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Genomic variation in pepper vein yellows viruses in Australia, including a new putative variant, PeVYV-10

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Abstract

Since the first identification and full sequence of the polerovirus pepper vein yellows virus in Australia in 2016, virus surveys of crops and weeds have sporadically identified PeVYV in different hosts and locations. Genomic comparisons of 14 PeVYV-like isolates using RT-PCR products spanning the 3’ end of the RdRp region (ORF 2), the intergenic region, ORF 3a, ORF 4, and ORF 3 (1388 nt) showed that four of the PeVYV isolates might be a new variant or PeVYV-like virus. From six PeVYV-positive plants, eight PeVYV-like sequences were obtained by high-throughput sequencing, as two hosts, 5352 and 5634, contained two slightly different PeVYV-like isolates. Three of the PeVYV-like isolates were most closely related to PeVYV-6 and PeVYV-5, and two isolates were closely related to PeVYV-9 and PeVYV-2. The other three isolates shared only 69-74% nucleotide sequence identity across the whole genome with any of the other PeVYVs, despite sharing 73-98%, 87-91%, and 84-87% amino acid sequence identity in ORF 3a, ORF 3, and the RdRp (ORF 2), respectively, suggesting that this virus is a new PeVYV-like virus, which we have tentatively called PeVYV-10. This is also the first report of a PeVYV-like virus infecting garlic.

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Acknowledgements

We thank Denis Persley and Sandy Watts for isolate collection, advice and technical support.

Funding

This study was funded by the Grains Research and Development Corporation, through funding from the Australian Government Department of Agriculture, Fisheries & Forestry, as part of its Rural R&D for Profit program, along with Cotton Research and Development Corporation, Hort Innovation Australia, Wine Australia, Sugar Research Australia and Forest and Wood Products Australia. Isolate Ita-7 was identified and isolated as part of a Ph.D. project supported by ACIAR project SMCN/2009/056 'Sustainable Productivity Improvements in Allium and Solanaceous Vegetable Crops in Indonesia and Sub-Tropical Australia'. Isolate 35744 was collected and identified as part of the VG16086 Area wide management of vegetable diseases: viruses and bacteria project funded by Hort Innovation and contributions from the Australian Government with co-investment from the Queensland Department of Agriculture and Fisheries; Victorian Department of Jobs, Precincts and Regions; The Northern Territory Department of Industry, Tourism & Trade; the Western Australia Department of Primary Industries and Regional Development and the University of Tasmania.

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Authors and Affiliations

  1. Queensland Department of Agriculture and Fisheries, Ecosciences Precinct, GPO Box 267, Brisbane, QLD, 4001, Australia

    Fiona Filardo, Murray Sharman & Paul Campbell

  2. Queensland Alliance for Agriculture and Food Science, Ecosciences Precinct, GPO Box 267, Brisbane, QLD, 4001, Australia

    Sari Nurulita

  3. Department of Agriculture Fisheries and Forestry, Northern Australia Quarantine Strategy, GPO Box 858, Canberra, ACT, 2601, Australia

    Lynne Jones

  4. Principal Research Fellow, School of Agriculture and Food Science, University of Queensland, Gatton, QLD, 4343, Australia

    Cherie Gambley

  5. Northern Territory Department of Industry, Tourism and Trade, Berrimah Farm Science Precinct, GPO Box 3000, Darwin, NT, 0801, Australia

    Samantha Bond

Authors
  1. Fiona Filardo
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  2. Sari Nurulita
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  6. Murray Sharman
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Contributions

FF wrote the manuscript and analysed the data. FF, SN, and PC performed high-throughput sequencing. FF and SN performed the 5’ and 3’ RACE. LJ contributed, identified, and photographed seven isolates. CG, SB, and MS contributed and identified isolates. PC provided supervision and grant funding. All authors read, revised, and approved the final manuscript.

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Correspondence to Fiona Filardo.

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Filardo, F., Nurulita, S., Jones, L. et al. Genomic variation in pepper vein yellows viruses in Australia, including a new putative variant, PeVYV-10. Arch Virol 169, 18 (2024). https://doi.org/10.1007/s00705-023-05943-y

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