WarmStart colorimetric RT-LAMP for the rapid, sensitive and specific detection of Enteroviruses A-D targeting the 5'UTR region.
Enteroviruses
RT-LAMP
colorimetric visualization
detection
isothermal amplification
Journal
Journal of applied microbiology
ISSN: 1365-2672
Titre abrégé: J Appl Microbiol
Pays: England
ID NLM: 9706280
Informations de publication
Date de publication:
Jan 2021
Jan 2021
Historique:
received:
02
05
2020
revised:
17
06
2020
accepted:
02
07
2020
pubmed:
9
7
2020
medline:
14
1
2021
entrez:
9
7
2020
Statut:
ppublish
Résumé
The aim of the present study was to develop a colorimetric LAMP assay for the detection of enteroviruses belonging to species A-D targeting the 5' untranslated region (5' UTR) of enteroviruses genome. The RNA was converted to cDNA by the reverse transcriptase and then amplified via LAMP by the WarmStart®Bst DNA polymerase, simultaneously in a single reaction tube, so we shortened the reaction time to 50 min. The sensitivity of the assay regarding Enterovirus B, C and D was determined to be 0·30 CCID This assay can be used as a diagnostic tool for the rapid, sensitive and specific detection of enteroviruses, easily implemented in small clinical and research laboratories since LAMP amplicons were visualized by colour changes eliminating the requirement for post-amplification processing steps. We developed a colorimetric assay ideal for field situations for the detection of enteroviruses, by targeting the 5' UTR. This assay demonstrated high specificity and sensitivity, based on its performance on 45 EV A-D reference strains, on 20 EV B clinical isolates and on three non-enteroviral RNA viruses.
Substances chimiques
5' Untranslated Regions
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
292-301Informations de copyright
© 2020 The Society for Applied Microbiology.
Références
Arita, M., Ling, H., Yan, D., Nishimura, Y., Yoshida, H., Wakita, T. and Shimizu, H. (2009) Development of a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) system for a highly sensitive detection of enterovirus in the stool samples of acute flaccid paralysis cases. BMC Infect Dis 9, 208.
Blomstrom, A.L., Hakhverdyan, M., Reid, S.M., Dukes, J.P., King, D.P., Belak, S. and Berg, M. (2008) A one-step reverse transcriptase loop mediated isothermal amplification assay for simple and rapid detection of swine vesicular disease virus. J Virol Methods 147, 188-193.
Bolanaki, E., Kottaridi, C., Markoulatos, P., Margaritis, L. and Katsorchis, T. (2005) A comparative amplification of five different genomic regions on Coxsackie A and B viruses. implications in clinical diagnostics. Mol Cell Probes 19, 127-135.
Casas, I., Powell, L., Klapper, P.E. and Cleator, G.M. (1995) New method for the extraction of viral RNA and DNA from cerebrospinal fluid for use in the polymerase chain reaction assay. J Virol Methods 53, 25-36.
Daskou, M., Dimitriou, T.G., Kouklamani-Giannouli, G., Nikolaidis, M., Mossialos, D., Amoutzias, G.D. and Markoulatos, P. (2020) Development of a reverse transcription loop-mediated isothermal amplification assay (RT-LAMP) that detects enteroviruses by targeting the highly conserved 5′-UTR region. Virus Genes 56, 194-201.
Ding, X., Nie, K., Shi, L., Zhang, Y., Guan, L., Zhang, D., Qi, S. and Ma, X. (2014) Improved detection limit in rapid detection of human enterovirus 71 and coxsackievirus A16 by a novel reverse transcription-isothermal multiple-self-matching-initiated amplification assay. J Clin Microbiol 52, 1862-1870.
Fischbach, J., Xander, N.C., Frohme, M. and Glokler, J.F. (2015) Shining a light on LAMP assays-a comparison of LAMP visualization methods including the novel use of berberine. Biotechniques 58, 189-194.
Hu, X., Zhang, Y., Zhou, X., Xu, B., Yang, M., Wang, M., Zhang, C., Li, J. et al. (2012) Simultaneously typing nine serotypes of enteroviruses associated with hand, foot, and mouth disease by a GeXP analyzer-based multiplex reverse transcription-PCR assay. J Clin Microbiol 50, 288-293.
Hymas, W.C., Aldous, W.K., Taggart, E.W., Stevenson, J.B. and Hillyard, D.R. (2008) Description and validation of a novel real-time RT PCR enterovirus assay. Clin Chem 54, 406-413.
Jaramillo-Gutierrez, G., Benschop, K.S., Claas, E.C., Jong, A.S., Van Loon, A.M., Pas, S.D. et al. (2013) September through October 2010 multi-centre study in the Netherlands examining laboratory ability to detect enterovirus 68, an emerging respiratory pathogen. J. Virol. Methods 190, 53-62.
Knipe, D.M. and Howley, P.M. (2013) Fields Virology, 6th edn. Philadelphia, PA: Lippincott Williams and Wilkins.
Kottaridi, C., Bolanaki, E. and Markoulatos, P. (2004) Amplification of Echoviruses genomic regions by different RT-PCR protocols-a comparative study. Mol Cell Probes 18(4), 263-269.
Kottaridi, C., Bolanaki, E., Siafakas, N. and Markoulatos, P. (2005) Evaluation of seroneutralization and molecular diagnostic methods for echovirus identification. Diagn Microbiol Infect Dis 53, 113-119.
