Coat protein phylogeny and systematics of potyviruses

Cassava brown streak virus evolves with a nucleotide-substitution rate that is typical for the family Potyviridae

The ipomoviruses (family Potyviridae) that cause cassava brown streak disease (cassava brown streak virus [CBSV] and Uganda cassava brown streak virus [UCBSV]) are damaging plant pathogens that affect the sustainability of cassava production in East and Central Africa. However, little is known about the rate at which the viruses evolve and when they emerged in Africa - which inform how easily these viruses can host shift and resist RNAi approaches for control. We present here the rates of evolution determined from the coat protein gene (CP) of CBSV (Temporal signal in a UCBSV dataset was not sufficient for comparable analysis). Our BEAST analysis estimated the CBSV CP evolves at a mean rate of 1.43 × 10-3 nucleotide substitutions per site per year, with the most recent common ancestor of sampled CBSV isolates existing in 1944 (95% HPD, between years 1922 - 1963). We compared the published measured and estimated rates of evolution of CPs from ten families of plant viruses and showed that CBSV is an average-evolving potyvirid, but that members of Potyviridae evolve more quickly than members of Virgaviridae and the single representatives of Betaflexiviridae, Bunyaviridae, Caulimoviridae and Closteroviridae.

Genome characterization of zucchini yellow mosaic virus infecting cucurbits reveals the presence of a new genotype in Trinidad and Tobago in the Caribbean region

Zucchini yellow mosaic virus (ZYMV) is a member of the genus Potyvirus that is becoming a serious pathogen of pumpkin and other cucurbits in Trinidad and Tobago and the entire Caribbean region. In this study, four ZYMV isolates infecting pumpkin in Trinidad and Tobago were characterized by complete genome sequencing. Phylogenetic analysis showed 5.9-6.0% nt and 7.7-7.9% aa sequence divergence in comparison to the most closely related isolates NAT and AG from Israel and SE04T from Slovakia. Based on the variations in the complete genome sequence as well as individual gene sequences, a new genotype, designated ZYMV-Trini, is proposed for these isolates. Among the gene sequences of ZYMV-Trini isolates, the greatest variation was observed in the HC-Pro gene, with 20.8% aa sequence divergence from their closest relatives, whereas the least variation was observed in the NIb, P3, and CP genes, with 1.8-2.2% aa sequence divergence. This study also showed that transmission of ZYMV can occur through seeds, but this was less common than transmission via the aphid Aphis gossypii. The progression of ZYMV in pumpkin seedlings was quantified by RT-qPCR, which showed a rapid surge in viral load after 37 days. From recombination analysis, it could be concluded that the isolates SE04T from Slovakia, NAT from Israel, and AG from Israel have made major contributions to the genome architecture of ZYMV-Trini isolates.

Turnip Mosaic Virus Coat Protein Deletion Mutants Allow Defining Dispensable Protein Domains for 'in Planta' eVLP Formation

The involvement of different structural domains of the coat protein (CP) of turnip mosaic virus, a potyvirus, in establishing and/or maintaining particle assembly was analyzed through deletion mutants of the protein. In order to identify exclusively those domains involved in protein-protein interactions within the particle, the analysis was performed by agroinfiltration "in planta", followed by the assessment of CP accumulation in leaves and the assembly of virus-like particles lacking nucleic acids, also known as empty virus-like particles (eVLP). Thus, the interactions involving viral RNA could be excluded. It was found that deletions precluding eVLP assembly did not allow for protein accumulation either, probably indicating that non-assembled CP protein was degraded in the plant leaves. Deletions involving the CP structural core were incompatible with particle assembly. On the N-terminal domain, only the deletion avoiding the subdomain involved in interactions with other CP subunits was incorporated into eVLPs. The C-terminal domain was shown to be more permissive to deletions. Assembled eVLPs were found for mutants, eliminating the whole domain. The C-terminal domain mutants were unusually long, suggesting some role of the domain in the regulation of particle length. The identification of the CP domains responsible for eVLP formation will allow for new approaches to protein stretch replacement with peptides or proteins of nanobiotechnological interest. Finally, specific cases of application are considered.

