Genomic variation in pepper vein yellows viruses in Australia, including a new putative variant, PeVYV-10.
Journal
Archives of virology
ISSN: 1432-8798
Titre abrégé: Arch Virol
Pays: Austria
ID NLM: 7506870
Informations de publication
Date de publication:
05 Jan 2024
05 Jan 2024
Historique:
received:
05
07
2023
accepted:
19
11
2023
medline:
5
1
2024
pubmed:
5
1
2024
entrez:
5
1
2024
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 38180533
doi: 10.1007/s00705-023-05943-y
pii: 10.1007/s00705-023-05943-y
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
18Informations de copyright
© 2024. Crown.
Références
Maina S, Edwards OR, Jones RAC (2016) First complete genome sequence of Pepper vein yellows virus from Australia. Genome Announc 4:e00450-e1416
pubmed: 27231375
pmcid: 4882956
Fiallo-Olivé E, Navas-Hermosilla E, Ferro CG, Zerbini FM, Navas-Castillo J (2018) Evidence for a complex of emergent poleroviruses affecting pepper worldwide. Adv Virol 163:1171–1178
Schliephake E, Graichen K, Rabenstein F (2000) Investigations on the vector transmission of the Beet mild yellowing virus (BMYV) and the Turnip yellows virus (TuYV). Zeitschrift für Pflanzenkrankheiten und Pflanzenschutz 107:81–87
Stevens M, Smith HG, Hallsworth PB (1995) Detection of the luteoviruses, beet mild yellowing virus and beet western yellows virus, in aphids caught in sugar-beet and oilseed rape crops, 1990–1993. Ann Appl Biol 127:309–320
doi: 10.1111/j.1744-7348.1995.tb06675.x
Brault V, van den Heuvel JF, Verbeek M, Ziegler-Graff V, Reutenauer A, Herrbach E, Garaud JC, Guilley H, Richards K, Jonard G (1995) Aphid transmission of beet western yellows luteovirus requires the minor capsid read-through protein P74. EMBO J 14:650–659
doi: 10.1002/j.1460-2075.1995.tb07043.x
pubmed: 7882968
pmcid: 398128
Herrbach E (1999) Vector-virus interaction. In: Smith HG, Barker H (eds) The luteoviridae. CAB International, London, pp 85–146
Jaag HM, Kawchuk L, Rohde W, Fischer R, Emans N, Prüfer D (2003) An unusual internal ribosomal entry site of inverted symmetry directs expression of a potato leafroll polerovirus replication-associated protein. Proc Natl Acad Sci 100:8939–8944
doi: 10.1073/pnas.1332697100
pubmed: 12835413
pmcid: 166417
van den Heuvel JF, Bruyère A, Hogenhout SA, Ziegler-Graff V, Brault V, Verbeek M, van der Wilk F, Richards K (1997) The N-terminal region of the luteovirus readthrough domain determines virus binding to Buchnera GroEL and is essential for virus persistence in the aphid. J Virol 71:7258–7265
doi: 10.1128/jvi.71.10.7258-7265.1997
pubmed: 9311800
pmcid: 192067
van der Wilk F, Verbeek M, Dullemans AM, van den Heuvel JFJM (1997) The genome-linked protein of potato leafroll virus is located downstream of the putative protease domain of the ORF1 product. Virology 234:300–303
doi: 10.1006/viro.1997.8654
pubmed: 9268161
Brault V, Périgon S, Reinbold C, Erdinger M, Scheidecker D, Herrbach E, Richards K, Ziegler-Graff V (2005) The polerovirus minor capsid protein determines vector specificity and intestinal tropism in the aphid. J Virol 79:9685–9693
doi: 10.1128/JVI.79.15.9685-9693.2005
pubmed: 16014930
pmcid: 1181584
Mayo MA, Miller WA (1999) The structure and expression of luteovirus genomes. In: Smith HG, Barker H (eds) The Luteoviridae. CAB International, Wallingford, pp 23–42
Smirnova E, Firth AE, Miller WA, Scheidecker D, Brault V, Reinbold C, Rakotondrafara AM, Chung BYW, Ziegler-Graff V (2015) Discovery of a small Non-AUG-initiated ORF in poleroviruses and luteoviruses that is required for long-distance movement. PLoS Pathog 11:e1004868
doi: 10.1371/journal.ppat.1004868
pubmed: 25946037
pmcid: 4422679
