During a survey of oat and barley crops in northern New South Wales (NSW) and southern Queensland (Qld), a novel member of the genus Luteovirus (family Tombusviridae) causing leaf reddening and yellow dwarf symptoms in oats and barley was found in both States. A near-complete genome of the virus tentatively named cereal red leaf virus (CrRLV; tentative species name Luteovirus foliarubra) was obtained through high throughput sequencing. The virus was genomically distinct from, but reacted with antibodies to, barley yellow dwarf virus-MAV. CrRLV was transmitted by Rhopalosiphon padi but not by R. maidis. Barley yellow dwarf virus-PAV was found in both NSW and Qld on barley and oats. Additionally, barley virus G was found for the first time in Qld and NSW, on barley, barley yellow dwarf virus-PAS for the first time in Qld, on barley, cereal yellow dwarf virus-RPS for the first time in NSW, on oats, and cereal yellow dwarf virus-RPV was found in NSW on oats and barley and for the first time in Qld, on oats.

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.

In this study, metagenomic sequence data was used to investigate the phytoplasma taxonomic diversity in vegetable-growing regions across Australia. Metagenomic sequencing was performed on 195 phytoplasma-positive samples, originating either from historic collections (n=46) or during collection efforts between January 2015 and June 2022 (n=149). The sampled hosts were classified as crop (n=155), weed (n=24), ornamental (n=7), native plant (n=6), and insect (n=3) species. Most samples came from Queensland (n=78), followed by Western Australia (n=46), the Northern Territory (n=32), New South Wales (n=17), and Victoria (n=10). Of the 195 draft phytoplasma genomes, 178 met our genome criteria for comparison using an average nucleotide identity approach. Ten distinct phytoplasma species were identified and could be classified within the 16SrII, 16SrXII (PCR only), 16SrXXV, and 16SrXXXVIII phytoplasma groups, which have all previously been recorded in Australia. The most commonly detected phytoplasma taxa in this study were species and subspecies classified within the 16SrII group (n=153), followed by strains within the 16SrXXXVIII group (‘Ca. Phytoplasma stylosanthis’; n=6). Several geographic- and host-range expansions were reported, as well as mixed phytoplasma infections of 16SrII taxa and ‘Ca. Phytoplasma stylosanthis’. Additionally, six previously unrecorded 16SrII taxa were identified, including five putative subspecies of ‘Ca. Phytoplasma australasiaticum’ and a new putative 16SrII species. PCR and sequencing of the 16S rRNA gene was a suitable triage tool for preliminary phytoplasma detection. Metagenomic sequencing, however, allowed for higher-resolution identification of the phytoplasmas, including mixed infections, than was afforded by only direct Sanger sequencing of the 16S rRNA gene. Since the metagenomic approach theoretically obtains sequences of all organisms in a sample, this approach was useful to confirm the host family, genus, and/or species. In addition to improving our understanding of the phytoplasma species that affect crop production in Australia, the study also significantly expands the genomic sequence data available in public sequence repositories to contribute to phytoplasma molecular epidemiology studies, revision of taxonomy, and improved diagnostics.

This is the first study to research management strategies for cotton leafroll dwarf virus (CLRDV) in the southeastern U.S. The efficacy of aphid vector management to reduce final CLRDV incidence was investigated concurrent with efforts to monitor aphid population dynamics and timing of CLRDV spread. Adjusting the planting date and insecticide applications did not reduce the final incidence of CLRDV, which was confirmed in 60–100% of plants per plot using RT-PCR. Aphid population density was reduced, but not eliminated with foliar insecticide applications. Aphis gossypii was the only species observed on cotton and was the dominant species collected in pan traps. Three distinct periods of virus spread were detected with sentinel plants including early, mid-and late-season. Most virus spread occurred during large aphid dispersal events.

Assays for the high throughput screening of crops for virus monitoring need to be quick, easy, and low cost. One method involves using tissue blot immunoassays (TBIA), where plant stems are blotted onto nitrocellulose membrane and screened with available antibodies against a range of viruses. TBIAs are inexpensive but limited by antibody availability and specificity. To circumvent the antibody limitations, we developed the tissue blot hybridization chain reaction (TB-HCR). As with TBIA, plant stems are blotted onto a nitrocellulose membrane, however, TB-HCR involves using nucleic acid probes instead of antibodies. We demonstrated for the first time that TB-HCR can be used for plant viruses by designing and testing probes against species from several virus genera including begomovirus, polerovirus, luteovirus, cucumovirus, and alfamovirus. We also explored different hairpin reporter methods such as biotin/streptavidin-AP and the Alexa Fluor-488 Fluorophore. TB-HCR has applications for low-cost diagnostics for large sample numbers, rapid diagnostic deployment for new viruses, and can be performed as a preliminary triage assay prior to downstream applications.

