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Occurrence and genetic diversity analysis of apple stem pitting virus isolated from apples in China

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Two primer pairs were used to detect apple stem pitting virus (ASPV) using a reverse transcription (RT)-PCR test. 82 out of the 141 randomly collected samples, from ten orchards in five provinces and regions of China, tested positive. In the positive samples forty-five (55%) were infected by ASPV and two other viruses. The full coat protein (CP) and the triple gene block (TGB) gene 1, 2 and 3 of partial ASPV isolates were subsequently cloned. The nucleotide and amino acid identities of 39 CP sequence variants from 31 Chinese apple samples were compared with that of previously reported ASPV isolates and were 67.4–96.0% and 68.4–97.7%, respectively. All ASPV sequence variants from Chinese apples separated into two clades with CP- and TGB-based phylogenetic trees, whilst the grouping of TGB2 and TGB3 trees was the same. Three recombinants (FS06-2, X5-2, and XLF-C-2) for CP and six (TH2-5, X8-2, FS05-2, X6-2 and XLF-A-1) recombinants for TGB were identified from the Chinese apple isolates. Two recombinants were found in the TGB sequence of isolate XLF-A-1. The results presented here may assist in the development of a more comprehensive screening tool for apple viruses.

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Correspondence to Ya-Feng Dong.

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This study was funded by CAAS-ASTIP.

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The author declares that she has no competing interests and no conflict of interest.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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Figure S1: Recombination events 5 (a) and 6 (b) in the ASPV TGB genes. RDP evidence for the recombinant origins of ASPV (100 bootstrap replicates, Jukes-Cantor distances); constructed using 200 nt sequence windows and a step size of 20 nt. (JPEG 84 kb)

Supplementary material 2 (DOC 181 kb)

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Hu, GJ., Dong, YF., Zhang, ZP. et al. Occurrence and genetic diversity analysis of apple stem pitting virus isolated from apples in China. Arch Virol 162, 2397–2402 (2017).

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