Kottaridi, C., Bolanaki, E., Mamuris, Z., Stathopoulos, C. and Markoulatos, P. (2006) Molecular phylogeny of PV1, 2A and 2B genes of echovirus isolates: epidemiological linkage and observations on genetic variation. Arch Virol 151, 1117-1132.
Kyriakopoulou, Z., Dedepsidis, E., Pliaka, V., Mastorakos, P., Stamati, A., Pratti, A., Levidiotou-Stefanou, S. and Markoulatos, P. (2010) Molecular identification and full genome analysis of an echovirus 7 strain isolated from the environment in Greece. Virus Genes 40, 183-192.
Kyriakopoulou, Z., Dedepsidis, E., Pliaka, V., Tsakogiannis, D., Ruether, I.G., Krikelis, A. and Markoulatos, P. (2011) Complete nucleotide sequence analysis of the VP1 genomic region of Echoviruses 6 isolated from sewage in Greece revealed 98% similarity with Echoviruses 6 that were characterized from an aseptic meningitis outbreak 1 year later. Clin Microbiol Infect 17:1170-1173.
Lang, M., Mirand, A., Savy, N., Henquell, C., Maridet, S., Perignon, R. et al. (2014) Acute flaccid paralysis following enterovirus D68 associated pneumonia, France. Euro Surveill 19, 2-6.
Lee, H.K. and Jeong, Y.S. (2004) Comparison of total culturable virus assay and multiplex integrated cell culture-PCR for reliability of waterborne virus detection. Appl Environ Microbiol 70, 3632-3636.
Lefkowitz, E.J., Dempsey, D.M., Hendrickson, R.C., Orton, R.J., Siddell, S.G. and Smith, D.B. (2017) Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic Acids Res 46, 708-717.
Nagamine, K., Hase, T. and Notomi, T. (2002) Accelerated reaction by loop-mediated isothermal amplification using loop primers. Mol Cell Probes 16, 223-229.
Notomi, T., Okayama, H., Masubuchi, H., Yonekawa, T., Watanabe, K., Amino, N. and Hase, T. (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28, e63.
Notomi, T., Mori, Y., Tomita, N. and Kanda, H. (2015) Loop-mediated isothermal amplification (LAMP): principle, features, and future prospects. J Microbiol 53, 1-5.
Pallansch, M., Oberste, S. and Whitton, L.J. (2013) Enteroviruses: polioviruses, coxsackieviruses, echoviruses, and newer enteroviruses. In Fields' Virology ed. Knipe, D.M. and Howley, P.M. 6th edn. Philadelphia, PA: Lippincott Williams &Wilkins.
Papaventsis, D., Siafakas, N., Markoulatos, P., Papageorgiou, G.T., Kourtis, C., Chatzichristou, E., Economou, C. and Levidiotou, S. (2005) Membrane adsorption with direct cell culture combined with reverse transcription-PCR as a fast method for identifying enteroviruses from sewage. Appl Environ Microbiol 71, 72-79.
Rohll, J.B., Percy, N., Lev, R., Evans, D.J., Almond, J.W. and Barclay, W.S. (1994) The 5΄-untranslated regions of Picornavirus RNAs contain independent functional domains essential for RNA replication and translation. J. Virol 68(7), 4389-4391.
Schuffenecker, I., Mirand, A., Josset, L., Henquell, C., Hecquet, D., Pilorge, L. et al. (2016) Epidemiological and clinical characteristics of patients infected with enterovirus D68, France. Euro Surveill 21, 4-15.
Shirato, K., Semba, S., El-Kafrawy, S.A., Hassan, A.M., Tolah, A.M., Takayama, I., Kageyama, T., Notomi, T. et al. (2018) Development of fluorescent reverse transcription loop-mediated isothermal amplification (RT-LAMP) using quenching probes for the detection of the Middle East respiratory syndrome coronavirus. J Virol Methods 258, 41-48.
Solomon, T., Lewthwaite, P., Perera, D., Cardosa, M.J., McMinn, P. and Ooi, M.H. (2010) Virology, epidemiology, pathogenesis, and control of enterovirus 71. Lancet Infect Dis 10, 778-790.
Suresh, S., Forgie, S. and Robinson, J. (2017) Non-polio enterovirus detection with acute flaccid paralysis: a systematic review. J Med Virol 90, 3-7.
Tanner, N.A., Zhang, Y. and Evans, T.C. Jr (2015) Visual detection of isothermal nucleic acid amplification using pH-sensitive dyes. Biotechniques 58, 59-68. https://doi.org/10.2144/000114253.
Tsai, J.D., Tsai, H.J., Lin, T.H., Chang, Y.Y., Yang, S.H. and Kuo, H.T. (2014) Comparison of the detection rates of RT-PCR and virus culture using a combination of specimens from multiple sites for enterovirus-associated encephalomyelitis during enterovirus 71 epidemic. Jpn J Infect Dis 67, 333-338.
Wong, Y.P., Othman, S., Lau, Y.L., Radu, S. and Chee, H.Y. (2018). Loop-mediated isothermal amplification (LAMP): a versatile technique for detection of micro-organisms. J Appl Microbiol 124:626-643.
World Health Organization (2004) Polio Laboratory Manual, 4th edn. Switzerland: WHO IVB/04.10, Geneva.