A method for simultaneous detection and identification of Brazilian dog- and vampire bat-related rabies virus by reverse transcription loop-mediated isothermal amplification assay

Saitou, Yasumasa; Kobayashi, Yuki; Hirano, Shinji; Mochizuki, Nobuyuki; Itou, Takuya; Ito, Fumio; Sakai, Takeo

doi:10.1016/j.jviromet.2010.04.008

Cited by 28 publications

(19 citation statements)

References 17 publications

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“…LAMP is being used increasingly for rapid detection and typing of emerging viruses (10,12,20,21). The use of reverse transcription (RT)-LAMP with HNB dye for visual detection of pandemic influenza A H1N1 virus 2009 was developed recently in our laboratory (16).…”

Section: Discussionmentioning

confidence: 99%

Visual Detection of High-Risk Human Papillomavirus Genotypes 16, 18, 45, 52, and 58 by Loop-Mediated Isothermal Amplification with Hydroxynaphthol Blue Dye

et al. 2011

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A simple, rapid, sensitive, qualitative, colorimetric loop-mediated isothermal amplification (LAMP) with hydroxynaphthol blue dye (HNB) was established to detect high-risk human papillomavirus (HPV) genotypes 16, 18, 45, 52, and 58. All initial validation studies with the control DNA proved to be type specific. The colorimetric type-specific LAMP assay could achieve a sensitivity of 10 to 100 copies at 63°C for 65 min, comparable to that of real-time PCR. In order to evaluate the reliability of HPV type-specific LAMP, the assay was further evaluated with HPV DNAs from a panel of 294 clinical specimens whose HPV status was previously determined with a novel one-step typing method with multiplex PCR. The tested panel comprised 108 HPV DNA-negative samples and 186 HPV-DNA-positive samples of 14 genotypes. The results showed that the sensitivity of HPV type-specific LAMP for HPV types 16, 18, 45, 52, and 58 was 100%, 100%, 100%, 100%, and 100%, respectively, and the specificity was 100%, 98.5%, 100%, 98.8%, and 99.2%, respectively, compared with a novel one-step typing method with multiplex PCR. No cross-reactivity with other HPV genotypes was observed. In conclusion, this qualitative and colorimetric LAMP assay has potential usefulness for the rapid screening of HPV genotype 16, 18, 45, 52, and 58 infections, especially in resource-limited hospitals or rural clinics of provincial and municipal regions in China.It is well established that virtually all cervical cancers are caused by persistent high-risk oncogenic human papillomavirus (HPV) infections in the cervix. Thus, cervical screening could be improved by testing for the DNA of high-risk types of HPV as a primary screening tool (3, 9, 24). So far, at least 14 high-risk HPV genotypes have been shown to cause cervical cancer; those most important for cervical cancer are HPV types 16, 18, 45, 31, 33, 52, 58, and 35 (6, 7, 26). HPV16 is by far the predominant type, causing more than 50% of cancers; HPV18 follows, causing 14%; and HPV45 causes approximately 2.8%. These genotypes are highly prevalent in all regions of the world and account for approximately 70% of all cancers of the cervix (2, 13, 25). HPV types 52 and 58 are rare in Western countries; however, they are prevalent in Asian populations, especially in China (5,14,15,28,29).Technologies available for HPV genotyping vary by method and platform and may offer type-specific characterization for a multitude of different high-and low-risk HPV types. For example, The Qiagen Hybrid Capture 2 HPV DNA (HC2) test and the Roche Amplicor HPV test (Amplicor) detect the DNA of 13 high-risk HPV types. The Linear Array HPV genotyping test allows for the discrimination of 37 HPV genotypes. The PapilloCheck HPV screening test (Greiner Bio-One GmbH, Frickenhausen, Germany) is a PCR-based DNA microarray system for the detection and identification of 24 HPV genotypes (4, 7, 13, 25). However, these methods might not be suitable in primary clinical settings in developing countries or for field use, because of the sophisticated ...

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Section: Discussionmentioning

confidence: 99%

Visual Detection of High-Risk Human Papillomavirus Genotypes 16, 18, 45, 52, and 58 by Loop-Mediated Isothermal Amplification with Hydroxynaphthol Blue Dye

et al. 2011

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“…Our data suggested that these isolates were similar in genetic characteristics throughout the entire genomes and that phylogenetic analyses based on complete genome should be continued to subdivide closely related isolates. Additionally, it seems that current genetic diagnosis methods, such as multiplex-RT-PCR and RT-LAMP, are adapted to be common to between these RABV from genetics standpoint [26,27]. Finally, these data may help in the prevention and control of rabies by facilitating multiple functional analyses based on reverse genetics and the development of novel genetic probes for diagnosis and therapeutics.…”

Section: Discussionmentioning

confidence: 99%

Determination and Molecular Analysis of the Complete Genome Sequence of Two Wild-Type Rabies Viruses Isolated from a Haematophagous Bat and a Frugivorous Bat in Brazil

