WarmStart colorimetric RT-LAMP for the rapid, sensitive and specific detection of Enteroviruses A-D targeting the 5'UTR region

Sample Treatment with Trypsin for RT-LAMP COVID-19 Diagnosis

The SARS-CoV-2 coronavirus is responsible for the COVID-19 pandemic resulting in a global health emergency. Given its rapid spread and high number of infected individuals, a diagnostic tool for a rapid, simple, and cost-effective detection was essential. In this work, we developed a COVID-19 diagnostic test, that incorporates a human internal control, based on the Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP). When working with synthetic SARS-CoV-2 RNA, the optimized RT-LAMP assay has a sensitivity of 10 viral copies and can be detected by fluorescence in less than 15 min or by the naked eye in 25 min using colorimetric RT-LAMP. To avoid the RNA extraction step, a pre-treatment of the sample was optimized. Subsequently, a validation was performed on 268 trypsin treated samples (including nasopharyngeal, buccal, and nasal exudates) and amplified with colorimetric RT-LAMP to evaluate its sensitivity and specificity in comparison with RT-qPCR of extracted samples. The validation results showed a sensitivity and specificity of 100% for samples with Ct ≤ 30. The rapid, simple, and inexpensive RT-LAMP SARS-CoV-2 extraction-free procedure developed may be an alternative test that could be applied for the detection of SARS-CoV-2 or adapted to detect other viruses present in saliva or nasopharyngeal samples with higher sensitivity and specificity of the antibody test.

Electromechanical RT-LAMP device for portable SARS-CoV-2 detection

Rapid point-of-care tests for infectious diseases are essential, especially in pandemic conditions. We have developed a point-of-care electromechanical device to detect SARS-CoV-2 viral RNA using the reverse-transcription loop-mediated isothermal amplification (RT-LAMP) principle. The developed device can detect SARS-CoV-2 viral RNA down to 10³ copies/mL and from a low amount of sample volumes (2 μL) in less than an hour of standalone operation without the need for professional labor and equipment. Integrated Peltier elements in the device keep the sample at a constant temperature, and an integrated camera allows automated monitoring of LAMP reaction in a stirring sample by using colorimetric analysis of unfocused sample images in the hue/saturation/value color space. This palm-fitting, portable and low-cost device does not require a fully focused sample image for analysis, and the operation could be stopped automatically through image analysis when the positive test results are obtained. Hence, viral infections can be detected with the portable device produced without the need for long, expensive, and labor-intensive tests and equipment, which can make the viral tests disseminated at the point-of-care.

Detection of emerging genotypes in Trichophyton mentagrophytes species complex: A proposal for handling biodiversity in dermatophytes

A resistant and hypervirulent dermatophyte from India has been described as a taxonomic novelty, Trichophyton indotineae, a species of the Trichophyton mentagrophytes complex. Rapid detection and correct identification of closely similar dermatophytes with different predilections are essential for efficient clinical management. We evaluated the efficacy of rapid diagnostic methods clinical and environmental strains in the T. mentagrophytes complex. The methods included Real-time-PCR, DermaGenius, LAMP, and MALDI-ToF MS, using rDNA ITS sequences as taxonomic standard. The results show that only MALDI-ToF MS can distinguish 96.97% T. indotineae from other closely related species. The complex comprises numerous clones which may differ in anonymous markers but with similar evolutionary behavior. Therefore, we recommend to distinguish species only when they show an appreciable degree of adaptation and thus are clinically significant. The distinction of remaining clonal diversity is an epidemiological query and can be solved by haplotype numbering.

Loop-mediated isothermal amplification (LAMP) colorimetric phenol red assay for rapid identification of α0-thalassemia: Application to population screening and prenatal diagnosis

Background

Identification of α⁰-thalassemia (SEA and THAI deletions) is essential in preventing and controlling of severe thalassemia diseases. We have developed the LAMP colorimetric assays for the detection of these two thalassemia defects and validated them in population screening and prenatal diagnosis.

Methods

Three LAMP colorimetric assays specific for α⁰-thalassemia (SEA deletion), α⁰-thalassemia (THAI deletion) and normal DNA sequence were developed. These assays were validated on 341 subjects who had initial thalassemia screening positive and various thalassemia genotypes. Prenatal diagnosis of α⁰-thalassemia (SEA deletion) was done on 33 fetuses at risk of having Hb Bart’s hydrops fetalis syndrome.

