A diagnostic accuracy study comparing RNA LAMP, direct LAMP, and rapid antigen testing from nasopharyngeal swabs

Evaluation of three rapid assays for detecting Mycoplasma pneumoniae in nasopharyngeal specimens

During the 2023 autumn-winter period in China, Mycoplasma pneumoniae (MP) infections have increased. To address this, rapid and accurate MP DNA detection methods are crucial. Three nucleic acid detection assays (Ustar, Coyote Flash10, Coyote Flash 20) that are widely used in China are currently being evaluated for their effectiveness in detecting MP DNA in nasopharyngeal specimens. Reference standard materials for MP and a total of 35 NPS collected from Peking Union Medical College Hospital were tested using the Ustar, Coyote Flash10 and Coyote Flash 20 assays to assess analytical sensitivity, analytical specificity, diagnostic performance and workflow. The assays showed differing limits of detection (LOD) based on the absolute quantification of reference standards, with LODs of 500 copies/mL for the Ustar assays and 200 copies/mL for both Coyote Flash10 and Coyote Flash 20 assays. Additionally, all three assays displayed excellently analytical specificity in detecting MP DNA.The clinical correlation analysis demonstrated that the Ustar assay exhibited a sensitivity of 90.00%, specificity of 100%, positive predictive value (PPV) of 100%, and negative predictive value (NPV) of 62.50%. In contrast, both the Coyote Flash10 and Coyote Flash 20 assays displayed perfect diagnostic accuracy with 100% sensitivities, specificities, PPVs, and NPVs. Despite variations in detection principles, sample volume, and pre-preparation among the three assays, they all had a turnaround time of less than 30 min with low-throughput processing. Overall, all three rapid nucleic acid detection assays displayed excellent clinical performance in detecting MP DNA, offering a solid foundation for the quick clinical diagnosis of MP infection.

Loop-Mediated Isothermal Amplification for Diagnosis of Zoonotic Malaria

Zoonotic malaria, caused by Plasmodium knowlesi, Plasmodium cynomolgi, Plasmodium coatneyi, and Plasmodium inui, is a significant global health concern. The gold standard microscopy, while widely used for malaria diagnosis, faces limitations in differentiating between malaria species. Polymerase chain reaction (PCR), despite its accuracy, is characterized by high costs and time-consuming procedures. This study aims to develop and validate a rapid and accurate diagnostic test for detecting four simian Plasmodium species by using loop-mediated isothermal amplification (LAMP). Loop-mediated isothermal amplification is a cost-effective and faster molecular testing alternative for malaria diagnosis. The project involved designing specific primers, testing sensitivity and specificity against various parasites (including human Plasmodium species, protozoa, and helminths), and evaluating the LAMP assay using 60 macaque samples infected with simian Plasmodium. The LAMP assay exhibited a sensitivity profile enabling the detection of P. knowlesi, P. coatneyi, and P. cynomolgi across a concentration gradient from 5 × 108 down to 5 × 105 parasites/µL. Notably, P. inui was detectable at 5 × 108 parasites/µL. Furthermore, the specificity of the primer tailored for the four simian Plasmodium species was proven, as it produced a positive amplification exclusively for the respective target species and generated negative results for nontarget species. The results indicated that the LAMP assay is capable of detecting simian Plasmodium within a short span of 60 minutes, without any false positives from other samples. This new test has the potential to revolutionize malaria diagnosis, surveillance, and control, thereby mitigating the impact of zoonotic malaria in regions of endemicity.

Evaluation of the SARS-CoV-2 RNA detection reagent LAMPdirect Genelyzer KIT using nasopharyngeal swab and saliva samples

The LAMPdirect Genelyzer KIT allows for the detection of SARS-CoV-2 RNA in saliva samples with a loop-mediated isothermal amplification (LAMP) method and generates results within 20 min. It has been approved by the Pharmaceuticals and Medical Devices Agency in Japan. In this study, the performance of the LAMPdirect Genelyzer KIT was compared with that of the RT-qPCR reference method using 50 nasopharyngeal swabs and 100 saliva samples. In addition, we evaluated the applicability of an alternative reverse transcriptase and the effects of an inactivation buffer. The total agreement rates were 80.0 % and 82.0 % for nasopharyngeal and saliva samples, respectively. When considering samples at the detection limit (50 copies/reaction) that increases the chance of transmission between humans, the total agreement rates were 100% and 94.1% for nasopharyngeal and saliva samples, respectively. The LAMP method is simple, fast, and inexpensive, making it useful for small medical institutions or rural areas.