The complete genome sequence of pineapple secovirus B (PSV-B), a new virus infecting pineapple (Ananas comosus) on the island of Oahu, Hawaii, was determined by high-throughput sequencing (HTS). The genome comprises two RNAs that are 5,956 and 3,808 nt long, excluding the 3'-end poly-A tails, both coding for a single large polyprotein. The RNA1 polyprotein contains five conserved domains associated with replication, while the RNA2 polyprotein is cleaved into the movement protein and coat protein. PSV-B is representative of a new species in the subgenus Cholivirus (genus Sadwavirus; family Secoviridae), as the level of amino acid sequence identity to recognized members of this subgenus in the Pro-Pol and coat protein regions is below currently valid species demarcation thresholds.

A carlavirus, closely related to cowpea mild mottle virus (CPMMV) and spread by silverleaf whitefly (SLW) was reported affecting fresh market beans in a major Australian growing district in 2016. Further investigations of this virus were completed through regular surveys of crops, weeds and SLW in this district from 2016–2019. Sequencing of the 3'end of the virus genome from a range of samples detected four variants, referred to as CPMMV:A:FB5288 and CPMMV:A:S1 to S3. The distribution of these four variants in survey samples showed the dominant variant in French bean crops as CPMMV:A:FB5288. The surveys also showed disease impacts were limited to autumn and varied over time. This variation is attributed to the influence of rainfall on adult insect vector levels. The experimental host range of CPMMV:A:FB5288 was shown to be limited to the Phaseoleae plant tribe and included the Australian native species, Glycine canescens. French bean varieties showed a range of susceptibilities to this dominant sequence variant from highly tolerant to very susceptible. The tolerant varieties provide the local industry with some options for disease management where previously there were none. Genetic diversity studies further highlight the need for taxonomic reform of the species referred to as CPMMV.

This review summarizes research on virus diseases of cereals and oilseeds in Australia since the 1950s. All viruses known to infect the diverse range of cereal and oilseed crops grown in the continent's temperate, Mediterranean, subtropical and tropical cropping regions are included. Viruses that occur commonly and have potential to cause the greatest seed yield and quality losses are described in detail, focusing on their biology, epidemiology and management. These are: barley yellow dwarf virus, cereal yellow dwarf virus and wheat streak mosaic virus in wheat, barley, oats, triticale and rye; Johnsongrass mosaic virus in sorghum, maize, sweet corn and pearl millet; turnip yellows virus and turnip mosaic virus in canola and Indian mustard; tobacco streak virus in sunflower; and cotton bunchy top virus in cotton. The currently less important viruses covered number nine infecting nine cereal crops and 14 infecting eight oilseed crops (none recorded for rice or linseed). Brief background information on the scope of the Australian cereal and oilseed industries, virus epidemiology and management and yield loss quantification is provided. Major future threats to managing virus diseases effectively include damaging viruses and virus vector species spreading from elsewhere, the increasing spectrum of insecticide resistance in insect and mite vectors, resistance-breaking virus strains, changes in epidemiology, virus and vectors impacts arising from climate instability and extreme weather events, and insufficient industry awareness of virus diseases. The pressing need for more resources to focus on addressing these threats is emphasized and recommendations over future research priorities provided.