Mochizuki

Kobayashi

Sato

et al. 2011

The Journal of Veterinary Medical Science

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ABSTRACT. The complete genome sequences of two Brazilian wild-type rabies viruses (RABV), a BR-DR1 isolate from a haematophagous bat (Desmodus rotundus) and a BR-AL1 isolate from a frugivorous bat (Artibeus lituratus), were determined. The genomes of the BR-DR1 and BR-AL1 had 11,923 and 11,922 nt, respectively, and both encoded the five standard genes of rhabdoviruses. The complete nucleotide sequence identity between the BR-DR1 and BR-AL1 isolates was 97%. The BR-DR1 and BR-AL1 isolates had some conserved functional sites revealed by the fixed isolates, whereas both isolates had unique amino acid substitutions in the antigenic region IV of the nucleocapsid gene. Therefore, it is speculated that both isolates were nearly identical in virologic character. According to our phylogenetic analysis based on the complete genomes, both isolates belonged to genotype 1, and to the previously defined "vampire batrelated RABV lineage" which consisted of mainly D. rotundus-and A. lituratus-isolates; however, a branch pattern with high bootstrap values suggested that BR-DR1 was more closely related to the 9001FRA isolate, which was collected from a dog bitten by a bat in French Guiana, than to BR-AL1. This result suggests that the vampire bat-related RABV lineage includes Brazilian vampire bat and Brazilian frugivorous bat RABV and is further divided into Brazilian vampire bat and Brazilian frugivorous bat RABV sub-lineages. The phylogenetic analysis based on the complete genomes was valuable in discriminating among very closely related isolates.KEY WORDS: complete genome, frugivorous bat, genetic analysis, haematophagous bat, wild-type rabies virus.

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“…Due to its enormous rate of amplification paired with a very high specificity, sensitivity, rapidity and low artifact susceptibility], the method together with its modifications have been strongly recommended for detection of a great number of strains of bacteria as well as viruses worldwide [14][15][16][17]. Although a large number of studies have been accomplished using LAMP or RT-LAMP including Potato virus Y [4], Potato Leafroll virus [18], Japanese yam mosaic potyvirus [19], Tomato Yellow Leaf Curl virus [20], Rabies virus [21], Macrobrachium rosenbergii nodavirus [22] and Cymbidium mosaic virus [23], all of which basically require more precise extraction protocol(s) about generating higher concentrations of DNA or RNA followed by the least amounts of probable contaminations which act as inhibitors in an amplification process. Notably, despite a few number of studies about immunocapture reverse transcription loopmediated isothermal amplification (IC-RT-LAMP) [17,24] because the technique has not been yet introduced for detection of PVY, an attempt was accordingly made to optimize a new protocol of it to save time and remove RNA extraction.…”

Section: Introductionmentioning

confidence: 99%

Colorimetric Immunocapture Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Rapid Detection of the Potato virus Y

Almasi¹

2013

J Plant Pathol Microbiol

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Loop-Mediated Isothermal Amplification (LAMP) assay is a novel technique for amplifying DNA under constant temperature, with high specificity, sensitivity, rapidity and efficiency. To diminish the time required for some diagnostic assays including Reverse Transcription PCR (RT-PCR), Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) and also DAS-ELISA into a minimum level, an innovative colorimetric IC-RT-LAMP and IC-RT-PCR protocol on the basis of Potato Virus Y (PVY) genome were used and optimized. Firstly, DAS-ELISA assay was performed to detect of the virus in a collection containing 95 suspicious samples. Lastly, five samples were detected as the positive samples. Then, the positive samples were verified by molecular methods. In this regard, all four RT-LAMP primers (i.e. F3, B3, FIP and BIP) together with RT-PCR primers (F and B) were selected on the basis of coat protein gene (CP) of PVY genome. Even though DAS-ELISA, RT-PCR and RT-LAMP assays could successfully detect positive infected plant samples, considering the time, safety, sensitivity, cost and simplicity, the last one was overall superior. Furthermore, the results demonstrated that the RT-LAMP assay was 100 times sensitive and 3 time faster compared to RT-PCR. LAMP assay was accomplished in the water bath either frees from any thermal cycler machine or sophisticated laboratories facility. Meanwhile, among six different visual dyes to accurately detect IC-RT-LAMP products, Hydroxynaphthol blue, GeneFinder TM and SYBR Green I could produce long stable colour change and brightness in a close tube-based approach to prevent cross-contamination risk, concluded eventually as the best ones. We accordingly propose this colorimetric assay as a highly reliable alternative viral recognition system regarding PVY recognition and probably other viral-based diseases.

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A method for simultaneous detection and identification of Brazilian dog- and vampire bat-related rabies virus by reverse transcription loop-mediated isothermal amplification assay

Cited by 28 publications

References 17 publications

Visual Detection of High-Risk Human Papillomavirus Genotypes 16, 18, 45, 52, and 58 by Loop-Mediated Isothermal Amplification with Hydroxynaphthol Blue Dye

Visual Detection of High-Risk Human Papillomavirus Genotypes 16, 18, 45, 52, and 58 by Loop-Mediated Isothermal Amplification with Hydroxynaphthol Blue Dye

Determination and Molecular Analysis of the Complete Genome Sequence of Two Wild-Type Rabies Viruses Isolated from a Haematophagous Bat and a Frugivorous Bat in Brazil

Colorimetric Immunocapture Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Rapid Detection of the Potato virus Y

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