Insights into the genetic diversity and evolution of Little cherry virus 1

Abstract

Little cherry virus 1 (LChV-1), a member of the recently proposed genus Velarivirus, is a sweet cherry pathogen that has been recently reported to infect other Prunus species and is associated with various plant disorders. In this work the incidence of the virus on its putative hosts and possible mechanisms driving its evolution were investigated. Due to problems encountered with LChV-1 detection, a new nested RT-PCR assay was developed and applied. The virus was found to be prevalent in cherry plantations in Greece and only occasionally detected in other Prunus species. Sequences corresponding to the partial RNA-dependent RNA polymerase (RdRp), heat-shock protein homologue (HSP70h) and coat protein (CP) genes were determined from Greek LChV-1 isolates originating from different hosts; these were analysed, along with published homologous genomic regions from other isolates. Phylogenetic analysis of the three genes revealed the segregation of four evolutionary distinct groups showing no host or geography-based clustering. Mean genetic distances among the four groups were high with the CP region showing the highest divergence, although intragroup variability levels were low. Nevertheless, estimations of the mean ratio of nonsynonymous substitutions per synonymous site to synonymous substitutions per synonymous site (dN/dS) for the partial RdRp, HSP70h and CP indicated that these genomic regions are under negative selection pressure. Interestingly, a recombination event was identified at the 3 0 end of RdRp on a Greek virus isolate, thus highlighting the role of this mechanism in the evolutionary history of LChV-1.

Updating the Quarantine Status of Prunus Infecting Viruses in Australia

“…Recombination is a powerful evolutionary driving force that results in the generation of new genotypes in RNA viruses [85,86]. Recombination events have been previously reported in RNA viruses in the family Betaflexiviridae and Closteroviridae [79,84,87,88] and in this study, multiple recombination events were identified amongst Australian isolates of ACLSV, CGRMV, CVA, LChV1, LChV2 and PBNSPaV. All the Australian recombinant isolates shared similar phylogenetic groupings with their major parental sequence which indicates close genetic connectivity within the population of these recombinants.…”

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

“…A third group is formed with the isolates Jerte, Ponferrada, Taian and YD [ 5 , 6 , 7 ]. Phylogenetic analyses using partial sequences of the RdRp, the HSP70h and the CP have classified LChV1 isolates into 4 clusters, including the three above mentioned ones [ 8 ]. Even though the intragroup diversity appears to be relatively low (3.3% to 7.4% in nts), the genetic distances between the different phylogenetic groups are higher (15% to 39% in nts) [ 3 , 5 , 6 , 7 , 8 ].…”

“…In the present study, seven novel LChV1 isolates were fully sequenced using HTS technologies. One of the isolates (G15 3) was recently partially characterized and shown to exhibit the highest genetic divergence from all so far known isolates [ 8 ]. The sequences of the other LChV1 isolates described herein were acquired during HTS analysis of several sweet or flowering cherry samples from three different countries.…”

Small RNA NGS Revealed the Presence of Cherry Virus A and Little Cherry Virus 1 on Apricots in Hungary

“…Infection of cherry by LChV-1 has been reported all over the world [ 37 , 38 , 39 , 40 ], usually as a coinfection with CVA. Moreover, its presence was also reported from different hosts (almond, peach and plum) [ 35 , 41 ] and recently from apricot [ 17 ]. It is graft-transmittable and although its close relative LChV-2 is transmitted by mealybugs, LChV-1 still lacks a confirmed vector.…”

“…It is graft-transmittable and although its close relative LChV-2 is transmitted by mealybugs, LChV-1 still lacks a confirmed vector. Its positive sense RNA genome has eight ORFs, including ORF3 encoding a heat-shock protein 70 homologue (HSP70h) and ORF5 and ORF6 encoding two coat proteins [ 41 ].…”