Integrated approach for detection of SARS-CoV-2 and its variant by utilizing LAMP and ARMS-PCR

A multiplex point-of-care test for discriminatory inference of SARS-CoV-2 Omicron lineages using reverse transcription loop-mediated isothermal amplification and lateral flow detection

The ongoing increase in genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages remains a significant global challenge, mainly due to the incompatibility of genetic sequencing with the technological and economic capabilities of most countries worldwide. Additionally, the continued circulation and emergence of numerous lineages of the Omicron variant with some specific mutations represent a challenge in developing straightforward tests for their discrimination. In this study, we developed a multiplex assay based on reverse transcription loop-mediated isothermal amplification with lateral flow assay detection (RT-LAMP-LFA). This assay aims to enhance the accessibility of genomic surveillance and to deliver more precise epidemiological data to support public health decision-making. To demonstrate its utility, we used the assay as a proof of concept for discriminating between the SARS-CoV-2 Omicron lineages BA.1 and BA.2. When comparing the results of the new assay with the gold standard method of genetic sequencing in a panel of clinical samples, the multiplex RT-LAMP-LFA demonstrated excellent diagnostic performance. For BA.1 lineage detection, the assay achieved 100% sensitivity, 100% specificity, and 100% accuracy, while for BA.2, it showed 100% sensitivity, 95% specificity, and 96% accuracy. The overall simplicity of the method combined with advantages such as short analysis time (40 min), low cost (∼$15 per test) and adaptability to the point-of-care format make the multiplex RT-LAMP-LFA assay an important screening tool for inferring SARS-CoV-2 Omicron lineage positive samples, thus alleviating the high demand for sequencing and expanding genomic surveillance, even in remote locations.

Standardization and Evaluation of the LAMP Technique for the Diagnosis of Canine Visceral Leishmaniasis in Conjunctival Swab Samples Using DNA Extracted by a Silica Column and Boiling

The diagnosis of canine visceral leishmaniasis (CVL) presents a challenge due to a variety of non-specific clinical signs. The available tests have low sensitivity. This study aimed to standardize and evaluate the loop-mediated isothermal amplification technique with K26 target (K26-LAMP) for diagnosis of CVL in conjunctival swab (CS) DNA samples extracted through a silica column commercial kit (SW-kit) and boiling (SW-DB) and to compare sensitivity with conventional PCR (kDNA-cPCR) and quantitative real-time PCR (18S-qPCR). Clinical samples of CSs were collected from 54 dogs after reactive serology tests. Positive parasitological and/or histological tests were used as inclusion criteria for a sensitivity analysis. A total of 79.2% (43/54) of dogs without clinical signs or with mild, moderate, or severe clinical signs were included in the study. The sensitivity results of K26-LAMP, kDNA-cPCR, and 18S-qPCR were 72.1%, 81.4%, and 80.5% with the SW-kit and 97.2%, 95.2%, and 57.1% with SW-DB, respectively. In all techniques, the proportion of positives was higher in the group with severe clinical disease, with statistically significant differences in the K26-LAMP and 18S-qPCR techniques being seen with the SW-kit. The results obtained with LAMP for CS samples are promising and its performance is similar to other techniques.

Development and evaluation of a rapid visual loop-mediated isothermal amplification assay for the tcdA gene in Clostridioides difficile detection

Background

The tcdA gene codes for an important toxin produced by Clostridioides difficile (C. difficile), but there is currently no simple and cost-effective method of detecting it. This article establishes and validates a rapid and visual loop-mediated isothermal amplification (LAMP) assay for the detection of the tcdA gene.

Methods

Three sets of primers were designed and optimized to amplify the tcdA gene in C. difficile using a LAMP assay. To evaluate the specificity of the LAMP assay, C. difficile VPI10463 was used as a positive control, while 26 pathogenic bacterial strains lacking the tcdA gene and distilled water were utilized as negative controls. For sensitivity analysis, the LAMP assay was compared to PCR using ten-fold serial dilutions of DNA from C. difficile VPI10463, ranging from 207 ng/µl to 0.000207 pg/µl. The tcdA gene of C.difficile was detected in 164 stool specimens using both LAMP and polymerase chain reaction (PCR). Positive and negative results were distinguished using real-time monitoring of turbidity and chromogenic reaction.

Results

At a temperature of 66 °C, the target DNA was successfully amplified with a set of primers designated, and visualized within 60 min. Under the same conditions, the target DNA was not amplified with the tcdA12 primers for 26 pathogenic bacterial strains that do not carry the tcdA gene. The detection limit of LAMP was 20.700 pg/µl, which was 10 times more sensitive than that of conventional PCR. The detection rate of tcdA in 164 stool specimens using the LAMP method was 17% (28/164), significantly higher than the 10% (16/164) detection rate of the PCR method (X2 = 47, p < 0.01).

Conclusion

LAMP method is an effective technique for the rapid and visual detection of the tcdA gene of C. difficile, and shows potential advantages over PCR in terms of speed, simplicity, and sensitivity. The tcdA-LAMP assay is particularly suitable for medical diagnostic environments with limited resources and is a promising diagnostic strategy for the screening and detection of C. difficile infection in populations at high risk.

Genomic and Phylogenetic Characterisation of SARS-CoV-2 Genomes Isolated in Patients from Lambayeque Region, Peru

OBJECTIVE

this study aims to identify and characterise genomic and phylogenetically isolated SARS-CoV-2 viral isolates in patients from Lambayeque, Peru.

METHODS

Nasopharyngeal swabs were taken from patients from the Almanzor Aguinaga Asenjo Hospital, Chiclayo, Lambayeque, Peru, which had been considered mild, moderate, and severe cases of COVID-19. Patients had to have tested positive for COVID-19, using a positive RT-PCR for SARS-CoV-2. Subsequently, the SARS-CoV-2 complete viral genome sequencing was carried out using Illumina MiSeq®. The sequences obtained from the sequence were analysed in Nextclade V1.10.0 to assign the corresponding clades, identify mutations in the SARS-CoV-2 genes and perform quality control of the sequences obtained. All sequences were aligned using MAFFT v7.471. The SARS-CoV-2 isolate Wuhan NC 045512.2 was used as a reference sequence to analyse mutations at the amino acid level. The construction of the phylogenetic tree model was achieved with IQ-TREE v1.6.12.

RESULTS

It was determined that during the period from December 2020 to January 2021, the lineages s C.14, C.33, B.1.1.485, B.1.1, B.1.1.1, and B.1.111 circulated, with lineage C.14 being the most predominant at 76.7% (n = 23/30). These lineages were classified in clade 20D mainly and also within clades 20B and 20A. On the contrary, the variants found in the second batch of samples of the period from September to October 2021 were Delta (72.7%), Gamma (13.6%), Mu (4.6%), and Lambda (9.1%), distributed between clades 20J, 21G, 21H, 21J, and 21I.

CONCLUSIONS

This study reveals updated information on the viral genomics of SARS-CoV-2 in the Lambayeque region, Peru, which is crucial to understanding the origins and dispersion of the virus and provides information on viral pathogenicity, transmission and epidemiology.