Isothermal Nucleic Acid Amplification Test Research Articles

1783. More than Which Molecular Test: Following the Directions in How and Who to Test in the Diagnosis of Influenza

BackgroundThe CDC and IDSA recommend testing hospitalized patients with suspected influenza using molecular assays, in part to implement precautions to prevent transmission. Both PCR and a rapid isothermal nucleic acid amplification test (NAAT) for influenza detection are available at the University of Utah Health (UU). The UU has required the more-sensitive PCR to discontinue isolation for suspect in patients, but we hypothesized the NAAT could be sufficient in most patients.MethodsA retrospective review of influenza diagnostics pre- and post-reinforcement of proper test procedures was performed across a university healthcare system, including a 650-bed tertiary care and 100-bed cancer hospital. During August 2018, providers and staff involved in testing were interviewed to describe their practices. Gaps were addressed in September 2018 with flyers outlining procedures, providing optimal sampling supplies, and EHR prompts for appropriate specimen type. A subset of UU patients tested by both NAAT and PCR within a 48 hour period were identified from the corporate data warehouse as Pre (September 2016 through March 2018) or Post reinforcement (October 2018 through March 2019). Agreement within PCR/NAAT test pairs was determined, with chart reviews of patients with discrepant results. Time of testing from the onset of symptoms was noted, and flu-like symptoms were defined as fever (>38°C) and cough or sore throat.ResultsPrior to reinforcement, most hospital staff were unaware of the optimal specimen type and collection swab for NAAT vs. PCR. Units initially lacked appropriate sampling supplies for NAAT. Providers complained of needing to confirm negative NAAT for inpatients with questionable symptoms, and supported the reinforcement to target follow-up PCR in those clearly symptomatic or immunocompromised. Concordance with NAAT and PCR pre- and post-reinforcement of proper test procedures when both methods were done is shown in the Figure.ConclusionDiagnosis of influenza is important in hospitalized patients. In addition to selecting a sensitive assay, attention to optimize test performance is critical. Our results suggest there is a need to train and monitor clinicians in identifying who to test and when, what specimen to collect and how, and in interpreting results. DisclosuresKimberly Hanson, MD, MHS, BioFire: Consultant, Grant/Research Support; T2 Biosystems: Consultant.

Colorimetric-Luminance Readout for Quantitative Analysis of Fluorescence Signals with a Smartphone CMOS Sensor.

Smartphones have shown promise as an enabling technology for portable and distributed point-of-care diagnostic tests. The CMOS camera sensor can be used for detecting optical signals, including fluorescence for applications such as isothermal nucleic acid amplification tests. However, such analysis is typically limited mostly to end point detection of single targets. Here we present a smartphone-based image analysis pipeline that utilizes the CIE xyY (chromaticity-luminance) color space to measure the luminance (in lieu of RGB intensities) of fluorescent signals arising from nucleic acid amplification targets, with a discrimination sensitivity (ratio between the positive to negative signals), which is an order of magnitude more than traditional RGB intensity based analysis. Furthermore, the chromaticity part of the analysis enables reliable multiplexed detection of different targets labeled with spectrally separated fluorophores. We apply this chromaticity-luminance formulation to simultaneously detect Zika and chikungunya viral RNA via end point RT-LAMP (Reverse transcription Loop-Mediated isothermal amplification). We also show real time LAMP detection of Neisseria gonorrhoeae samples down to a copy number of 3.5 copies per 10 μL of reaction volume in our smartphone-operated portable LAMP box. Our chromaticity-luminance analysis is readily adaptable to other types of multiplexed fluorescence measurements using a smartphone camera.

Multicenter evaluation of the Alere™ i influenza A&B assay using respiratory specimens collected in viral transport media

Rapid and accurate detection of influenza virus is critical for proper patient management. The Alere™ i Influenza A&B assay is an isothermal nucleic acid amplification test capable of detecting influenza A and B viruses directly from respiratory specimens. In this multicenter clinical trial conducted in the US, we evaluated the clinical performance of the Alere™ i Influenza A&B assay against that of the Prodesse ProFlu+ assay. A total of 1243 fresh, leftover nasal or nasopharyngeal swabs eluted in viral transport medium were tested by both assays. Sensitivity and specificity of the Alere™ i Influenza A&B assay were 97.8% (95% CI 94.6–99.2) and 96.6% (95% CI 95.2–97.5) for influenza A and 92.9% (95% CI 85.5–96.9) and 98.3% (95% CI 97.4–98.0) for influenza B. The Alere™ i Influenza A&B assay is an ideal molecular assay for influenza virus detection due to its high sensitivity and specificity with minimal hands-on and turn-around-time.

Integrated self-regulating resistive heating for isothermal nucleic acid amplification tests (NAAT) in Lab-on-a-Chip (LoC) devices.

