Development of insulated isothermal PCR for rapid on-site malaria detection

Advances in Malaria Diagnostic Methods in Resource-Limited Settings: A Systematic Review

Malaria continues to pose a health challenge globally, and its elimination has remained a major topic of public health discussions. A key factor in eliminating malaria is the early and accurate detection of the parasite, especially in asymptomatic individuals, and so the importance of enhanced diagnostic methods cannot be overemphasized. This paper reviewed the advances in malaria diagnostic tools and detection methods over recent years. The use of these advanced diagnostics in lower and lower-middle-income countries as compared to advanced economies has been highlighted. Scientific databases such as Google Scholar, PUBMED, and Multidisciplinary Digital Publishing Institute (MDPI), among others, were reviewed. The findings suggest important advancements in malaria detection, ranging from the use of rapid diagnostic tests (RDTs) and molecular-based technologies to advanced non-invasive detection methods and computerized technologies. Molecular tests, RDTs, and computerized tests were also seen to be in use in resource-limited settings. In all, only twenty-one out of a total of eighty (26%) low and lower-middle-income countries showed evidence of the use of modern malaria diagnostic methods. It is imperative for governments and other agencies to direct efforts toward malaria research to upscale progress towards malaria elimination globally, especially in endemic regions, which usually happen to be resource-limited regions.

HPB-Chip: An accurate high-throughput qPCR-based tool for rapidly profiling waterborne human pathogenic bacteria in the environment

Waterborne pathogens are threatening public health globally, but profiling multiple human pathogenic bacteria (HPBs) in various polluted environments is still a challenge due to the absence of rapid, high-throughput and accurate quantification tools. This work developed a novel chip, termed the HPB-Chip, based on high-throughput quantitative polymerase chain reactions (HT-qPCR). The HPB-Chip with 33-nL reaction volume could simultaneously complete 10,752 amplification reactions, quantifying 27 HPBs in up to 192 samples with two technical replicates (including those for generating standard curves). Specific positive bands of target genes across different species and single peak melting curves demonstrated high specificity of the HPB-Chip. The mixed plasmid serial dilution test validated its high sensitivity with the limit of quantification (LoD) of averaged 82 copies per reaction for 25 target genes. PCR amplification efficiencies and R2 coefficients of standard curves of the HPB-Chip averaged 101 % and 0.996, respectively. Moreover, a strong positive correlation (Pearson' r: 0.961-0.994, P < 0.001) of HPB concentrations (log10 copies/L) between HPB-Chip and conventional qPCR demonstrated high accuracy of the HPB-Chip. Subsequently, the HPB-Chip has been successfully applied to absolutely quantify 27 HPBs in municipal and hospital wastewater treatment plants (WWTPs) after PMA treatment. A total of 17 HPBs were detected in the 6 full-scale WWTPs, with an additional 19 in the hospital WWTP. Remarkably, Acinetobacter baumannii, Legionella pneumophila, and Arcobacter butzler were present in the final effluent of each municipal WWTP. Overall, the HPB-Chip is an efficient and accurate high-throughput quantification tool to comprehensively and rapidly quantify 27 HPBs in the environment.

Evaluation of a Sample-to-Result POCKIT Central SARS-CoV-2 PCR System

The emergence of COVID-19 has caused unprecedented impacts on global public health and many other aspects. Meanwhile, many types of methods have been developed to detect the causative agent, SARS-CoV-2; this has greatly advanced the technologies in the diagnostic field. Here, we describe the development and validation of a sample-in-result-out POCKIT Central SARS-CoV-2 PCR system for detecting SARS-CoV-2 in comparison with a commercial reference real-time RT-PCR assay (TaqPath COVID-19 Combo Kit). Both assays were specific and did not cross-react with non-SARS-CoV-2 agents. Both assays were able to detect various SARS-CoV-2 strains including some variants. Based on testing serial dilutions of SARS-CoV-2 USA-WA1/2020 isolate, the limit of detection was 0.8 TCID₅₀/mL (1.87 × 10³ genomic copies/mL) for POCKIT Central SARS-CoV-2 PCR and 0.16 TCID₅₀/mL (3.75 × 10² genomic copies/mL) for the reference PCR. Subsequently, 183 clinical samples were tested by both assays and the diagnostic sensitivity, specificity, and agreement of the POCKIT Central SARS-CoV-2 PCR were 91.7%, 100%, and 94.0%, respectively, when compared to the reference PCR. The compact sample-to-result POCKIT Central SARS-CoV-2 PCR system is a simplified and efficient point-of-care tool for SARS-CoV-2 detection. In addition, this platform can be readily adapted to detect other human and animal viruses.

Rapid Detection of Fusarium oxysporum Using Insulated Isothermal PCR and a Rapid, Simple DNA Preparation Protocol

We developed an insulated isothermal PCR (iiPCR) method for the efficient and rapid detection of Fusarium oxysporum (Fo), which is a fungus that infects various hosts and causes severe crop losses. The Fo iiPCR method was sensitive enough to detect up to 100 copies of standard DNA template and 10 fg of Fo genomic DNA. In addition, it could directly detect 1 pg of mycelium and 10 spores of Fo without DNA extraction. Our study compared the performance of Fo iiPCR to that of three published in planta molecular detection methods—conventional PCR, SYBR green-based real-time PCR, and hydrolysis probe-based real-time PCR—in field detection of Fo. All diseased field samples yielded positive detection results with high reproducibility when subjected to an Fo iiPCR test combined with a rapid DNA extraction protocol compared to Fo iiPCR with an automated magnetic bead-based DNA extraction protocol. Intraday and interday assays were performed to ensure the stability of this new rapid detection method. The results of detection of Fo in diseased banana pseudostem samples demonstrated that this new rapid detection method was suitable for field diagnosis of Fusarium wilt and had high F1 scores for detection (the harmonic mean of precision and recall of detection) for all asymptomatic and symptomatic Fo-infected banana samples. In addition, banana samples at four growth stages (seedling, vegetative, flowering and fruiting, and harvesting) with mild symptoms also showed positive detection results. These results indicate that this new rapid detection method is a potentially efficient procedure for on-site detection of Fo.

