Applicability of a colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for SARS-CoV-2 detection in high exposure risk setting

Lateral flow paired with RT-LAMP: A speedy solution for Influenza A virus detection in swine

Influenza A Virus in swine (IAV-S) is a zoonotic pathogen that is nearly ubiquitous in commercial swine in the USA. Swine possess sialic acid receptors that allow co-infection of human and avian viruses with the potential of pandemic reassortment. We aimed to develop a fast and robust testing method for IAV-S detection on swine farms. Two primers of the RT-LAMP assay were labeled for use in a lateral flow readout. A commercially available lateral flow kit was used to read the amplicon product. With a runtime of ∼ 45 minutes, the limit of detection for the assay is comparable with an RT-qPCR Cq less than 35, with a sensitivity of 83.5 % and a specificity of 89.6 %. This assay allows veterinarians and producers with limited access to diagnostic services to perform and detect Matrix gene amplification on-site with low equipment costs. The time from sample collection to detection is less than one hour, making this method an accessible, convenient, and affordable tool to prevent the spread of zoonotic disease.

SARS-CoV-2 RT-LAMP in saliva: enhancing the results via a combination of cooling and specimen dilution procedure

Colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a potential and relatively simple rapid diagnostics method for COVID-19 detection. This study aims to evaluate and optimize the RT-LAMP performance on saliva specimens based on a commercially available kit.Modifications on an established protocol (Protocol A) were used, including Proteinase K supplementation (Protocol B); pre-treatment using nuclease-free water and proteinase K (Protocol C); Saliva cooling (Protocol D); saliva dilution after pre-treatment (Protocol E); lastly a combination of saliva cooling and dilution (Protocol F). Protocol performances were evaluated by comparing success rates (SR), diagnostic accuracy (DA), sensitivity, specificity, and predictive values. Additionally, a correlation between the Ct value by RT-qPCR and RT-LAMP performance was analyzed.. A total of 106 specimens were used in this study. Protocols B and C showed 100% unreadable results, therefore were paused. Protocol F showed the highest SR (87.65%) compared to other protocols, with a slight compromise to DA (81.69%), sensitivity (57.14%), specificity (97.67%), PPV (94.12%), and NPV (77.78%). In the sub-analysis of the low Ct value group (Ct < 30), Protocol F demonstrated a higher success rate (86.57%) compared to protocol A (64.18%); increased 3.08% sensitivity and 2.42% NPV; comparable DA; minor reduction in specificity (A = 100%; F = 97.67%) and PPV (A = 100%; F = 92.31%). A combination of saliva cooling-dilution substantially increased the tested kit's success rate, despite a slight decrease in specificity and PPV. Findings confirmed the saliva cooling-dilution procedure was beneficial to the test's SR, sensitivity, and NPV in the low Ct value group.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-024-00870-1.

Impact of Omicron variant sublineage BA.2.75 on the OnSite COVID-19 Ag Rapid Test: the applicability of rapid antigen test with universal transport media

BACKGROUND

Rapid antigen testing (RAT) is one of the most powerful tools for SARS-CoV-2 detection. The OnSite COVID-19 Ag Rapid Test is an antigen-based, point-of-care test approved by the WHO for Emergency Use Listing. The Nucleocapsid (N) gene mutations found in the emerging Omicron sublineages lead to the question of RAT performance.

OBJECTIVE

To ensure the diagnostic performance of the study RAT during rapidly mutated Omicron variants.

RESULTS

We independently evaluated the performance of this assay in 1098 archived samples collected in Thailand during October 2022-February 2023, which were 798 and 300 COVID-19 real-time RT-PCR positive and negative, respectively. The assay performed with 100% sensitivity and 100% specificity using a cycle threshold (Ct) of <20 for the RT-PCR. The sensitivity decreased to 88% when using Ct <30. Most of the SARS-CoV-2 found were Omicron BA.2 (99%), harboring six known N mutations (P13L, E31del, S33del, R203K, G204R and S413R). Eight samples containing hybrid variants (XBB.1*, XBB.2 and XBJ) were detected by the study RAT. This RAT detects all Omicron sublineages known to be circulating in Thailand.

CONCLUSIONS

These results confirmed the good performance of the study RAT for detecting Omicron variants and its appropriateness for individual diagnosis and for genomic surveillance.

Development of an integrated sample amplification control for salivary point-of-care pathogen testing

BACKGROUND

The COVID-19 pandemic has led to a rise in point-of-care (POC) and home-based tests, but concerns over usability, accuracy, and effectiveness have arisen. The incorporation of internal amplification controls (IACs), essential control for translational POC diagnostics, could mitigate false-negative and false-positive results due to sample matrix interference or inhibition. Although emerging POC nucleic acid amplification tests (NAATs) for detecting SARS-CoV-2 show impressive analytical sensitivity in the lab, the assessment of clinical accuracy with IACs is often overlooked. In some cases, the IACs were run spatially, complicating assay workflow. Therefore, the multiplex assay for pathogen and IAC is needed.

RESULTS

We developed a one-pot duplex reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay for saliva samples, a non-invasive and simple collected specimen for POC NAATs. The ORF1ab gene of SARS-CoV-2 was used as a target and a human 18S ribosomal RNA in human saliva was employed as an IAC to ensure clinical reliability of the RT-LAMP assay. The optimized assay could detect SARS-CoV-2 viral particles down to 100 copies/μL of saliva within 30 min without RNA extraction. The duplex RT-LAMP for SARS-CoV-2 and IAC is successfully amplified in the same reaction without cross-reactivity. The valid results were easily visualized in triple-line lateral flow immunoassay, in which two lines (flow control and IAC lines) represent valid negative results and three lines (flow control, IAC, and test line) represent valid positive results. This duplex assay demonstrated a clinical sensitivity of 95%, specificity of 100%, and accuracy of 96% in 30 clinical saliva samples.