Comparison of the diagnostic accuracy of the Pluslife Mini Dock RHAM technology with Abbott ID Now and Cepheid GenXpert: A retrospective evaluation study

Rapid and sensitive detection of pathogens is critical in interrupting the transmission chain of infectious diseases. Currently, real-time (RT-)PCR represents the gold standard for the detection of SARS-CoV-2. RNase HII-assisted amplification (RHAM) is a promising technology, enabling reliable point-of-care (PoC) testing; however, its diagnostic accuracy has not yet been investigated. The present study compared the Pluslife Mini Dock (RHAM technology), with Abbott ID Now and Cepheid GeneXpert IV. The positive percent agreement (PPA) and negative percent agreement (NPA) were determined in 100 SARS-CoV-2 positive and 210 SARS-CoV-2 negative samples. Further, the reliability of the Pluslife Mini Dock was investigated in different SARS-CoV-2 variants (Delta and Omicron subvariants). The PPA was 99.00% for Pluslife, 100.00% for Abbott ID Now, and 99.00% for Cepheid GeneXpert, with an NPA of 100.00%, 98.90%, and 93.72%, respectively. Abbott ID Now demonstrated the highest rate of invalid results. All SARS-CoV-2 analysed variants were detected by the Pluslife device. Altogether, the Pluslife Mini Dock demonstrated a PPA of 99.16% (235/237) for CT < 36 and an NPA of 100.00% (313/313), respectively. In conclusion, the Pluslife Mini Dock demonstrated better analytical performance than Abbott ID Now and Cepheid GeneXpert IV, representing a highly accurate and rapid PoC alternative to RT-PCR.

Evaluation of the EasyNAT SARS-CoV-2 assay PCR test for the diagnosis of SARS-CoV-2 infection

Reverse transcription polymerase chain reaction (RT-PCR) tests are commonly utilized in commercial settings but pose challenges due to labor-intensive procedures and extended response times during peak demand. In contrast, real-time fluorescence and isothermal amplification assays using Crossing Priming Amplification (CPA) offer faster genetic material analysis, eliminate subjectivity, and require less manipulation and personnel training. This study aimed to validate the EasyNAT SARS-CoV-2 Assay, a diagnostic kit based on CPA, using oral and nasopharyngeal samples. The EasyNAT kit was compared to the Xpert Xpress SARS-CoV-2 kit, evaluating 873 samples obtained during routine analysis at the Microbiology Laboratory of the Hospital Costa del Sol (Marbella, Spain). The overall sensitivity and specificity for the EasyNAT SARS-CoV-2 Assay were 79.1% (95%CI 74.5-83.7) and 99.5% (95%CI 98.7-100), respectively; with, validity index of 91.9%, positive predictive value of 98.9%, negative predictive value of 88.9%, positive likelihood ratio of 144.5, negative likelihood ratio of 0.21 and a total Youden Index of 0.79. Notably, sensitivity improved in fresh samples (91.4%), along with a high Youden Index (0.91). The EasyNAT SARS-CoV-2 Assay achieved a higher percentage of concordance in positive samples with Xpert Xpress SARS-CoV-2 when analyzing cycle threshold (Ct) intervals below 30 compared to intervals equal or greater than 30, and demons. In conclusion, the EasyNAT SARS-CoV-2 Assay demonstrated high sensitivity and agreement with Xpert Xpress SARS-CoV-2, particularly in fresh samples or when the signal was detected at Ct intervals below 30, indicating higher viral loads. This makes it suitable for rapid screening in various settings, including those with limited access to conventional molecular laboratory setting.

Laboratory Evaluation of a SARS-CoV-2 RT-LAMP Test

There is a need to have more accessible molecular diagnostic tests for the diagnosis of severe acute respiratory syndrome coronavirus 2 disease in low- and middle-income countries. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) may provide an attractive option as this technology does not require a complex infrastructure. In this study, the diagnostic performance of a SARS-CoV-2 RT-LAMP was evaluated using RT-PCR-confirmed clinical specimens of COVID-19-positive (n = 55) and -negative patients (n = 55) from the Netherlands. The observed sensitivity of the RT-LAMP test was 97.2% (95% CI: 82.4-98.0%) and the specificity was 100% (95% CI: 93.5-100%). The positive predictive value of the RT-LAMP was 100%, the negative predictive value 93.2% (95% CI: 84.3-97.3%), and the diagnostic accuracy was 96.4% (95% CI: 91.0-99.0%). The agreement between the RT-LAMP and the RT-PCR was "almost perfect" (κ-value: 0.92). The evaluated RT-LAMP might provide an attractive alternative molecular diagnostic tool for SARS-CoV-2 in resource limited settings.