Resistance of Musa balbisiana Accessions of the Philippines to Banana Bunchy Top Virus.

Banana bunchy top disease (BBTD) is caused by banana bunchy top virus (BBTV), the most important virus affecting banana. Currently, no cultivar or accession of banana has complete resistance to BBTD. A total of 36 wild Musa spp. accessions, including 34 Musa balbisiana and 2 M. acuminata subsp. errans ("Agutay"), were screened for resistance against BBTV. In greenhouse tests using viruliferous banana aphids (Pentalonia nigronervosa), all M. balbisiana accessions remained symptomless, and BBTV was not detected in any of these plants by PCR at 3 and 6 months postinoculation. In contrast, 100% disease incidence was recorded in M. acuminata subsp. errans and in cv. Lakatan susceptible control plants. The PCR-negative M. balbisiana plants were then transferred to a field with high BBTV inoculum pressure where they remained symptomless and PCR-negative for up to 5 years, while all cv. Lakatan developed BBTD. Wild M. balbisiana accessions showed a high level of resistance and possibly immunity to BBTV and are expected to provide a resource for conventional and marker-assisted breeding.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Genome sequence of pineapple secovirus B, a second sadwavirus reported infecting Ananas comosus.

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.

Bermuda grass latent virus in Australia: genome sequence, sequence variation, and new hosts.

Bermuda grass latent virus (BGLV; genus Panicovirus) is identified for the first time in Australia and in only the second country after the USA. A full-length genome sequence was obtained, which has 97% nucleotide sequence identity to that of the species exemplar isolate. Surveys for BGLV, utilising a newly designed universal panicovirus RT-PCR assay for diagnosis, demonstrated widespread infection by this virus in a broad variety of Bermuda grass cultivars (Cynodon dactylon and C. dactylon × C. transvaalensis) grown in both New South Wales and Queensland. The virus was also detected in Rhodes grass (Chloris gayana) and Kikuyu grass (Cenchrus clandestinus), which are both important pasture grasses in subtropical Australia, and the latter is also grown as turf. Furthermore, the Rhodes grass plant, which had strong mosaic symptoms, was also infected with sugarcane mosaic virus, warranting further investigations as to whether synergistic interactions occur between these two viruses.

Viruses Infecting Greenhood Orchids (Pterostylidinae) in Eastern Australia.

The Australasian biogeographic realm is a major centre of diversity for orchids, with every subfamily of the Orchidaceae represented and high levels of endemism at the species rank. It is hypothesised that there is a commensurate diversity of viruses infecting this group of plants. In this study, we have utilised high-throughput sequencing to survey for viruses infecting greenhood orchids (Pterostylidinae) in New South Wales and the Australian Capital Territory. The main aim of this study was to characterise Pterostylis blotch virus (PtBV), a previously reported but uncharacterised virus that had been tentatively classified in the genus Orthotospovirus. This classification was confirmed by genome sequencing, and phylogenetic analyses suggested that PtBV is representative of a new species that is possibly indigenous to Australia as it does not belong to either the American or Eurasian clades of orthotospoviruses. Apart from PtBV, putative new viruses in the genera Alphaendornavirus, Amalgavirus, Polerovirus and Totivirus were discovered, and complete genome sequences were obtained for each virus. It is concluded that the polerovirus is likely an example of an introduced virus infecting a native plant species in its natural habitat, as this virus is probably vectored by an aphid, and Australia has a depauperate native aphid fauna that does not include any species that are host-adapted to orchids.

Characterisation of novel endogenous geminiviral elements in macadamia.

BACKGROUND: The presence of geminivirus sequences in a preliminary analysis of sRNA sequences from the leaves of macadamia trees with abnormal vertical growth (AVG) syndrome was investigated. RESULTS: A locus of endogenous geminiviral elements (EGE) in the macadamia genome was analysed, and the sequences revealed a high level of deletions and/or partial integrations, thus rendering the EGE transcriptionally inactive. The replication defective EGE in the macadamia genome indicates its inability to be the source of new viral infections and thus cause AVG or any other disease in macadamia. The EGE sequences were detected in two edible Macadamia species that constitute commercial cultivars and the wild germplasm of edible and inedible species of Macadamia. This strongly suggests that the integration preceded speciation of the genus Macadamia. A draft genome of a locus of EGE in Macadamia was developed. The findings of this study provide evidence to suggest the endogenization of the geminiviral sequences in the macadamia genome and the ancestral relationship of EGE with Macadamia in the Proteaceae family. Random mutations accumulating in the EGE inform that the sequence is evolving. CONCLUSIONS: The EGE in Macadamia is inactive and thus not a direct cause of any diseases or syndromes including AVG in macadamia. The insertion of the EGE in the macadamia genome preceded speciation of the genus Macadamia.