SIGNIFICANCE

IACs play a crucial role in ensuring user confidence with respect to the accuracy and reliability of at-home and POC molecular diagnostics. We demonstrated the multiplex capability of SARS-COV-2 and human18S ribosomal RNA RT-LAMP without complicating assay design. This generic platform can be extended in a similar manner to include human18S ribosomal RNA IACs into different clinical sample matrices.

Bioscreening specific peptide-expressing phage and its application in sensitive dual-mode immunoassay of SARS-CoV-2 spike antigen

Biorecognition components with high affinity and selectivity are vital in bioassay to diagnose and treat epidemic disease. Herein a phage display strategy of combining single-amplification-panning with non-amplification-panning was developed, by which a phage displaying cyclic heptapeptide ACLDWLFNSC (peptide J4) with good affinity and specificity to SARS-CoV-2 spike protein (SP) was identified. Molecular docking suggests that peptide J4 binds to S2 subunit by hydrogen bonding and hydrophobic interaction. Then the J4-phage was used as the capture antibody to establish phage-based chemiluminescence immunoassay (CLIA) and electrochemical impedance spectroscopy (EIS) analytical systems. The as-proposed dual-modal immunoassay platform exhibited good sensitivity and reliability in SARS-CoV-2 SP and pseudovirus assay. The limit of detection for SARS-CoV-2 SP by EIS immunoassay is 0.152 pg/mL, which is dramatically lower than that of 42 pg/mL for J4-phage based CLIA. Further, low to 40 transducing units (TU)/mL, 10 TU/mL SARS-CoV-2 pseudoviruses can be detected by the proposed J4-phage based CLIA and electrochemical immunosensor, respectively. Therefore, the as-developed dual mode immunoassays are potential methods to detect SARS-CoV-2. It is also expected to explore various phages with specific peptides to different targets for bioanalysis.

Establishment and application of a loop-mediated isothermal amplification-lateral flow dipstick (LAMP-LFD) method for detecting Clostridium piliforme

BACKGROUND

Clostridium piliforme (causative agent of Tyzzer disease) infects various animals, including primates, and hence a threat to animal and human health worldwide. At present, it is detected using traditional methods, such as path morphology, polymerase chain reaction and enzyme-linked immunosorbent assay. Therefore, it is necessary to develop convenient, efficient visual molecular biological methods for detecting C. piliforme.

OBJECTIVES

To establish a method with good specificity, high sensitivity and simple operation for the detection of C. piliforme.

METHODS

In this study, we designed internal and external primers based on the conserved 23S rRNA region of C. piliforme to develop a biotin-labelled diarrhoea-suffered loop-mediated isothermal amplification (LAMP) system for detecting of C. piliforme and assessed the specificity, sensitivity and repeatability of the LAMP system.

RESULTS

The LAMP system did not exhibit cross-reactivity with 24 other common pathogenic species, indicating that it had good specificity. The minimum concentration of sensitivity was 1 × 10-7  ng/μL. Mouse models (Meriones unguiculatus) of Tyzzer disease were established and a LAMP-lateral flow dipstick (LAMP-LFD) was developed for detecting C. piliforme. The detection rate of C. piliforme was 5.08% in clean-grade animals and 9.96% in specific-pathogen-free-grade animals from Jiangsu, Zhejiang and Shanghai. In addition, the detection rates of C. piliforme were 10.1%, 8.6% and 20%, in animals from Hangzhou, Wenzhou and Shaoxing, respectively. The detection rate of C. piliforme was higher in experimental animals used in schools than in those used in companies and research institutes.

CONCLUSIONS

The LAMP-LFD method established in this study can be used to detect C. piliforme in animals handled in laboratory facilities of universities, pharmaceutical enterprises and research and development institutions.

Development of an Integrated Sample Amplification Control for Salivary Point-of-Care Pathogen Testing

Background

The COVID-19 pandemic has led to a rise in point-of-care (POC) and home-based tests, but concerns over usability, accuracy, and effectiveness have arisen. The incorporation of internal amplification controls (IACs), essential control for translational POC diagnostics, could mitigate false-negative and false-positive results due to sample matrix interference or inhibition. Although emerging POC nucleic acid amplification tests (NAATs) for detecting SARS-CoV-2 show impressive analytical sensitivity in the lab, the assessment of clinical accuracy with IACs is often overlooked. In some cases, the IACs were run spatially, complicating assay workflow. Therefore, the multiplex assay for pathogen and IAC is needed.

Results

We developed a one-pot duplex reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay for saliva samples, a non-invasive and simple collected specimen for POC NAATs. The ORF1ab gene of SARS-CoV-2 was used as a target and a human 18S ribosomal RNA in human saliva was employed as an IAC to ensure clinical reliability of the RT-LAMP assay. The optimized assay could detect SARS-CoV-2 viral particles down to 100 copies/μL of saliva within 30 minutes without RNA extraction. The duplex RT-LAMP for SARS-CoV-2 and IAC is successfully amplified in the same reaction without cross-reactivity. The valid results were easily visualized in triple-line lateral flow immunoassay, in which two lines (flow control and IAC lines) represent valid negative results and three lines (flow control, IAC, and test line) represent valid positive results. This duplex assay demonstrated a clinical sensitivity of 95%, specificity of 100%, and accuracy of 96% in 30 clinical saliva samples.

Significance

IACs play a crucial role in ensuring user confidence with respect to the accuracy and reliability of at-home and POC molecular diagnostics. We demonstrated the multiplex capability of SARS-COV-2 and human18S ribosomal RNA RT-LAMP without complicating assay design. This generic platform can be extended in a similar manner to include human18S ribosomal RNA IACs into different clinical sample matrices.