Zucchini yellow mosaic virus: biological properties, detection procedures and comparison of coat protein gene sequences

Between 2006 and 2010, 5324 samples from at least 34 weed, two cultivated legume and 11 native species were collected from three cucurbit-growing areas in tropical or subtropical Western Australia. Two new alternative hosts of zucchini yellow mosaic virus (ZYMV) were identified, the Australian native cucurbit Cucumis maderaspatanus, and the naturalised legume species Rhyncosia minima. Low-level (0.7%) seed transmission of ZYMV was found in seedlings grown from seed collected from zucchini (Cucurbita pepo) fruit infected with isolate Cvn-1. Seed transmission was absent in >9500 pumpkin (C. maxima and C. moschata) seedlings from fruit infected with isolate Knx-1. Leaf samples from symptomatic cucurbit plants collected from fields in five cucurbit-growing areas in four Australian states were tested for the presence of ZYMV. When 42 complete coat protein (CP) nucleotide (nt) sequences from the new ZYMV isolates obtained were compared to those of 101 complete CP nt sequences from five other continents, phylogenetic analysis of the 143 ZYMV sequences revealed three distinct groups (A, B and C), with four subgroups in A (I-IV) and two in B (I-II). The new Australian sequences grouped according to collection location, fitting within A-I, A-II and B-II. The 16 new sequences from one isolated location in tropical northern Western Australia all grouped into subgroup B-II, which contained no other isolates. In contrast, the three sequences from the Northern Territory fitted into A-II with 94.6-99.0% nt identities with isolates from the United States, Iran, China and Japan. The 23 new sequences from the central west coast and two east coast locations all fitted into A-I, with 95.9-98.9% nt identities to sequences from Europe and Japan. These findings suggest that (i) there have been at least three separate ZYMV introductions into Australia and (ii) there are few changes to local isolate CP sequences following their establishment in remote growing areas. Isolates from A-I and B-II induced chlorotic symptoms in inoculated leaves of Chenopodium quinoa, but an isolate from A-II caused symptomless infection. One of three commercial ZYMV-specific antibodies did not detect all Australian isolates reliably by ELISA. A multiplex real-time PCR using dual-labelled probes was developed, which distinguished between Australian ZYMV isolates belonging to phylogenetic groups A-I, A-II and B-II.     

Molecular variability and genetic structure of the population of <Emphasis Type="Italic">Onion yellow dwarf virus</Emphasis> infecting garlic in Iran

Onion yellow dwarf virus (OYDV) is one of the most important viral diseases of garlic crops worldwide. This study surveyed the occurrence of OYDV in 26 garlic ecotypes collected from different regions in Iran during 2008–2009. Using an electron microscope, we detected filamentous particles with about 700–800 nm in length and 12 nm in width in five samples. These features are typical of the genus Potyvirus. The coat protein (CP) gene from 26 samples was PCR amplified, cloned, sequenced, and compared with the sequences available in GenBank. Phylogenetic analysis using 235 deduced amino acids of the CP gene showed that virus isolates fell into two groups, group A and group B. Members of group A were divided into two subgroups: A-I and A-II. The subgroup A-I appears to be a new subgroup comprising 17 Iranian isolates. The identity levels among the amino acid of 26 Iranian isolates ranged between 90 and 100%. The results indicated that the genetic diversity found in Iran is due to local OYDV populations rather than introduction from other geographical regions. This study is the first report about the molecular structure and geographically diverse range of OYDV populations in this country.     

The phylogenetic structure of the cluster of tobamovirus species serologically related to ribgrass mosaic virus (RMV) and the sequence of streptocarpus flower break virus (SFBV)