Biological, Pathological, and Molecular Characteristics of a New Potyvirus, Dendrobium Chlorotic Mosaic Virus, Infecting Dendrobium Orchid

Dendrobium smillieae is one of the popular orchids in Taiwan. This report describes a new potyvirus tentatively named Dendrobium chlorotic mosaic virus (DeCMV) causing chlorotic and mosaic symptoms in D. smillieae. Enzyme-linked immunosorbent assay (ELISA) tests using six antisera against orchid-infecting viruses revealed that only a monoclonal antibody against the potyvirus group reacted positively with crude saps prepared from a symptomatic dendrobium orchid. Potyvirus-like, flexuous, filamentous particles were observed under an electron microscope, measuring approximately 700 to 800 nm in length and 11 to 12 nm in diameter. Sequence analyses revealed that DeCMV coat protein gene shared 59.6 to 66.0% nucleotide sequence identity and 57.6 to 66.0% amino acid sequence identity, whereas the DeCMV complete genome shared 54.1 to 57.3% nucleotide sequence identity and 43.7 to 49.5% amino acid sequence identity with those other known potyviruses. These similarity levels were much lower than the criteria set for species demarcation in potyviruses. Thus, DeCMV can be considered a new potyvirus. The whole DeCMV genome contains 10,041 nucleotides (GenBank accession no. MK241979) and encodes a polyprotein that is predicted to produce 10 proteins by proteolytic cleavage. In a pathogenicity test, results of inoculation assays demonstrated that DeCMV can be transmitted to dendrobium orchids by grafting and mechanical inoculation, as verified by ELISA and western blot analyses using the DeCMV polyclonal antiserum and by reverse transcription polymerase chain reaction using the coat protein gene-specific primers. The inoculated orchids developed similar chlorotic and mosaic symptoms. In conclusion, DeCMV is a novel orchid-infecting potyvirus, and this is the first report of a new potyvirus that infects dendrobium orchids in Taiwan.

Genetic diversity and biological characterization of sugarcane streak mosaic virus isolates from Iran

Sugarcane streak mosaic virus (SCSMV; genus Poacevirus, family Potyviridae) is a major causal agent of sugarcane mosaic disease in Asia. A survey of SCSMV was conducted in cultivated fields in Khuzestan province, southwestern Iran. Sixty-five sugarcane leaf samples showing mosaic symptoms were collected and investigated by RT-PCR. Almost one-fourth of the samples were found to be infected by SCSMV. To verify molecular variability, 12 SCSMV isolates were sequenced and analyzed by comparing partial NIb-CP gene sequences. The nucleotide identity among Iranian isolates was 83.1-99.8%, indicating high nucleotide variability, while amino acid identity was 95.2-100%, which suggesting selection for amino acid conservation. They shared nucleotide identities of 76.2-99.1% with those of other SCSMV isolates available in GenBank, the highest with isolates from Pakistan (PAK), India (IND671) and China (M117, KT257289). Further analysis was conducted based on complete CI coding region to gain more insight into the phylogenetic relationships of Iranian SCSMV compared to those from other Asian countries. Iranian isolates shared identities of 79.8-89.0% (nucleotide) and 94.8-98.6% (amino acid) with those from other geographical regions in the CI gene. The highest nucleotide identity of Iranian isolates was with isolates PAK (Pakistan), M121 (JQ975096, China) and IND671 (India), respectively. The phylogenetic trees (based on CI and NIb-CP) revealed the segregation of SCSMV isolates into two major divergent evolutionary lineages that reflect geographical origin of the isolates (with minor exception). Phylogenetic analyses grouped Iranian SCSMV isolates together with isolates from Pakistan, India and just one Chinese isolate in group II. Biological results showed that Iranian SCSMV isolates infect sugarcane, sorghum, maize and some wild grasses, causing mosaic symptoms on the leaves.

Identification of host factors potentially involved in RTM-mediated resistance during potyvirus long distance movement

The long distance movement of potyviruses is a poorly understood step of the viral cycle. Only factors inhibiting this process, referred to as "Restricted TEV Movement" (RTM), have been identified in Arabidopsis thaliana. On the virus side, the potyvirus coat protein (CP) displays determinants required for long-distance movement and for RTM-based resistance breaking. However, the potyvirus CP was previously shown not to interact with the RTM proteins. We undertook the identification of Arabidopsis factors which directly interact with either the RTM proteins or the CP of lettuce mosaic virus (LMV). An Arabidopsis cDNA library generated from companion cells was screened with LMV CP and RTM proteins using the yeast two-hybrid system. Fourteen interacting proteins were identified. Two of them were shown to interact with CP and the RTM proteins suggesting that a multiprotein complex could be formed between the RTM proteins and virions or viral ribonucleoprotein complexes. Co-localization experiments in Nicotiana benthamiana showed that most of the viral and cellular protein pairs co-localized at the periphery of chloroplasts which suggests a putative role for plastids in this process.