Canine parvovirology - A brief updated review on structural biology, occurrence, pathogenesis, clinical diagnosis, treatment and prevention

Canine parvovirus (CPV) is a major cause of hemorrhagic diarrhea and mortality in puppies worldwide. There are 2 types of Parvovirus which affects canines: Canine parvovirus 2 (CPV-2) and Canine parvovirus 1 (CPV-1) or the Minute Virus of Canine (MVC). CPV-2 originated from Feline panleukopenia virus and has undergone genetic variation to give rise to its three variants (CPV-2a, CPV-2b and CPV-2c). Amino acid substitutions in VP2 capsid protein have led virus to adapt new host range. The original CPV-2 was known to be dominant in Japan, Belgium, Australia as well as USA and later circulated throughout the world. Clinically, CPV-2 infection is characterized by anorexia, lethargy, depression, vomiting, leukopenia and severe hemorrhagic diarrhea. Several diagnostic tests have been developed to detect parvoviral infections which are categorized into immunological tests (latex agglutination test, SIT-SAT and ELISA etc.) and molecular based tests (PCR, mPCR and RT-PCR etc.). To control and manage the disease several treatments like fluid therapies, antibiotics, and adjunctive treatments are available and some are in various stages of development. Apart from this, many vaccines are also commercially available and some are in developmental stages. The present review contains detailed information regarding structural biology, occurrence, pathogenesis, clinical diagnosis, treatments and prevention in order to understand the need and the growing importance of CPV-2.

Evaluation of an automated insulated isothermal polymerase chain reaction system for rapid and reliable, on-site detection of African swine fever virus

OBJECTIVE

To evaluate the utility of an automated insulated isothermal PCR (iiPCR) system for rapid and reliable on-site detection of African swine fever virus (ASFV) in swine biological samples.

SAMPLE

Lymph node, tissue homogenate, whole blood, serum, spleen, and tonsil samples collected from swine in North and South Vietnam.

PROCEDURES

Analytic sensitivity of the iiPCR system was determined by serial dilution and analysis of 2 samples (swine tissue homogenate and blood) predetermined to be positive for ASFV. Analytic specificity was assessed by analysis of 2 samples predetermined to be negative for ASFV and positive or negative for other swine pathogens (classical swine fever virus, porcine reproductive and respiratory syndrome virus, foot-and-mouth disease virus, and porcine circovirus type 2). Diagnostic performance of the iiPCR system for detection of ASFV was determined by analysis of the various tissue sample types. For all tests, a real-time PCR assay was used as the reference method.

RESULTS

The iiPCR system was able to detect ASFV in swine blood or tissue homogenate at dilutions up to 10⁶, whereas the real-time PCR assay was able to detect dilutions of up to 10⁵ or 10⁶. The iiPCR system had high analytic specificity for detection of ASFV versus other swine pathogens. Between 97% and 100% agreement was found between results of the iiPCR system for the various tissue samples and results of real-time PCR assay.

CONCLUSIONS AND CLINICAL RELEVANCE

The evaluated iiPCR system was found to be a rapid, reliable, and sample-flexible method for ASFV detection and may be useful for disease surveillance and quarantine in national strategies for early ASF control.

Isothermal Nucleic Acid Amplification Technologies for the Detection of Equine Viral Pathogens

Simple Summary

Equine viral diseases remain a prominent concern for human and equine health globally. Many of these viruses are of primary biosecurity concern to countries that import equines where these viruses are not present. In addition, several equine viruses are zoonotic, which can have a significant impact on human health. Current diagnostic techniques are both time consuming and laboratory-based. The ability to accurately detect diseases will lead to better management, treatment strategies, and health outcomes. This review outlines the current modern isothermal techniques for diagnostics, such as loop-mediated isothermal amplification and insulated isothermal polymerase chain reaction, and their application as point-of-care diagnostics for the equine industry.

Abstract

The global equine industry provides significant economic contributions worldwide, producing approximately USD $300 billion annually. However, with the continuous national and international movement and importation of horses, there is an ongoing threat of a viral outbreak causing large epidemics and subsequent significant economic losses. Additionally, horses serve as a host for several zoonotic diseases that could cause significant human health problems. The ability to rapidly diagnose equine viral diseases early could lead to better management, treatment, and biosecurity strategies. Current serological and molecular methods cannot be field-deployable and are not suitable for resource-poor laboratories due to the requirement of expensive equipment and trained personnel. Recently, isothermal nucleic acid amplification technologies, such as loop-mediated isothermal amplification (LAMP) and insulated isothermal polymerase chain reaction (iiPCR), have been developed to be utilized in-field, and provide rapid results within an hour. We will review current isothermal diagnostic techniques available to diagnose equine viruses of biosecurity and zoonotic concern and provide insight into their potential for in-field deployment.

