Tomato Brown Rugose Fruit Virus Pandemic.

Tomato brown rugose fruit virus (ToBRFV) is an emerging tobamovirus. It was first reported in 2015 in Jordan in greenhouse tomatoes and now threatens tomato and pepper crops around the world. ToBRFV is a stable and highly infectious virus that is easily transmitted by mechanical means and via seeds, which enables it to spread locally and over long distances. The ability of ToBRFV to infect tomato plants harboring the commonly deployed Tm resistance genes, as well as pepper plants harboring the L resistance alleles under certain conditions, limits the ability to prevent damage from the virus. The fruit production and quality of ToBRFV-infected tomato and pepper plants can be drastically affected, thus significantly impacting their market value. Herein, we review the current information and discuss the latest areas of research on this virus, which include its discovery and distribution, epidemiology, detection, and prevention and control measures, that could help mitigate the ToBRFV disease pandemic.

New Weed Hosts for Tomato Brown Rugose Fruit Virus in Wild Mediterranean Vegetation.

Tomato brown rugose fruit virus (ToBRFV; genus, Tobamovirus, family, Virgaviridae) was first reported in 2015 infecting tomatoes grown under protected cropping in the Jordan Valley. Since then, ToBRFV has been detected in tomatoes grown in both protected and open fields across Jordan. The increased incidence of ToBRFV prompted this investigation of the potential role of natural weed hosts in the dissemination of ToBRFV. A survey was conducted in the Jordan Valley and highlands to determine possible reservoir hosts of ToBRFV in fields and greenhouse complexes in which tomatoes were grown. Detection of ToBRFV infection was made by double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) and further confirmation by reverse-transcription polymerase chain reaction (RT-PCR), followed by DNA cloning and sequencing, and bioassays. Thirty weed species belonging to twenty-six genera from sixteen families were tested. Twelve species belonging to eight families were infected of which ten species are newly reported hosts for ToBRFV. Seed transmission of ToBRFV in Solanum nigrum was confirmed in a grow-out experiment. To our knowledge, this is the first report of the natural occurrence of ToBRFV on weed hosts. Identification of natural reservoirs of ToBRFV can help to develop management practices focused on weed plant species to prevent ToBRFV transmission. The extent to which ToBRFV survives in diverse alternate weed host species outside tomato growing seasons in different world regions requires further research in order to establish the risk associated with the possible contribution of weeds as a reservoir for primary infections in tomato crops.

Complete nucleotide sequence of a begomovirus associated with an alphasatellite and a betasatellite naturally infecting okra in Jordan.

The complete nucleotide sequences of a monopartite begomovirus and an associated alphasatellite and betasatellite isolated from naturally infected okra (Abelmoschus esculentus) plants originating from Jordan were determined. The sequences of the begomovirus, alphasatellite, and betasatellites were determined to be 2,764, 1,307, and 1,354 nucleotides in length, respectively. Sequence Demarcation Tool (SDT) and phylogenetic analysis revealed that the begomovirus isolate shared the highest (99.5-99.8%) nt sequence identity with isolates of cotton leaf curl Gezira virus (CLCuGeV), a begomovirus found to exclusively infect cotton in Africa, and recently, in Asia and the Middle East. The DNA sequences of the alphasatellite and betasatellite exhibited the highest nt sequence identity (98.7-98.9% and 92.2-95.3%, respectively) to cotton leaf curl Gezira alphasatellite and cotton leaf curl Gezira betasatellite, respectively. This is the first identification of an African begomovirus, associated with DNA satellites, infecting okra in Jordan.

Draft Genome Sequence of the Plant Growth-Promoting Pseudomonas punonensis Strain D1-6 Isolated from the Desert Plant Erodium hirtum in Jordan.

Pseudomonas punonensis strain D1-6 was isolated from roots of the desert plant Erodium hirtum, near the Dead Sea in Jordan. The genome of strain D1-6 reveals several key plant growth-promoting and herbicide-resistance genes, indicating a possible specialized role for this endophyte.

Occurrence of organochlorine pesticide residues in eggs, chicken and meat in Jordan.

