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<p>Survey in Java Island tested 19 shallots (<i>Allium cepa</i> var. <i>aggregatum</i>) sampled from six regencies of Indonesia using a specific primer pair for iris yellow spot virus (IYSV, <i>Orthotospovirus</i>), and universal primer pairs for allexiviruses, carlaviruses, and potyviruses. Four garlic (<i>A. sativum</i>) imported from China samples collected from markets were used as comparative host. Through nucleotide sequencing, garlic virus C (GarV-C, <i>Allexivirus</i>), shallot yellow stripe virus (SYSV, <i>Potyvirus</i>), shallot latent virus (SLV, <i>Carlavirus</i>) and IYSV were identified in shallots, while garlic common latent virus (GarCLV, <i>Carlavirus</i>) and SLV were in garlic samples. Phylogenetic trees based on different genome regions divided global GarV-C isolates into SW3.3&#xa0;A, SW3.3B, and GVC 1 phylogroups. Indonesian SYSV and SLV isolates were genetically separated with those from other countries. IYSV isolates from Indonesia were positioned closely with isolates from Bosnia and Herzegovina, and USA. GarV-C and IYSV were identified for the first time in shallot in Indonesia here.</p>

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Molecular identification and phylogenetic analysis of four viruses infecting shallot in Java Island, Indonesia

  • 期刊论文

  • 发表日期：

    2026年2月11日

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  • Siska Nur Siti Yuliandini,
  • Alif Lammim Al Azhar,
  • Dyana Rahma Ningrum,
  • Paramita Maris,
  • Sari Nurulita,
  • Mahmoud A. Amer,
  • Adyatma Irawan Santosa

摘要

Survey in Java Island tested 19 shallots (Allium cepa var. aggregatum) sampled from six regencies of Indonesia using a specific primer pair for iris yellow spot virus (IYSV, Orthotospovirus), and universal primer pairs for allexiviruses, carlaviruses, and potyviruses. Four garlic (A. sativum) imported from China samples collected from markets were used as comparative host. Through nucleotide sequencing, garlic virus C (GarV-C, Allexivirus), shallot yellow stripe virus (SYSV, Potyvirus), shallot latent virus (SLV, Carlavirus) and IYSV were identified in shallots, while garlic common latent virus (GarCLV, Carlavirus) and SLV were in garlic samples. Phylogenetic trees based on different genome regions divided global GarV-C isolates into SW3.3 A, SW3.3B, and GVC 1 phylogroups. Indonesian SYSV and SLV isolates were genetically separated with those from other countries. IYSV isolates from Indonesia were positioned closely with isolates from Bosnia and Herzegovina, and USA. GarV-C and IYSV were identified for the first time in shallot in Indonesia here.