Disease outbreaks caused by turnip yellows virus (TuYV), a member of the genus Polerovirus, family Luteoviridae, regularly occur in canola and pulse crops throughout Australia. To understand the genetic diversity of TuYV for resistance breeding and management, genome sequences of 28 TuYV isolates from different hosts and locations were determined using high-throughput sequencing (HTS). We aimed to identify the parts of the genome that were most variable and clarify the taxonomy of viruses related to TuYV. Poleroviruses contain seven open reading frames (ORFs): ORF 0–2, 3a, and 3–5. Phylogenetic analysis based on the genome sequences, including isolates of TuYV and brassica yellows virus (BrYV) from the GenBank database, showed that most genetic variation among isolates occurred in ORF 5, followed by ORF 0 and ORF 3a. Phylogenetic analysis of ORF 5 revealed three TuYV groups; P5 group 1 and group 3 shared 45–49% amino acid sequence identity, and group 2 is a recombinant between the other two. Phylogenomic analysis of the concatenated ORFs showed that TuYV is paraphyletic with respect to BrYV, and together these taxa form a well-supported monophyletic group. Our results support the hypothesis that TuYV and BrYV belong to the same species and that the phylogenetic topologies of ORF 0, 3a and 5 are incongruent and may not be informative for species demarcation. A number of beet western yellow virus (BWYV)- and TuYV-associated RNAs (aRNA) were also identified by HTS for the first time in Australia.

This study examined the natural and experimental host range and aphid and graft transmission of the tentative polerovirus phasey bean mild yellows virus (PBMYV). Eleven complete coding sequences from PBMYV isolates were determined from a range of hosts and locations. We found two genetically distinct variants of PBMYV. PBMYV-1 was the originally described variant, and PBMYV-2 had a large putative recombination in open reading frame 5 such that PBMYV-1 and PBMYV-2 shared only 65-66% amino acid sequence identity in the P5 protein. The virus was transmitted by a clonal colony of cowpea aphids ( Aphis craccivora ) and by grafting with infected scions but was not transmitted by a clonal colony of green peach aphids ( Myzus persicae ). PBMYV was found in natural infections in 11 host species with a range of symptoms and severity, including seven important grain legume crops from across a wide geographic area in Australia. PBMYV was common and widespread in the tropical weed phasey bean ( Macroptilium lathyroides ), but it is likely that there are other major alternative hosts for the virus in temperate regions of Australia. The experimental host range of PBMYV included the Fabaceae hosts chickpea ( Cicer arietinum ), faba bean ( Vicia faba ), pea ( Pisum sativum ), and phasey bean, but transmissions failed to infect several other members of the families Asteraceae, Cucurbitaceae, Fabaceae and Solanaceae. PBMYV was commonly found in grain legume crops in eastern and western Australia, sometimes at greater than 90% incidence. This new knowledge about PBMYV warrants further assessments of its economic impact on important grain legume crops.

In Sudan yellowing viruses are key production constraints in pulse crops. Field surveys were carried out to identify luteovirids affecting chickpea crops in the major production regions (Gezira Scheme and River Nile State). A total of 415 chickpea plant samples with yellowing and stunting symptoms were collected during the 2013, 2015 and 2018 growing seasons. Serological results (Tissue-blot immunoassays) showed that Luteoviridae and Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) were the most common viruses, with rare infections with Faba bean necrotic yellows virus (FBNYV, genus Nanovirus, family Nanoviridae). Some samples reacted only with a broad-spectrum luteovirid monoclonal antibody (5G4-MAb), and others showed cross reactions between the specific monoclonal antibodies, suggesting the occurrence of new luteovirid variants. Serological results were confirmed by amplification with reverse transcription-polymerase chain reaction (RT-PCR) and sequencing of the partial coat protein gene. Molecular analyses provided a basic, sufficient and reliable characterization for four viruses affecting chickpea that belong to Polerovirus (family Luteoviridae). These were Cucurbit aphid-borne yellows virus (CABYV), Pepper vein yellows virus (PeVYV), Pepo aphid-borne yellows virus (PABYV) and Cotton leafroll dwarf virus (CLRDV), that shared high similarity with the type sequences. Phylogenetic analyses also revealed high similarity to luteovirid species. This study has established reliable, rapid and sensitive molecular tools for the detection of luteovirid species.