Clinical validation of an automated reverse transcription-insulated isothermal PCR assay for the detection of severe acute respiratory syndrome coronavirus 2

To determine clinical performance of the single-target SARS-CoV-2 orf 1 ab reverse transcription-insulated isothermal PCR (RT-iiPCR) assay, the positive percentage agreement between this assay and a laboratory real-time RT-PCR assay was 96.8% (30 of 31; 95% confidence interval [CI], 90.5%-100%) and the negative percentage agreement was 97.1% (67 of 69; 95% CI, 93.1%-100%).

Development and use of a reverse transcription insulated isothermal PCR assay for detection and characterization of bovine torovirus in yaks

Bovine torovirus (BToV) is an important diarrhea-causing pathogen affecting bovines. To facilitate BToV detection, a reverse transcription insulated isothermal PCR (RT-iiPCR) assay was developed that targets the BToV M gene with high specificity and reproducibility. The assay has a limit of detection of 23 copies/μL. Out of 69 diarrheic fecal samples from yaks collected on six farms in Tibet and Sichuan provinces in China, 11.59% (8/69) tested positive for BToV using this assay. The full-length spike (S) and hemagglutinin-esterase (HE) genes of three positive samples were subsequently sequenced. Notably, an identical recombination event was identified in the S1 subunit of the S protein of three isolates. All of the HE genes were found to belong to genotype III and shared the same unique aa variation (P44S) in the esterase domain. This study is the first confirmation of BToV in yaks and the first report of an S gene recombination event in BToV. Our findings will enhance the current understanding of the molecular characteristics and genetic evolution of BToV.

Application of embryo biopsy and sex determination via polymerase chain reaction in a commercial equine embryo transfer program in Argentina

Embryo biopsy for fetal sexing has clinical application, but few reports are available of its use within an active embryo transfer program. We evaluated results on biopsy of 459 embryos over one breeding season. There were no significant differences in pregnancy rate between biopsied and non-biopsied embryos (72% vs 73%) or for biopsied embryos recovered at the centre (73%) compared with those shipped overnight (72%). However, the pregnancy rate decreased significantly in shipped embryos biopsied ≥20h after collection. Overall, 86% of biopsies provided a sex diagnosis. The likelihood of a positive genomic (g) DNA result was significantly higher for biopsies from large blastocysts (96%) than from smaller embryos (70-85%). In total, 38% of biopsies were positive for Y chromosome DNA (Y-DNA) and were diagnosed as male. Subsequently, 95% of Y-DNA-positive embryos were confirmed as male and 78% of Y-DNA-negative embryos were confirmed as female. The accuracy of prediction of female (Y-DNA negative) was significantly higher when the biopsy sample was probed for Y-DNA only compared with probing for both gDNA and Y-DNA. We estimate that by transferring only Y-DNA-negative embryos, 3% of potential female pregnancies may have been lost, and production of male pregnancies was reduced by 72%.

Rapid identification of melioidosis agent by an insulated isothermal PCR on a field-deployable device

Background

Burkholderia pseudomallei causes melioidosis, a serious illness that can be fatal if untreated or misdiagnosed. Culture from clinical specimens remains the gold standard but has low diagnostic sensitivity.

Method

In this study, we developed a rapid, sensitive and specific insulated isothermal Polymerase Chain Reaction (iiPCR) targeting bimA gene (Burkholderia Intracellular Motility A; BPSS1492) for the identification of B. pseudomallei. A pair of novel primers: BimA(F) and BimA(R) together with a probe were designed and 121 clinical B. pseudomallei strains obtained from numerous clinical sources and 10 ATCC non-targeted strains were tested with iiPCR and qPCR in parallel.

Results

All 121 B. pseudomallei isolates were positive for qPCR while 118 isolates were positive for iiPCR, demonstrating satisfactory agreement (97.71%; 95% CI [93.45–99.53%]; k = 0.87). Sensitivity of the bimA iiPCR/POCKIT assay was 97.52% with the lower detection limit of 14 ng/µL of B. pseudomallei DNA. The developed iiPCR assay did not cross-react with 10 types of non-targeted strains, indicating good specificity.

Conclusion

This bimA iiPCR/POCKIT assay will undoubtedly complement other methodologies used in the clinical laboratory for the rapid identification of this pathogen.

Free convective PCR: From principle study to commercial applications-A critical review

Polymerase chain reaction (PCR) is an extremely important tool for molecular diagnosis, as it can specifically amplify nucleic acid templates for sensitive detection. As another division of PCR, free convective PCR was invented in 2001, which can be performed in a capillary tube pseudo-isothermally within a significantly short time. Convective PCR thermal cycling is implemented by inducing thermal convection inside the capillary tube, which stratifies the reaction into spatially separate and stable melting, annealing, and extension zones created by the temperature gradient. Convective PCR is a promising tool that can be used for nucleic acid diagnosis as a point-of-care test (POCT) due to the significantly simplified heating strategy, reduced cost, and shortened detection time without sacrificing sensitivity and accuracy. Here, we review the history of free convective PCR from its invention to development and its commercial applications.

