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.

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.

Phytoplasma disease outbreaks were common and widespread in grain legume crops including mung bean (Vigna radiata), soybean (Glycine max) and peanut (Arachis hypogaea) in late 2016 and early 2017. Mung bean crops were affected in all major production areas spanning a distance of over 1,200 km from north to south with numerous crops having greater than 40% disease incidence near Dalby. Several soybean crops from Cecil Plains were also affected by phytoplasma in late autumn 2016. Almost 100% of plants were affected in some paddocks and virtually no yield. During the 2016/17 summer, some vegetable and pawpaw crops also had damaging outbreaks of disease. Several tomato crops in south-east Queensland had incidences of “big-bud” disease in excess of 50%. Capsicum and eggplant crops also had phytoplasma at higher than normal levels. In coastal Queensland, pawpaw (Carica papaya) crops had about 30% of plants affected by yellow crinkle disease but up to 80% in some younger plants. The P1/P7 region of the 16S gene was amplified from several different crop types. Resulting sequences had close to 100% nucleotide identity to pigeon pea little leaf phytoplasma, Candidatus Phytoplasma aurantifolia (16Sr-II group), which has been previously reported in Australia from pigeon pea (Canjanus cajan) and stylosanthes. A known leaf hopper vector of phytoplasma, Orosius orientalis, was collected from some affected mung bean crops but it is not certain it was associated with these disease outbreaks. To our knowledge, this is the most significant, widespread outbreak of phytoplasma in broad acre crops to occur in this region of Australia. It is unclear what the underlying reasons are for this sudden increase in disease incidence. We are continuing further studies to determine: the diversity of phytoplasma across crop and weed hosts and geographical range, which insect species are vectors, and possible management options.

The Bowen region of Northern Queensland is an important winter production area for tomatoes in Australia. There are three economically important viruses in the region that affect tomato, Tomato yellow leaf curl virus (TYLCV), Tomato spotted wilt virus (TSWV) and Potato leafroll virus (PLRV), which are vectored by whiteflies, thrips and aphids, respectively. An area wide management approach is required to lower the primary inoculum throughout the district. To this end, we undertook investigations into the virus incidence and alternative hosts for the virus and vectors in different cropping regions throughout the district, as well as local management options such as insecticide application and possible non-host cover crops for the wet-season break in production. The initial incidence of Potato leafroll virus was very high, most probably due to abnormal weather patterns for the district, and has ceased to be a problem. Tomato yellow leaf curl virus is a continual problem even at the beginning of the season, indicating large reservoir host(s) in the environment. Only four alternative hosts have been identified: Stachytarpheta jamaicensis (TSWV), Solanum americanum (PLRV and TYLCV) Trianthema portulacastrum (TYLCV), and Amaranthus viridis(TLYCV). Different insecticide and application options were trialled for protection against Tomato yellow leaf curl virus, with the best possible option yielding marketable fruit more than ninety percent of a resistant hybrid. A trial of yield vs time of infection of TYLCV found that whitefly exclusion for 6 weeks post-transplant yielded an average increase of nearly three kilograms of marketable fruit per plant. A number of pulse crops have been confirmed as non-hosts of tomato yellow leaf curl for use as cover crops in the wet-season break. Most of the production has moved to dual resistant TYLCV/TSWV hybrids, though an area wide management program still needs to be established to reduce the primary inoculum throughout the district, giving growers more varietal options, especially early in the season.

Pineapple mealybug wilt-associated virus 1 (PMWaV-1), 2 (PMWaV-2) and 3 (PMWaV-3) have been detected in Australian commercial pineapple crops, along with a previously undescribed ampelovirus, forwhich the name Pineapple mealybug wilt-associated virus 5 (PMWaV-5) is proposed. Partial sequences extending from open reading frame 1 b through to the heat shock protein homologue were obtained for PMWaV-1, -3 and -5. Phylogenetic analyses of selected regions of these sequences indicated that PMWaV-5 is a distinct species and most closely related to PMWaV-1. The amino acid sequence variation observed in the RNA-dependent RNA polymerase region of PMWaV-1 isolates was 95.8–98.4% and of PMWaV-3 isolates was 92.2–99.5%. p ]In surveys of mealybug wilt disease (MWD) affected crops, none of the four viruses was clearly associated with the disease at all survey sites. A statistically significant association (P <0.001) between the presence of PMWaV-2 and symptoms was observed at one survey site (site 3), but the virus was at a low incidence at the remaining three survey sites. By contrast, although PMWaV-1 and −3 were equally distributed between symptomless and MWD-affected plants at site 3, there was a statistically significant (P < 0.001) association between each of these two viruses and MWD at sites 1 and 4. At site 2, there was a statistically significant (P < 0.001) association only between PMWaV-3 and MWD. PMWaV-1 was the most commonly found of the four viruses and conversely PMWaV-5 was only occasionally found. Australian isolates of PMWaV-1, -2 and -3 were transmitted by the mealybug species Dysmicoccus brevipes.

A previously published partial sequence of pineapple bacilliform virus was shown to be from a retrotransposon (family Metaviridae) and not from a badnavirus as previously thought. Two newly discovered sequence groups isolated from pineapple were associated with bacilliform virions and were transmitted by mealybugs. Phylogenetic analyses indicated that they were members of new badnavirus species. A third caulimovirid sequence was also amplified from pineapple, but available evidence suggests that this DNA is not encapsidated, but more likely derived from an endogenous virus.