Cotton bunchy top disease causes sporadic but serious losses in cotton ( Gossypium hirsutum ) in Australia but little has been reported about the diversity, distribution, host range and detection of the causal agent, cotton bunchy top virus (CBTV). We have obtained the complete coding sequence of two poleroviruses from symptomatic cotton to cover all seven putative open reading frames. These species are called CBTV-1 and CBTV-2 and all seven predicted gene products differ by 25% to 49% amino acid identity, indicating they are distinct polerovirus species. A multiplex PCR for CBTV-1 and CBTV-2 was used to screen more than 700 plant samples from 36 species to identify 16 new field and experimental host species. Serological detection by tissue blot immune assay was successful when the two viruses were transmitted to chickpea ( Cicer arietinum ), but was unreliable for detecting the viruses in cotton. Volunteer and ratoon cotton were identified as common reservoirs of CBTV nearby to cotton cropping areas. Other species that may be regionally important reservoirs include Malva parviflora , Euphorbia hirta and Gossypium sturtianum . Both CBTV species were common and widespread in all major cotton production regions and the genetic diversity within each species was low for the genome region spanning from the 3’ end of open reading frame (ORF) 2 and complete ORF 3. From a total of 257 cotton plants displaying symptoms typical of cotton bunchy top, 256 (99.6%) were positive for CBTV-2 and 93 of these (36%) were mixed infections of CBTV-2 and CBTV-1. As a single infection, CBTV-1 was non-symptomatic, indicating that CBTV-2 is the causal agent of typical cotton bunchy top disease.