The absence of eukaryotic initiation factor eIF(iso)4E affects the systemic spread of a Tobacco etch virus isolate in Arabidopsis thaliana

Translation initiation factor eIF4E exerts an important role during infection of viral species in the family Potyviridae. Particularly, a eIF(iso)4E family member is required for Arabidopsis thaliana susceptibility to Turnip mosaic virus, Lettuce mosaic virus, and Tobacco etch virus (TEV). In addition, a resistance mechanism named restriction of TEV movement (RTM) in A. thaliana controls the systemic spread of TEV in Col-0 ecotype. Here, we describe that TEV-TAMPS, a Mexican isolate, overcomes the RTM resistance mechanism reported for TEV-7DA infection of the Col-0 ecotype but depends on eIF(iso)4E for its systemic spread. To understand at which level eIF(iso)4E participates in A. thaliana TEV-TAMPS infection, the viral RNA replication and translation were measured. The absence or overexpression of eIF(iso)4E did not affect viral translation, and replication was still observed in the absence of eIF(iso)4E. However, the TEV-TAMPS systemic spread was completely abolished in the null mutant. The viral protein genome-linked (VPg) precursor NIa was found in coimmunoprecipitated complexes with both, eIF(iso)4E and eIF4E. However, the viral coat protein (CP) was only present in the eIF(iso)4E complexes. Since both the VPg and the CP proteins are needed for systemic spread, we propose a role of A. thaliana eIF(iso)4E in the movement of TEV-TAMPS within this host.

Analysis of 3'-Terminal Region of Bean common mosaic virus Strains Infecting Common Bean in India

Four strains (NL-1, NL-1n, NL-7 and NL-7n) of Bean common mosaic virus (BCMV) prevalent on common bean (Phaseolus vulgaris) in Himachal Pradesh, a north-western Himalayan state of India were compared at the 3' terminal region of the viral genome to elucidate variation and relationship among these strains. 3' terminal region comprising of partial nuclear inclusion b (NIb) (171-233 bp), complete coat protein (CP) (860 bp) and 3' untranslated region (UTR) (208-244 bp) shared 96-98% nucleotide and 96-99% amino acids identity among various strains of BCMV. Multiple alignment as well as cluster dendrograms of the 3' terminal region placed the test isolates in BCMV species of genus Potyvirus. Phylogenetic analysis of complete CP as well as 3' UTR also showed Indian strains to be distinct strains. Sequence homology, multiple alignment and evolutionary divergence of 3' terminal region could not differentiate the pathogenic strain groups, thereby establishing least role of this region in strain characterization of the virus. Comparisons of CP and 3' UTR region of BCMV strains and other members of genus Potyvirus clearly indicated the little utility of 3' terminal region in distinction of virus strains. Implications of coat protein region in viral strain distinction are also discussed.

Molecular genetic analysis of virus isolates from wild and cultivated plants demonstrates that East Africa is a hotspot for the evolution and diversification of sweet potato feathery mottle virus

Sweet potato feathery mottle virus (SPFMV, genus Potyvirus) is globally the most common pathogen of cultivated sweet potatoes (Ipomoea batatas; Convolvulaceae). Although more than 150 SPFMV isolates have been sequence-characterized from cultivated sweet potatos across the world, little is known about SPFMV isolates from wild hosts and the evolutionary forces shaping SPFMV population structures. In this study, 46 SPFMV isolates from 14 wild species of genera Ipomoea, Hewittia and Lepistemon (barcoded for the matK gene in this study) and 13 isolates from cultivated sweet potatoes were partially sequenced. Wild plants were infected with the EA, C or O strain, or co-infected with the EA and C strains of SPFMV. In East Africa, SPFMV populations in wild species and sweet potato were genetically undifferentiated, suggesting inter-host transmission of SPFMV. Globally, spatial diversification of the 178 isolates analysed was observed, strain EA being largely geographically restricted to East Africa. Recombination was frequently detected in the 6K2-VPg-NIaPro region of the EA strain, demonstrating a recombination 'hotspot'. Recombination between strains EA and C was rare, despite their frequent co-infections in wild plants, suggesting purifying selection against strain EA/C recombinants. Positive selection was predicted on 17 amino acids distributed over the entire coat protein in the globally distributed strain C, as compared to only four amino acids in the coat protein N-terminus of the EA strain. This selection implies a more recent introduction of the C strain and a higher adaptation of the EA strain to the local ecosystem. Thus, East Africa appears as a hotspot for evolution and diversification of SPFMV.

