Whole-genome sequencing and variant analysis of apple stem pitting virus isolated from Shanxi province, China

Variants of Apple stem pitting virus (ASPV), which are distributed widely worldwide, have a marked effect on apple yield and quality. Surveys of the occurrence of ASPV have led to greater understanding of its genome architecture and the mechanisms underlying its evolution. In this study, we used reverse transcription-polymerase chain reaction to detect ASPV in 409 apple leaf samples collected from Shanxi province. The incidence of ASPV ranged from 36.33% (in Linyi) to 55.37% (in Pingyao). A total of 15 new ASPV isolates were identified; the full-length genome sequence comprised 9328 nucleotides and encoded a putative polypeptide of 3050 amino acids (including the 5' and 3' ends). Shanxi-2 had highest nucleotide identity (94.37%) with KU308398.1, and Shanxi-1 had the lowest (77.74%) with MK239268.1. Phylogenetic analysis classified ASPV isolates (n=23) into two groups, with no significant correlation of geographic distribution. Moreover, 16 potential recombination events were identified. Estimation of selection pressures within the ASPV population revealed negative selection pressure in five coding regions (encoding RNA-dependent RNA polymerases, triple gene block protein 1, triple gene block protein 2, triple gene block protein 3, a coat protein) within the genome. Genetic recombination and negative selection represent important evolutionary mechanisms shaping the genetic structure of the ASPV population. ASPV shows wide distribution and genetic diversity in Shanxi, China. The results of this study provide important clues for evaluating the epidemiological characteristics of ASPV, as well as valuable information for developing sustainable virus management strategies.