Pome fruit viruses at the Canadian Clonal Genebank and molecular characterization of Apple chlorotic leaf spot virus isolates

A survey for apple and pear viruses was carried out at the Canadian Clonal Genebank (CCG), Harrow, Ontario, Canada, during the fall/winter of 2007 and spring of 2008. Leaves and/or dormant cuttings were randomly collected from 438 to 122 accessions of apple and pear, respectively. Samples were tested by Double Antibody Sandwich-Enzyme Linked Immunosorbent Assay (DAS-ELISA) for the presence of Apple chlorotic leaf spot virus (ACLSV), Apple stem pitting virus (ASPV), Apple stem grooving virus (ASGV) and Apple mosaic virus (ApMV). Infection rates for apples were ACLSV (48.1%), ASGV (10%), ASPV (6.6%) and ApMV (7.1%), and for pears ACLSV (42.6%). ACLSV was detected and characterization by multiplex RT-PCR with primers targeting a fragment of 677 bp corresponding to the partial coat protein (CP), movement protein (MP) and untranslated (3′UTR) region in 22 accessions of apple and pear. Multiplex RT-PCR showed a higher sensitivity over the ELISA test. The nucleotide and amino acid deduced partial CP identities ranged from 82.6–100% to 91–100%, respectively, while partial MP identities was 62.5–100% at aa level based on the amplified fragment appropriate for partial MP using a frame shift, among 22 ACLSV isolates. Phylogenetic analyses based on the partial CP region clustered CCG ACLSV isolates in two different groups, while those based on the partial MP region embraced CCG ACLSV isolates in two sub-clusters within the same group. This is the first report on the detection of ACLSV, ASPV, ASGV and ApMV at CCG, and the molecular characterization of ACLSV isolates in apple and pear plants from worldwide countries to deduce possible heterogeneity and evolution.

► Pentaplex RT-PCR showed more sensitive in detection ACLSV, ASGV, ASPV and ApMV at CCG than ELISA.
► Sequence identities were 82.6–100% at nt, and 91–100% at aa level for 22 CCG ACLSV isolates.
► ACLSV CCG isolates were grouped into two clusters at nt and deduced part CP level.
► ACLSV CCG isolates were grouped into B6 and P205 type based on five amino acids combination.
► ACLSV CCG isolates were grouped into two sub-clusters at deduced part MP level.