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High throughput multiplex real time PCR assay for the simultaneous quantification of DNA and RNA viruses infecting cassava plants

High throughput multiplex real time PCR assay for the simultaneous quantification of DNA and RNA viruses infecting cassava plants

Otti, Gerald, Bouvaine, Sophie, Kimata, Bernadetha, Mkamillo, Geoffrey, Kumar, Lava, Tomlins, Keith and Maruthi, M.N. ORCID: 0000-0002-8060-866X (2016) High throughput multiplex real time PCR assay for the simultaneous quantification of DNA and RNA viruses infecting cassava plants. Journal Of Applied Microbiology (Online first). ISSN 1364-5072 (Print), 1365-2672 (Online) (doi:https://doi.org/10.1111/jam.13043)

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Abstract

Aims: To develop a multiplex TaqMan-based real-time PCR assay (qPCR) for the simultaneous detection and quantification of both RNA and DNA viruses affecting cassava (Manihot esculenta) in eastern Africa.

Methods and Results: The diagnostic assay was developed for two RNA viruses; Cassava brown streak virus (CBSV) and Uganda cassava brown streak virus (UCBSV) and two predominant DNA viruses; African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV), which cause the economically important cassava brown streak disease (CBSD) and cassava mosaic disease (CMD), respectively. Our method, developed by analysing PCR products of viruses, was highly sensitive to detect target viruses from very low quantities of 4 to 10 femtograms. Multiplexing did not diminish the sensitivity or accuracy compared to uniplex alternatives. The assay reliably detected and quantified four cassava viruses in field samples where CBSV and UCBSV synergy was observed in majority of mixed-infected varieties.

Conclusions: We have developed a high-throughput qPCR diagnostic assay capable of specific and sensitive quantification of predominant DNA and RNA viruses of cassava in eastern Africa.

Significance and Impact of Study: The qPCR methods are a great improvement on the existing methods and can be used for monitoring virus spread as well as for accurate evaluation of the cassava varieties for virus resistance.

Item Type: Article
Additional Information: This is the peer reviewed version of the following article: High throughput multiplex real time PCR assay for the simultaneous quantification of DNA and RNA viruses infecting cassava plants, which has been published in final form at http://dx.doi.org/10.1111/jam.13043 . This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving
Uncontrolled Keywords: Cassava diseases, Virus detection and quantification, TaqMan assays, Real-time PCR
Faculty / Department / Research Group: Faculty of Engineering & Science > Natural Resources Institute > Agricultural Biosecurity Research Group
Last Modified: 02 May 2017 15:59
Selected for GREAT 2016: None
Selected for GREAT 2017: GREAT b
Selected for GREAT 2018: None
Selected for GREAT 2019: None
URI: http://gala.gre.ac.uk/id/eprint/14252

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