Development of a film-based immunochromatographic microfluidic device for malaria diagnosis

In this study, a novel film-based immunochromatographic microfluidic device (IMD) has been developed for malaria diagnosis. A microfluidic channel was patterned on a polyethylene terephthalate (PET) double-sided adhesive film using a plotting cutter and was assembled with a polycarbonate (PC) film. The PC film used for the probe immobilization layer was activated using oxygen plasma treatment to modify the film surface with avidin-biotin linker to immobilize a capture antibody. A fluorescent labeled Pan type mAb conjugate was prepared for signal indicator after undergoing a sandwich enzyme-linked immunosorbent assay (ELISA). Target antigens include Plasmodium falciparum (P. falciparum) lactate dehydrogenase (LDH) and Plasmodium vivax (P. vivax) LDH which were injected into the sample inlet. Target antigens combined with the conjugate and then flowed to the detection chamber where two test dots and a control dot (Ctrl) exist. In the presence of P. falciparum LDH, three detection dots including test dot 1 (T1), test dot 2 (T2) and Ctrl revealed fluorescence signals where P. falciparum mAb, Pan type pLDH mAb and goat anti-mouse IgG were immobilized, respectively. When P. vivax LDH was present, T2 and Ctrl dots showed fluorescence signals while no signal was detected with the negative control. P. falciparum LDH and P. vivax LDH were successfully detected on the IMD with a detection limit of 50 ng/mL and 100 ng/mL, respectively. The IMD provides a point-of-care diagnosis platform which is able to analyze pathogenic bacteria and viruses that can be applied in the field of clinical diagnosis and food safety testing.

Development and evaluation of reverse transcription-insulated isothermal PCR assay to detect duck hepatitis A virus type A in liver samples using the POCKITTM system

Duck hepatitis A virus (DHAV) infection is characterized by severe hepatitis. In recent years, DHAV-A has become widespread in Asia and has led to economic losses. Conventional methods of DHAV-A detection must often be performed in the laboratory with inconvenience equipment. We have developed a rapid reverse transcription insulated isothermal (RT-iiPCR) technique for the on-site detection of DHAV-A based on the POCKIT^TM system in a convenient minitype device. We optimized the PCR primers and probes for the amplification of the DHAV-A 3C/3D genes, and successfully amplified a specific fragment of DHAV-A, but no fragment from 18 other duck pathogens. The limit of detection for viral RNA was 49 copies per reaction, and the sensitivity and specificity were each 100% in the analysis of 60 liver samples. By comparison, the sensitivities of RT-iiPCR was comparable in sensitivity to existing rRT-PCR. Furthermore, the RT-iiPCR results were 98.3% in agreement with those of the rRT-PCR, with a kappa value of 0.938. In conclusion, this new method not only offers a higher sensitivity and specificity than existing techniques, but also time-saving and better suited to field diagnoses because device is portable.

A fully automated sample-to-answer PCR system for easy and sensitive detection of dengue virus in human serum and mosquitos

BACKGROUND

The insulated isothermal PCR (iiPCR) technology enables consistent PCR amplification and detection in a simple heating device. A pan-dengue virus (DENV) RT-iiPCR, targeting the 5' untranslated region, was validated previously on the semi-automated POCKIT combo system (involving separate devices for nucleic acid extraction and PCR amplification/detection) to offer performance comparable to a laboratory real-time PCR. Working on the same technologies, a compact automated sample-in-answer-out system (POCKIT Central Nucleic Acid Analyser) has been available commercially for iiPCR, minimizing human error risks and allowing easy molecular bio-detection near points of need. Here, we evaluated the analytical and clinical performance of the pan-DENV RT-iiPCR on the fully automated system by comparison to those on the semi-automated system.

METHODOLOGY/PRINCIPAL FINDINGS

Testing sera containing serial diluted DENV-1, -2, -3, or -4 cell culture stock, the pan-DENV RT-iiPCR system had similar 100% detection endpoints on the two systems; i.e. at 1, 10, 1 and 10 PFU/ml, respectively, on the fully automated system, and at 10, 1, 10 and 10 PFU/ml, respectively, on the semi-automated system. Furthermore, both fully automated and semi-automated PCR system can detect all four DENV serotypes in mosquitos. Clinical performance of the reagent on the two systems was evaluated by testing 60 human serum samples. Both systems detected the same 40 samples (ten DENV-1, -2, -3, and -4 positive each) and did not detect the other 20; 100% agreement (κ = 1) was found between the two systems.

CONCLUSIONS/SIGNIFICANCE

With performance comparable to a previously validated system, the fully-automated PCR system allows applications of the pan-DENV reagent as a useful tool near points of need to facilitate easy, fast and effective detection of dengue virus and help mitigate versatile public health challenges in the control and management of dengue disease.

A reverse transcription-insulated isothermal PCR assay for the detection of duck hepatitis A virus type 3 based on the POCKIT™ system

Duck hepatitis A virus type 3 (DHAV-3) infection is characterized by severe hepatitis. In recent years, DHAV-3 has become widespread in Asia and has led to economic losses. Conventional methods for DHAV-3 detection usually depend on the use of larger equipment that is not portable and is not fit for on-site diagnoses. In this study, a rapid reverse transcription insulated isothermal (RT-iiPCR) technique was developed for the on-site detection of DHAV-3 based on the POCKIT™ system in a convenient device. The concentration of primer pairs and probes were optimized for amplification of the DHAV-3 VP3 gene of DHAV-3, with no amplification of 12 other duck pathogens. The detection limit of viral RNA was 3.85 × 10¹ copies/μL, and the analytical sensitivity and specificity levels were both 100% in the detection of 40 liver samples. Furthermore, 97.5% of the RT-iiPCR results were in agreement with those of rRT-PCR, with a kappa value of 0.93. This method is time-saving and better suited to field diagnoses because of its portable device.

An RT-PCR panel for rapid serotyping of dengue virus serotypes 1 to 4 in human serum and mosquito on a field-deployable PCR system

Background

Dengue fever, a mosquito-borne disease, is caused by dengue virus (DENV) which includes four major serotypes (DENV-1, -2, -3, and -4). Some serotypes cause more severe diseases than the other; severe dengue is associated with secondary infections by a different serotype. Timely serotyping can provide early warning of dengue epidemics to improve management of patients and outbreaks. A mobile insulated isothermal PCR (iiPCR) system is available to allow molecular detection of pathogens near points of need.

