Bean Common Mosaic Virus Subgroup Research Articles

A Genetic Study of Spillovers in the Bean Common Mosaic Subgroup of Potyviruses.

Nine viruses of the bean common mosaic virus subgroup of potyviruses are major international crop pathogens, but their phylogenetically closest relatives from non-crop plants have mostly been found only in SE Asia and Oceania, which is thus likely to be their "centre of emergence". We have compared over 700 of the complete genomic ORFs of the crop pandemic and the non-crop viruses in various ways. Only one-third of crop virus genomes are non-recombinant, but more than half the non-crop virus genomes are. Four of the viruses were from crops domesticated in the Old World (Africa to SE Asia), and the other five were from New World crops. There was a temporal signal in only three of the crop virus datasets, but it confirmed that the most recent common ancestors of all the crop viruses were before inter-continental marine trade started after 1492 CE, whereas all the crown clusters of the phylogenies are from after that date. The non-crop virus datasets are genetically more diverse than those of the crop viruses, and Tajima's D analyses showed that their populations were contracting, and only one of the crop viruses had a significantly expanding population. dN/dS analyses showed that most of the genes and codons in all the viruses were under significant negative selection, and the few that were under significant positive selection were mostly in the PIPO-encoding region of the P3 protein, or the PIPO protein itself. Interestingly, more positively selected codons were found in non-crop than in crop viruses, and, as the hosts of the former were taxonomically more diverse than the latter, this may indicate that the positively selected codons are involved in host range determination; AlphaFold3 modelling was used to investigate this possibility.

A Zinc Finger Motif in the P1 N Terminus, Highly Conserved in a Subset of Potyviruses, Is Associated with the Host Range and Fitness of Telosma Mosaic Virus.

P1 is the first protein translated from the genomes of most viruses in the family Potyviridae, and it contains a C-terminal serine-protease domain that cis-cleaves the junction between P1 and HCPro in most cases. Intriguingly, P1 is the most divergent among all mature viral factors, and its roles during viral infection are still far from understood. In this study, we found that telosma mosaic virus (TelMV, genus Potyvirus) in passion fruit, unlike TelMV isolates present in other hosts, has two stretches at the P1 N terminus, named N1 and N2, with N1 harboring a Zn finger motif. Further analysis revealed that at least 14 different potyviruses, mostly belonging to the bean common mosaic virus subgroup, encode a domain equivalent to N1. Using the newly developed TelMV infectious cDNA clones from passion fruit, we demonstrated that N1, but not N2, is crucial for viral infection in both Nicotiana benthamiana and passion fruit. The regulatory effects of N1 domain on P1 cis cleavage, as well as the accumulation and RNA silencing suppression (RSS) activity of its cognate HCPro, were comprehensively investigated. We found that N1 deletion decreases HCPro abundance at the posttranslational level, likely by impairing P1 cis cleavage, thus reducing HCPro-mediated RSS activity. Remarkably, disruption of the Zn finger motif in N1 did not impair P1 cis cleavage and HCPro accumulation but severely debilitated TelMV fitness. Therefore, our results suggest that the Zn finger motif in P1s plays a critical role in viral infection that is independent of P1 protease activity and self-release, as well as HCPro accumulation and silencing suppression. IMPORTANCE Viruses belonging to the family Potyviridae represent the largest group of plant-infecting RNA viruses, including a variety of agriculturally and economically important viral pathogens. Like all picorna-like viruses, potyvirids employ polyprotein processing as the gene expression strategy. P1, the first protein translated from most potyvirid genomes, is the most variable viral factor and has attracted great scientific interest. Here, we defined a Zn finger motif-encompassing domain (N1) at the N terminus of P1 among diverse potyviruses phylogenetically related to bean common mosaic virus. Using TelMV as a model virus, we demonstrated that the N1 domain is key for viral infection, as it is involved both in regulating the abundance of its cognate HCPro and in an as-yet-undefined key function unrelated to protease processing and RNA silencing suppression. These results advance our knowledge of the hypervariable potyvirid P1s and highlight the importance for infection of a previously unstudied Zn finger domain at the P1 N terminus.

Complete genome sequence of passiflora virus Y infecting passion fruit in China.