Taxonomy update for the family Alphasatellitidae: new subfamily, genera, and species.

Alphasatellites (family Alphasatellitidae) are circular, single-stranded DNA molecules (~1-1.4 kb) that encode a replication-associated protein and have commonly been associated with some members of the families Geminiviridae, Nanoviridae, and Metaxyviridae (recently established). Here, we provide a taxonomy update for the family Alphasatellitidae following the International Committee on Taxonomy of Viruses (ICTV) Ratification Vote held in March 2021. The taxonomic update includes the establishment of the new subfamily Petromoalphasatellitinae. This new subfamily includes three new genera as well as the genus Babusatellite, which previously belonged to the subfamily Nanoalphasatellitinae. Additionally, three new genera and 14 new species have been established in the subfamily Geminialphasatellitinae, as well as five new species in the subfamily Nanoalphasatellitinae.

Genome sequence and geographic distribution of a new nepovirus infecting Stenotaphrum secundatum in Australia.

The genome sequence of a new subgroup C nepovirus from Stenotaphrum secundatum in Australia is described. This virus, tentatively named Stenotaphrum nepovirus (SteNV), was present in separate plants as a mixed infection with either sugarcane mosaic virus or Panicum mosaic virus. The virus genome was divided between two RNA segments, 7,824 and 7,104 nucleotides (nt) in length, which each encode a single long polyprotein with putative 3C-like cysteine protease sites of the type H/G, H/S or L/S. The 3' untranslated region of RNA2, at 2,155 nt, is the longest observed for any subgroup C nepovirus. Phylogenetic analyses using protease-polymerase and coat protein amino acid alignments suggest that SteNV is most closely related to cherry leaf roll virus. Using a newly developed RT-PCR assay, this virus was detected at multiple localities in New South Wales, Queensland and Western Australia, and in a second host species, Digitaria didactyla. No consistent association between virus infection and symptoms could be established. The economic importance, pathogenicity and transmission of this novel virus species warrant further investigation.

ICTV Virus Taxonomy Profile: Nanoviridae.

Nanoviridae is a family of plant viruses (nanovirids) whose members have small isometric virions and multipartite, circular, single-stranded (css) DNA genomes. Each of the six (genus Babuvirus) or eight (genus Nanovirus) genomic DNAs is 0.9-1.1 kb and is separately encapsidated. Many isolates are associated with satellite-like cssDNAs (alphasatellites) of 1.0-1.1 kb. Hosts are eudicots, predominantly legumes (genus Nanovirus), and monocotyledons, predominantly in the order Zingiberales (genus Babuvirus). Nanovirids require a virus-encoded helper factor for transmission by aphids in a circulative, non-propagative manner. This is a summary of the ICTV Report on the family Nanoviridae, which is available at ictv.global/report/nanoviridae.

Identification of putative viroplasms within banana cells infected by banana streak MY virus.

The badnavirus replication cycle is poorly understood and most knowledge is based on extrapolations from model viruses such as Cauliflower mosaic virus (CaMV). However, in contrast to CaMV, badnaviruses are thought not to produce viroplasms and therefore it has been a mystery as to where virion assembly occurs. In this study, ultrathin sections of a banana leaf infected with a badnavirus, banana streak MY virus (BSMYV), were examined by transmission electron microscopy. Electron-dense inclusion bodies (EDIBs) were sporadically distributed in parenchymatous tissues of the leaf, most commonly in the palisade and spongy mesophyll cells. These EDIBs had a characteristic structure, comprising an electron-dense core, a single, encircling lacuna and an outer ring of electron-dense material. However, much less frequently, EDIBs with two or three lacunae were observed. In the outer ring, densely packed virions were visible with a shape and size consistent with that expected for badnaviruses. Immunogold labelling was done with primary antibodies that detected the N-terminus of the capsid protein and strong labelling of the outer ring but not the central core or lacuna was observed. It is concluded that the EDIBs that were observed are equivalent in function to the viroplasms of CaMV, although obviously different in composition as there is not a paralogue of the transactivation/viroplasm protein in the badnavirus genome. It is postulated that production of a viroplasm could be a conserved characteristic of all members of the Caulimoviridae.