Previous trials of antiplatelet therapy for the prevention of venous thromboembolism have individually been inconclusive, but a meta-analysis of their results indicated reductions in the risks of deep-vein thrombosis and of pulmonary embolism in various high-risk groups. The aim of this large randomised placebo-controlled trial was to confirm or refute these apparent benefits.During 1992-1998, 148 hospitals in Australia, New Zealand, South Africa, Sweden and the UK randomised 13,356 patients undergoing surgery for hip fracture, and 22 hospitals in New Zealand randomised a further 4088 patients undergoing elective arthroplasty. Study treatment was 160 mg daily aspirin or placebo, started preoperatively and continued for 35 days. Patients received any other thromboprophylaxis thought necessary. Follow-up was of mortality and of in-hospital morbidity up to day 35.Among the patients with hip fracture, allocation to aspirin produced proportional reductions in pulmonary embolism of 43% (95% CI 18-60; p=0.002) and in symptomatic deep-vein thrombosis of 29% (3-48; p=0.03). Pulmonary embolism or deep-vein thrombosis was confirmed in 105 (1.6%) of 6679 patients assigned aspirin compared with 165 (2.5%) of 6677 assigned placebo, which represents an absolute reduction of 9 (SE 2) per 1000 and a proportional reduction of 36% (19-50; p=0.0003). Similar proportional effects were seen in all major subgroups, including patients receiving subcutaneous heparin. Aspirin prevented 4 (1) fatal pulmonary emboli per 1000 patients (18 aspirin-group vs 43 placebo-group deaths), representing a proportional reduction of 58% (27-76; p=0.002), with no apparent effect on deaths from any other vascular cause (hazard ratio 1.04 [95% CI 0.86-1.26]) or non-vascular cause (1.01 [0.84-1.23]). Deaths due to bleeding were few (13 aspirin vs 15 placebo), but there was an excess of 6 (3) postoperative transfused bleeding episodes per 1000 patients assigned aspirin (p=0.04). Among elective-arthroplasty patients, rates of venous thromboembolism were lower, but the proportional effects of aspirin were compatible with those among patients with hip fracture.These results, along with those of the previous meta-analysis, show that aspirin reduces the risk of pulmonary embolism and deep-vein thrombosis by at least a third throughout a period of increased risk. Hence, there is now good evidence for considering aspirin routinely in a wide range of surgical and medical groups at high risk of venous thromboembolism.

Non-manual methods of lysing single second-stage juveniles (J2s) of Meloidogyne and direct squashing of nematodes were assessed for consistency by the success of subsequent amplification of mitochondrial DNA by polymerase chain reaction. Microwave heating and boiling resulted in amplification of DNA from only 10% of J2s; treatment with proteinase K, 20%; direct squashing, 50%; and 24 h incubation in NaOH, 81%. Components of mixtures of mtDNA types could be detected consistently by DNA amplification only if they constituted at least 30% of the mixture.

Colombian datura virus was identified from the ornamental plant Brugmansia sp., showing leaf mosaic symptoms. The nucleotide sequence of the 3′ untranslated region and the amino acid sequence of the 3′ portion of the coat protein were 100% identical to those from a Hungarian isolate of the virus. This represents the first record of this virus in Australia.

Infection of commercial garlic crops by viruses is common and substantially reduces crop quality and yield. Viruses found in garlic include members of the Poty-, Carla- and Allexivirus genera, and a Tospovirus, Iris yellow spot virus (IYSV). Virus spread in garlic crops is facilitated though vegetative propagation of infected bulbs, and through vectors, such as aphids, mites and thrips. Extensive international research has identified viruses infecting garlic, and their impacts on yield, however, there is limited knowledge for Australian garlic. This study evaluates the distribution of viruses in Australian field garlic and vegetative planting material across multiple growing districts located in Queensland, New South Wales, South Australia, and Victoria. Molecular screening of crop samples was carried out using genus-specific RT-PCR-based assays, followed by species-specific hybridisation assays. The samples were tested for three potyviruses, Onion yellow dwarf virus (OYDV), Shallot yellow strip virus (SYSV), and Leek yellow stripe virus (LYSV), three carlaviruses, Garlic common latent virus (GarCLV), Garlic latent virus (GarLV) and Shallot latent virus (SLV), and five allexiviruses, Garlic viruses A, B, C and X (GarVA, -B, -C, and –X) and Shallot virus X (ShVX). Virus incidence within planting material was near 100%, with plants carrying at least one virus from each of the three genera tested. The most common infections were potyviruses, OYDV and LYSV, and carlaviruses, SLV and GarCLV. The genetic diversity of local viruses was evaluated through sequencing of the viral coat protein (CP) across a selection of isolates. Increased knowledge of virus population dynamics in Australian crops, their vectors and weed hosts, contributes to our understanding of virus epidemiology and supports quarantine efforts attempting to limit the entry and spread of new viruses into Australia. Additionally, this study supports further development of virus free garlic germplasm in Australia and contributes targeted pest management strategies for industry.