The complete genome sequence of passiflora virus Y (PaVY) from passion fruit growing in Guangdong province, China, was determined. The entire positive single-strand RNA genome comprises 9681 nucleotides (nt) excluding the poly(A) tail and encodes a polyprotein of 3084 amino acids flanked by 5' and 3' untranslated regions of 169 and 257 nt, respectively. In sequence comparisons and phylogenetic analysis, PaVY appears to represent a new species in the bean common mosaic virus subgroup of the genus Potyvirus. This is the first report of the complete genome sequence of PaVY and the first report of this virus in China.

Description and genetic variation of a distinct species of Potyvirus infecting saffron (Crocus sativus L.) plants in major production regions in Iran

Saffron (Crocus sativus L.), a highly valuable crop famous for the unique taste, aroma, colour and medicinal properties of the stigmas, is widely cultivated in Iran. During 2011–2016, a total of 965 samples were randomly collected from six important saffron growing provinces of Iran to test for the presence of viruses. Assays revealed the presence of a distinct species of the genus Potyvirus, which has been tentatively named saffron latent virus (SaLV). Phylogenetic analysis of the SaLV complete genome sequence, 9,693 nucleotides (nt) excluding poly(A) tail, revealed that this virus grouped into Bean common mosaic virus subgroup in the genus Potyvirus with the closest relative being Bean common mosaic necrosis virus. A number of distinct plant species were evaluated for the host range of SaLV; Chenopodium amaranticolor and Chenopodium quinoa were found to be systemic hosts of SaLV. There were no nucleotide sites that indicated any recombination events, and the analysis of the coat protein (CP) sequence of 50 samples, collected from different geographical origins, did not show spatially structured diversity. Overall, our data shows strong negative selection pressure in CP, estimated by nucleotide sequences. The relevance of SaLV for saffron production in Iran remains to be established.

Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae

Genome structure and sequence are notably conserved between members of the family Potyviridae. However, some genomic regions of these viruses, such as that encoding the P1 protein, show strikingly high variability. In this study, some partially conserved motifs were identified upstream of the quite well-conserved protease domain located near the P1 C terminus. The irregular distribution of these motifs suggests that the potyviral P1 proteins have undergone complex evolutionary diversification. Evidence was found of recombination events in the P1 N-terminal region, similar to those reported in potyviruses of the bean common mosaic virus subgroup, but also affecting other potyviruses. Moreover, intergeneric recombination events affecting potyviruses and ipomoviruses were also observed. Evidence that these recombination events could be linked to host adaptation is provided. Specific sequence features and differences in net charge help to classify the P1 proteins of members of the family Potyviridae into two groups: those from potyviruses and rymoviruses and those from tritimoviruses. The ipomovirus Cucumber vein yellowing virus has two P1 copies arranged in tandem, the most N-terminal one being of the potyvirus type and the other being of the tritimovirus type. These findings suggest that both recombination and gene duplication have contributed to P1 evolution and helped to facilitate successful adaptation of members of the family Potyviridae to a wide range of host species.

The Complete Nucleotide Sequence of a Pakistani Isolate of Watermelon Mosaic Virus Provides Further Insights into the Taxonomic Status in the Bean Common Mosaic Virus Subgroup

Watermelon mosaic virus (WMV) is a potyvirus with a worldwide distribution, but is mostly found in temperate and Mediterranean regions. The complete nucleotide (nt) sequence of a Pakistani isolate of WMV (WMV-Pk) was determined and compared with French isolate (WMV-Fr) and other closely related potyviruses. WMV-Pk showed overall identities of 94.4% (nt) and 96% (amino acid; aa) with the WMV-Fr. However, variability was observed in the 5' UTR and P1 region. Although sequence identities over most of the genome were well above 90% at both the nt and aa levels, reaching 99.6% (aa) in the CP and 100% (aa) in the 6K1 and 6K2, thereby suggesting that WMV-Pk and WMV-Fr are identical strains, but the sequence identities in the P1 region were only 80.6% (aa) and 82.8% (nt), while that in the 5' UTR was 82%. These differences may be due to different mutation phenomena of a common ancestor virus or mutations caused by different selection pressures in two different agro-ecological zones. The sequence of WMV-Pk is very close to that of Soybean mosaic virus (SMV) over most of the genome, except for the N-terminal region, which is subject to recombination between SMV and Peanut stripe virus (PSV)/Bean common mosaic virus (BCMV), as revealed by Simplot and phylogenetic analyses of N- and C-terminal P1, HC-Pro, and 5' UTR regions of the genome.