Summary. Ribgrass mosaic virus (RMV), turnip vein-clearing virus (TVCV) and Youcai mosaic virus (YoMV; formerly designated as oilseed rape mosaic virus; ORMV) belong to the genus Tobamovirus and are arranged in one out of three subgroups because of their common host range, serological cross-reactivity and amino acid composition of their coat proteins. The recently defined species Wasabi mottle virus (WMoV) is closely related to the same subgroup. The distinction of the four species is difficult and the lack of sequence information of a wide range of isolates has led to an unclear nomenclature. To clarify this situation we sequenced the coat protein genes from 18 isolates which were serologically related to members of the species of this cluster. The size of the coat protein was conserved with the exception of one isolate which revealed an N-terminal extension due to the mutation of three stop-codons. Phylogenetic analysis of these CP ORFs resulted in a tree with three clusters each containing at least one of the approved species RMV, TVCV and 1ptYoMV/WMoV in which our isolates were distributed. The tree was congruent and did support the present taxonomic status of species within this subgroup. For practical purpose we developed a subgroup 3 specific primer pair and a species differentiating restriction fragment length polymorphism (RFLP). Sequencing of the genome of Streptocarpus flower break virus (SFBV) which is serologically distantly related to the subgroup 3 viruses revealed a distinct genome organization. Therefore we propose that this virus should be regarded as a member of a species not belonging to any of the subgroups so far established.     

Genetic structure and molecular variability of potato virus M populations

To investigate the genetic diversity of potato virus M (PVM; genus Carlavirus, family Betaflexiviridae), the complete nucleotide sequence of the coat protein gene of 30 PVM isolates from a major potato-growing region in Iran were determined. Phylogenetic analysis of these Iranian PVM isolates together with those available in the GenBank database suggested two divergent evolutionary lineages that did not reflect the origin of the isolates, and these were designated as PVM-o and PVM-d. Examination of the genetic variability of the coat protein of Iranian isolates and their counterparts whose sequences are available in the Genbank database revealed 16 genotype groups in the PVM population. Analysis of the synonymous-to-nonsynonymous ratio showed strong purifying selection in the CP gene in the genotype groups of divergent clades.     

Molecular characterization and evolutionary analysis of <Emphasis Type="Italic">soybean mosaic virus</Emphasis> infecting <Emphasis Type="Italic">Pinellia ternata</Emphasis> in China

Twenty-nine Pinellia ternata specimens were collected from representative areas in China, including the major production provinces of Zhejiang, Henan, Shanxi, Hunan, Shandong and Hubei. Seven isolates related to soybean mosaic virus (SMV), which could be pathogenic on P. ternata and some soybean [Glycine max (L.) Merr.] cultivars, were detected using double antibody sandwich immunosorbent assay (DAS-ELISA) and RT-PCR amplification performed with degenerate primer of potyviruses. It is revealed that the common potyvirus infecting P. ternata is, indeed, only SMVs rather than Dasheen mosaic virus (DsMV) as previously reported. Further molecular phylogenetic analysis of the coat protein (CP) genes of these SMV isolates from P. ternata and G. max, along with some other potyvirus members, such as DsMV and Watermelon mosaic virus (WMV) reconstructed the evolutionary route on both nucleotide and amino acid levels. Similarity and homology of nucleotide sequences for SMV CP genes demonstrated high host correlation and low partial habitat correlation, while those of amino acid sequences also showed that the host correlation was more notable than the habitat correlation. The amino acid sequence of conserved region within CP determines the main function, which shows high homology between species. This study outspreaded from the viruses themselves and their relationship to the infected hosts and revealed the evolutionary strategies, especially the rapid variation or recombination of SMV of P. ternata, in order to adapt itself naturally to the special host. The GenBank Accession numbers of the sequences reported in this article are DQ360817-DQ360823.     

Molecular characterization of coat protein gene of Garlic common latent virus isolates from India: an evidence for distinct phylogeny and recombination

The coat protein (CP) gene of five Indian Garlic common latent virus (GarCLV) isolates was sequenced and it was 960 bp long in all the five isolates, encoding a protein of 319 amino acids. Comparative nucleotide sequence analysis revealed diversity of 4.3 % among the Indian isolates and of 11.9 % among all isolates worldwide. Amino acid sequence comparison showed a significant variability in the N-terminal of CP of GarCLV. Various protein analysis tools identified thirteen conserved domains and motifs including Carlavirus and Potexvirus-specific Flexi CP and Flexi N CP. Phylogenetic analysis clustered GarCLV isolates in the subgroup II with isolates from Australia, Brazil, Japan, and South Korea. Intraspecies recombination study revealed that only one of the Indian isolates was a recombinant. Interspecies recombination study suggested the absence of genetic exchange from Carlavirus species to GarCLV; conversely, GarCLV was identified as a putative donor for at least two other Carlavirus species. This is the first report of molecular variability and recombination in GarCLV isolates.     

