Biological and molecular characterization of a novel carmovirus isolated from angelonia

International Trade and Local Effects of Viral and Bacterial Diseases in Ornamental Plants

Since the 1950s, there have been major changes in the scope, value, and organization of the ornamental plant industry. With fewer individual producers and a strong trend toward consolidation and globalization, increasing quantities of diverse plant genera and species are being shipped internationally. Many more ornamentals are propagated vegetatively instead of by seed, further contributing to disease spread. These factors have led to global movement of pathogens to countries where they were not formerly known. The emergence of some previously undescribed pathogens has been facilitated by high-throughput sequencing, but biological studies are often lacking, so their roles in economic diseases are not yet known. Case studies of diseases in selected ornamentals discuss the factors involved in their spread, control measures to reduce their economic impact, and some potential effects on agronomic crops. Advances in diagnostic techniques are discussed, and parallels are drawn to the international movement of human diseases.

Accurate and sensitive diagnosis of geminiviruses through enrichment, high-throughput sequencing and automated sequence identification

Existing diagnostic techniques used to identify plant-infecting DNA viruses and their associated molecules are often limited in their specificity and can be challenged by samples containing multiple viruses. We adapted a simple method of amplifying circular viral DNA and, in combination with high-throughput sequencing and bioinformatic analysis, used it as a virus diagnostic method. We validated this diagnostic method with a plant sample infected with a tomato yellow leaf curl geminivirus infectious clone and also compared PCR- and high-throughput-sequencing diagnostics on a geminivirus-infected field sample, showing that both methods gave similar results. Finally, we analyzed infected field samples of pepper from Mexico and tomato from India using this approach, demonstrating that it is both sensitive and capable of simultaneously identifying multiple discrete DNA viruses and subviral DNA elements in densely infected samples.

The complete nucleotide sequence and genome organization of a novel carmovirus--honeysuckle ringspot virus isolated from honeysuckle

A virus associated with yellow-to-purple ringspot on honeysuckle plants has been detected and tentatively named honeysuckle ringspot virus (HnRSV). The complete nucleotide sequence of HnRSV from infected honeysuckle has been determined. The genomic RNA of HnRSV is 3,956 nucleotides in length and is predicted to contain five open reading frames (ORFs). Comparisons of the amino acid sequences of the ORFs of HnRSV with those of members of the family Tombusviridae show that HnRSV is closely related to members of the genus Carmovirus. Phylogenetic analysis based on the amino acid sequences of RdRp and coat protein and nucleotide sequences of the whole genome revealed that HnRSV forms a subgroup with the carmoviruses. Together, our results support the classification of HnRSV as a member of a new species in the genus Carmovirus, family Tombusviridae.

Surprising Results from a Search for Effective Disinfectants for Tobacco mosaic virus-Contaminated Tools

Over 100 years after its discovery, Tobacco mosaic virus (TMV) remains an economically important pathogen for producers of many vegetatively propagated crops including petunias (Petunia × hybrida). To directly address this concern, we have developed a robust system to determine efficacy of disinfectants for treating TMV-contaminated cutting tools using a combination of preliminary screens and replicated trials. Contrary to widely held beliefs, wild-type (wt) TMV and four additional tobamovirus species infected four petunia cultivars without producing obvious viral symptoms. In contrast, a petunia isolate of TMV with 99.0% (nucleotide) and 99.4% (amino acid) coat protein sequence identity to wt TMV produced symptoms on all but one tested cultivar. We also show that TMV transmission can occur up to the twentieth petunia plant cut following a single cutting event on a TMV-infected plant. Although many new products are now available, treatment of TMV-contaminated tools with a 20% (wt/vol) solution of nonfat dry milk (NFDM) plus 0.1% Tween 20 or a 1:10 dilution of household bleach (0.6% sodium hypochlorite), two "old standbys", completely eliminated TMV transmission to petunias. Treatment of contaminated tools with 1% (wt/vol) Virkon S or 20% NFDM also significantly reduced the incidence of infected petunias. Other treatments identified in the preliminary screens are candidates for the second phase of screening that simulates contamination during the process of taking cuttings.

Complete nucleotide sequence and genome organization of Calibrachoa mottle virus (CbMV)--a new species in the genus Carmovirus of the family Tombusviridae

Complete genomic sequence of the viral RNA of Calibrachoa mottle virus (CbMV) has been determined. The CbMV genome has a positive-sense single-stranded RNA of 3919 nucleotides in length and encodes five open reading frames (ORFs). ORF1 encodes a protein with predicted molecular weight of 28 kDa (p28). ORF2 extends through the amber stop codon of ORF1 to give a protein with a predicted molecular weight of 87 kDa (p87). The readthrough domain of p87 contains the GDD motif common to RNA-dependent RNA polymerases (RdRp). ORF3 and ORF4 encode two small overlapping polypeptides of 8 kDa (p8) and 9 kDa (p9), respectively. The 3'-proximal ORF5 encodes a capsid protein (CP) of 37 kDa (p37). The untranslated 5'- and 3'-terminal regions are composed of 34 and 234 non-coding nucleotides, respectively. Comparisons of amino acid sequences of the ORFs of CbMV with members of Tombusviridae show that CbMV is closely related to members of the genus Carmovirus. Phylogenetic analyses based on the amino acid sequences of RdRp and coat protein and nucleotide sequences of the whole genome reveal that CbMV forms a subgroup with several carmoviruses. Therefore, the genome organization, physico-chemical properties, sequence alignments and phylogenetic analysis support the classification of CbMV as a new species in the genus Carmovirus, family Tombusviridae.

Complete nucleotide sequence of Nootka lupine vein-clearing virus

The complete genome sequence of Nootka lupine vein-clearing virus (NLVCV) was determined to be 4,172 nucleotides in length containing four open reading frames (ORFs) with a similar genetic organization of virus species in the genus Carmovirus, family Tombusviridae. The order and gene product size, starting from the 5'-proximal ORF consisted of: (1) polymerase/replicase gene, ORF1 (p27) and ORF1RT (readthrough) (p87), (2) movement proteins ORF2 (p7) and ORF3 (p9), and, (3) the 3'-proximal coat protein ORF4, (p37). The genomic 5'- and 3'-proximal termini contained a short (59 nt) and a relatively longer 405 nt untranslated region, respectively. The longer replicase gene product contained the GDD motif common to RNA-dependent RNA polymerases. Phylogenetically, NLVCV formed a subgroup with the following four carmoviruses when separately comparing the amino acids of the coat protein or replicase protein: Angelonia flower break virus (AnFBV), Carnation mottle virus (CarMV), Pelargonium flower break virus (PFBV), and Saguaro cactus virus (SgCV). Whole genome nucleotide analysis (percent identities) among the carmoviruses with NLVCV suggested a similar pattern. The species demarcation criteria in the genus Carmovirus for the amino acid sequence identity of the polymerase (<52%) and coat (<41%) protein genes restricted NLVCV as a distinct species, and instead, placed it as a tentative strain of CarMV, PFBV, or SgCV when both the polymerase and CP were used as the determining factors. In contrast, the species criteria that included different host ranges with no overlap and lack of serology relatedness between NLVCV and the carmoviruses, suggested that NLVCV was a distinct species. The relatively low cutoff percentages allowed for the polymerase and CP genes to dictate the inclusion/exclusion of a distinct carmovirus species should be reevaluated. Therefore, at this time we have concluded that NLVCV should be classified as a tentative new species in the genus Carmovirus, family Tombusviridae.