Organochlorine pesticide (OCP) residues in 519 samples; comprising eggs, chicken and meat (lamb and beef), collected from Jordan were determined. All samples were analyzed for their residual contents of aldrin, dichlorodiphenyltrichloroethane and metabolites (DDTs), dieldrin, endosulfan isomers, endrin, hexachlorocyclohexane isomers (HCHs), heptachlor, heptachlor epoxide and hexachlorobenzene (HCB). The samples were Soxhlet extracted for 8h in 250mL petroleum ether. The cleanup of the samples was performed by Florisil column chromatography and analysis was done on a gas chromatography equipped with an electron capture detector (GC-ECD). The results indicated that 28% (38/134), 20% (23/115) and 49% (131/270) of the examined eggs, chicken and meat samples, respectively, were contaminated with OCP residues. HCHs and DDTs are the most prominently noticed compounds, as they were detected at a high incidence. On the other hand, heptachlor, heptachlor epoxide, HCB, aldrin and endrin compounds were only present in less than 7% of the analyzed samples. These residues are present despite complete ban on the use of OCPs for agricultural purposes in Jordan. No residues of op'-DDD, op'-DDT, dieldrin, alpha-endosulfan and beta-endosulfan were detected.

Organochlorine pesticide residues in dairy products in Jordan.

The use of aldrin, dieldrin, endrin, heptachlor and hexachlorobenzene (HCB) has been banned in Jordan officially in 1981, and of dichlorodiphenyltrichloroethane (DDT) in 1995. However, residues of such compounds can still be found in the environment and in foodstuffs. Dairy products are an important exposure route for organochlorine pesticides (OCPs) to humans. For this reason, the presence of OCP residues in 233 dairy product samples; comprising milk, butter, cheese, labaneh and yoghurt collected from Jordan was determined. All samples were analyzed for their residual contents of aldrin, DDT and metabolites (DDTs), dieldrin, endosulfan isomers, endrin, hexachlorocyclohexane isomers (HCHs), heptachlor and HCB. Levels of these compounds were determined by gas chromatography with electron capture detector (GC-ECD). The results indicated that 9% (21/233), 8.5% (20/233), 6% (14/233) and 2.1% (5/233) of the examined samples were contaminated with beta-HCH, pp'-DDE, alpha-HCH and gamma-HCH, respectively. Heptachlor and alpha-endosulfan were only present in less than 2% of the analyzed samples. None of the samples revealed the presence of aldrin, op'-DDD, pp'-DDD, op'-DDE, op'-DDT, pp'-DDT, dieldrin, beta-endosulfan, endrin and HCB at their detection limits. The order for the contamination in the analyzed dairy products was labaneh>cheese>yoghurt>butter>milk. This study has provided the preliminary information on the concentration of OCPs in dairy products for the first time in Jordan. The results will help in a scientific assessment of the implications of pesticide residues with regards to human risks in Jordan.

Further complexity of the genus Crinivirus revealed by the complete genome sequence of Lettuce chlorosis virus (LCV) and the similar temporal accumulation of LCV genomic RNAs 1 and 2.

The sequence of Lettuce chlorosis virus (LCV) (genus Crinivirus) was determined and found to contain unique open reading frames (ORFs) and ORFs similar to those of other criniviruses, as well as 3' non-coding regions that shared a high degree of identity. Northern blot analysis of RNA extracted from LCV-infected plants identified subgenomic RNAs corresponding to six prominent internal ORFs and detected several novel LCV-single stranded RNA species. Virus replication in tobacco protoplasts was investigated and results indicated that LCV replication proceeded with novel crinivirus RNA accumulation kinetics, wherein viral genomic RNAs exhibited a temporally similar expression pattern early in the infection. This was noticeably distinct from the asynchronous RNA accumulation pattern previously observed for Lettuce infectious yellows virus (LIYV), the type member of the genus, suggesting that replication of the two viruses likely operate via dissimilar mechanisms.

Partial Sequence and Survey Analysis Identify a Multipartite, Negative-Sense RNA Virus Associated with Fig Mosaic.