Analysis of Iranian <Emphasis Type="Italic">Potato virus S</Emphasis> isolates

Two hundred forty potato samples with one or more symptoms of leaf mosaic, distortion, mottling and yellowing were collected between 2005 and 2008 from seven Iranian provinces. Forty-four of these samples tested positive with double-antibody sandwich enzyme-linked immunosorbent assays (DAS-ELISA) using a Potato virus S (PVS) polyclonal antibody. Of these 12 isolates of PVS were selected based on the geographical location for biological and molecular characterization. The full coat protein (CP) and 11K genes from 12 PVS isolates were PCR amplified, cloned and sequenced. All 12 PVS isolates showed mosaic symptoms on Nicotiana debneyii and N. tabacum cv. Whiteburly and local lesion on Chenopodium amaranticolor, C. quinoa and C. album. The Iranian isolates share between 93 and 100% pairwise nucleotide identity with other PVS^O isolates. Based on maximum likelihood phylogenetic analysis coupled with pairwise identity analysis, we propose 15 genotypes for the PVS^O strain and 3 genotypes for the PVS^A strain.     

Distribution and molecular diversity of three cucurbit-infecting poleroviruses in China

Cucurbit aphid-borne yellows virus (CABYV) and Melon aphid-borne yellows virus (MABYV) have been found to be associated with cucurbit yellowing disease in China. Our report identifies for the first time a third distinct polerovirus, tentatively named Suakwa aphid-borne yellows virus (SABYV), infecting Suakwa vegetable sponge. To better understand the distribution and molecular diversity of these three poleroviruses infecting cucurbits, a total of 214 cucurbitaceous crop samples were collected from 25 provinces in China, and were investigated by RT-PCR and sequencing. Of these, 108 samples tested positive for CABYV, while 40 samples from five provinces were positive for MABYV, and SABYV was detected in only 4 samples which were collected in the southern part of China. Forty-one PCR-amplified fragments containing a portion of the RdRp gene, intergenic NCR and CP gene were cloned and sequenced. Sequence comparisons showed that CABYV isolates shared 78.0–79.2% nucleotide sequence identity with MABYV isolates, and 69.7–70.8% with SABYV. Sequence identity between MABYV and SABYV was 73.3–76.5%. In contrast, the nucleotide identities within each species were 93.2–98.7% (CABYV), 98.1–99.9% (MABYV), and 96.1–98.6% (SABYV). Phylogenetic analyses revealed that the polerovirus isolates fit into three distinct groups, corresponding to the three species. The CABYV group could be further divided into two subgroups: the Asia subgroup and the Mediterranean subgroup, based on CP gene and partial RdRp gene sequences. Recombination analysis suggested that MABYV may be a recombinant virus.     

Genetic diversity of the movement and coat protein genes of South American isolates of Prunus necrotic ringspot virus

Prunus necrotic ringspot virus (PNRSV) is distributed worldwide, but no molecular data have been previously reported from South American isolates. The nucleotide sequences corresponding to the movement (MP) and coat (CP) proteins of 23 isolates of PNRSV from Chile, Brazil, and Uruguay, and from different Prunus species, have been obtained. Phylogenetic analysis performed with full-length MP and CP sequences from all the PNRSV isolates confirmed the clustering of the isolates into the previously reported PV32-I, PV96-II and PE5-III phylogroups. No association was found between specific sequences and host, geographic origin or symptomatology. Comparative analysis showed that both MP and CP have phylogroup-specific amino acids and all of the motifs previously characterized for both proteins. The study of the distribution of synonymous and nonsynonymous changes along both open reading frames revealed that most amino acid sites are under the effect of negative purifying selection.     

