Table 1.
Oligonucleotide primers used for overlapping RT-PCR amplification to determine nucleotide sequences of the AdV-1 variants.
Table 2.
Sequence identities of Actinidia deliciosa virus 1 variant 1 and 2 with other members of the family Closteroviridae.
Fig 1.
Schematic illustration of the structure of the genomes of AdV-1 variants and other relevant members of the family Closteroviridae.
The names of proteins or motifs corresponding to acronyms are as follows: PRO (leader papain-like protease), MTR (methyltransferase), HEL (helicase), RdRp (RNA-dependent RNA polymerase), HSP70h (heat shock protein 70 homolog), CP(coat protein).
Fig 2.
Multiple sequence alignments of RdRp proteins from AdV-1 variants and other species in the family Closteroviridae.
Gaps (·) had been introduced to optimize alignment. The unique 26-aa inserts are boxed in red. The RdRp proteins of Actinidia virus 1 (KX857665), Persimmon virus B variant 1 (NC025967), Persimmon virus B variant 2 (AB923925), Citrus tristeza virus (KU883267), Raspberry mottle virus (NC008585), Mint virus 1 (NC006944), Beet pseudo-yellows virus (NC005209), Bean yellow disorder virus (NC010560), Grapevine leafroll-associated virus 1 (NC016509), Pineapple mealybug wilt-associated virus 1 (AF414119), Cordyline virus 1 (HM588723), and Grapevine leafroll-associated virus 7 (HE588185) are abbreviated as AcV-1, PeVB v1, PeVB v2, CTV, RMV, MV-1, BPYV, BYDV, GLRaV-1, PMWaV-1, CoV-1 and GLRaV-7, respectively.
Fig 3.
Phylogenetic trees of the amino acid sequences of RdRp (A), HSP70h (B), and CP (C) from representative members of the family Closteroviridae.
Bipolaris maydis chrysovirus 1 RaRd (BMC-1 in A), Theobroma cacao HSP70 (TcHSP70 in B), and Peanut stunt virus CP (PSV in C) were used as outgroups. Bootstrap support values are displayed at nodes. Virus names and their abbreviations were Actinidia virus 1 (AcV-1), Persimmon virus B variant 1 and 2 (PeVB v1 and PeVB v2), Blueberry virus A (BVA), Grapevine rootstock stem lesion associated virus (GRSLaV), Carnation yellow fleck virus (CYFV), Mint virus 1 (MV-1), Carnation necrotic fleck virus(CNFV), Tobacco virus 1 (ToV-1), Ctrawberry chlorotic fleck associated virus (SCFaV), Beet yellow stunt virus (BYSV), Citrus tristeza virus (CTV), Raspberry mottle virus (RMV), Carrot yellow leaf virus (CYLV), Beet yellow virus (BYV), Plum bark necrosis stem pitting-associated virus (PBNSPaV), Little cherry virus 2 (LCV-2), Pineapple mealybug wilt-associated virus 1, 2 and 3 (PMWaV-1, -2, and -3), Grapevine leafroll-associated virus 1, 2, 3, 4, 5, 6, 7, and 9 (GLRaV-1, -2, -3, -4, -5, -6, -7, and -9), Little cherry virus 1 (LChV-1), Cordyline virus 1 (CoV-1), Bean yellow disorder virus (BYDV), Cucurbit chlorotic yellows virus (CCYV), Lettuce chlorosis virus (LCV), Tomato chlorosis virus (ToCV), Cucurbit yellow stunting disorder virus (CYSDV), Potato yellow vein virus (PYVV), Beet pseudo-yellows virus (BPYV), and Diodia vein chlorosis virus (DVCV). Accession numbers of the sequences are listed after the slashes.