The genomic sequence of Wisteria vein mosaic virus and its similarities with other potyviruses

The complete nucleotide sequence of a Beijing isolate of Wisteria vein mosaic virus was determined to be 9695 nucleotides in length excluding the poly(A) tail. Sequence analysis predicted a single large open reading frame of 9279 nucleotides potentially encodes a polyprotein of 3092 amino acids. Phylogenetic analysis based on the genomic and deduced amino acid sequences support the current status of Wisteria vein mosaic virus (WVMV) as a distinct virus of the genus Potyvirus and a member of the Bean common mosaic virus (BCMV) subgroup. Sequence comparisons of WVMV and other members of the BCMV subgroup showed that WVMV is most closely related to both soybean mosaic virus and watermelon mosaic virus.

Detection and characterisation of a second potyvirus from Thunberg fritillary in China

Plants of Thunberg fritillary (Fritillaria thunbergii Miq.) from Zhejiang Province, were found to be co-infected with two distinct potyviruses. One was an isolate of the recently reported Thunberg fritillary mosaic virus (TFMV; Wei et al., (2005) Arch Virol 150: 1271-1280), while the other was a distinct virus that did not react with TFMV antiserum nor with antisera to 17 other potyviruses, except for a weak reaction with antibodies produced to soybean mosaic virus (SMV) Pinellia strain. Both viruses could be transmitted mechanically to their original host but not to any of a range of commonly used indicator plants. No local lesion host was identified that would enable the viruses to be propagated independently. The complete sequences of both viruses were determined; that of the new virus (9656 nt) had the typical genome organisation and recognised sequence motifs of a potyvirus, encoding a putative polyprotein of 351 kDa. Phylogenetic analysis, sequence comparisons, and the pattern of polyprotein cleavage sites all indicated that it was a member of the Bean common mosaic virus subgroup. The most closely related species are Soybean mosaic virus and Wisteria vein mosaic virus, with 68-69% amino acid identity between their polyproteins. This is sufficiently different for the new virus to be regarded as a distinct species, which we have tentatively named Fritillary virus Y.

Identification and molecular characterization of Zantedeschia mild mosaic virus, a new calla lily-infecting potyvirus

Tissue-cultured seedlings of calla lily (Zantedeschia spp.) with mild mosaic symptom were observed in Taiwan. A new potyvirus, Zantedeschia mild mosaic virus (ZaMMV), was identified in the diseased plants based on the result of ELISA, virion morphology and sequence data. In the host range test, ZaMMV only infected Philodendron selloum and Zantedeschia spp. causing systemic mosaic and mild mosaic symptom, respectively. The 3'-terminal region of the virus was amplified by RT-PCR from total RNA using a potyvirus-specific degenerate primer and an oligo-dT primer. Sequence analysis revealed that the highest amino acid sequence identity of the capsid protein (CP) gene between ZaMMV and thirty potyviruses was 55%, and the highest nucleotide identity of 3' untranslated region (3'UTR) was 52%. Therefore, in terms of species demarcating criteria, ZaMMV is a new species of the genus Potyvirus. From the result of phylogenetic analysis, ZaMMV should be a member of the Bean common mosaic virus subgroup. According to the deduced amino acid sequence of ZaMMV, the N terminus of the CP contained 39 glutamine residues before DAG motif. This unique sequence has never been discovered in plant viruses.

First Report of Bean common mosaic necrotic virus Infecting Bean Plants in Aguascalientes and Veracruz, Mexico.

Bean common mosaic necrosis virus (BCMNV) is a pathogen of Phaseolus vulgaris L. BCMNV was previously classified in serogroup A (for necrotic strains) of the Bean common mosaic virus (BCMV) subgroup; serogroup B included non-necrotic strains of BCMV. Both serogroups are currently classified as two different species in the BCMV subgroup of the Poytvirus genus; strains of either species will produce mosaic symptoms and, in the presence of hypersensitive I gene, necrosis in bean plants (1). Prior to this classification, BCMV was reported in Mexico by the presence of mosaic and necrotic symptoms (2). To investigate the presence of BCMNV in Mexico, samples were collected in two of the main bean producing states. The total extracted RNA was used for reverse transcription polymerase chain reaction using primers complementary to the middle portion of the NIa gene (5') and the 3' UTR of the NL3 Michigan isolate (accession number U19287). Two cDNA segments of 2 and 3 kb were obtained from infected plants from the state of Aguascalientes, in the highlands of central Mexico, and from the state of Veracruz, in the lowlands of the Gulf of Mexico, respectively. The cDNAs were cloned and sequenced. Alignment analysis of these sequences with the NL3 strain of BCMNV showed a similarity of 96.4 and 96.7%, respectively. The similarity between the Aguascalientes (accession number AJ01265) and Veracruz isolates was 99.6%, indicating that both are variants of the same species. On the other hand, alignment analysis of these isolates with some published BCMV strain sequences (i.e., accession numbers L15332 and U55315) displayed low similarities of 52.9 and 64.4%, respectively. These comparisons indicate that the Aguascalientes and Veracruz viral isolates belong to the BCMNV species and is the causal agent of mosaic and necrosis observed on the bean plants in those states.