Isothermal nucleic acid amplification tests (NAAT) in a Lab-on-a-Chip (LoC) format promise to bring high-accuracy, non-instrumented rapid tests to the point of care. Reliable rapid tests for infectious diseases allow for early diagnosis and treatment, which in turn enables better containment of potential outbreaks and fewer complications. A critical component to LoC NAATs is the heating element, as all NAAT protocols require incubation at elevated temperatures. We propose a cheap, integrated, self-regulating resistive heating solution that uses 2xAAA alkaline batteries as the power source, can maintain temperatures in the 60–63°C range for at least 25 minutes, and reaches the target range from room temperature in 5 minutes. 4 heating element samples with different electrical characteristics were evaluated in a thermal mock-up for a LoC NAAT device. An optimal heating element candidate was chosen based on temperature profiling. The optimal candidate was further evaluated by thermal modelling via finite element analysis of heat transfer and demonstrated suitable for isothermal nucleic acid amplification.

Lyophilized visually readable loop-mediated isothermal reverse transcriptase nucleic acid amplification test for detection Ebola Zaire RNA

Recent viral outbreaks highlight the need for reliable, yet broadly deployable diagnostics for detection of epidemic and emerging pathogens. In this study we designed and optimized methods to visually detect viral nucleic acid by isothermal amplification and SYBR dye intercalation. We designed and tested loop-mediated isothermal amplification (LAMP) primers and lyophilized reactions to optimize the detection of Zaire Ebola Virus (ZEBOV) and further evolved the LAMP platform to allow room-temperature storage for deployment in resource limited settings. Our results demonstrated excellent sensitivity and specificity for viral nucleic acid sequences with lower limits of detection of less than 100 copies. Moreover, lyophilized reaction mixtures retained activity for prolonged periods under dry conditions at room temperature. This approach offers a way for detection of emerging viruses in resource limited settings.

Comparison of a new visual isothermal nucleic acid amplification test with PCR and skin snip analysis for diagnosis of onchocerciasis in humans

Accurate, simple and affordable diagnostics are needed to detect Onchocerca volvulus infection in humans. A newly developed colorimetric loop-mediated isothermal amplification (LAMP) assay was compared to PCR and skin snip analysis for diagnosis of onchocerciasis. The robustness and simplicity of the assay indicates that it may be a useful field tool for surveillance in endemic countries.

On-Chip Isothermal Nucleic Acid Amplification on Flow-Based Chemiluminescence Microarray Analysis Platform for the Detection of Viruses and Bacteria.

This work presents an on-chip isothermal nucleic acid amplification test (iNAAT) for the multiplex amplification and detection of viral and bacterial DNA by a flow-based chemiluminescence microarray. In a principle study, on-chip recombinase polymerase amplification (RPA) on defined spots of a DNA microarray was used to spatially separate the amplification reaction of DNA from two viruses (Human adenovirus 41, Phi X 174) and the bacterium Enterococcus faecalis, which are relevant for water hygiene. By establishing the developed assay on the microarray analysis platform MCR 3, the automation of isothermal multiplex-amplification (39 °C, 40 min) and subsequent detection by chemiluminescence imaging was realized. Within 48 min, the microbes could be identified by the spot position on the microarray while the generated chemiluminescence signal correlated with the amount of applied microbe DNA. The limit of detection (LOD) determined for HAdV 41, Phi X 174, and E. faecalis was 35 GU/μL, 1 GU/μL, and 5 × 10(3) GU/μL (genomic units), which is comparable to the sensitivity reported for qPCR analysis, respectively. Moreover the simultaneous amplification and detection of DNA from all three microbes was possible. The presented assay shows that complex enzymatic reactions like an isothermal amplification can be performed in an easy-to-use experimental setup. Furthermore, iNAATs can be potent candidates for multipathogen detection in clinical, food, or environmental samples in routine or field monitoring approaches.

Prospective evaluation of the Alere i Influenza A&B nucleic acid amplification versus Xpert Flu/RSV

The rapid and accurate detection of influenza virus in respiratory specimens is required for optimal management of patients with acute respiratory infections. Because of the variability of the symptoms and the numerous other causes of influenza-like illness, the diagnosis of influenza cannot be made on the basis of clinical criteria alone. Thus, rapid influenza diagnostic tests have been developed such as the Alere i Influenza A&B isothermal nucleic acid assay. We prospectively evaluated the performance of the Alere i Influenza A&B assay in comparison with our routine Xpert Flu/RSV assay. Positive samples were subtyped according to the protocol from the National Influenza Center (Paris, France). A total of 96 respiratory nasal swab samples were analyzed: with both methods, 38 were positive and 56 were negative. Samples were prospectively collected from January 20 to April 8, 2015, from patient (86 adult and 10 pediatric patients) presenting with an influenza-like illness through the French influenza season. In comparison with the Xpert Flu/RSV assay, the overall sensitivity and specificity of the Alere i Influenza A&B assay were 95% and 100%, respectively. Our results indicate that the Alere i Influenza A&B assay has a good overall analytical performance and a high degree of concordance with the PCR-based Xpert Flu/RSV assay. The Alere i Influenza A&B isothermal nucleic acid amplification test is a powerful tool for influenza detection due to its high sensitivity and specificity as well as its ability to generate results within 15min.

