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<p><i>Cherry virus A</i> (CVA) belongs to the genus <i>Capillovirus</i> in the family Betaflexiviridae. It exhibits a relatively high infection rate in sweet cherry orchards in China, and most infections occur as mixed viral infections. In this study, long-fragment-specific primers were designed to perform segmented RT-PCR amplification on the CVA Shihezi isolate (CVA-SHZ) from Xinjiang, enabling the acquisition of the first complete genome sequence of CVA from Shihezi, Xinjiang, China. The results revealed that the genome of the Xinjiang Shihezi isolate is 7,373 nucleotides in length (excluding the poly(A) tail), which shares the same genomic organization as the four representative full-length CVA sequences previously deposited in GenBank and encodes two open reading frames (ORFs). Sequence alignment showed that the nucleotide sequence identity between CVA-SHZ and the Chinese isolates ChTA11 and ChTA12 was 98.7% for both; with the Indian isolate (FN691959.1) it was 81.6%; and with the German isolate (X82547.1) it reached 97.7%. Alignment analysis of the nucleotide and amino acid sequences of functional regions within ORF1 revealed that the domain of unknown function (DUF1717) displays relatively high sequence variability. In the phylogenetic tree, the CVA-SHZ isolate clustered most closely with the two Chinese isolates, ChTA12 and ChTA11, forming a distinct small clade. Together with the German isolate, this clade constitutes a well-supported major branch, whereas the Indian isolate JK (FN691959.1) occupies a more distant evolutionary position.</p>

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Complete genome sequence analysis of cherry isolate CVA-SHZ from Shihezi, Xinjiang, China

  • 期刊论文

  • 发表日期：

    2026年6月15日

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  • Dengpan Zhou,
  • Yanan Zhao,
  • Xiaojun Wang,
  • Yan Gu

摘要

Cherry virus A (CVA) belongs to the genus Capillovirus in the family Betaflexiviridae. It exhibits a relatively high infection rate in sweet cherry orchards in China, and most infections occur as mixed viral infections. In this study, long-fragment-specific primers were designed to perform segmented RT-PCR amplification on the CVA Shihezi isolate (CVA-SHZ) from Xinjiang, enabling the acquisition of the first complete genome sequence of CVA from Shihezi, Xinjiang, China. The results revealed that the genome of the Xinjiang Shihezi isolate is 7,373 nucleotides in length (excluding the poly(A) tail), which shares the same genomic organization as the four representative full-length CVA sequences previously deposited in GenBank and encodes two open reading frames (ORFs). Sequence alignment showed that the nucleotide sequence identity between CVA-SHZ and the Chinese isolates ChTA11 and ChTA12 was 98.7% for both; with the Indian isolate (FN691959.1) it was 81.6%; and with the German isolate (X82547.1) it reached 97.7%. Alignment analysis of the nucleotide and amino acid sequences of functional regions within ORF1 revealed that the domain of unknown function (DUF1717) displays relatively high sequence variability. In the phylogenetic tree, the CVA-SHZ isolate clustered most closely with the two Chinese isolates, ChTA12 and ChTA11, forming a distinct small clade. Together with the German isolate, this clade constitutes a well-supported major branch, whereas the Indian isolate JK (FN691959.1) occupies a more distant evolutionary position.