensitive enough to detect as little as 1.5 copies/μl of complementary DNA (cDNA), making it suitable for application using casework samples. It was also highly specific for body fluids, as non-specific amplification did not occur. In addition, saliva-semen mixtures with ratios ranging from 1:50 to 50:1 were successfully identified. When comparing the results of RT-qPCR and RT-ddPCR, some samples were difficult to interpret because of the high Ct values of RT-qPCR. However, when the same samples were analyzed using RT-ddPCR, saliva and semen were distinctly identified. Thus, RT-ddPCR is useful for mixed samples (e.g., in sexual assault cases) with low amounts of DNA, which often leads to ambiguous results when using RT-qPCR. Other body fluids (e.g., vaginal fluid and menstrual blood) can also be identified by including additional markers. This study demonstrates the potential of RT-ddPCR for applications in forensic science.

TERTmonitor Efficacy and Performance in Detecting Mutations by Droplet Digital PCR

BACKGROUND

The screening of TERT promoter (TERTp) mutations is essential in cancer research and diagnostics, due to its prevalence in tumours associated with low self-renewal rates. TERTmonitor is a diagnosis kit primarily designed for real-time qPCR qualitative detection of -124C>T and -146C>T TERTp mutations, which are highly prevalent in several malignancies, particularly in bladder carcinoma.

OBJECTIVE

This study aims to investigate TERTmonitor performance in droplet digital PCR (ddPCR) in urine samples from bladder cancer patients.

METHODS

A total of 45 urine samples were examined by real-time qPCR and ddPCR techniques, and their performances were compared.

RESULTS

TERTmonitor had similar performance in both real-time qPCR and ddPCR platforms. Specifically, the methods exhibited a concordance rate of 95.45% and 90% for -124C>T and -146C>T mutations, respectively. Importantly, an enhanced sensitivity in certain scenarios was exhibited by ddPCR when compared to real-time qPCR, detecting mutations that the latter failed to identify in approximately 4.55% and 10% of the samples for -124C>T and -146C>T mutations, respectively. This enhanced sensitivity of ddPCR was particularly evident in samples with low-frequency mutations.

CONCLUSIONS

The findings highlight the usefulness of TERTmonitor for cancer surveillance either in real-time qPCR or ddPCR platforms.

The incidence of donor white blood cell survival (transfusion-associated microchimerism) in Australian pediatric patients

INTRODUCTION

Donor leucocyte survival following red blood cell (RBC) transfusion, known as transfusion-associated microchimerism (TAM), can occur in some patients. In Australia, despite the introduction of leucocyte filtration (leucodepletion) during RBC manufacture, TAM has been detected in adult trauma patients. However, the incidence of TAM in Australian pediatric patients has not been analyzed.

METHODS

Patients aged 0-16 years were recruited across two cohorts. Retrospective participants had RBC transfusion between January 1, 2002 and November 15, 2017 and prospective participants received RBC transfusion between December 1, 2016 and November 25, 2020. Twelve bi-allelic insertion/deletion (InDel) polymorphisms were used to detect microchimerism amplification patterns using real-time PCR (RT-PCR) and droplet digital PCR (ddPCR).

RESULTS

Of the retrospective cohort (n = 40), six patients showed amplification of InDel sequences indicating potential microchimerism. For three patients, minor InDel sequences were detected using RT-PCR only, two patients had minor InDel amplification using ddPCR only, and one patient had minor InDel amplification that was confirmed using both techniques. Amplification of minor sequences occurred in three patients who had received a bone marrow transplant in addition to RBC transfusion. In the prospective cohort (n = 25), no InDel amplification indicating potential microchimerism was detected using RT-PCR.

DISCUSSION

Cell-based therapies had been administered in three patients where microchimerism amplification patterns were detected. Three patients have microchimerism that may be attributed to RBC transfusion. In prospective patients, who received leucodepleted and gamma-irradiated RBC units, no potential microchimerism amplification were detected. ddPCR may be a suitable technique for TAM analysis but requires further evaluation.