RNA and nucleotide sequence-based analyses were used to identify viruses in fig mosaic (FM)-affected fig (Ficus carica) trees. Nucleotide sequence analyses of 267 cloned cDNAs identified sequences corresponding to four viruses representing four distinct taxa from fig trees in California. Virus sequences corresponding to members of the family Closteroviridae were most common (55 sequences). We also found two sequences for an Umbravirus, one sequence corresponding to a Luteovirus-associated RNA, and two sequences that showed homology to European mountain ash ringspot-associated virus (EMARAV). Reverse transcription-polymerase chain reaction (RT-PCR) and northern hybridization analyses were used to confirm the presence of specific virus RNAs in fig trees. A survey of 184 fig trees from a germplasm collection, a commercial orchard, backyards, and feral fig trees showed that one virus was most common (detected in 96% of tested samples), while none of the other virus sequences were detected in more than 36% of the fig trees. Based on its association with FM-affected trees, nucleotide sequence-based phylogenetic association, and previous reported properties, we suggest the name of this virus as Fig mosaic-associated virus (FMaV).

Rose spring dwarf-associated virus has RNA structural and gene-expression features like those of Barley yellow dwarf virus.

We determined the complete nucleotide sequence of the Rose spring dwarf-associated virus (RSDaV) genomic RNA (GenBank accession no. EU024678) and compared its predicted RNA structural characteristics affecting gene expression. A cDNA library was derived from RSDaV double-stranded RNAs (dsRNAs) purified from infected tissue. Nucleotide sequence analysis of the cloned cDNAs, plus for clones generated by 5'- and 3'-RACE showed the RSDaV genomic RNA to be 5808 nucleotides. The genomic RNA contains five major open reading frames (ORFs), and three small ORFs in the 3'-terminal 800 nucleotides, typical for viruses of genus Luteovirus in the family Luteoviridae. Northern blot hybridization analysis revealed the genomic RNA and two prominent subgenomic RNAs of approximately 3 kb and 1 kb. Putative 5' ends of the sgRNAs were predicted by identification of conserved sequences and secondary structures which resembled the Barley yellow dwarf virus (BYDV) genomic RNA 5' end and subgenomic RNA promoter sequences. Secondary structures of the BYDV-like ribosomal frameshift elements and cap-independent translation elements, including long-distance base pairing spanning four kb were identified. These contain similarities but also informative differences with the BYDV structures, including a strikingly different structure predicted for the 3' cap-independent translation element. These analyses of the RSDaV genomic RNA show more complexity for the RNA structural elements for members of the Luteoviridae.

Complete nucleotide sequences and genome characterization of a novel double-stranded RNA virus infecting Rosa multiflora.

The three double-stranded (ds) RNAs were detected in Rosa multiflora plants showing rose spring dwarf (RSD) symptoms. Northern blot analysis revealed three dsRNAs in preparations of both dsRNA and total RNA from R. multiflora plants. The complete sequences of the dsRNAs (referred to as dsRNA 1, dsRNA 2 and dsRNA 3) were determined based on a combination of shotgun cloning of dsRNA cDNAs and reverse transcription-polymerase chain reaction (RT-PCR). The largest dsRNA (dsRNA 1) was 1,762 bp long with a single open reading frame (ORF) that encoded a putative polypeptide containing 479 amino acid residues with a molecular mass of 55.9 kDa. This polypeptide contains amino acid sequence motifs conserved in the RNA-dependent RNA polymerases (RdRp) of members of the family Partitiviridae. Both dsRNA 2 (1,475 bp) and dsRNA 3 (1,384 bp) contained single ORFs, encoding putative proteins of unknown function. The 5' untranslated regions (UTR) of all three segments shared regions of high sequence homology. Phylogenetic analysis using the RdRp sequences of the various partitiviruses revealed that the new sequences would constitute the genome of a virus in family Partitiviridae. This virus would cluster with Fragaria chiloensis cryptic virus and Raphanus sativus cryptic virus 2. We suggest that the three dsRNA segments constitute the genome of a novel cryptic virus infecting roses; we propose the name Rosa multiflora cryptic virus (RMCV). Detection primers were developed and used for RT-PCR detection of RMCV in rose plants.