Book Chapter

Development and Validation of Real-Time RT-LAMP Assays for the Specific Detection of Zika Virus

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

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.

Keywords
Zika virus; Isothermal amplification; Real-time detection; RT-LAMP; LAVA software; Primer Explorer V4

StatusPublished
FundersEuropean Commission (Horizon 2020)
Title of seriesMethods in Molecular Biology
Number in series2142
Publication date31/12/2020
Publication date online05/05/2020
URLhttp://hdl.handle.net/1893/31109
PublisherSpringer
Place of publicationNew York
ISSN of series1940-6029
ISBN9781071605806
eISBN9781071605813