Genetic diversity among viruses associated with sugarcane mosaic disease in Tucumán, Argentina

Sugarcane leaves with mosaic symptoms were collected in 2006--07 in Tucumán (Argentina) and analyzed by reverse-transcriptase polymerase chain reaction (RT-PCR) restriction fragment length polymorphism (RFLP) and sequencing of a fragment of the Sugarcane mosaic virus (SCMV) and Sorghum mosaic virus (SrMV) coat protein (CP) genes. SCMV was detected in 96.6% of samples, with 41% showing the RFLP profile consistent with strain E. The remaining samples produced eight different profiles that did not match other known strains. SCMV distribution seemed to be more related to sugarcane genotype than to geographical origin, and sequence analyses of CP genes showed a greater genetic diversity compared with other studies. SrMV was detected in 63.2% of samples and most of these were also infected by SCMV, indicating that, unlike other countries and other Argentinean provinces, where high levels of co-infection are infrequent, co-existence is common in Tucumán. RFLP analysis showed the presence of SrMV strains M (68%) and I (14%), while co-infection between M and H strains was present in 18% of samples. Other SCMV subgroup members and the Sugarcane streak mosaic virus (SCSMV) were not detected. Our results also showed that sequencing is currently the only reliable method to assess SCMV and SrMV genetic diversity, because RT-PCR-RFLP may not be sufficiently discriminating.

Rapid evolutionary dynamics of zucchini yellow mosaic virus

Zucchini yellow mosaic virus (ZYMV) is an economically important virus of cucurbit crops. However, little is known about the rate at which this virus has evolved within members of the family Cucurbitaceae, or the timescale of its epidemiological history. Herein, we present the first analysis of the evolutionary dynamics of ZYMV. Using a Bayesian coalescent approach we show that the coat protein of ZYMV has evolved at a mean rate of 5.0 x 10(-4) nucleotide substitutions per site, per year. Notably, this rate is equivalent to those observed in animal RNA viruses. Using the same approach we show that the lineages of ZYMV sampled here have an ancestry that dates back no more than 800 years, suggesting that human activities have played a central role in the dispersal of ZYMV. Finally, an analysis of phylogeographical structure provides strong evidence for the in situ evolution of ZYMV within individual countries.

Natural infection of Alternanthera tenella (Amaranthaceae) by a new potyvirus

A virus was isolated from joyweed (Alternanthera tenella Colla-Amaranthaceae), a common weed in tropical and sub-tropical regions. Examination by electron microscopy showed long flexuous particles with an average length of 756 nm in crude sap. Serological results showed positive reaction with antisera to PVY-O. A fragment of 1772 nucleotides was sequenced. The CP sequence shares 76% of identity with the CP of Potato virus Y strain NTN. These results confirm that the virus is a new potyvirus infecting A. tenella, and the name Alternanthera mild mosaic virus (AltMMV) is proposed.

Analysis of the molecular and biological variability of zucchini yellow mosaic virus isolates from Slovakia and Czech Republic

The diversity of ZYMV isolates was analysed by the biological and molecular characterisation of 11 isolates sampled from cucumber, squash and zucchini between 2001 and 2006 in various localities of Slovakia and Czech Republic. Analysis of the molecular variability targeting three separate genomic regions of the ZYMV genome [P1, P3 and (Cter)NIb-(Nter)CP] revealed a remarkable low level of nucleotide variability between isolates, despite their temporal and spatial distinction. Phylogenetic analysis based on the 5'-terminal part of the CP gene highlighted the close relatedness of Slovak, Czech and other central European isolates. Low level of genetic diversity within central European ZYMV isolates is in contrast to the diversity observed for isolates from other geographical regions, in particular Asia. No evidence of recombination in the ZYMV genome was detected. Sequence comparison between aggressive and moderate ZYMV isolates revealed one amino acid difference in the N-terminal part of the P3 protein, potentially involved in the tolerance breaking.