HomePlant DiseaseVol. 104, No. 9First Report of Cotton Leafroll Dwarf Virus Affecting Chickpea (Cicer arietinum) in Uzbekistan PreviousNext DISEASE NOTES OPENOpen Access licenseFirst Report of Cotton Leafroll Dwarf Virus Affecting Chickpea (Cicer arietinum) in UzbekistanSafaa G. Kumari, Murray Sharman, Abdulrahman Moukahel, Zafar Ziyaev, and Seid AhmedSafaa G. Kumari†Corresponding author: S. G. Kumari; E-mail Address: s.kumari@cgiar.orghttp://orcid.org/0000-0002-4492-6257International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol Station, Beqa'a, Zahle, Lebanon, Murray SharmanDepartment of Agriculture and Fisheries, Brisbane, Queensland, Australia, Abdulrahman MoukahelInternational Center for Agricultural Research in the Dry Areas (ICARDA), Terbol Station, Beqa'a, Zahle, Lebanon, Zafar ZiyaevKashkadarya Scientific Research Institute of Grain Breeding and Seed Production, Karshi, Uzbekistan, and Seid AhmedInternational Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, MoroccoAffiliationsAuthors and Affiliations Safaa G. Kumari1 † Murray Sharman2 Abdulrahman Moukahel1 Zafar Ziyaev3 Seid Ahmed4 1International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol Station, Beqa'a, Zahle, Lebanon 2Department of Agriculture and Fisheries, Brisbane, Queensland, Australia 3Kashkadarya Scientific Research Institute of Grain Breeding and Seed Production, Karshi, Uzbekistan 4International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco Published Online:6 Jul 2020https://doi.org/10.1094/PDIS-01-20-0085-PDNAboutSections ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Chickpea (Cicer arietinum L.; family Fabaceae) plants with symptoms typical of virus infection (chlorosis, stunting, necrosis, yellowing, and reddening) were collected during disease surveys in June 2012 (386 samples from 23 fields) and May to June 2013 (288 samples from 19 fields) from the major chickpea-growing regions (Tashkent, Sirdarya, Jizzah, Samarkand, and Surkhandarya) of Uzbekistan. All samples were tested first by tissue-blot immunoassay (TBIA) (Makkouk and Kumari 1996) with a broad-spectrum legume luteovirus monoclonal antibody (MAb) (5G4; Katul 1992). For comparison of relative reactions, blots from positive legume luteoviruses (bean leafroll virus [BLRV], beet western yellows virus [BWYV], and chickpea chlorotic stunt virus [CpCSV]) and heathy plants were included for each TBIA. To identify the individual legume luteoviruses, the samples with positive reaction to MAb 5G4 were retested further using specific MAbs to BWYV (A5977 from Agdia, U.S.A.), BLRV (4B10; Katul 1992), a mixture of three MAbs (1-1G5, 1-3H4, and 1-4B12) to an Ethiopian isolate of CpCSV, and a mixture of three MAbs (5-2B8, 5-3D5, and 5-5B8) to a Syrian isolate of CpCSV (Abraham et al. 2009). Total RNA was extracted from 35 chickpea samples that showed positive reaction to 5G4 MAb only, or to 5G4 and other MAbs. Reverse transcription-polymerase chain reaction (RT-PCR) was performed using polerovirus group-specific primers AS3 (5′-CACGCGTCIACCTATTTIGGRTTITG-3′) (Abraham et al. 2008) and Pol3870F (5′-ATCACBTTCGGGCCGWSTYTWTCAGA-3′), as described by Sharman et al. (2015), except with the use of MyTaq Red DNA Polymerase (Bioline, U.K.). RT-PCR amplicons of the partial coat protein gene of the expected size (376 bp) were directly sequenced. Four out of 35 tested samples had 96 to 97% nucleotide (nt) sequence identity with the Brazilian (GQ401140 and KP176644) and Argentinean (KF359947) isolates of cotton leafroll dwarf virus (CLRDV, genus Polerovirus, family Luteoviridae). To confirm CLRDV infection in these chickpea samples, they were tested by RT-PCR using CLRDV-specific primer CLRDV3675F (5′-CCACGTAGRCGCAACAGGCGT-3′) and Pol3982R (5′-CGAGGCCTCGGAGATGAACT-3′) (Sharman et al. 2015). Amplicons of the expected size (310 bp) were obtained from all four samples and were sequenced in both directions. These four samples (UzCp137-13, UzCp148-13, UzCp149-13, and UzCp154-13) were collected in 2013 from one field in the Surkhandarya region, and their nucleotide sequences were deposited in GenBank under accession numbers MK461134, MK461135, MK461136, and MK461137, respectively. After removal of primers, the resulting consensus sequences were 268 nucleotides in length and shared greater than 99% nt identity among them, and as such further analysis was done for sample UzCp137-13, for which the closest match by BLAST was 98% nt identity to a CLRDV isolate from Argentina (KF359947). To our knowledge, this is the first report of CLRDV in chickpea from Uzbekistan. Mukherjee et al. (2016) studied the genetic similarity between CLRDV and chickpea stunt disease associated virus (CpSDaV) in India and found the coat protein gene sequences of both viruses to be almost identical (89.4 to 100% depending on the virus isolates), suggesting that CpSDaV is likely a strain of CLRDV. Chickpea stunt is a major disease of chickpeas in India, and thus CLRDV will be of huge concern to both chickpea and cotton production in Uzbekistan.The author(s) declare no conflict of interest.References:Abraham, A. D., et al. 2008. Afr. J. Biotechnol. 7:414. Google ScholarAbraham, A. D., et al. 2009. Arch. Virol. 154:791. https://doi.org/10.1007/s00705-009-0374-0 Crossref, ISI, Google ScholarKatul, L. 1992. Characterization by serology and molecular biology of bean leaf roll virus and faba bean necrotic yellows virus. Ph.D. thesis, University of Göttingen, Göttingen, Germany. Google ScholarMakkouk, K. M., and Kumari, S. G. 1996. Arab J. Plant Prot. 14:3. https://asplantprotection.org/wp-content/uploads/2018/07/V14-1_3-9.pdf. Google ScholarMukherjee, A. K., et al. 2016. Plant Pathol. J. 32:580. https://doi.org/10.5423/PPJ.NT.09.2015.0197 Crossref, ISI, Google ScholarSharman, M., et al. 2015. Australas. Plant Dis. Notes 10:24. https://doi.org/10.1007/s13314-015-0174-1 Crossref, ISI, Google ScholarThe author(s) declare no conflict of interest.Funding: This work was partially supported by CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS) and Grains Research and Development Corporation-GRDC (project DAN00202).DetailsFiguresLiterature CitedRelated Vol. 104, No. 9 September 2020SubscribeISSN:0191-2917e-ISSN:1943-7692 DownloadCaptionRipening strawberry infected by Colletotrichum acutatum (M. Dowling et al.). Photo credit: M. Dowling. Diaporthe leaf spot caused by Diaporthe humulicola on hop cone tissue (E. Allan-Perkins et al.). Photo credit: M. Salvas. Metrics Article History Issue Date: 26 Aug 2020Published: 6 Jul 2020Accepted: 1 Apr 2020 Pages: 2532-2532 Information© 2020 The American Phytopathological SocietyFundingCGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS)Grains Research and Development Corporation-GRDCGrant/Award Number: DAN00202Keywordsvirusesepidemiologydisease development and spreadfield crops and legumesThe author(s) declare no conflict of interest.Cited byFirst Report of Cotton Leafroll Dwarf Virus Infecting Hibiscus syriacus in South KoreaDavaajargal Igori, Ah Young Shin, Se Eun Kim, Suk Yoon Kwon, and Jae Sun Moon3 October 2022 | Plant Disease, Vol. 106, No. 11Prospective Alternate Hosts of an Emerging Polerovirus in Cotton Landscapes in the Southeastern United States13 October 2022 | Viruses, Vol. 14, No. 10Antibodies for the Coat Protein of Cotton Leafroll Dwarf Virus Detect Commelina sp. as an Intermediary Host for Cotton Blue Disease13 July 2022 | Frontiers in Plant Science, Vol. 13The Viral Threat in Cotton: How New and Emerging Technologies Accelerate Virus Identification and Virus Resistance Breeding5 April 2022 | Frontiers in Plant Science, Vol. 13Plant Pathogens which Threaten Food Security: Viruses of Chickpea and Other Cool Season Legumes in West Asia and North Africa4 February 2020 | Food Security, Vol. 12, No. 3