Methodology/Principle findings

In this study, side-by-side comparison with the CDC DENV-1-4 Real Time RT-PCR (qRT-PCR) was performed to evaluate the performance of four singleplex DENV-1–4 serotyping reverse transcription-iiPCR (RT-iiPCR) reagents for DENV subtyping on the mobile PCR system. The four RT-iiPCRs did not react with Zika virus and chikungunya virus; tests with serial dilutions of the four DENV serotypes made in human serum showed they had detection endpoints comparable to those of the reference method, indicating great analytical sensitivity and specificity. Clinical performance of the RT-iiPCR reagents was evaluated by testing 40 serum samples each (around 20 target serotype-positive and 20 DENV-negative); all four reagents had high agreement (97.5–100%) with the reference qRT-PCR. Moreover, testing of mosquitoes separately infected experimentally with each serotype showed that the four reagents detected specifically their target DENV serotypes in mosquito.

Conclusions/Significance

With analytical and clinical performance comparable to the reference qRT-PCR assay, the four index RT-iiPCR reagents on the field-deployable PCR system can serve as a useful tool for DENV detection near points of needs.

Rapid detection of equine infectious anaemia virus nucleic acid by insulated isothermal RT-PCR assay to aid diagnosis under field conditions

BACKGROUND

Control of equine infectious anaemia (EIA) currently depends on serological diagnosis of infected equids. However, recently infected equids may not produce detectable anti-EIAV antibodies up to 157 days post infection and so present a high transmission risk. Therefore, direct nucleic acid detection methods are urgently needed to improve EIAV surveillance and management programs in counties where the disease is endemic.

OBJECTIVES

To evaluate a field-deployable, reverse transcription-insulated isothermal PCR (RT-iiPCR) assay targeting the conserved 5' untranslated region (5' UTR)/exon 1 of the tat gene of EIAV.

STUDY DESIGN

The analytical and clinical performance of the newly developed EIAV RT-iiPCR was evaluated by comparison with a EIAV real-time RT-PCR (RT-qPCR) along with the AGID test.

METHODS

Analytical sensitivity was determined using in vitro transcribed RNA containing the target area of the 5' UTR/tat gene and samples from two EIAV-positive horses. Specificity was verified using nine common equine viruses. Clinical performance was evaluated by comparison with EIAV RT-qPCR and AGID using samples derived from 196 inapparent EIAV carrier horses.

RESULTS

EIAV RT-iiPCR did not react with other commonly encountered equine viruses and had equivalent sensitivity (95% detection limit of eight genome equivalents), with a concordance of 95.41% to conventional EIAV RT-qPCR. However, the RT-qPCR and RT-iiPCR had sensitivities of 43.75 and 50.00%, respectively, when compared to the AGID test.

MAIN LIMITATIONS

Low viral loads commonly encountered in inapparent EIAV carriers may limit the diagnostic sensitivity of RT-PCR-based tests.

CONCLUSIONS

Although EIAV RT-iiPCR is not sufficiently sensitive to replace the current AGID test, it can augment control efforts by identifying recently exposed or "serologically silent" equids, particularly as the latter often represent a significant transmission risk because of high viral loads. Furthermore, the relatively low cost and field-deployable design enable utilisation of EIAV RT-iiPCR even in remote regions.

Considerations for incorporating real-time PCR assays into routine marine biosecurity surveillance programmes: a case study targeting the Mediterranean fanworm (Sabella spallanzanii) and club tunicate (Styela clava) 1

Molecular techniques may provide effective tools to enhance marine biosecurity surveillance. Prior to routine implementation, evidence-based consideration of their benefits and limitations is needed. In this study, we assessed the efficiency and practicality of visual diver surveys and real-time PCR assays (targeting DNA and RNA) for detecting two marine invasive species whose infestation levels varied between species and location: Sabella spallanzanii and Styela clava. Filtered water samples (n = 171) were collected in parallel with dive surveys at two locations as part of the New Zealand Marine High Risk Site Surveillance programme: Nelson Harbour (27 sites) and Waitemata Harbour (30 sites). Diver surveys resulted in a greater number of detections compared to real-time PCR: S. clava - 21 versus 5 sites in Nelson, 6 versus 1 in Auckland; S. spallanzanii - 18 versus 10 in Auckland, no detections in Nelson. Occupancy modelling derived detection probabilities for the real-time PCR for S. clava were low (14%), compared to S. spallanzanii (66%). This could be related to abundances, or species-specific differences in DNA shedding. Only one RNA sample was positive, suggesting that most detections were from extracellular DNA or non-viable fragments. While molecular methods cannot yet replace visual observations, this study shows they provide useful complementary information.

Rapid Diagnosis of Babesia gibsoni by Point-of-Need Testing by Insulated Isothermal PCR in Dogs at High Risk of Infection

Background

Dogs seized by law enforcement agencies during dogfighting investigations are at increased risk of Babesia gibsoni infection. A rapid and cost‐effective diagnostic test would increase the feasibility of mass screening of dogs for infection and monitoring treatment efficacy in B. gibsoni‐infected dogs.

Objective

To determine the performance of a point‐of‐need insulated isothermal PCR (iiPCR) test for diagnosis of B. gibsoni in dogs rescued in dogfighting investigations.

Animals

Two hundred and thirty‐three dogs seized in dogfighting investigations.