Nucleotide sequence analysis of Plum pox virus isolate W3174: evidence of a new strain

The nucleotide sequence of Plum pox virus (PPV) isolate W3174 was determined. The virus genome consists of 9788 nucleotides (nt), excluding the poly(A) tail at the 3'-terminus, with 5'- and 3'-untranslated regions (UTRs) of 146 and 219 nt, respectively. The deduced polyprotein consists of 3141 amino acid (aa) residues, with the coat protein region consisting of 993 nt (331 aa). In comparisons with PPV-D, -M, -EA and -C isolates, nucleotide identity levels ranged from 79 to 80% for the entire genome and from 78 to 79%, 78 to 81%, and 92 to 95% for the NIb, CP, and 3'-UTR regions, respectively. The majority of nucleotide substitutions in the NIb region of W3174 are silent, while substitutions in the CP region are not silent, giving aa identities of 89-91% and 79-81%, respectively. The HC-Pro region contains the KITC and PTK motifs, and the DAG motif is located at positions 12-14 of the deduced CP aa sequence, all associated with aphid transmission. Phylogenetic analysis based on the complete genome sequence, the NIb, CP, and 3'-UTR region were performed. PPV-W3174 consistently formed a distinct clade or group, when compared to members of all four recognized strains of PPV, indicating that it is genetically distinct. These results are consistent with serological and nucleic acid-based strain typing data and justify recognition of this isolate as representative of a new strain identified as PPV-W.

Characterization of a novel potyvirus isolated from maize in Israel

A potyvirus (proposed name of Zea mosaic virus [ZeMV]) isolated from maize in Israel was analyzed by serology, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of capsid proteins, symptomatology, and sequencing. Parts of the nuclear inclusion b, coat protein, and 3' regions were sequenced; the amino acid sequence of ZeMV capsid was determined by time-of-flight mass spectrometry (TOFMS). The results of these analyses were compared with those of similar analyses of the following potyviruses: Maize dwarf mosaic virus (MDMV), Sugarcane mosaic virus strain MDB (SCMV-MDB), Johnsongrass mosaic virus(JGMV), Sorghum mosaic virus (SrMV), and an isolate of MDMV from Israel. Indirect enzyme-linked immunosorbent assay using ZeMV antiserum detected only ZeMV, and reciprocal tests using MDMV, JGMV, or SrMV antisera failed to detect ZeMV. ZeMV cross-reacted weakly when SCMV-MDB antiserum was used. The mass of ZeMV capsid was determined to be 36,810 Da by SDS-PAGE and 34,216 Da by TOFMS. The ZeMV systemically infected johnsongrass (Sorghum halepense), but did not infect oat (Avena sativa), pearl millet (Pennisetum glaucum), barley (Hordeum vulgare), or rye (Secale cereale). Necrosis was caused in 19 sorghum lines by SrMV, in 15 by ZeMV, in 14 by MDMV, and in 5 by JGMV and SCMV-MDB. The nucleic acid and amino acid sequences of ZeMV clearly showed that it is not a strain of JGMV, MDMV, SCMV, or SrMV.

Variability of P1 protein of zucchini yellow mosaic virus for strain differentiation and phylogenetic analysis with other potyviruses

The complete nucleotide sequence of a Singapore isolate of zucchini yellow mosaic potyvirus (ZYMV-S) was determined from viral cDNA clones. The complete genome is 9603 nucleotides in length excluding the poly (A) tail. Computer analysis of the sequence revealed a single large open reading frame (ORF) that presumably encodes a polyprotein of 3082 amino acids with a calculated molecular weight of 350 kDa. Analysis of the helper component (HC) protein showed that the highly conserved motif K-I-T-C which is involved in aphid transmission appeared as K-L-S-C. There is also a change of D-A-G to G-A-G triplet near the N-terminal of the coat protein (CP). Amino acid sequence identity comparison of ZYMV-S gene products with the California and Reunion Island isolates of ZYMV revealed a minimum range of 65-75% to a maximum range of 95-98%. Comparison with other distinct potyviruses showed a low degree of identity from 19-74%. The 5' untranslated region (UTR) of ZYMV-S showed 67% and 72% identity when compared with the California and Reunion Island isolates, respectively. The sequence variability in the 5' UTR of ZYMV can be exploited for strain differentiation and phylogenetic analysis. ZYMV-S shared 94% and 82% identity in the 3' UTR as compared to the California and Reunion Island isolates, respectively. The P1 protein of ZYMV-S shared moderate sequence variability among ZYMV isolates but high sequence variability among all potyviruses. In addition, phylogenetic analysis using the P1 protein indicated that highly variable proteins in the viral genome could also be employed in the study of potyvirus taxonomy and used for strain differentiation.