Faba bean polerovirus 1 (FBPV-1); a new polerovirus infecting legume crops in Australia.

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.

Glucose-6-Phosphate Dehydrogenase Deficiency is Associated with Cardiovascular Disease in U.S. Military Centers.

Glucose-6-phosphate dehydrogenase (G6PD) protects erythrocytes from oxidative stress and hemolysis; G6PD deficiency is the most prevalent enzymopathy. The United States military routinely performs tests to prevent exposing G6PD-deficient personnel to antimalarial drugs that might cause life-threatening hemolytic reactions. In addition, G6PD is a key determinant of vascular function, and its deficiency can lead to impaired nitric oxide production and greater vascular oxidant stress-precursors to atherosclerosis and cardiovascular disease. Using military medical records, we performed a retrospective, cross-sectional study to investigate whether deficient G6PD levels are associated with a higher prevalence of cardiovascular disease than are normal levels, and, if so, whether the relationship is independent of accepted cardiovascular risk factors. We analyzed the medical records of 737 individuals who had deficient G6PD levels and 16,601 who had normal levels. Everyone had been screened at U.S. military medical centers from August 2004 through December 2007. We evaluated our dependent variable (composite cardiovascular disease) at the individual level, and performed binary logistic regression of our independent variable (G6PD status) and control variables (modifiable cardiovascular risk factors). The adjusted odds ratio of 1.396 (95% CI, 1.044-1.867; P <0.05) indicated that G6PD-deficient individuals have 39.6% greater odds of developing cardiovascular disease than do those with normal levels. Early intervention may reduce the incidence of cardiovascular disease in military personnel and civilians who have deficient G6DP levels.

Off-tarp emissions, distribution, and efficacy of carbonated fumigants in a low permeability film tarped field.

Carbonated fumigants have been shown to distribute quickly and uniformly in sandy soils and improve pest control efficacy for annual crops. Low permeability films, such as VaporSafe® (TIF), could further improve fumigant dispersion by effectively retaining the fumigant in soil; however, there is a concern that the TIF can lead to higher off-tarp edge emissions. An orchard field trial was conducted to determine the off-tarp emissions, distribution, efficacy, and fate of carbonated Telone® C35 [63.4% 1,3-dichloropropene (1,3-D), 34.7% chloropicrin (CP)] that was shank-injected at 46cm soil depth. Treatments included carbonated fumigants at full- or 2/3 rates and a full rate of regular (nitrogen-pressurized) fumigants covered with standard polyethylene (PE) film, TIF, or no surface seal. Fumigant emissions at the regular tarp edge (25cm from the shank line) peaked at 3.98µgm-2s-1 for 1,3-D and 0.05µgm-2s-1 for CP. The addition of a TIF tarp extension (to 85cm from the shank line) reduce peak off-tarp emissions to <1 and <0.03µgm-2s-1 for 1,3-D and CP, respectively. Fumigant concentration under TIF was usually at least twice that under PE regardless of carbonation. Carbonation at 345KPa with 1.5% of dissolved CO2 did not significantly improve fumigant dispersion in soil profile compared to the conventional nitrogen pressurization. In a citrus nematode bioassay, only the 2/3 rate of carbonated fumigation treatment sealed with PE failed to control nematodes at 25cm away from shank line. This research indicates that a 60-cm TIF extension can effectively reduce off-tarp edge emissions in strip fumigation treatments. While the adaptability of carbonation of fumigants is still questionable, further research efforts are needed in finding effective solutions to control plant parasitic nematodes, which remain a challenge in orchard fumigation.

Ongoing geographical spread of Tomato yellow leaf curl virus.

Tomato yellow leaf curl virus (TYLCV) seriously impacts tomato production throughout tropical and sub-tropical regions of the world. It has a broad geographical distribution and continues to spread to new regions in the Indian and Pacific Oceans including Australia, New Caledonia and Mauritius. We undertook a temporally-scaled, phylogeographic analysis of all publicly available, full genome sequences of TYLCV, together with 70 new genome sequences from Australia, Iran and Mauritius. This revealed that whereas epidemics in Australia and China likely originated through multiple independent viral introductions from the East-Asian region around Japan and Korea, the New Caledonian epidemic was seeded by a variant from the Western Mediterranean region and the Mauritian epidemic by a variant from the neighbouring island of Reunion. Finally, we show that inter-continental scale movements of TYLCV to East Asia have, at least temporarily, ceased, whereas long-distance movements to the Americas and Australia are probably still ongoing.

