A universal PCR primer to detect members of the Potyviridae and its use to examine the taxonomic status of several members of the family

A new point mutation in the HC-Pro of potato virus Y is involved in tobacco vein necrosis

Tobacco vein necrosis (TVN) is a complex phenomenon regulated by different genetic determinants mapped in the HC-Pro protein (amino acids N330, K391 and E410) and in two regions of potato virus Y (PVY) genome, corresponding to the cytoplasmic inclusion (CI) protein and the nuclear inclusion protein a-protease (NIa-Pro), respectively. A new determinant of TVN was discovered in the MK isolate of PVY which, although carried the HC-Pro determinants associated to TVN, did not induce TVN. The HC-Pro open reading frame (ORF) of the necrotic infectious clone PVY N605 was replaced with that of the non-necrotic MK isolate, which differed only by one amino acid at position 392 (T392 instead of I392). The cDNA clone N605_MKHCPro inoculated in tobacco induced only weak mosaics at the systemic level, demostrating that the amino acid at position 392 is a new determinant for TVN. No significant difference in accumulation in tobacco was observed between N605 and N605_MKHCPro. Since phylogenetic analyses showed that the loss of necrosis in tobacco has occurred several times independently during PVY evolution, these repeated evolutions strongly suggest that tobacco necrosis is a costly trait in PVY.

Overview on century progress in research on mosaic disease of apple (Malus domestica Borkh) incited by apple mosaic virus/apple necrotic mosaic virus

Apple mosaic is widely distributed disease throughout the apple growing regions leading to the major adverse effects both qualitatively and quantitatively. Earlier the apple mosaic virus-ApMV was regarded as the only causal agent of the disease, but recently a novel virus apple necrotic mosaic virus-ApNMV have been reported as the causal pathogen from various apple growing countries. Accurate diagnosis of disease and detection of ApMV and ApNMV are of utmost importance, because without this ability we can neither understand nor control this disease. Both the viruses are mostly controlled through quarantine, isolation, sanitation and certification programs depending on sensitive and specific detection methods available. Here we review the 100-year progress in research on apple mosaic disease, which includes history, yield losses, causal agents, their genome organization, replication, traditional to recent detection methods, transmission, distribution and host range of associated viruses and management of the disease.

One-Step Reverse-Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Assay for the Detection of Canna Yellow Streak Virus

Canna yellow streak virus (CaYSV) is a potyvirus that causes severe damage to the ornamental plant canna in the United Kingdom and Brazil. Here, we identified CaYSV in China by isolating total RNA from an infected plant, amplifying the virus genome segments, and cloning and sequencing the amplicons. After assembly, the full-length genome of the virus was obtained and uploaded to the NCBI database. Phylogenetic analysis results showed that the Guizhou isolate (OL546222) was most closely related to the KS isolate (MG545919.1). Virus detection is essential for virus disease control but the subclinical infection of CaYSV on canna in its early development increases the difficulty of CaYSV diagnosis. The goal of this study was to develop an efficient method for detection of CaYSV. We designed the primers, optimized the reaction conditions, and finally established a one-step reverse-transcription loop-mediated isothermal amplification (RT-LAMP) method. The product of RT-LAMP can be analyzed by both agarose gel electrophoresis and visible color change. The established one-step RT-LAMP assay showed high specificity and sensitivity in detecting CaYSV. This RT-LAMP method was also applied in analysis of 61 field samples collected from Guizhou and Jiangsu Provinces. The results showed that the infection rates of CaYSV on canna samples from these two provinces were very high (63 and 96% respectively).

Complete genome sequence analysis of a new potyvirus isolated from Paris polyphylla var. yunnanensis

The complete genome sequence of a new potyvirus from Paris polyphylla var. yunnanensis was determined. Its genomic RNA consists of 9571 nucleotides (nt), excluding the 3'-terminal poly(A) tail, containing the typical open reading frame (ORF) of potyviruses and encoding a putative large polyprotein of 3061 amino acids. The virus shares 54.20%-59.60% nt sequence identity and 51.80%-57.90% amino acid sequence identity with other potyviruses. Proteolytic cleavage sites and conserved motifs of potyviruses were identified in the polyprotein and within individual proteins. Phylogenetic analysis indicated that the virus was most closely related to lily yellow mosaic virus. The results suggest that the virus should be classified as a member of a novel species within the genus Potyvirus, and we have tentatively named this virus "Paris yunnanensis mosaic chlorotic virus" (PyMCV).

Complete genome sequence of polygonatum mosaic-associated virus 1, a novel member of the genus Potyvirus in China

The complete genome sequence of a putative novel potyvirus, tentatively named "polygonatum mosaic-associated virus 1" (PMaV1), was sequenced from naturally infected Polygonatum cyrtonema Hua in China. PMaV1 has a typical genome organization of potyviruses with a single large open reading frame (nt 119-9448) that encodes a 3109-aa polyprotein that is predicted to be cleaved into 10 mature proteins by virus-encoded proteases. Pairwise comparisons revealed that PMaV1 shares 71.50% complete genome sequence identity with Polygonatum kingianum virus 4 and 80.00% amino acid sequence identity with Polygonatum kingianum virus 3 of the genus Potyvirus. Phylogenetic analysis indicated that PMaV1 clustered with other potyviruses and that it was most closely related to Polygonatum kingianum virus 3 and Polygonatum kingianum virus 4. These results suggest that PMaV1 is a new member of the genus Potyvirus of the family Potyviridae (Nucleotide sequence data reported are available in the GenBank databases under the accession number OP380926).

