Characterisation of the little cherry virus 1 isolate infecting almonds in the Czech Republic

Little cherry virus 1 (LChV1) of the genus Velarivirus is an important pathogen associated with the little cherry disease. It infects various species of the genus Prunus, mainly the sweet cherry and the sour cherry. Recently, plums and apricots have also been reported as natural hosts. In the present work, the LChV1 isolate causing chlorotic mosaics in almonds is characterised. The nearly complete (+)ssRNA genome sequence of the Alm138 isolate, obtained by Sanger sequencing, is 16 878 nt long showing a typical velarivirus structure with 8 ORFs. Among them, the taxonomically important ORFs, ORF1a/1b encoding the polyprotein is 8 421 nt long, with a 0/+1 frameshift position at 6 923; ORF3 encoding the heat shock protein HSP70h is 1 656 nt long, and ORF6 encoding the coat protein duplicate is 1 989 nt long. The genome sequence showed its highest identity with LChV1 isolates Apr184R (96.2%), 19SP003B (92.2%) and Kyoto-2 (92.1%). A similar situation was also found for the ORF1, HSP70h, and CP nucleotide and amino acid sequences. A phylogenetic analysis identified Alm138 as a member of the G5 phylogenetic group, supporting its close relationships with the Czech Apr184R apricot isolate and the other members of this group. This report describes the first little cherry virus 1 isolate infecting almonds and confirms the presence of isolates of the G5 phylogroup within Europe.