Genetic variation analysis of apple chlorotic leaf spot virus coat protein reveals a new phylogenetic type and two recombinants in China.

In this study, we generated sequences of the apple chlorotic leaf spot virus (ACLSV) coat protein (CP) gene. Genetic variation and phylogenetic analyses were carried out on these sequences along with others reported previously. ACLSV populations clustered into four types: in three of the four types, combinations of three amino acids at positions of 40, 75 and 79 were conserved. The fourth phylogenetic type, newly identified here, was characterized by co-variation of Ser(40)-Tyr(75)-Ser(79). Statistically significant genetic differentiation and infrequent gene flow were detected among the four types. Two natural recombinants were detected for the first time among ACLSV isolates/genotypes from China.