Methods

Cross‐sectional study. Whole blood samples were tested for B. gibsoni and Babesia spp. by iiPCR. Results were compared to a reference standard comprised of concordant results from real‐time PCR in a commercial diagnostic laboratory and antibody titers.

Results

The iiPCR system was quick to learn, portable, and had a short processing time of <2 hours. Sensitivity and specificity of the iiPCR assay for B. gibsoni were 90% (95% confidence interval [CI] 81–95%) and 99% (CI, 95–100%), respectively. Sensitivity and specificity of the iiPCR assay for Babesia spp. were 87% (CI, 78–93%) and 98% (CI, 0.94–99%), respectively.

Conclusions and Clinical Importance

The iiPCR system produced few false‐positive results, indicating that positive results are likely to represent true infections when used in high‐risk animals. The iiPCR system can fail to identify 10–15% of truly infected dogs. However, the portability, speed, and economy of the iiPCR system compared to testing through a reference laboratory can allow rescue groups to screen and identify infection in more dogs.

Potential Point-of-Care Testing for Dengue Virus in the Field

The four serotypes of dengue virus (DENV) cause one of the most important and rapidly emerging mosquito-borne viral diseases in humans. Of the currently available diagnostic tests for dengue, the reverse transcription-PCR (RT-PCR) assay is the most sensitive and specific, and so it is commonly used as the gold standard. However, the requirement of a sophisticated and expensive thermal cycler makes it very difficult to use as a point-of-care diagnostic test in resource-limited regions where dengue is endemic. Tsai et al. (J Clin Microbiol 56:e01865-17, 2018, https://doi.org/10.1128/JCM.01865-17) report the analytical and clinical performances of a reverse transcription-insulated isothermal PCR (RT-iiPCR) assay with a portable nucleic acid analyzer for rapid detection of the four DENV serotypes; its reproducibility and complete agreement on clinical samples with the multiplex RT-PCR assay developed by the Centers for Disease Control and Prevention suggest that the dengue RT-iiPCR is a potential point-of-care test. Compared with other DENV RNA detection methods, the unique isothermal PCR design of RT-iiPCR, together with further improvements, would represent a promising new type of field-deployable diagnostic test for dengue.

Validation of the Pockit Dengue Virus Reagent Set for Rapid Detection of Dengue Virus in Human Serum on a Field-Deployable PCR System

Dengue virus (DENV) infection, a mosquito-borne disease, is a major public health problem in tropical countries. Point-of-care DENV detection with good sensitivity and specificity enables timely early diagnosis of DENV infection, facilitating effective disease management and control, particularly in regions of low resources. The Pockit dengue virus reagent set (GeneReach Biotech), a reverse transcription insulated isothermal PCR (RT-iiPCR), is available to detect all four serotypes of DENV on the field-deployable Pockit system, which is ready for on-site applications. In this study, analytical and clinical performances of the assay were evaluated. The index assay did not react with 14 non-DENV human viruses, indicating good specificity. Compared to the U.S. CDC DENV-1-4 real-time quantitative RT-PCR (qRT-PCR) assay, testing with serial dilutions of virus-spiked human sera demonstrated that the index assay had detection endpoints that were separately comparable with the 4 serotypes. Excellent reproducibility was observed among repeat tests done by six operators at three sites. In clinical performance, 195 clinical sera collected around Kaohsiung city in 2012 and 21 DENV-4-spiked sera were tested with the RT-iiPCR and qRT-PCR assays in parallel. The 121 (11 DENV-1, 78 DENV-2, 11 DENV-3, and 21 DENV-4) qRT-PCR-positive and 95 qRT-PCR-negative samples were all positive and negative by the RT-iiPCR reagent results, respectively, demonstrating high (100%) interrater agreement (95% confidence interval [CI_95%], ∼98.81% to 100%; κ = 1). With analytical and clinical performance equivalent to those of the reference qRT-PCR assay, the index PCR assay on the field-deployable system can serve as a highly sensitive and specific on-site tool for DENV detection.

Evaluation of a field-deployable reverse transcription-insulated isothermal PCR for rapid and sensitive on-site detection of Zika virus

Background

The recent emergence of Zika virus (ZIKV) in Brazil and its precipitous expansion throughout the Americas has highlighted the urgent need for a rapid and reliable on-site diagnostic assay suitable for viral detection. Such point-of-need (PON), low-cost diagnostics are essential for ZIKV control in vulnerable areas with limited resources.

Methods

We developed and evaluated a ZIKV-specific field-deployable RT-iiPCR reagent set targeting the E gene for rapid detection of ZIKV in ZIKV-spiked human and mosquito specimens, and compared its performance to the Center for Disease Control and Prevention (CDC) and Pan American Health Organization (PAHO) RT-qPCR assays targeting the E and NS2B genes, respectively.

Results

These assays demonstrated exclusive specificity for ZIKV (African and Asian lineages), had limits of detection ranging from 10 to 100 in vitro transcribed RNA copies/μl and detection endpoints at 10 plaque forming units/ml of infectious tissue culture fluid. Analysis of human whole blood, plasma, serum, semen, urine, and mosquito pool samples spiked with ZIKV showed an agreement of 90% (k = 0.80), 92% (k = 0.82), 95% (k = 0.86), 92% (k = 0.81), 90% (k = 0.79), and 100% (k = 1), respectively, between the RT-iiPCR assay and composite results from the reference RT-qPCR assays. Overall, the concurrence between the ZIKV RT-iiPCR and the reference RT-qPCR assays was 92% (k = 0.83).

