Development of a loop-mediated isothermal amplification assay for rapid detection of BK virus.

Department of Pediatrics, Children's Hospital of Pittsburgh, 3705 Fifth Avenue, Pittsburgh, PA 15213, USA.
Journal of Clinical Microbiology (Impact Factor: 4.23). 06/2007; 45(5):1581-7. DOI: 10.1128/JCM.01024-06
Source: PubMed

ABSTRACT Loop-mediated isothermal amplification (LAMP) is a novel method for rapid amplification of DNA. Its advantages include rapidity and minimal equipment requirement. The LAMP assay was developed for BK virus (BKV), which is a leading cause of morbidity in renal transplant recipients. The characteristics of the assay, including its specificity and sensitivity, were evaluated. BKV LAMP was performed using various incubation times with a variety of specimens, including unprocessed urine and plasma samples. A ladder pattern on gel electrophoresis, typical of successful LAMP reactions, was observed specifically only for BKV and not for other viruses. The sensitivity of the assay with 1 h of incubation was 100 copies/tube of a cloned BKV fragment. Additionally, a positive reaction was visually ascertained by a simple color reaction using SYBR green dye. BKV LAMP was also successful for urine and plasma specimens without the need for DNA extraction. Due to its simplicity and specificity, the LAMP assay can potentially be developed for "point of care" screening of BKV.

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    MethodsX. 10/2014; 1:137-143.
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    ABSTRACT: This study investigated loop-mediated isothermal amplification (LAMP) detection of Plasmodium falciparum and Plasmodium vivax in urine and saliva of malaria patients. From May to November 2011, 108 febrile patients referred to health centers in Sistan and Baluchestan Province of south-eastern Iran participated in the study. Saliva, urine, and blood samples were analyzed with nested PCR and LAMP targeting the species-specific nucleotide sequence of small subunit ribosomal RNA gene (18S rRNA) of P. falciparum and P. vivax and evaluated for diagnostic accuracy by comparison to blood nested PCR assay. When nested PCR of blood is used as standard, microscopy and nested PCR of saliva and urine samples showed sensitivity of 97.2%, 89.4% and 71% and specificity of 100%, 97.3% and 100%, respectively. LAMP sensitivity of blood, saliva, and urine was 95.8%, 47% and 29%, respectively, whereas LAMP specificity of these samples was 100%. Microscopy and nested PCR of saliva and LAMP of blood were comparable to nested PCR of blood (к=0.95, 0.83, and 0.94, respectively), but agreement for nested PCR of urine was moderate (к=0.64) and poor to fair for saliva LAMP and urine LAMP (к=0.38 and 0.23 respectively). LAMP assay showed low sensitivity for detection of Plasmodium DNA in human saliva and urine compared to results with blood and to nested PCR of blood, saliva, and urine. However, considering the advantages of LAMP technology and of saliva and urine sampling, further research into the method is worthwhile. LAMP protocol and precise preparation protocols need to be defined and optimized for template DNA of saliva and urine.
    Acta tropica 04/2014; · 2.79 Impact Factor
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    ABSTRACT: Malaria can be diagnosed in saliva and urine using mitochondrial PCR detection of Plasmodium DNA. Blood, saliva and urine were collected from 99 febrile patients referred to health centers in Sistan and Baluchestan Province, southeastern Iran, from May to November 2011. The mitochondrial cytochrome b gene of Plasmodium falciparum and Plasmodium vivax was targeted in saliva, urine and blood samples using nested PCR. Nested PCR proved to be more sensitive than microscopy for the diagnosis of sub-microscopic and mixed-species infections. The results of nested PCR amplifications of saliva and urine samples showed the same specificity of 97% and sensitivity of 91% and 70%, respectively. Nested PCR amplifications of saliva samples and microscopy showed the greatest area under the receiver operating characteristic (ROC) curve and were more accurate than nested PCR amplifications of urine samples. Nested PCR amplification of saliva samples showed good levels of detection of mitochondrial Plasmodium DNA as compared to nested PCR of blood (к=0.84; AUC=0.94), which was used as a reference standard. Based on the results of nested PCR as well as the advantages of saliva sampling, we suggest that saliva could be an alternative to blood, in malaria diagnosis, in cases where repeat sampling is required. Further studies are needed to validate these findings.
    Transactions of the Royal Society of Tropical Medicine and Hygiene 04/2014; · 1.93 Impact Factor

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