Differentiation Among Potyviruses Infecting Sweet Potato Based on Genus-and Virus-Specific Reverse Transcription Polymerase Chain Reaction

Knowledge of virus diseases affecting sweet potato has been complicated due to the frequent occurrence of mixed infections and difficulties in isolating and purifying sweet potato viruses. A combined assay of reverse transcription and polymerase chain reaction (PCR) utilizing degenerate genus-specific primers POT1 and POT2 was applied to 18 sweet potato clones from China. The primers were designed to amplify the variable 5' terminal region of the potyvirus coat protein gene. Molecular analysis of the amplified fragments identified the Chinese strains of sweet potato feathery mottle virus (SPFMV-CH), sweet potato latent virus (SPLV-CH), and sweet potato virus G (SPVG-CH). Among the detected potyviruses, a distantly related strain of SPFMV-CH, tentatively named SPFMV-CH2, was identified in sweet potatoes from China. On the basis of sequence identity, SPFMV-CH2 was closely related to the common (-C) strain of that virus. Identification of a closely related strain of SPVG-CH in one sweet potato clone from China further illustrated the usefulness of broad-spectrum PCR for detecting uncharacterized viruses. The acquisition of sequence information permitted the design of virus-specific primers for detecting and differentiating SPFMV, SPLV, and SPVG.

Evidence for the assignment of two strains of SPLV to the genus Potyvirus based on coat protein and 3' non-coding region sequence data

The use of potyvirus-specific primers and subsequent application of the RACE procedure allowed the cloning of the 3' terminal 1088 nucleotides of the genomic RNA of the Taiwan isolate of sweetpotato latent virus (SPLV-T) and the 3' genomic 1085 nucleotides of a SPLV-like virus from China (SPLV-CH). The sequence of an internal part of the presumptive nuclear inclusion b gene was also determined for both isolates. Detailed sequence analyses revealed the presence of consensus motifs which indicated that SPLV-CH and SPLV-T should be regarded as members of the genus Potyvirus. Multiple sequence alignments and phylogenetic analyses were also performed and unambiguously assessed these isolates as strains of a distinct Potyvirus. SPLV was not related to other potyviruses infecting sweetpotato nor to any other sequenced virus. From the presence of the DAG box, SPLV-CH is expected to be a typical aphid transmitted Potyvirus whereas a conceivable explanation is proposed for the non-aphid transmission of SPLV-T.

Phylogenetic justification for splitting the Rymovirus genus of the taxonomic family Potyviridae

The Potyviridae family has been divided into four genera on the basis of vector transmission, as follows: Potyvirus genus (aphid), Rymovirus genus (mite), Bymovirus genus (fungus) and Ipomovirus genus (whitefly). However recent sequence comparisons of the coat protein and 3' NCR regions of the potyviruses have demonstrated that the rymoviruses appear to be a group of two unrelated clusters namely Ryegrass Mosaic Virus (RGMV), Agropyron Mosaic Virus (AgMV) and Hordeum Mosaic Virus (HoMV) in one group and Wheat Streak Mosaic Virus (WSMV) and Brome Streak Mosaic Virus (BrSMV) in the second group. We therefore propose that RGMV, AgMV and HoMV remain in the genus Rymovirus and WSMV and BrSMV form a separate genus, possibly the Whestrevirus genus.

Comparison of the nucleotide sequences of the 3'-terminal regions of one aphid and two non-aphid transmissible isolates of potato A potyvirus

The sequences of the 3'-terminal 1145 nucleotides of two non-aphid transmissible (NAT) isolates (Ali and Juliniere) and one aphid transmissible (AT) isolate (Rouge) of potato virus A (PVA) RNA were determined. Those sequences contained the complete coding region of the coat protein (CP) followed by a 3'-nontranslated region (3'-NTR) of 225 (Ali and Juliniere) and 227 (Rouge) nucleotides. The obtained sequences were compared to those of the 3'-regions of four published PVA isolates and a virus described as tamarillo mosaic virus (TamMV) which on the basis of sequence data is a strain of PVA. The analysis of the 3'-terminal region of PVA isolates indicated that the CP N-terminal variable domain (32 residues) divides PVA isolates into two subgroups, where only tripeptide DAG correlates with aphid transmissibility. In addition to DAG/DAS sequence we found four other amino acids at the N-terminus of PVA CP, which are conserved in two subgroups. The central region (core part and C-termini) of CP is highly conserved among all PVA isolates (96.6 to 99.6%). 3'-NTR, separates PVA-isolates into two subgroups on the basis of its length and homology.