Identification and in silico characterisation of defective molecules associated with isolates of banana bunchy top virus.

Banana bunchy top virus (BBTV) is a multi-component single-stranded DNA virus. From 267 potentially infected Musa plants, 24 apparently 'defective' BBTV components have been identified. Interestingly, 23/24 of these defective molecules were apparently derived from DNA-R. All of the identified defective molecules had retained at least part of the CR-SL and CR-M but had insertions and/or deletions that in most cases resulted in open reading frame disruptions. Our detection of three monophyletic but diverse (and therefore likely circulating) defective DNA-R lineages suggests that, in many cases, defective DNA-R molecules might remain associated with BBTV genomes for prolonged periods.

Fumigation efficacy and emission reduction using low-permeability film in orchard soil fumigation.

BACKGROUND: Many orchards use fumigation to control soilborne pests prior to replanting. Controlling emissions is mandatory to reduce air pollution in California. This research evaluated the effects of plastic film type [polyethylene (PE) or totally impermeable film (TIF)], application rate of Telone C35 [full (610 kg ha(-1) ), 2/3 or 1/3 rates] and carbonation at 207 kPa on fumigant transport (emission and in soil) and efficacy. RESULTS: While increasing fumigant concentrations under the tarp, TIF reduced emissions >95% (∼2% and <1% of total applied 1,3-dichloropropene and chloropicrin respectively) relative to bare soil, compared with ∼30% reduction by PE. All fumigation treatments, regardless of film type, provided good nematode control above 100 cm soil depth; however, nematode survival was high at deeper depths. Weed emergence was mostly affected by tarping and fumigant rate, with no effects from the carbonation. CONCLUSION: TIF can effectively reduce fumigant emissions. Carbonation under the studied conditions did not improve fumigant dispersion and pest control. The 2/3 rate with TIF controlled nematodes as effectively as the full rate in bare soil or under the PE film to 100 cm soil depth. However, control of nematodes in deeper soil remains a challenge for perennial crops.

Effects of CO2 dissolution on phase distribution and degradation of dimethyl disulfide in soils under grape production.

BACKGROUND: Dimethyl disulfide (DMDS) is a fumigant recently registered in parts of the United States. The fumigant has high pesticidal activity, but does not disperse in soils as well as other fumigants. This study assessed the use of CO2 as a propellant to improve soil dispersion and diffusion by evaluating the partitioning and degradation of DMDS after carbonation in four vineyard soils collected in California. RESULTS: The soil with the highest organic carbon content (Clarksburg) had the highest soil-water partition coefficient (Kd ) (P < 0.001), which increased after carbonation. However, DMDS sorption decreased in the Mecca and Fowler soils. Henry's law constant (Kh ), which measures a compound's potential for partitioning between air and water, doubled from 0.04 to 0.10 with the addition of CO2 , indicating less DMDS solubility. Carbonation did not negatively affect DMDS's half-lives in the different soils. CONCLUSION: While trials are needed for validation of field-scale impacts, carbonation had mixed effects on soil partitioning and no discernable impact on degradation, but greatly decreased DMDS water solubility. This indicates that carbonation could improve some facets of DMDS diffusion and dispersion, depending on soil properties (carbon content and moisture), without greatly affecting its other behaviors.

The global distribution of Banana bunchy top virus reveals little evidence for frequent recent, human-mediated long distance dispersal events.

Banana bunchy top virus (BBTV; family Nanoviridae, genus Babuvirus) is a multi-component single-stranded DNA virus, which infects banana plants in many regions of the world, often resulting in large-scale crop losses. We analyzed 171 banana leaf samples from fourteen countries and recovered, cloned, and sequenced 855 complete BBTV components including ninety-four full genomes. Importantly, full genomes were determined from eight countries, where previously no full genomes were available (Samoa, Burundi, Republic of Congo, Democratic Republic of Congo, Egypt, Indonesia, the Philippines, and the USA [HI]). Accounting for recombination and genome component reassortment, we examined the geographic structuring of global BBTV populations to reveal that BBTV likely originated in Southeast Asia, that the current global hotspots of BBTV diversity are Southeast Asia/Far East and India, and that BBTV populations circulating elsewhere in the world have all potentially originated from infrequent introductions. Most importantly, we find that rather than the current global BBTV distribution being due to increases in human-mediated movements of bananas over the past few decades, it is more consistent with a pattern of infrequent introductions of the virus to different parts of the world over the past 1,000 years.

Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: high rates of intra-species recombination - a driving force in the emergence of new strains.

In Sudan Chickpea chlorotic dwarf virus (CpCDV, genus Mastrevirus, family Geminiviridae) is an important pathogen of pulses that are grown both for local consumption, and for export. Although a few studies have characterised CpCDV genomes from countries in the Middle East, Africa and the Indian subcontinent, little is known about CpCDV diversity in any of the major chickpea production areas in these regions. Here we analyse the diversity of 146 CpCDV isolates characterised from pulses collected across the chickpea growing regions of Sudan. Although we find that seven of the twelve known CpCDV strains are present within the country, strain CpCDV-H alone accounted for ∼73% of the infections analysed. Additionally we identified four new strains (CpCDV-M, -N, -O and -P) and show that recombination has played a significant role in the diversification of CpCDV, at least in this region. Accounting for observed recombination events, we use the large amounts of data generated here to compare patterns of natural selection within protein coding regions of CpCDV and other dicot-infecting mastrevirus species.

Phylodynamic evidence of the migration of turnip mosaic potyvirus from Europe to Australia and New Zealand.

Turnip mosaic virus (TuMV) is a potyvirus that is transmitted by aphids and infects a wide range of plant species. We investigated the evolution of this pathogen by collecting 32 isolates of TuMV, mostly from Brassicaceae plants, in Australia and New Zealand. We performed a variety of sequence-based phylogenetic and population genetic analyses of the complete genomic sequences and of three non-recombinogenic regions of those sequences. The substitution rates, divergence times and phylogeographical patterns of the virus populations were estimated. Six inter- and seven intralineage recombination-type patterns were found in the genomes of the Australian and New Zealand isolates, and all were novel. Only one recombination-type pattern has been found in both countries. The Australian and New Zealand populations were genetically different, and were different from the European and Asian populations. Our Bayesian coalescent analyses, based on a combination of novel and published sequence data from three non-recombinogenic protein-encoding regions, showed that TuMV probably started to migrate from Europe to Australia and New Zealand more than 80 years ago, and that distinct populations arose as a result of evolutionary drivers such as recombination. The basal-B2 subpopulation in Australia and New Zealand seems to be older than those of the world-B2 and -B3 populations. To our knowledge, our study presents the first population genetic analysis of TuMV in Australia and New Zealand. We have shown that the time of migration of TuMV correlates well with the establishment of agriculture and migration of Europeans to these countries.

Emissions from soil fumigation in two raised bed production systems tarped with low permeability films.

Raised beds are used to produce some high-value annual fruit and vegetable crops such as strawberry in California (CA) and tomato in Florida (FL), USA. Pre-plant soil fumigation is an important tool to control soil-borne pests in the raised beds. However, fumigant emissions have detrimental environmental consequences. Field trials were conducted to evaluate emissions of 1,3-dichloropropene (1,3-D) and chloropicrin (CP) in two different production systems with raised beds covered by different tarps. In the CA trial, InLine (60.8% 1,3-D and 33.3% CP) was drip-applied at 340 kg ha(-1) to 5 cm deep in the beds (30 cm high and 107 cm wide) tarped with polyethylene (PE) or virtually impermeable film (VIF). In the FL trial, carbonated Telone C35 (63.4% 1,3-D and 34.7% CP) was shank-applied at 151 kg ha(-1) to 20 cm deep in the beds (22 cm high and 76 cm wide) tarped with totally impermeable film (TIF). Emissions from tarped beds relative to furrows were contrary between the two trials. For the CA trial, the emission was 47% of applied 1,3-D and 27% of applied CP from PE tarped beds and 31% of applied 1,3-D and 15% of applied CP from VIF tarped beds, while that from uncovered furrows was<0.4% for both chemicals in both fields. In the FL trial, only 0.1% 1,3-D was emitted from the TIF tarped beds, but 27% was measured from the uncovered furrows. Factors contributing to the differences in emissions were chiefly raised-bed configuration, tarp permeability, fumigant application method, soil properties, soil water content, and fumigant carbonation. The results indicate that strategies for emission reduction must consider the differences in agronomic production systems. Modifying raised bed configuration and fumigant application technique in coarse textured soils with TIF tarping can maximize fumigation efficiency and emission reduction.