High-Throughput Sequencing Reveals Further Diversity of Little Cherry Virus 1 with Implications for Diagnostics

Abstract

Little cherry virus 1 (LChV1, Velarivirus, Closteroviridae) is a widespread pathogen of sweet or sour cherry and other Prunus species, which exhibits high genetic diversity and lacks a putative efficient transmission vector. Thus far, four distinct phylogenetic clusters of LChV1 have been described, including isolates from different Prunus species. The recent application of high throughput sequencing (HTS) technologies in fruit tree virology has facilitated the acquisition of new viral genomes and the study of virus diversity. In the present work, several new LChV1 isolates from different countries were fully sequenced using different HTS approaches. Our results reveal the presence of further genetic diversity within the LChV1 species. Interestingly, mixed infections of the same sweet cherry tree with different LChV1 variants were identified for the first time. Taken together, the high intra-host and intra-species diversities of LChV1 might affect its pathogenicity and have clear implications for its accurate diagnostics.

High-Throughput Sequencing Assists Studies in Genomic Variability and Epidemiology of Little Cherry Virus 1 and 2 infecting Prunus spp. in Belgium

“…For LChV1, maximum likelihood phylogenetic trees derived from the aligned partial RdRp, CP and complete genome nucleotide sequences from our study and from NCBI provided key information about their relationship within the LChV-1 group. Firstly, according to RdRp and CP nt sequences and using the same readily published phylogenetic methodology [2], we could reconstruct the entire LChV-1 phylogenetic landscape with the nt sequence of all LChV-1 Belgian isolates grouped into two distant large sub-clusters, closely related (97%–100% nt identity) to other GenBank sequences of LChV-1 from Greece (No2ISTO, HG792418) and Germany (V2356, JX669615) belonging to Group 1 and 2 (Figure 1 and Figure S2), in accordance with earlier studies [2,36,41]. Secondly, given the extensive spread of these notably divergent LChV-1 isolates infecting different Prunus species across Belgium and the lack of congruence according to the geographic or host-plant origin, these observations suggest that the virus was not recently introduced to Belgium.…”

“…All other sampled Prunus species were confirmed to be latently infected. Their etiology varied considerably between scion and rootstock varieties and also according to season, year of sampling and sometimes co-infection as observed in earlier reports [2,3,8,21,22,27,28,29,30,31,32,33,34,35,36,41].…”

“…The wide intra- and inter-host genetic diversity of LChV-1 and LChV-2 has been characterized only in a few countries [2,3,4,27,28,29,30,31,32,33,34,35,36]. Both viruses are confirmed to be present in Belgium, however no comprehensive phylogenetic characterization of the LChD has been published so far.…”

The population structure of Rose rosette virus in the USA

“…High-throughput sequencing (HTS) is a valuable tool, providing low-cost, efficient sequencing for diverse applications such as ocean microbiome and gut microflora [5]. In plant virology, HTS is mostly applied in virus detection and discovery [6][7][8][9][10], but a major drawback in the methodology is the output of a high percentage of non-viral sequence, limiting sequencing depth and identification of virus variants [11,12]. HTS of PCR amplicons minimizes host sequence interference and has been used successfully to study the population structure of fungal and animal viruses [13][14][15][16].…”

Comprehensive Real-Time RT-PCR Assays for the Detection of Fifteen Viruses Infecting Prunus spp.

“…The genetic diversity of plant viruses is well known (reviewed in [3,4]). For example, divergent variants of LChV-1 and LChV-2 have been characterized via high throughput sequencing (HTS), which affects the epidemiology and symptomatology associated with these viruses [5,6]. PNRSV and PDV isolates can be classified in several phylogroups based on their coat protein (CP) or RNA-dependent RNA polymerase (RdRp) genes [7,8].…”