Molecular evidence that the whitefly-transmitted sweetpotato mild mottle virus belongs to a distinct genus of the Potyviridae

Complementary DNA representing 2 108 nucleotides at the 3' end of the genomic RNA of the whitefly-transmitted sweetpotato mild mottle virus (SPMMV) was cloned after PCR. Sequence analysis revealed an open reading frame of 1 797 nucleotides which codes for a protein of 599 amino acids, followed by a 3' non-coding region of 311 nucleotides. Alignment of the deduced amino acid sequence with corresponding sequences of other members of the Potyviridae demonstrated that part of the presumptive RNA-dependent RNA polymerase and the coat protein coding regions of SPMMV are found at the 3' end of its genome, in that order. Alignment of the amino acid sequence of the core of SPMMV coat protein with those of selected members of the Potyviridae showed limited identity, thus demonstrating--with phylogenetic analysis--that SPMMV belongs to a distinct genus of the family Potyviridae.

Inheritance of resistance to potyviruses in Phaseolus vulgaris L. III. Cosegregation of phenotypically similar dominant responses to nine potyviruses

We have identified monogenic dominant resistance to azuki bean mosaic poty virus (AzMV), passionfruit woodiness potyvirus-K (PWV-K), zucchini yellow mosaic potyvirus (ZYMV), and a dominant factor that conditioned lethal necrosis to Thailand Passiflora potyvirus (ThPV), in Phaseolus vulgaris 'Black Turtle Soup 1'. Resistance to AzMV, PWV-K, ZYMV, watermelon mosaic potyvirus, cowpea aphid-borne mosaic potyvirus, blackeye cowpea mosaic potyvirus, and lethal necrosis to soybean mosaic potyvirus and ThPV cosegregated as a unit with the I gene for resistance to bean common mosaic potyvirus.

The complete nucleotide sequences of the coat protein cistron and the 3' non-coding region of a newly-identified potyvirus infecting sweetpotato, as compared to those of sweetpotato feathery mottle virus

Complementary DNA representing 728 nucleotides of the 3' end of the genomic RNA of sweetpotato virus G (SPV-G) a newly-identified potyvirus infecting sweetpotato, was cloned and sequenced. This sequence was combined with that previously determined for the 5' terminal part of the coat protein cistron of the virus. The whole sequence contained a single open reading frame (ORF) of 1065 nucleotide, with the capacity to encode a coat protein of 355 amino acids, significantly larger than that of other potyviruses. The ORF was followed by an untranslated region of 222 nucleotides and a poly (A) tail. The coat protein of SPV-G was only distantly related to that of known potyviruses, with the exception of sweetpotato feathery mottle virus (SPFMV). Indeed, sequence identity in the C-terminal three quarters of the coat protein (more than 80%) and in the 3' untranslated region (more than 70%) indicate that SPV-G should be considered as closely related to, though distinct from SPFMV. This subset relationship is similar to that previously reported for members of the bean yellow mosaic virus subgroup or the bean common mosaic virus subgroup.

Variability in the length of the amino terminal sequence contributes to the capsid protein diversity among dasheen mosaic potyvirus isolates

Western blot analysis of several dasheen mosaic virus isolates revealed molecular weight differences among their capsid proteins (CPs). Sequence analysis of the CP gene showed that the CP of isolate TEN was 15 amino acids shorter than that of isolate LA due to a 57-base deletion and a 12-base insertion into the 5' end of the TEN CP gene. Our data suggest that frequent deletions and insertions are responsible for the CP size diversity among DMV isolates.

A phylogenetic and evolutionary justification for three genera of Geminiviridae

Gene-by-gene phylogenetic analyses of all of the viruses for which sequences are known, as well as analysis of the coding capacities, clearly demonstrated that there are two major groups of viruses in the taxonomic family Geminiviridae. These are of the Subgroup I type, with one genomic component, which mainly infect monocots and are leafhopper-transmitted; and of the Subgroup III type, with one or two genomic components, which infect dicots and are whitefly-transmitted. The existence of "New World" and "Old World" clusters of Subgroup III viruses was confirmed, as well as the possession by the latter of an AV1 ORF not present in New World viruses. A third minor generic group is defined by viruses of the Subgroup II type, which have a single genomic component, infect dicots, and are leafhopper-transmitted. The latter group appear to be the result of an ancient recombination event between a Subgroup III-like and a Subgroup I-like virus. The question of whether one- and two-component Subgroup III viruses should be in the same taxon appears hard to resolve: the only distinguishing feature of the one-component Subgroup III viruses is that they apparently have no second component, as gene-for-gene comparisons of the "A" components of the viruses with other Subgroup III viruses place them within a larger Old World group of viruses, most of which are two component. The possibility exists that these viruses may either have independently lost their B components, or possess a B component that has simply not yet been found. Possible nomenclatural changes to accommodate viruses with the same name which are not closely related to one another, and possible evolutionary scenarios to account for the observed familial, generic and specific diversity of geminiviruses, are discussed.

