Molecular and pathobiological characterization of 61 Potato mop‐top virus full‐length cDNAs reveals great variability of the virus in the centre of potato domestication, novel genotypes and evidence for recombination

Pruthvi Kalyandurg,Aderito Monjane,Giovanna Müller,Jan Kreuze,Ladislao Palomino,Eugene I Savenkov,Ian Barker,Nina I Lukhovitskaya,Carlos Chuquillanqui,Jose Fernando Gil,Betty Flores

doi:10.1111/mpp.12552

Abstract

SummaryThe evolutionary divergence of Potato mop‐top virus (PMTV), a tri‐partite, single‐stranded RNA virus, is exceptionally low, based on the analysis of sequences obtained from isolates from Europe, Asia and North America. In general, RNA viruses exist as dynamic populations of closely related and recombinant genomes that are subjected to continuous genetic variation. The reason behind the low genetic variation of PMTV remains unclear. The question remains as to whether the low variability is a shared property of all PMTV isolates or is a result of the limited number of isolates characterized so far. We hypothesized that higher divergence of the virus might exist in the Andean regions of South America, the centre of potato domestication. Here, we report high variability of PMTV isolates collected from 12 fields in three locations in the Andean region of Peru. To evaluate PMTV genetic variation in Peru, we generated full‐length cDNA clones, which allowed reliable comparative molecular and pathobiological characterization of individual isolates. We found significant divergence of the CP‐RT and 8K sequences. The 8K cistron, which encodes a viral suppressor of RNA silencing, was found to be under diversifying selection. Phylogenetic analysis determined that, based on the CP‐RT sequence, all PMTV isolates could be categorized into three separate lineages (clades). Moreover, we found evidence for recombination between two clades. Using infectious cDNA clones of the representatives of these two clades, as well as reassortants for the RNA‐CP genomic component, we determined the pathobiological differences between the lineages, which we coined as S (for severe) and M (for mild) types. Interestingly, all isolates characterized previously (from Europe, Asia and North America) fall into the S‐type clade, whereas most of the Peruvian isolates belong to the M‐type. Taken together, our results support the notion of the single introduction of PMTV from the centre of potato origin to Europe, and subsequent spread of the S‐type into Asia and USA. This is also supported by the suggested novel classification of isolates based on genetic constellations.

Highlights

RNA viruses within a host are faced with continuous changes in host gene expression and metabolism, and trigger numerous different antiviral reactions, e.g. RNA silencing
We speculated that the high genomic stability and low sequence variation of Potato mop-top virus (PMTV), to preserve genome integrity, might be a result of constraints imposed by the need to transport three RNA genomic components and the mode of PMTV movement in the plant as polar virions, which require rather intricate interactions between the minor coat protein, viral movement protein and, possibly, certain host factors at one extremity of the virus particles, leaving little room for variation (Torrance et al, 2009)
The same samples were analysed by enzyme-linked immunosorbent assay (ELISA) using monoclonal antisera against PMTV coat protein (CP)

Summary

Introduction

RNA viruses within a host are faced with continuous changes in host gene expression and metabolism, and trigger numerous different antiviral reactions, e.g. RNA silencing. In order to cope with antiviral responses and to evade them, RNA virus genomes exhibit extremely high mutation rates owing to the lack of proofreading activity and elevated error rate (1024–1026 errors per nucleotide) residue of their RNA-dependent RNA polymerases (RdRps). We speculated that the high genomic stability and low sequence variation of PMTV, to preserve genome integrity, might be a result of constraints imposed by the need to transport three RNA genomic components and the mode of PMTV movement in the plant as polar virions, which require rather intricate interactions between the minor coat protein ( known as CP-RT), viral movement protein and, possibly, certain host factors at one extremity of the virus particles, leaving little room for variation (Torrance et al, 2009). MOLECULARPLANTPATH OL OGYPUBL ISH EDBYBRIT IS HSOCIETYF OR P L AN TPATHOL OG Y AN D JO HNWILEY & SO NSLTD

Results

Discussion

Conclusion