Conclusions

The ZIKV RT-iiPCR has a performance comparable to the reference CDC and PAHO RT-qPCR assays but provides much faster results (~1.5 h) with a field-deployable system that can be utilized as a PON diagnostic with the potential to significantly improve the quality of the health care system in vulnerable areas.

Electronic supplementary material

The online version of this article (10.1186/s12879-017-2852-4) contains supplementary material, which is available to authorized users.

malERA: An updated research agenda for diagnostics, drugs, vaccines, and vector control in malaria elimination and eradication

Since the turn of the century, a remarkable expansion has been achieved in the range and effectiveness of products and strategies available to prevent, treat, and control malaria, including advances in diagnostics, drugs, vaccines, and vector control. These advances have once again put malaria elimination on the agenda. However, it is clear that even with the means available today, malaria control and elimination pose a formidable challenge in many settings. Thus, currently available resources must be used more effectively, and new products and approaches likely to achieve these goals must be developed. This paper considers tools (both those available and others that may be required) to achieve and maintain malaria elimination. New diagnostics are needed to direct treatment and detect transmission potential; new drugs and vaccines to overcome existing resistance and protect against clinical and severe disease, as well as block transmission and prevent relapses; and new vector control measures to overcome insecticide resistance and more powerfully interrupt transmission. It is also essential that strategies for combining new and existing approaches are developed for different settings to maximise their longevity and effectiveness in areas with continuing transmission and receptivity. For areas where local elimination has been recently achieved, understanding which measures are needed to maintain elimination is necessary to prevent rebound and the reestablishment of transmission. This becomes increasingly important as more countries move towards elimination.

Evaluation and Clinical Validation of Two Field-Deployable Reverse Transcription-Insulated Isothermal PCR Assays for the Detection of the Middle East Respiratory Syndrome-Coronavirus

Middle East respiratory syndrome (MERS) is an emerging zoonotic viral respiratory disease that was first identified in Saudi Arabia in 2012. In 2015, the largest MERS outbreak outside of the Middle East region occurred in the Republic of Korea. The rapid nosocomial transmission of MERS-coronavirus (MERS-CoV) in Korean health care settings highlighted the importance and urgent need for a rapid and reliable on-site diagnostic assay to implement effective control and preventive measures. Here, the evaluation and validation of two newly developed reverse transcription-insulated isothermal PCR (RT-iiPCR) methods targeting the ORF1a and upE genes of MERS-CoV are described. Compared with World Health Organization-recommended singleplex real-time quantitative RT-PCR (RT-qPCR) assays, both RT-iiPCR assays had comparable analytical sensitivity for the detection of MERS-CoV RNA in tissue culture fluid and in sputum samples spiked with infectious virus. Furthermore, clinical evaluation was performed with sputum samples collected from subjects with acute and chronic respiratory illnesses, including patients infected with MERS-CoV. The overall agreement values between the two RT-iiPCR assays and the reference RT-qPCR assays were 98.06% (95% CI, 94.43%-100%; κ = 0.96) and 99.03% (95% CI, 95.88%-100%; κ = 0.99) for ORF1a and upE assays, respectively. The ORF1a and upE MERS-CoV RT-iiPCR assays coupled with a field-deployable system provide a platform for a highly sensitive and specific on-site tool for diagnosis of MERS-CoV infections.

Application of nanodiagnostics in point-of-care tests for infectious diseases

Although tremendous efforts have been put into the treatment of infectious diseases to prevent epidemics and mortality, it is still one of the major health care issues that have a profound impact on humankind. Therefore, the development of specific, sensitive, accurate, rapid, low-cost, and easy-to-use diagnostic tools is still in urgent demand. Nanodiagnostics, defined as the application of nanotechnology to medical diagnostics, can offer many unique opportunities for more successful and efficient diagnosis and treatment for infectious diseases. In this review, we provide an overview of the nanodiagnostics for infectious diseases from nanoparticle-based, nanodevice-based, and point-of-care test (POCT) platforms. Most importantly, emphasis focused on the recent trends in the nanotechnology-based POCT system. The current state-of-the-art and most promising point-of-care nanodiagnostic technologies, including miniaturized diagnostic magnetic resonance platform, magnetic barcode assay system, cell phone-based polarized light microscopy platform, cell phone-based dongle platform, and paper-based POCT platform, for infectious diseases were fully examined. The limitations, challenges, and future trends of the nanodiagnostics in POCTs for infectious diseases are also discussed.

Translation of a laboratory-validated equine herpesvirus-1 specific real-time PCR assay into an insulated isothermal polymerase chain reaction (iiPCR) assay for point-of-need diagnosis using POCKIT™ nucleic acid analyzer

Equine herpesvirus myeloencephalopathy (EHM), a major problem for the equine industry in the United States, is caused by equine herpesvirus-1 (EHV-1). In addition, EHV-1 is associated with upper respiratory disease, abortion, and chorioretinal lesions in horses. Here we describe the development and evaluation of an inexpensive, user-friendly insulated isothermal PCR (iiPCR) method targeting open reading 30 (ORF30) to detect both neuropathogenic and non-neuropathogenic strains on the field-deployable POCKIT™ device for point-of-need detection of EHV-1. The analytical sensitivity of the EHV-1 iiPCR assay was 13 genome equivalents per reaction. The assay did not cross react with ten non-target equine viral pathogens. Performance of the EHV-1 iiPCR assay was compared to two previously described real-time PCR (qPCR) assays in two laboratories by using 104 archived clinical samples. All 53 qPCR-positive and 46 of the 51 qPCR-negative samples tested positive and negative, respectively, by the iiPCR. The agreement between the two assays was 95.19% (confidence interval 90.48-99.90%) with a kappa value of 0.90. In conclusion, the newly developed EHV-1 iiPCR assay is robust to provide specificity and sensitivity comparable to qPCR assays for the detection of EHV-1 nucleic acid in clinical specimens.