The orthotospovirus, capscium chlorosis virus (CaCV) was shown to be common and widespread in the weed host Ageratum conyzoides in eastern coastal regions of Queensland, Australia with up to 92% of plants infected. This is the first report of A. conyzoides being an important host of CaCV in Australia. CaCV was also found as natural infections of Arachis hypogaea (peanut), Ananas comosus (pineapple), Sonchus oleraceus, Tagetes minuta and Emilia sonchifolia. This is the first report of CaCV infecting pineapple and being associated with severe disease symptoms. Thrips palmi, Frankliniella schultzei and Microcephalothrips abdominalis were shown to transmit CaCV while no transmission was achieved using F. occidentalis.

Alfalfa plants in the field can display a range of virus-like symptoms, especially when grown over many years for seed production. Most known alfalfa viruses have RNA genomes, some of which can be detected using diagnostic assays, but many viruses of alfalfa are not well characterized. This study aims to identify the RNA and DNA virus complexes associated with alfalfa plants in Australia. To maximize the detection of RNA viruses, we purified double-stranded RNA (dsRNA) for high throughput sequencing and characterized the viromes of ten alfalfa samples that showed diverse virus-like symptoms. Using Illumina sequencing of tagged cDNA libraries from immune-captured dsRNA, we identified sequences of the single-stranded RNA viruses, alfalfa mosaic virus (AMV), bean leafroll virus, a new emaravirus tentatively named alfalfa ringspot-associated virus, and persistent dsRNA viruses belonging to the families Amalgaviridae and Partitiviridae. Furthermore, rolling circle amplification and restriction enzyme digestion revealed the complete genome of chickpea chlorosis Australia virus, a mastrevirus (family Geminiviridae) previously reported only from chickpea and French bean that was 97% identical to the chickpea isolate. The sequence data also enabled the assembly of the first complete genome (RNAs 1-3) of an Australian AMV isolate from alfalfa.