Results

The LAMP colorimetric assays for α⁰-thalassemia (SEA and THAI deletions) could be clearly interpreted by naked eyes. The assay for α⁰-thalassemia (SEA deletion) showed a 100% (62/62 x 100) sensitivity and 98.2% (274/279 x 100) specificity whereas, that of the α⁰-thalassemia (THAI deletion) showed 100% (1/1 x 100) sensitivity and 99.7% (339/340 x 100) specificity. We obtained a 100% concordant prenatal diagnosis results using LAMP assays of α⁰-thalassemia (SEA deletion) in 33 fetuses as compared to the conventional PCR analysis.

Conclusions

The LAMP colorimetric assays developed are simple, rapid, and do not require sophisticated equipment. Inclusion of the LAMP tests in the existing screening protocol significantly reduce the screening cost and the molecular analysis workload, which should prove useful in the prevention and control program of hemoglobinopathies in the region.

Identification of Gyromitra infula: A Rapid and Visual Method Based on Loop-Mediated Isothermal Amplification

With mushroom poisoning emerging as one of the most serious food safety problems worldwide, a rapid identification method of poisonous mushrooms is urgently required to investigate the source of poisoning. Gyromitra infula, a kind of poisonous mushroom, contains gyromitrin toxin, which causes epileptogenic neurotoxicity and hemolytic disease. This study aimed to establish a rapid and visual method of G. infula identification based on loop-mediated isothermal amplification (LAMP). A set of specific LAMP primers was designed, and its specificity in G. infula was confirmed against various mushroom species, including its closely related species and other macrofungi. The sensitivity assay showed that the minimum concentration of genomic DNA detected by LAMP was 1 ng/μl. The method’s applicability was conducted by preparing mushroom samples that were boiled and digested in artificial gastric juice. The results showed that the content as low as 1% G. infula can be successfully detected. This method can be completed within 90 min, and the reaction results can be directly observed by the naked eyes. Hence, the identification method of G. infula established based on LAMP in this study is accurate, rapid, sensitive, and low-cost, which is required for clinical treatment or forensic analysis when mushroom poisoning occurs.

Enteroviral Infections in the First Three Months of Life

Enteroviruses (EVs) are an important source of infection in the paediatric age, with most cases concerning the neonatal age and early infancy. Molecular epidemiology is crucial to understand the circulation of main serotypes in a specific area and period due to their extreme epidemiological variability. The diagnosis of EVs infection currently relies on the detection of EVs RNA in biological samples (usually cerebrospinal fluid and plasma, but also throat swabs and feces) through a polymerase chain reaction assay. Although EVs infections usually have a benign course, they sometimes become life threatening, especially when symptoms develop in the first few days of life. Mortality is primarily associated with myocarditis, acute hepatitis, and multi-organ failure. Neurodevelopmental sequelae have been reported following severe infections with central nervous system involvement. Unfortunately, at present, the treatment of EVs infections is mainly supportive. The use of specific antiviral agents in severe neonatal infections has been reported in single cases or studies including few neonates. Therefore, further studies are needed to confirm the efficacy of these drugs in clinical practice.

Rapid molecular diagnostics of large deletional β0-thalassemia (3.5 kb and 45 kb) using colorimetric LAMP in various thalassemia genotypes

Background

β-thalassemia is an inherited disorder that is reported worldwide. Two common β⁰-thalassemia mutations (3.5 kb and 45 kb deletions) are prevalent in Southeast Asia and Thailand. Identification of these defects is essential to population screening and prenatal diagnosis. We aimed to develop colorimetric LAMP based on a phenol red indicator and validate it on various thalassemia genotypes.

Method

Colorimetric LAMP assays for detecting β⁰-thalassemia 3.5- and 45-kb deletions were developed and validated on 254 routine clinical samples. The results of the assays could be interpreted by the naked eye and compared with the gold standard gap-PCR.

Results

A total of 254 samples related to seven phenotypes and 27 different genotype groups showed 100% concordance between the colorimetric LAMP assays and gap-PCR for detecting β⁰-thalassemia (3.5- and 45-kb deletions). The sensitivity, specificity, NPV, and PPV were calculated as 100% for both β⁰-thalassemia 3.5- and 45-kb deletion detection. The comparison of the usefulness of colorimetric LAMP assays and conventional methods was demonstrated in this study.

Conclusions

The developed colorimetric LAMP assays are rapid, simple, and highly cost effective and can be interpreted by the naked eye. These assays should be applied for screening deletional β⁰-thalassemia in routine settings or small community hospitals in remote areas where thalassemia is highly heterogeneous.