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

Fiona Filardo; Sari Nurulita; Lynne Jones; Cherie Gambley; Samantha Bond; Murray Sharman; Paul Campbell

doi:10.1007/s00705-023-05943-y

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

Arch Virol. 2024 Jan 5;169(1):18. doi: 10.1007/s00705-023-05943-y.

Authors

Fiona Filardo¹, Sari Nurulita², Lynne Jones³, Cherie Gambley⁴, Samantha Bond⁵, Murray Sharman⁶, Paul Campbell⁶

Affiliations

¹ Queensland Department of Agriculture and Fisheries, Ecosciences Precinct, GPO Box 267, Brisbane, QLD, 4001, Australia. fiona.filardo@daf.qld.gov.au.
² Queensland Alliance for Agriculture and Food Science, Ecosciences Precinct, GPO Box 267, Brisbane, QLD, 4001, Australia.
³ Department of Agriculture Fisheries and Forestry, Northern Australia Quarantine Strategy, GPO Box 858, Canberra, ACT, 2601, Australia.
⁴ Principal Research Fellow, School of Agriculture and Food Science, University of Queensland, Gatton, QLD, 4343, Australia.
⁵ Northern Territory Department of Industry, Tourism and Trade, Berrimah Farm Science Precinct, GPO Box 3000, Darwin, NT, 0801, Australia.
⁶ Queensland Department of Agriculture and Fisheries, Ecosciences Precinct, GPO Box 267, Brisbane, QLD, 4001, Australia.

PMID: 38180533
DOI: 10.1007/s00705-023-05943-y

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.

MeSH terms

Australia
Crops, Agricultural*
Genomics
Luteoviridae* / genetics
RNA-Dependent RNA Polymerase

Substances

RNA-Dependent RNA Polymerase