Cowpea aphid borne mosaic virus-Morocco and South African Passiflora virus are strains of the same potyvirus

High performance liquid chromatography (HPLC) profiles of tryptic peptides and partial amino acid sequence analysis have been employed to establish the taxonomic status of the Moroccan isolate of cowpea aphid-borne mosaic virus (CABMV). Some previous reports have suggested CABMV to be very closely related to blackeye cowpea mosaic virus (B1CMV) while other reports have concluded that this relationship is distant. In this report a tryptic digest of the coat protein of CABMV-Morocco was compared with those of the coat proteins of B1CMV-Type, B1CMV-W, the mild mottle strain of peanut stripe virus (PStV-MM) and the NY15 strain of bean common mosaic virus (BCMV-NY15), all of which are now recognised as strains of BCMV. The comparisons also included the NL-3 strain of bean necrosis mosaic virus (BNMV-NL3), which had previously been classified as a strain of BCMV. The HPLC peptide profiles indicated that CABMV-Morocco was distinct from BCMV and BNMV. Amino acid sequence analysis of peptides accounting for more than half of the coat protein confirmed that CABMV-Morocco was not a strain of BNMV or BCMV but was a distinct member of the BCMV subset of viruses that previously has been shown to include BCMV, BNMV, soybean mosaic virus, zucchini yellow mosaic virus, passionfruit woodiness virus and South African Passiflora virus (SAPV). Comparison of the partial sequence data with these and other published sequences revealed that the coat protein of CABMV-Morocco is very similar to that of SAPV suggesting that they are strains of the same virus. Since CABMV was described over 25 years earlier than SAPV, the name CABMV should take precedence and SAPV should be renamed CABMV-SAP, the South African Passiflora strain of CABMV.

Taxonomic relationships between distinct potato virus Y isolates based on detailed comparisons of the viral coat proteins and 3'-nontranslated regions

Detailed comparisons were made of the sequences of the coat protein (CP) cistrons and 3'-nontranslated regions (3'-NTR) of 21 (geographically) distinct isolates of potato virus Y (PVY) and a virus isolate initially described as pepper mottle virus (PepMoV). Multiple sequence alignments and phylogenetic relationships based on these alignments resulted into a subgrouping of virus isolates which largely corresponded with the historical strain differentiation based on biological criteria as host range, symptomatology and serology. Virus isolates belonging to the same subgroup shared a number of characteristic CP amino acid and 3'-NTR nucleotide residues indicating that, by using sequences from the 3'-terminal region of the potyvirus genome, a distinction could be made between different isolates of one virus species as well as between different virus species. RNA secondary structure analysis of the 3'-NTR of twelve PVY isolates revealed four major stem-loop structures of which, surprisingly, the loop sequences gave a similar clustering of isolates as resulting from the overall comparisons of CP and 3'-NTR sequences. This implies a biological significance of these structural elements.

Cloning, sequencing, and expression in Escherichia coli of the coat protein gene of a new potyvirus infection South African Passiflora

Complementary DNA representing 1418 nucleotides (nt) of the 3'-poly(A)-proximal tract of the genomic RNA of a potyvirus causing woodiness disease in South African passion fruit, was cloned and sequenced. The sequence contained a single long open reading frame (ORF) of 1188 nt with no initiation codon, and a 3'-non-coding region (3'-NCR) of 230 nt followed by a poly-adenylate tract. Comparison of the ORF with other potyviral coat protein (CP) sequences led to the prediction that a 279 residue CP of MW 31722 is encoded by 836 nt at the 3'-terminus of the ORF. This virus is not merely a South African strain of passion fruit woodiness virus (PWV): the deduced CP sequence is only distantly related to CPs of other sequenced strains of PWV, although it is part of a distinct subgroup of potyviruses related to PWV. The virus was therefore designated as South African passiflora virus (SAPV). The DNA containing the putative CP was cloned into the pUEX2 bacterial expression vector and expressed in Escherichia coli as a beta-gal-CP fusion protein. The fusion protein reacted with polyclonal antisera raised against the native virus, and antisera raised against partially purified fusion protein reacted with viral CP in Western blots.

A summary of potyvirus taxonomy and definitions

The current taxonomic status of the family Potyviridae is presented with suggestions for resolving some taxonomic problems. Terms such as strain, pathotype, serotype, variant, mutant, and isolate are discussed in relation to the family.