Multicenter clinical evaluation of the novel Alere™ i Influenza A&B isothermal nucleic acid amplification test

BackgroundRapid detection of influenza infection is important for patient management and timely anti-viral therapy. Rapid antigen detection tests for influenza have inferior sensitivity when compared to nucleic acid-based amplification tests. An isothermal nucleic acid amplification test that offers the potential for rapid molecular testing at the clinical point-of-care with simple equipment can improve influenza detection rates. ObjectivesTo evaluate the performance of Alere™ i Influenza A&B isothermal nucleic acid amplification test to detect influenza A and B in comparison to viral cell culture as reference method. Study designA prospective, multicenter, clinical study to evaluate the clinical performance of the Alere™ i Influenza A&B assay in a point-of-care setting using prospectively enrolled specimens from both children and adults was conducted in seven sites. ResultsIn comparison with viral cell culture, the overall sensitivity and specificity of the Alere™ i Influenza A&B assay was 97.8% and 85.6% for the detection of influenza A, and 91.8% and 96.3% for the detection of influenza B, respectively. Following resolution of discrepant results by real-time RT-PCR the sensitivity and specificity of the Alere™ i Influenza A&B assay improved to 99.3% and 98.1% for influenza A, and 97.6% and 100% for influenza B, respectively. ConclusionsThe Alere™ i Influenza A&B isothermal nucleic acid amplification test is an ideal point-of-care test for influenza detection in children and adults due to its high sensitivity and specificity and ability to generate results within 15min from specimen receipt.

Development and Comparison of a Rapid Isothermal Nucleic Acid Amplification Test for Typing of Herpes Simplex Virus Types 1 and 2 on a Portable Fluorescence Detector

We have developed a rapid and simple molecular test, the IsoGlow HSV Typing assay, for the detection and typing of herpes simplex virus (type 1 and 2) from genital or oral lesions. Clinical samples suspended in viral transport mediums are simply diluted and then added to a helicase-dependent amplification master mix. The amplification and detection were performed on a portable fluorescence detector called the FireFly instrument. Detection of amplification products is based on end-point analysis using cycling probe technology. An internal control nucleic acid was included in the amplification master mix to monitor the presence of amplification inhibitors in the samples. Because the device has only two fluorescence detection channels, two strategies were developed and compared to detect the internal control template: internal control detected by melting curve analysis using a dual-labeled probe, versus internal control detection using end-point fluorescence release by a CPT probe at a lower temperature. Both have a total turnaround time of about 1 hour. Clinical performance relative to herpes viral culture was evaluated using 176 clinical specimens. Both formats of the IsoGlow HSV typing assay had sensitivities comparable to that of the Food and Drug Administration-cleared IsoAmp HSV (BioHelix Corp., Beverly MA) test and specificity for the two types of HSV comparable to that of ELVIS HSV (Diagnostic Hybrids, Athens, OH).

A rapid and simple isothermal nucleic acid amplification test for detection of herpes simplex virus types 1 and 2

Background A simple and rapid IsoAmp ® HSV assay has been developed for qualitative detection of herpes simplex virus (HSV) types 1 and 2 from genital lesions. Sample preparation involved a simple dilution step and the diluted specimens were directly added to the device and amplified by isothermal helicase-dependent amplification (HDA). Amplification products were then detected by a DNA strip embedded in a disposable cassette without any instrument. The total test turn-around time is less than 1.5 h from specimen processing to result reporting. Objectives To evaluate the analytical and clinical performance of the IsoAmp ® HSV assay as well as the robustness and reproducibility of the assay. Study design The analytical sensitivity of the IsoAmp ® HSV assay was determined using both HSV-1 and HSV-2. Clinical performance was evaluated using 135 frozen specimens collected from patients with suspected HSV infection in genital area. Results The analytical sensitivity of the assays was 5.5 and 34.1 copies/reaction for HSV-1 and HSV-2 respectively with a 95% confidence interval. When the herpes viral culture was used as the reference standard, the clinical sensitivity and specificity of the IsoAmp ® HSV assay were 100.0% and 96.3% respectively. The inter-laboratory reproducibility achieved an overall 97.5% agreement by testing a total of 80 blinded HSV-1 samples among five laboratories. Conclusion Adequate analytical and clinical performance of the IsoAmp ® HSV assay was demonstrated. This assay is simple to perform and has acceptable inter-laboratory reproducibility.