The nucleotide sequence of the 3′-terminal region of dasheen mosaic virus (Caladium isolate) and expression of its coat protein in Escherichia coli for antiserum production

A caladium isolate of dasheen mosaic virus (DsMV-Ch) was cloned as cDNA from genomic RNA. The sequence of the 3'-terminal 3158 nucleotides, which consisted of the 3'-terminus of the NIa gene, the NIb gene, the coat protein (CP) gene, and a 246-nucleotide non-coding region, was between 57-68% similar at the nucleotide level and 72-82% similar at the amino acid level when compared with other potyviruses. Phylogenetic analysis of aligned, selected potyviral CP sequences indicate that DsMV-Ch is similar to DsMV isolates infecting taro and closely related to the bean common mosaic virus subgroup in the genus Potyvirus. A recombinant DsMV-Ch CP (approximately 39 kDa) expressed in E. coli was used as an immunogen and the resulting antiserum reacted with DsMV and several other potyviruses in Western blots and indirect ELISA.

Purification, Host Range, Serology, and Partial Sequencing of Dendrobium Mosaic Potyvirus, A New Member of the Bean Common Mosaic Virus Subgroup

Dendrobium mosaic potyvirus (DeMV) was successfully transmitted from honohono orchids (Dendrobium superbum Reichb. f.) to Nicotiana benthamiana. The coat protein of the virus purified from N. benthamiana had a molecular weight of 34 × 10 3 in sodium dodecyl sulfatepolyacrylamide gel electrophoresis analysis, and the viral RNA was approximately 9.5 kb in size in denatured agarose gel electrophoresis. With a polyclonal antiserum produced against purified DeMV particles, DeMV was found to be widespread in honohono orchids in Hawaii. Based on serological reactions in indirect enzyme-linked immunosorbent assay with monoclonal antibodies, DeMV is a potyvirus of the bean common mosaic virus (BCMV) subgroup. DeMV-specific cDNA clones were obtained and sequenced. Sequence comparison using the coat protein amino acid sequence and the 3' untranslated region sequence showed that DeMV shares 88 to 91 % and 85 to 95 % identity, respectively, with those sequences of BCMV subgroup members. Data from host range studies suggest that DeMV behaves similarly to other potyviruses in the BCMV subgroup such as azuki bean mosaic virus (AzMV) and blackeye cowpea mosaic virus (BICMV). Based on available information, DeMV is considered a member of the BCMV subgroup

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.

Serological and biological relationships among viruses in the bean common mosaic virus subgroup.

Bean common mosaic virus (BCMV), blackeye cowpea mosaic virus (B1CMV), cowpea aphid-borne mosaic virus (CABMV), azuki bean mosaic virus (AzMV), and peanut stripe virus (PStV) are five species of the genus Potyvirus, family Potyviridae which are seed-transmitted in beans or cowpeas. Eighteen isolates of BCMV, five isolates of B1CMV, four isolates of CABMV, and one isolate each of AzMV, and PStV were compared serologically using a panel of 13 monoclonal antibodies (MAbs) raised against BCMV, B1CMV, CABMV, or PStV in indirect enzyme-linked immunosorbent assay (ELISA). Four MAbs detected all virus isolates; one detected all isolates except those of CABMV. Three MAbs were specific only for serotype A isolates of BCMV. Four MAbs detected all serotype B isolates of BCMV plus all isolates of B1CMV, AzMV, and PStV. None of the antibodies distinguished among these four viruses. However, in biological tests with 11 bean cultivars selected for differentiating BCMV pathotypes, all isolates of B1CMV, AzMV, and PStV could be differentiated from the BCMV serotype B isolates by their reactions on a few bean cultivars in host group I and the cowpea cultivar California Blackeye #5. Potential problems that can arise from the use of nonauthenticated isolates are also discussed.