Genetic diversity and distribution of tomato-infecting begomoviruses in Iran

The incidence and severity of tomato leaf curl disease (TLCD) is increasing worldwide. Here we assess the diversity and distribution within tomato producing areas of Iran of begomoviruses that cause this disease. Tomato with typical TLCD symptoms and asymptomatic weeds were collected in 2005 and 2006 and tested for the presence of begomovirus DNA using polymerase chain reaction (PCR). Analysis of cloned and sequenced PCR products revealed that both mono- and bipartite begomoviruses are associated with TLCD in Iran. Furthermore, our results confirmed the symptomless infection with mono- and bipartite begomoviruses of two weed species, Chrozophora hierosolymitana Spreng (Euphobiaceae) and Herniaria sp. (Caryophyllaceae). Eighteen Iranian begomovirus isolates were classified into two major groups and two or three subgroups according to the 5′-proximal 200 nucleotides of the coat protein (CP) gene or the N-terminal 600 nucleotides of the Rep gene. Whereas most of the monopartite isolates showed closest similarity to tomato yellow leaf curl virus-Gezira (TYLCV-Ge), the three bipartite isolates were most similar to Tomato leaf curl New Delhi virus (ToLCNDV). Mixed mono- and a bipartite begomovirus infections were detected in both tomato and C. hierosolymitana. Our results indicate that the tomato producing areas in central, southern, and southeastern Iran are threatened by begomoviruses originating from both the Mediterranean basin and the Indian subcontinent.     

Molecular analysis of coat protein coding region of tobacco stunt virus shows that it is a strain of <Emphasis Type="Italic">Lettuce big-vein virus</Emphasis> in the genus <Emphasis Type="Italic">Varicosavirus</Emphasis>

Summary. To evaluate the relationship between tobacco stunt virus (TStV) and Lettuce big-vein virus (LBVV), we determined nucleotide sequences of the coat protein (CP) coding region of five TStV and three LBVV isolates and compared them with those of one Japanese and four Spanish isolates of LBVV. CP coding regions were identical in size and the nucleotide and amino acid sequence identities between TStV and LBVV were 95.6–96.5% and 97.2–98.7%, respectively. Phylogenetic analysis of nucleotide sequences indicated that TStV was very closely related to LBVV and a strain of LBVV rather than a distinct species.     

Characterisation of<Emphasis Type="Italic"> potato virus Y</Emphasis> isolates from Iran

A survey of Potato virus Y (PVY) was conducted in cultivated fields in six Iranian provinces between January 2005 to July 2007. Two hundred samples from potato and tomato were collected and analyzed by enzyme-linked immunosorbent assay (ELISA) for potyviruses. Almost one fourth of the samples were found to be infected by PVY. Analysis of these PVY-positive samples using three monoclonal antibodies (MAbs) facilitating the simultaneous detection of three main strains namely the ordinary (PVY^O), strain (PVY^N) and C (PVY^C) strains. However, the fourth strain (PVY^NTN) and some others recombinant isolates were also identified by molecular methods. Host range and symptoms analysis using sap inoculation of four different strains of PVY onto a range of plants revealed that the four strains showed biological properties that seemed to be consistent with their molecular grouping. Fourteen isolates of PVY were chosen based on the host and geographical location, primer specificity and serology for further biological and molecular characterisation. The coat protein (CP) and P1 genes and 3′-non-translated region (3′NTR) from 14 representative isolates were sequenced and analysed with the sequences available in GenBank. Composite analysis of the P1, CP and 3′-UTR sequences with all full genome sequences of PVY revealed that there are three potential strains of PVY in Iran, PVY^O, PVY^N-W and PVY^NTN. Isolate KER.SA_N was the most divergent of all the 14 isolates reacted with PVY^N specific MAbs but grouped with PVY^O strains in maximum likelihood phylogentic analysis. The PVY^NTN isolates from Iran more closely related to the European than North American PVY^NTN isolates.     

Identification and characterization of a new vitivirus from grapevine

New virus-like sequences, TvAQ7 and TvP15, were found in a Japanese grapevine accession of OKY-AQ7 (cv. Aki Queen) and of OKY-P15 (cv. Pione) by nested RT-PCR to simultaneously amplify a segment of the RNA-dependent RNA polymerase (RdRp) gene from members of the genera Vitivirus and Foveavirus. The TvAQ7 genome, except for an exact 5′ terminus, is composed of about 7.6 kb containing five potential open reading frames. The genomic organization resembles those of grapevine virus A and other known vitiviruses. The 199-amino-acid sequence deduced from the ORF4 of TvAQ7 has 38.5–54.0% identity with the coat protein (CP) of known grapevine vitiviruses and 86.9% identity with TvP15. Phylogenetic analysis based on amino acid sequences of the CP showed that TvAQ7 and TvP15 were closely related to the vitiviruses. In addition, we confirmed that TvAQ7 and TvP15 were transmitted from infected grapevine to healthy seedlings by the mealybug Pseudococcus comstocki Kuwanae. On the basis of our findings, TvAQ7 and TvP15 should be considered isolates of a new species of the genus Vitivirus, and both isolates are probably genetic variants of the new species. We propose to name this virus grapevine virus E (GVE).     