Applying improved ddPCR to reliable quantification of MPXV in clinical settings

Monkeypox virus (MPXV) poses a global health threat. Droplet digital PCR (ddPCR) holds potential as an accurate diagnostic tool for clinical microbiology. However, there is limited literature on the applicability of ddPCR in clinical settings. In this study, the clinical features of patients with MPXV during the initial outbreak in China in June 2023 were reviewed, and an optimized ddPCR method with dilution and/or inhibitor removal was developed to enhance MPXV detection efficiency. Eighty-two MPXV samples were tested from nine different clinical specimen types, including feces, urine, pharyngeal swabs, anal swabs, saliva, herpes fluid, crust, and semen, and the viral load of each specimen was quantified. A comparative analysis was performed with qPCR to assess sensitivity and specificity and to investigate the characteristics of MPXV infection by analyzing viral loads in different clinical specimens. Consequently, common pharyngeal and gastrointestinal symptoms were observed in patients with MPXV. The optimized ddPCR method demonstrated relatively high sensitivity for MPXV quantification in the clinical materials, with a limit of detection of 0.1 copies/μL. This was particularly evident in low-concentration samples like whole blood, semen, and urine. The optimized ddPCR demonstrated greater detection accuracy compared with normal ddPCR and qPCR, with an area under the curve (AUC) of 0.939. Except for crust samples, viral loads in the specimens gradually decreased as the disease progressed. Virus levels in feces and anal swabs kept a high detection rate at each stage of post-symptom onset, and feces and anal swabs samples may be suitable for clinical diagnosis and continuous monitoring of MPXV.

IMPORTANCE

The ddPCR technique proved to be a sensitive and valuable tool for accurately quantifying MPXV viral loads in various clinical specimen types. The findings provided valuable insights into the necessary pre-treatment protocols for MPXV diagnosis in ddPCR detection and the potentially suitable sample types for collection. Therefore, such results can aid in comprehending the potential characteristics of MPXV infection and the usage of ddPCR in clinical settings.

Using a combination of quantitative culture, molecular, and infrastructure data to rank potential sources of fecal contamination in Town Creek Estuary, North Carolina

Estuarine water quality is declining worldwide due to increased tourism, coastal development, and a changing climate. Although well-established methods are in place to monitor water quality, municipalities struggle to use the data to prioritize infrastructure for monitoring and repair and to determine sources of contamination when they occur. The objective of this study was to assess water quality and prioritize sources of contamination within Town Creek Estuary (TCE), Beaufort, North Carolina, by combining culture, molecular, and geographic information systems (GIS) data into a novel contamination source ranking system. Water samples were collected from TCE at ten locations on eight sampling dates in Fall 2021 (n = 80). Microbiological water quality was assessed using US Environmental Protection Agency (U.S. EPA) approved culture-based methods for fecal indicator bacteria (FIB), including analysis of total coliforms (TC), Escherichia coli (EC), and Enterococcus spp. (ENT). The quantitative microbial source tracking (qMST) human-associated fecal marker, HF183, was quantified using droplet digital PCR (ddPCR). This information was combined with environmental data and GIS information detailing proximal sewer, septic, and stormwater infrastructure to determine potential sources of fecal contamination in the estuary. Results indicated FIB concentrations were significantly and positively correlated with precipitation and increased throughout the estuary following rainfall events (p < 0.01). Sampling sites with FIB concentrations above the U.S. EPA threshold also had the highest percentages of aged, less durable piping materials. Using a novel ranking system combining concentrations of FIB, HF183, and sewer infrastructure data at each site, we found that the two sites nearest the most aged sewage infrastructure and stormwater outflows were found to have the highest levels of measurable fecal contamination. This case study supports the inclusion of both traditional water quality measurements and local infrastructure data to support the current need for municipalities to identify, prioritize, and remediate failing infrastructure.

eDNA-based monitoring of Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans with ddPCR in Luxembourg ponds: taking signals below the Limit of Detection (LOD) into account

BACKGROUND

Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) are two pathogenic fungi that are a significant threat to amphibian communities worldwide. European populations are strongly impacted and the monitoring of the presence and spread of these pathogens is crucial for efficient decision-making in conservation management.

RESULTS

Here we proposed an environmental DNA (eDNA) monitoring of these two pathogenic agents through droplet digital PCR (ddPCR) based on water samples from 24 ponds in Luxembourg. In addition, amphibians were swabbed in eight of the targeted ponds in order to compare the two approaches at site-level detection. This study allowed the development of a new method taking below-Limit of Detection (LOD) results into account thanks to the statistical comparison of the frequencies of false positives in no template controls (NTC) and below-LOD results in technical replicates. In the eDNA-based approach, the use of this method led to an increase in Bd and Bsal detection of 28 and 50% respectively. In swabbing, this resulted in 8% more positive results for Bd. In some samples, the use of technical replicates allowed to recover above-LOD signals and increase Bd detection by 35 and 33% respectively for eDNA and swabbing, and Bsal detection by 25% for eDNA.

CONCLUSIONS

These results confirmed the usefulness of technical replicates to overcome high levels of stochasticity in very low concentration samples even for a highly sensitive technique such as ddPCR. In addition, it showed that below-LOD signals could be consistently recovered and the corresponding amplification events assigned either to positive or negative detection via the method developed here. This methodology might be particularly worth pursuing in pathogenic agents' detection as false negatives could have important adverse consequences. In total, 15 ponds were found positive for Bd and four for Bsal. This study reports the first record of Bsal in Luxembourg.