In 2016, severe pod distortion and leaf mottling in green beans (Phaseolus vulgaris) for the fresh market (Figs. 1-2; isolate Q5288) occurred in the Fassifern production area in south Queensland, Australia. Disease incidence in crops was 60-100%, resulting in losses of up to ÄD 400,000. A sample of soybean (Glycine max cv. Zam-1) displaying similar leaf symptoms (Fig. 3; isolate Q5294) was collected from a crop, about 50 km from the infected bean crops. Disease incidence in this crop was 5-10%. Both isolates were transmitted by manual inoculation and by Bemisia tabaci (MEAM1) from infected bean plants to uninfected soybean and bean. All test plants developed symptoms similar to the original samples. The inoculated plants tested negative for potyvirus using an ImmunoStrip test (Agdia, USA) and a group-specific RT-PCR (Langeveld et al., 3; Gibbs & Mackenzie, 2). Flexuous virions 600-700 nm in length (Fig. 4) were observed in the inoculated plants The virion morphology is consistent with carlaviruses and the samples tested positive in DAS-ELISA with antibodies (DSMZ, Germany) for the carlavirus, Cowpea mild mottle virus (CPMMV). The virus has since been detected in Australia's major winter bean production area, some 1000 km distant from the original detection site. In 2019, the carlavirus was also identified from Bundaberg in south Queensland where disease incidence exceeded 50% with significant production losses from deformed, unmarketable pods. The detection of the virus in regions producing 80% of Australia's fresh green beans and the high susceptibility of major commercial varieties has prompted new research on virus epidemiology and management. Amplicons covering part of the coat protein gene through to the 3' end of the genome were obtained by RT-PCR amplification using the oligo-dT primer Poty 1 (Gibbs & Mackenzie, 2) as the reverse primer for both isolates and the forward primer Carla7190F (5'-GGNYTNGGNGTICCIACIGARCAYGT-3'; designed to detect a range of carlaviruses) for Q5288 and CPMMV7277F (5'-GATTCHAGYGGBACHTTYGAYTGGA-3'; designed from CPMMV sequences) for Q5294. The amplicons were directly sequenced and gave fragments of 916 bp (GenBank Accession No. MK910291) for Q5288 and 837 bp (MK910292) for Q5294. These sequences are only 71% identical. Using BLAST analyses (Zhang et al., 2000), the sequences most closely matched CPMMV from Brazil (KC884249) at 85% identity, and CPMMV from India (AF024629) at 76%, for Q5288 and Q5294, respectively.The ICTV demarcation threshold for species within the Carlavirus genus is less than 72% identity between coat protein or polymerase sequences. A comparison of the partial coat protein nucleotide sequences indicated the Australian isolates fall within CPMMV with similar identities to each other (78.9%) and the type species originally reported from Ghana (Brunt & Kenten, 1) (NC_014730), 78.1% (Q5288) and 78.9% (Q5294). Further analyses reveal the CPMMV type species is very diverse from other isolates and the ICTV criteria is not met for the polymerase gene (Table 1). This is the first report of a carlavirus infecting plants in the Fabaceae in Australia. The Australian isolates are genetically distinct from each other and to international CPMMV isolates. Further refinement of the taxonomy of carlaviruses infecting hosts in this genus, including these Australian isolates is required. This work was funded by Hort Innovation using the vegetable research and development levy and contributions from the Australian Government.

Macroptilium atropurpureum (siratro) samples from Queensland, Australia were collected as part of virus surveys and screened using tissue blot immunoassays for the presence of luteoviridae viruses. Sequencing of a reverse transcription polymerase chain reaction (RT-PCR) product, generated with degenerate primers for poleroviruses, revealed the non-symptomatic virus in siratro was a novel polerovirus, given the proposed name siratro latent polerovirus (SLPV). SLPV-specific RT-PCR showed that SLPV was widely distributed in siratro throughout Queensland. SLPV was transmitted via Aphis craccivora (cowpea aphids) to siratro and Pisum sativum (field pea). The complete genome of one isolate of SLPV was found to be 6090 nucleotides in length and shared only 69% nucleotide identity with its closest match, phasey bean mild yellows virus. Poleroviruses contain six major open reading frames (ORFs) labelled ORF 0–5. The SLPV genome has a similar arrangement. However, the region that should encode for ORF 0 is missing an AUG start codon. Sequencing of this region, from eight SLPV isolates, from different geographic regions, showed all lacked the ORF 0 AUG site and some isolates contained point mutations and deletions in this region, thus inhibiting translation of ORF 0. These results suggest that SLPV does not have a functional ORF 0 which may affect viral pathogenicity and restrict host range. This is the first report, to date, of a polerovirus with an apparently non-functional ORF 0 region.

A new polerovirus species with the proposed name faba bean polerovirus 1 (FBPV-1) was found in winter legume crops and weeds in New South Wales, Australia. We describe the complete genome sequence of 5,631 nucleotides, containing all putative open reading frames, from two isolates, one from faba bean (Vicia faba) and one from chickpea (Cicer arietinum). FBPV-1 has a genome organization typical of poleroviruses with six open reading frames. However, recombination analysis strongly supports a recombination event in which the 5′ portion of FBPV-1, which encodes for proteins P0, P1 and P1-P2, appears to be from a novel parent with a closest nucleotide identity of only 66% to chickpea chlorotic stunt virus. The 3′ portion of FBPV-1 encodes for proteins P3, P4 and P3-P5 and shares 94% nucleotide identity to a turnip yellows virus isolate from Western Australia.

We present here the complete genome sequence of a novel mastrevirus isolated from Cicer arietinum (chickpea) from Australia. We propose the name chickpea redleaf virus 2.