Genetic variability and phylogenetic analysis of hosta virus X

Triple gene block 1 (TGB1) and coat protein (CP) sequences of 30 hosta virus X (HVX) isolates from Tennessee (TN), USA, were determined and compared with available sequences in GenBank. The CPs of all known HVX isolates, including those from TN, shared 98.3–100% and 98.2–100% nucleotide and amino acid sequence identity, respectively, whereas TGB1 shared 97.4–100% nucleotide and 97–100% amino acid sequence identity. TGB1 of TN isolates were all longer by one codon from that of a Korean isolate, which is the only sequence publicly available. Phylogenetic analysis of nucleotide and amino acid sequences of TGB1 and CP of all known HVX isolates, separately or combined, revealed a close relationship, suggesting that all of them are derived from a common ancestor. Phylogenetic analysis with the type member of each genus of the family Flexiviridae confirmed that HVX is a member of a distinct species of the genus Potexvirus.     

Genetic variability in the coat protein genes of lettuce big-vein associated virus and Mirafiori lettuce big-vein virus

Summary. Available data suggests that lettuce big-vein disease is caused by the ophiovirus Mirafiori lettuce big-vein virus (MLBVV) but not by the varicosavirus Lettuce big-vein-associated virus (LBVaV), although the latter is frequently associated with the disease. Since the disease occurs worldwide, the putative coat protein (CP) open reading frames of geographically distinct isolates of MLBVV and LBVaV were sequenced. Comparison of both nucleotide and amino acid sequences showed a high level of sequence similarity among LBVaV isolates. Phylogenetic analysis of LBVaV CP nucleotide sequences showed that most of the Spanish isolates clustered in a phylogenetic group whereas English isolates were more similar to the USA isolate. An Australian isolate was closely related to the Dutch isolate. Genetic diversity among MLBVV CP nucleotide sequences was higher ranging from 0.2% to 12%. Phylogenetic analysis of MLBVV CP nucleotide sequences revealed two distinct subgroups. However, this grouping was not correlated with symptom development on lettuce or the geographic origin of the MLBVV isolates. Finally, a quick method based on RFLP analysis of RT-PCR amplicons was developed for assigning MLBVV isolates to the two subgroups.     

Identification of new isolates of <Emphasis Type="Italic">Turnip mosaic virus</Emphasis> that cluster with less common viral strains

Summary Turnip mosaic virus (TuMV) was found infecting cultivated brassicas and wild and cultivated ornamental Brassicaceae plants in different regions of Spain. Five new TuMV isolates, originating from different host plant species (Brassica cretica, Brassica juncea, Brassica napus, Eruca vesicaria subsp. sativa and Sisymbrium orientale), have been identified. The nucleotide sequences of the coat protein (CP) genes of the five isolates were determined. Phylogenetic analysis of the CP sequences showed that the five isolates grouped into two different clusters. The three isolates from the central region of Spain clustered with a previously reported Pisum sativum isolate from southeastern Spain, whereas the other two isolates from the eastern region clustered with two Italian and two Greek isolates. Both clusters were genetically distinct and belonged to the multi-lineage group OBR. The OBR group contains mainly TuMV isolates from hosts other than Brassica spp. and Raphanus sativus and mostly originating from Mediterranean countries. These new sequences provide further phylogenetic resolution of the OBR group. Although new TuMV isolates have been found in Spain, they were not associated with any serious disease outbreaks.     

Strawberry necrotic shock virus is a distinct virus and not a strain of <Emphasis Type="Italic">Tobacco streak virus</Emphasis>

Summary. Fragaria (strawberry) and Rubus species (blackberry, wild blackberry, red raspberry and black raspberry) were thought to be infected with distinct isolates of Tobacco streak virus (TSV). Employing serology and nucleic acid hybridization it has been shown that these isolates form a cluster distinct from other strains of TSV. In this study we have cloned and sequenced the complete RNA 3 of an isolate of TSV from strawberry (Fragaria) as well as the coat protein (CP) gene of 14 additional isolates of TSV originating from Fragaria and Rubus species. Our data suggest that the isolates of TSV that infect Fragaria and Rubus belong to a distinct virus for which we propose the name Strawberry necrotic shock virus (SNSV). The RNA 3 of SNSV contains 2248 nucleotides, 43 more than the type isolate of TSV from white clover (TSV-WC), with a CP gene that is 669 nucleotides long, in contrast to the 714–7 nucleotides of the TSV CP sequences found in the database. The movement protein gene of SNSV is 897 nucleotides in length, 27 more than that of the TSV-WC isolate of TSV. The CP genes of the 15 Fragaria and Rubus isolates that we studied form two distinct phylogenetic clusters that share about 95% amino acid sequence identity, while they only share 60–65% amino acid sequence identity with TSV-WC.     