Digital PCR Partition Classification

BACKGROUND

Partition classification is a critical step in the digital PCR data analysis pipeline. A range of partition classification methods have been developed, many motivated by specific experimental setups. An overview of these partition classification methods is lacking and their comparative properties are often unclear, likely impacting the proper application of these methods.

CONTENT

This review provides a summary of all available digital PCR partition classification approaches and the challenges they aim to overcome, serving as a guide for the digital PCR practitioner wishing to apply them. We additionally discuss strengths and weaknesses of these methods, which can further guide practitioners in vigilant application of these existing methods. This review provides method developers with ideas for improving methods or designing new ones. The latter is further stimulated by our identification and discussion of application gaps in the literature, for which there are currently no or few methods available.

SUMMARY

This review provides an overview of digital PCR partition classification methods, their properties, and potential applications. Ideas for further advances are presented and may bolster method development.

Adaptation of Droplet Digital PCR-Based HIV Transcription Profiling to Digital PCR and Association of HIV Transcription and Total or Intact HIV DNA

In most people living with HIV (PLWH) on effective antiretroviral therapy (ART), cell-associated viral transcripts are readily detectable in CD4+ T cells despite the absence of viremia. Quantification of HIV RNA species provides insights into the transcriptional activity of proviruses that persist in cells and tissues throughout the body during ART ('HIV reservoir'). One such technique for HIV RNA quantitation, 'HIV transcription profiling', developed in the Yukl laboratory, measures a series of HIV RNA species using droplet digital PCR. To take advantage of advances in digital (d)PCR, we adapted the 'HIV transcription profiling' technique to Qiagen's dPCR platform (QIAcuity) and compared its performance to droplet digital (dd)PCR (Bio-Rad QX200 system). Using RNA standards, the two technologies were tested in parallel and assessed for multiple parameters including sensitivity, specificity, linearity, and intra- and inter-assay variability. The newly validated dPCR assays were then applied to samples from PLWH to determine HIV transcriptional activity relative to HIV reservoir size. We report that HIV transcriptional profiling was readily adapted to dPCR and assays performed similarly to ddPCR, with no differences in assay characteristics. We applied these assays in a cohort of 23 PLWH and found that HIV reservoir size, based on genetically intact proviral DNA, does not predict HIV transcriptional activity. In contrast, levels of total DNA correlated with levels of most HIV transcripts (initiated, proximally and distally elongated, unspliced, and completed, but not multiply spliced), suggesting that a considerable proportion of HIV transcripts likely originate from defective proviruses. These findings may have implications for measuring and assessing curative strategies and clinical trial outcomes.

Exploring the eDNA dynamics of the host-pathogen pair Pacifastacus leniusculus (Decapoda) and Aphanomyces astaci (Saprolegniales) under experimental conditions

The oomycete Aphanomyces astaci causes crayfish plague, a disease threatening native European crayfish. It is carried and transmitted by American crayfish species, which are the original hosts of A. astaci. In recent years, environmental DNA (eDNA) methods have been successfully implemented to monitor the spread of both A. astaci and its hosts. However, still little is known about how population density and other environmental factors influence the detectability of this host-pathogen complex. In a mesocosm experiment, we tested the influence of crayfish density, temperature and food availability on the detectability of eDNA for A. astaci and its host, signal crayfish Pacifastacus leniusculus. We also compared eDNA results with crayfish population density measured by catch per unit effort (CPUE) from two lakes with varying crayfish density and A. astaci prevalence. The mesocosm experiment revealed that a limited set of controlled factors can substantially change the detectable amount of eDNA, even though the physical presence of the target organisms remains the same. In cold, clear water, eDNA quantities of both targets increased far more than in a linear fashion with increased crayfish density. However, the presence of food decreased the detectability of crayfish eDNA, presumably through increased microbial-induced eDNA degradation. For A. astaci, where eDNA typically represents living spores, food did not affect the detectability. However, high water temperature strongly reduced it. The increased complexity and variability of factors influencing eDNA concentration under natural conditions, compared to a controlled experimental environment, suggests that establishing a reliable relationship between eDNA quantities and crayfish density is difficult to achieve. This was also supported by field data, where we found minimal correspondence between eDNA quantity and CPUE data. A comparison between quantitative real-time PCR (qPCR) analysis and droplet-digital PCR (ddPCR) analysis revealed higher detection success of the targets in field samples when using qPCR. Overall, our results support eDNA as an effective tool for presence-absence monitoring, but it seems less suited for biomass quantification and population density estimates. Detection of A. astaci and P. leniusculus is not influenced uniformly by respective environmental factors. Consequently, we recommend a strategy of monitoring both targets, where the detection of one may point towards the presence of the other.