Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/31109
Appears in Collections:Aquaculture Book Chapters and Sections
Title: Development and Validation of Real-Time RT-LAMP Assays for the Specific Detection of Zika Virus
Author(s): Lopez-Jimena, Benjamin
Bakheit, Mohammed
Bekaert, Michaël
Harold, Graham
Frischmann, Sieghard
Fall, Cheikh
Diagne, Cheikh Tidiane
Faye, Oumar
Faye, Ousmane
Sall, Amadou Alpha
Weidmann, Manfred
Contact Email: m.w.weidmann@stir.ac.uk
Editor(s): Kobinger, Gary
Racine, Trina
Sponsor: European Commission (Horizon 2020)
Citation: Lopez-Jimena B, Bakheit M, Bekaert M, Harold G, Frischmann S, Fall C, Diagne CT, Faye O, Faye O, Sall AA & Weidmann M (2020) Development and Validation of Real-Time RT-LAMP Assays for the Specific Detection of Zika Virus. In: Kobinger G & Racine T (eds.) Zika Virus: Methods and Protocols. Methods in Molecular Biology, 2142. New York: Springer, pp. 147-164. https://doi.org/10.1007/978-1-0716-0581-3_13
Keywords: Zika virus
Isothermal amplification
Real-time detection
RT-LAMP
LAVA software
Primer Explorer V4
Issue Date: 2020
Series/Report no.: Methods in Molecular Biology, 2142
Abstract: Two one-step real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for the detection of Zika virus (ZIKV) were developed, based on two different primer design approaches: (1) open source, based on a combination of sequence diversity clustering (phylogeny and principal component analysis) and LAVA algorithm, using 45 whole genome ZIKV sequences retrieved from the National Center for Biotechnology Information (NCBI) database; (2) standard software for LAMP primer design (Primer Explorer V4), using 59 sequences of the ZIKV 3′ UTR. The assays were firstly evaluated with External Quality Assessment panels from INSTAND e.V. (Germany) and EVD-LabNet (The Netherlands) including 4 and 12 unknown samples, respectively, and secondly, with 9 human, mosquito, and monkey ZIKV isolates from Africa (Senegal, Ivory Coast, and Uganda) and America (Brazil). The limit of detection as determined by probit analysis was 181 molecules for both RT-LAMP assays, and 100% reproducibility in the assays was obtained for 103 molecules (4/8 repetitions were positive for 102 molecules). Both assays were specific, amplifying only ZIKV RNA and not cross-detecting other arboviruses included in this study.
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DOI Link: 10.1007/978-1-0716-0581-3_13

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