Genetic diversity and phylogenetic relationships of apple chlorotic leaf spot virus isolates from Malus, Pyrus and Prunus hosts in Latvia

Abstract

AbstractThe prevalence of apple chlorotic leaf spot virus (ACLSV) in different Rosaceae species, mainly from cultivated apple (Malus domestica), pear (Pyrus communis), plum (Prunus domestica), apricot (Prunus armeniaca) and wild plants of genus Amelanchier, Cotoneaster, Crataegus, Malus, Prunus and Sorbus were studied. ACLSV was found in cultivated M. domestica, P. communis, P. domestica and wild‐growing Malus, including M. sylvestris. Thirty‐four sequences of the ACLSV coat protein gene were obtained and compared with 372 homologous sequences from GenBank to evaluate the genetic diversity of the virus in Latvia and worldwide. The sequence identities varied from 79.6% to 98.4% at the nucleotide level and 84.5% to 100% at the amino acid level. Phylogenetic analyses clustered ACLSV pome fruit isolates into three genetic types but isolates from stone fruits into four phylogenetic groups. Three genetic types of ACLSV pome and stone fruit isolates were identified in Latvia. Two of them were previously characterized as type B6 and P205. The third genetic type was newly recognized among the stone fruit isolates and distinguished from other virus isolates by amino acid substitutions in three positions, Ser14, Asn23 and Leu72. Two natural recombinants, LV27 and NZ5, were detected among ACLSV isolates from Latvia, and recombination events were identified for the first time in wild‐growing Malus, confirming that recombination is a common process in the ACLSV population.