Ziegler-Graff V, Brault V, Mutterer JD, Simonis MT, Herrbach E, Guilley H, Richards KE, Jonard G (1996) The coat protein of beet western yellows luteovirus is essential for systemic infection but the viral gene products P29 and P19 are dispensable for systemic infection and aphid transmission. Mol Plant Microbe Interact 9(6):501–510
doi: 10.1094/MPMI-9-0501
Filardo F, Nancarrow N, Kehoe M, McTaggart AR, Congdon B, Kumari S, Aftab M, Trębicki P, Rodoni B, Thomas J, Sharman M (2021) Genetic diversity and recombination between turnip yellows virus strains in Australia. Adv Virol 166:813–829
Massawe DP, Stewart LR, Kamatenesi J, Asiimwe T, Redinbaugh MG (2018) Complete sequence and diversity of a maize-associated Polerovirus in East Africa. Virus Genes 54:432–437
doi: 10.1007/s11262-018-1560-5
pubmed: 29687187
LaTourrette K, Holste NM, Garcia-Ruiz H (2021) Polerovirus genomic variation. Virus Evol. https://doi.org/10.1093/ve/veab102
doi: 10.1093/ve/veab102
pubmed: 35299789
pmcid: 8923251
Peng Q, Li W, Zhou X, Sun C, Hou Y, Hu M, Fu S, Zhang J, Kundu JK, Lei L (2023) Genetic diversity analysis of brassica yellows virus causing aberrant color symptoms in oilseed rape. Plants (Basel) 12:1008
doi: 10.3390/plants12051008
pubmed: 36903869
Nurulita S, Geering ADW, Crew KS, Harper SM, Thomas JE (2022) Detection of two poleroviruses infecting garlic (Allium sativum) in Australia. Australas Plant Path 51:461–465
doi: 10.1007/s13313-022-00870-z
Sharman M, Lapbanjob S, Sebunruang P, Belot JL, Galbieri R, Giband M, Suassuna N (2015) First report of Cotton leafroll dwarf virus in Thailand using a species-specific PCR validated with isolates from Brazil. Australas Plant Dis Notes 10:1–4
doi: 10.1007/s13314-015-0174-1
Abraham AD, Varrelmann M, Vetten HJ (2008) Molecular evidence for the occurrence of two new luteoviruses in cool season food legumes in Northeast Africa. Afr J Biotechnol 7:414–420
Knierim D, Deng TC, Tsai WS, Green SK, Kenyon L (2010) Molecular identification of three distinct Polerovirus species and a recombinant Cucurbit aphid-borne yellows virus strain infecting cucurbit crops in Taiwan. Plant Pathol 59:991–1002
doi: 10.1111/j.1365-3059.2010.02327.x
Tamura K, Stecher G, Kumar S (2021) MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 38:3022–3027
doi: 10.1093/molbev/msab120
pubmed: 33892491
pmcid: 8233496
Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526
pubmed: 8336541
Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16:1616–1626
doi: 10.1101/gad.1004402
pubmed: 12101121
pmcid: 186362
Filardo FF, Thomas JE, Webb M, Sharman M (2019) Faba bean polerovirus 1 (FBPV-1); a new polerovirus infecting legume crops in Australia. Adv Virol 164:1915–1921
Krueger, F. (2021). Trim Galore. In GitHub repository. GitHub. https://github.com/FelixKrueger/TrimGalore.com/fenderglass/Flye
Bester R, Cook G, Breytenbach JHJ, Steyn C, De Bruyn R, Maree HJ (2021) Towards the validation of high-throughput sequencing (HTS) for routine plant virus diagnostics: measurement of variation linked to HTS detection of citrus viruses and viroids. Virol J 18:61
doi: 10.1186/s12985-021-01523-1
pubmed: 33752714
pmcid: 7986492
Gibbs A, Mackenzie A (1997) A primer pair for amplifying part of the genome of all potyvirids by RT-PCR. J Virol Methods 63:9–16
doi: 10.1016/S0166-0934(96)02103-9
pubmed: 9015271
Ghosh S, Kanakala S, Lebedev G, Kontsedalov S, Silverman D, Alon T, Mor N, Sela N, Luria N, Dombrovsky A, Mawassi M, Haviv S, Czosnek H, Ghanim M (2019) Transmission of a new polerovirus infecting pepper by the whitefly Bemisia tabaci. J Virol. https://doi.org/10.1128/JVI.00488-19
doi: 10.1128/JVI.00488-19
pubmed: 31142671
pmcid: 6675903