DNA Microarray Detection of 18 Important Human Blood Protozoan Species

Background

Accurate detection of blood protozoa from clinical samples is important for diagnosis, treatment and control of related diseases. In this preliminary study, a novel DNA microarray system was assessed for the detection of Plasmodium, Leishmania, Trypanosoma, Toxoplasma gondii and Babesia in humans, animals, and vectors, in comparison with microscopy and PCR data. Developing a rapid, simple, and convenient detection method for protozoan detection is an urgent need.

Methodology/Principal Findings

The microarray assay simultaneously identified 18 species of common blood protozoa based on the differences in respective target genes. A total of 20 specific primer pairs and 107 microarray probes were selected according to conserved regions which were designed to identify 18 species in 5 blood protozoan genera. The positive detection rate of the microarray assay was 91.78% (402/438). Sensitivity and specificity for blood protozoan detection ranged from 82.4% (95%CI: 65.9% ~ 98.8%) to 100.0% and 95.1% (95%CI: 93.2% ~ 97.0%) to 100.0%, respectively. Positive predictive value (PPV) and negative predictive value (NPV) ranged from 20.0% (95%CI: 2.5% ~ 37.5%) to 100.0% and 96.8% (95%CI: 95.0% ~ 98.6%) to 100.0%, respectively. Youden index varied from 0.82 to 0.98. The detection limit of the DNA microarrays ranged from 200 to 500 copies/reaction, similar to PCR findings. The concordance rate between microarray data and DNA sequencing results was 100%.

Conclusions/Significance

Overall, the newly developed microarray platform provides a convenient, highly accurate, and reliable clinical assay for the determination of blood protozoan species.

More than 1 billion people are infected with blood protozoan diseases worldwide. The most common blood protozoa in humans, animals, and vectors include Plasmodium, Leishmania, Trypanosoma, Toxoplasma gondii and Babesia. Due to similar morphology among different blood protozoan species, misdiagnosis always occurs. Most molecular techniques are only carried out in laboratories, with a small number of samples detected simultaneously. Meanwhile, common detection methods may not be convenient for field investigation of large amounts of samples. In order to better manage blood protozoan infection, proper tools are required for the monitoring of these pathogens. Here, a comprehensive and sensitive DNA microarray was developed and tested, which allowed the parallel detection of 18 blood protozoan species.

Field-Deployable Reverse Transcription-Insulated Isothermal PCR (RT-iiPCR) Assay for Rapid and Sensitive Detection of Foot-and-Mouth Disease Virus

Foot‐and‐mouth disease (FMD) is a highly contagious viral disease of cloven‐hoofed animals, which can decimate the livestock industry and economy of countries previously free of this disease. Rapid detection of foot‐and‐mouth disease virus (FMDV) is critical to containing an FMD outbreak. Availability of a rapid, highly sensitive and specific, yet simple and field‐deployable assay would support local decision‐making during an FMDV outbreak. Here we report validation of a novel reverse transcription‐insulated isothermal PCR (RT‐iiPCR) assay that can be performed on a commercially available, compact and portable POCKIT^™ analyser that automatically analyses data and displays ‘+’ or ‘−’ results. The FMDV RT‐iiPCR assay targets the 3D region of the FMDV genome and was capable of detecting 9 copies of in vitro‐transcribed RNA standard with 95% confidence. It accurately identified 63 FMDV strains belonging to all seven serotypes and showed no cross‐reactivity with viruses causing similar clinical diseases in cloven‐hoofed animals. The assay was able to identify FMDV RNA in multiple sample types including oral, nasal and lesion swabs, epithelial tissue suspensions, vesicular and oral fluid samples, even before the appearance of clinical signs. Clinical sensitivity of the assay was comparable or slightly higher than the laboratory‐based real‐time RT‐PCR assay in use. The assay was able to detect FMDV RNA in vesicular fluid samples without nucleic acid extraction. For RNA extraction from more complex sample types, a commercially available taco^™ mini transportable magnetic bead‐based, automated extraction system was used. This assay provides a potentially useful field‐deployable diagnostic tool for rapid detection of FMDV in an outbreak in FMD‐free countries or for routine diagnostics in endemic countries with less structured laboratory systems.

Development of a TaqMan Probe-Based Insulated Isothermal Polymerase Chain Reaction (iiPCR) Assay for Detection of Fusarium oxysporum f. sp. cubense Race 4

This study developed a novel and inexpensive detection method based on a TaqMan probe-based insulated isothermal polymerase chain reaction (iiPCR) method for the rapid detection of Panama disease caused by Fusarium oxysporum f. sp. cubense (Foc) race 4, which is currently among the most serious fungal vascular diseases worldwide. By using the portable POCKIT™ device with the novel primer set iiFoc-1/iiFoc-2, the Foc race 4 iiPCR assay (including DNA amplification and signal monitoring) could be completed within one hour. The developed Foc race 4 iiPCR assay is thus a user-friendly and efficient platform designed specifically for the detection of Foc race 4. The detection limit of this optimized Foc iiPCR system was estimated to be 1 copy of the target standard DNA as well as 1 fg of the Foc genomic DNA. This approach can serve as a rapid detection method for in planta detection of Foc race 4 in field-infected banana. It was concluded that this molecular detection procedure based on iiPCR has good potential for use as an efficient detection method.