Cloning and sequencing of the coat protein gene of tobacco ringspot virus isolates from UK and Iran

The coat protein (CP) gene and the 3' untranslated region (UTR) of genomic RNA 2 of Tobacco ringspot virus (TRSV, the genus Nepovirus, subgroup a) isolates from the UK and Iran were cloned from total viral RNA and sequenced. Comparison of these isolates with an isolate from the USA revealed a high degree of nucleotide and amino acid identity which extends the knowledge of molecular relationships between these three TRSV isolates. The UK isolate shared the highest nucleotide identity (95%) with the US isolate as compared to a lower identity with the Iranian isolate (92%). The highest identity (98%) was found between the UK and US isolates at amino acid level. Comparative analysis of the Iranian, UK and US isolates revealed some differences concerning some members of other subgroups of nepoviruses. For example, the N-terminal FDAYXR and the C-terminal FYGRXS motifs conserved among some nepoviruses, which occur adjacent to each other in folded CP molecules, were not detected in the Iranian, UK or US TSRV isolates. These isolates shared similarity only with Tomato ringspot virus (TomRSV) belonging to the subgroup c of nepoviruses. Another similarity of these isolates with TomRSV and Raspberry ringspot virus (RRSV) was the presence of a 34 nucleotide (nt) long sequence within the 3'-UTR.     

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

Summary.  A caladium isolate of dasheen mosaic virus (DsMV-Ch) was cloned as cDNA from genomic RNA. The sequence of the 3′-terminal 3 158 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 (∼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. Received March 19 Accepted June 26, 1998     

Characterization of a new curtovirus,pepper yellow dwarf virus,from chile pepper and distribution in weed hosts in New Mexico

Over 4,950 asymptomatic weed samples from more than 20 weed species that are host plants for curtoviruses were collected from ten chile pepper fields in southern New Mexico (NM) during 2003, 2004 and 2005 to identify whether they were infected with curtoviruses and to determine which curtoviruses were distributed in the weed population. Polymerase chain reaction using primers designed to detect a portion of the coat protein (cp) gene were used to detect curtoviruses, and infected plants were further tested for specific curtoviruses using primers designed to detect to a portion of the replication-associated protein (rep) gene. Amplification of the cp gene was successful from 3.7, 1.17, and 1.9% of the weed samples in 2003, 2004, and 2005, respectively. Seventy-three amplicons from those samples were sequenced and compared to well-characterized curtoviruses. Analysis of the rep nucleotide sequences showed that ~32.9% of the weed isolates tested were closely related to beet mild curly top virus (BMCTV). Approximately 12.4% were closely related to beet severe curly top virus (BSCTV). The rest of the weed isolates (54.7%), which shared a very high level of nucleotide sequence identity to each other, represent a new curtovirus species. Using eight primers designed for PCR, complete genomes of three curtoviruses isolated from chile pepper samples representing the three groups of curtoviruses in southern New Mexico were sequenced. Comparisons of whole sequences of the genomes revealed that the DG2SW171601 isolate (2,929 nucleotides) was nearly identical to BMCTV-W4 (~98% nucleotide sequence identity). The LRME27601 isolate (2,927 nucleotides) was most closely related to BSCTV (~92% nucleotide sequence identity). The LJN17601 isolate (2,959 nucleotides) shared only from 49.9 to 88.8% nucleotide sequence identity with other well-characterized curtoviruses. Based on the accepted cut-off of 89%, we propose that the LJN17601 isolate is a member of a new curtovirus species. Chile peppers infected with this virus in the field express chlorotic stunting symptoms, so we propose the name pepper yellow dwarf virus (PeYDV). This new curtovirus species may be the result of mutations in the genome and recombination between BMCTV-W4 and BSCTV.