The Incidence and Genetic Diversity of Apple Mosaic Virus (ApMV) and Prune Dwarf Virus (PDV) in Prunus Species in Australia.

Wycliff Kinoti,Narelle Nancarrow,Brendan Rodoni,Fiona Constable,Kim Plummer

doi:10.3390/v10030136

Wycliff Kinoti, Narelle Nancarrow + Show 3 more

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https://doi.org/10.3390/v10030136

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Journal: Viruses	Publication Date: Mar 19, 2018
Citations: 8	License type: CC BY 4.0

Affiliation: La Trobe University, AgriBio, Agriculture Victoria

Abstract

Apple mosaic virus (ApMV) and prune dwarf virus (PDV) are amongst the most common viruses infecting Prunus species worldwide but their incidence and genetic diversity in Australia is not known. In a survey of 127 Prunus tree samples collected from five states in Australia, ApMV and PDV occurred in 4 (3%) and 13 (10%) of the trees respectively. High-throughput sequencing (HTS) of amplicons from partial conserved regions of RNA1, RNA2, and RNA3, encoding the methyltransferase (MT), RNA-dependent RNA polymerase (RdRp), and the coat protein (CP) genes respectively, of ApMV and PDV was used to determine the genetic diversity of the Australian isolates of each virus. Phylogenetic comparison of Australian ApMV and PDV amplicon HTS variants and full length genomes of both viruses with isolates occurring in other countries identified genetic strains of each virus occurring in Australia. A single Australian Prunus infecting ApMV genetic strain was identified as all ApMV isolates sequence variants formed a single phylogenetic group in each of RNA1, RNA2, and RNA3. Two Australian PDV genetic strains were identified based on the combination of observed phylogenetic groups in each of RNA1, RNA2, and RNA3 and one Prunus tree had both strains. The accuracy of amplicon sequence variants phylogenetic analysis based on segments of each virus RNA were confirmed by phylogenetic analysis of full length genome sequences of Australian ApMV and PDV isolates and all published ApMV and PDV genomes from other countries.

Highlights

Apple mosaic virus (ApMV) and Prune dwarf virus (PDV) are members of the genus Ilarvirus, which have a positive-sense, single-stranded tripartite RNA genome organization composed of RNA1, RNA2, and RNA3 [1]
prune dwarf virus (PDV) strains occurring in Australian Prunus trees
The low incidence of apple mosaic virus (ApMV) (3%) observed amongst the 127 Australian Prunus tree samples is similar to findings of several studies in other countries [2,35,36,37]

Summary

Introduction

Apple mosaic virus (ApMV) and Prune dwarf virus (PDV) are members of the genus Ilarvirus (familyBromoviridae), which have a positive-sense, single-stranded tripartite RNA genome organization composed of RNA1, RNA2, and RNA3 [1]. RNA3 is bi-cistronic encoding for the movement protein (MP) and coat protein (CP) that is expressed via sub-genomic RNA4 [2,3]. ApMV and PDV infect a wide variety of herbaceous and woody hosts, including Prunus species, and can cause diseases of economic importance [7]. ApMV infection causes significant crop yield reduction of up to 25% in some commercial Prunus species [10]. PDV infection can induce a variety of symptoms which may include chlorosis, mosaic, ringspot symptoms on leaves, and stunting [7]. Amongst the Prunus infecting ilarviruses, PDV has the most significant economic impact with infections attributed to yield losses of up to 100% in some commercial crops [7,11]

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