Molecular characterization of Canna yellow streak virus with divergent coat protein N-terminal fragment in Iraq

BACKGROUND

Canna yellow streak virus (CaYSV, family Potyviridae) infects many canna cultivars, which have been widely cultivated in the Iraqi gardens for ornamental purposes. The genetic variability within multiple genomic regions of CaYSV population has been demonstrated in the 3' part, particularly in the coat protein (CP). This work was aimed to characterize CaYSV and investigate its variability from canna plants in Iraq.

METHOD AND RESULTS

Leaves of canna plants grown in several gardens in Baghdad were tested by potyvirus group antibodies and RT-PCR. Analysis of the nucleotide (nt) sequences corresponding to the 3' part of the virus genome revealed the highest identity (81.6-90.6%) with known CaYSV isolates. Phylogenetic analysis of the coat protein (CP) gene sequence placed the Iraqi isolates in a separate clade with members of group A. This distinction was evidenced by unique amino acid changes found within the N-terminal motif of the CP. This is the first report of phylogenetically distinct CaYSV in Iraq.

CONCLUSIONS

This is the first report of phylogenetically distinct CaYSV with divergent CP N-terminus in Iraq.

First report of zucchini tigre mosaic virus infecting four cucurbit crops in China

Cucurbits including ridge gourd (Luffa acutangula), Chieh-qua (Benincasa hispida Cogn. var. Chieh-qua How), Trichosanthes anguina, and sponge gourd (L. cylindrica) are important vegetables in most Asian countries. The 90 viruses known to infect cucurbits include 15 species in genus Potyvirus. In October 2020, nine cucurbit samples with leaf distortion, blister and mottle were collected from the same field of Foshan City, Guangdong Province, China. All samples were tested by western blot with potyvirus-specific antibody (Agdia lnc., Elkhart, IN) and RT-PCR with potyvirus degenerate primers Sprimer/M4T (Chen et al. 2001). Seven out of nine samples were positive for potyvirus in both tests, including one ridge gourd, one Chieh-qua, one sponge gourd, two bottle gourd (Lagenaria siceraria) and two T. anguina. All PCR products (~700-bp) were cloned and sequenced. Sequences of seven amplicons (OM522614 to OM522618, OP090158 to OP090159) containing partial nib and cp genes shared 80.3-100% nucleotide (nt) identity among themselves, and 81.2-97.7% nt identity with ZTMV isolates from China (MN267689, LC371337, MK988416). Except for one Chieh-qua sample, papaya ringspot virus (PRSV) was detected in the same samples where ZTMV was found through sequencing of the amplicons mentioned above. The obtained sequences (OM808942 to OM808945, OP090170 to OP090171) were 95.4-100% identical with PRSV isolates from China. Further RT-PCR was conducted with ZTMV-specific primers ZTMVdF/ZTMVdR targeting partial P3 and 6K1 genes, and PRSV-specific primers PRSV3778F/PRSV4630R targeting partial P3, full-length 6K1 and partial CI genes for all nine samples. Consistently, seven samples were positive for ZTMV, among which one Chieh-qua sample was infected with only ZTMV and six samples were co-infected with ZTMV and PRSV. Interspecific recombination event has been reported for ZTMV (Peng et al. 2021), to detect the recombinants, RT-PCR was conducted for all nine samples with primers ZTMV600F/ZTMV2400R covering the interspecies recombination site (Peng et al. 2021). A fragment (~1.8 kb) was amplified from one T. anguina sample and sequenced (OP090172), which had 97.0% nt identity with the reported recombinant ZTMV-KF17 (MK988415). To fulfill Koch's postulates, a Chieh-qua sample detected with ZTMV but not PRSV, was used for mechanical inoculation on Chieh-qua seedlings. Blister and leaf distortion similar to the field symptoms were observed 21 days post-inoculation. ZTMV infection was verified by RT-PCR with primer pairs Sprimer/M4T and ZTMVdF/ZTMVdR, respectively, followed by sequencing. No amplicon was detected with primer pairs PRSV3778F/PRSV4630R and ZTMV600F/ZTMV2400R. To study the incidence of ZTMV and PRSV, 33 samples including T. anguina, ridge gourd and Chieh-qua were collected from three different fields in Foshan City in May 2022, and were tested by RT-PCR with ZTMV and PRSV primers aforementioned. 30.3% (10/33) of the samples were positive for ZTMV, 39.4% (13/33) tested positive for PRSV, and 21.2% (7/33) were co-infected with the two viruses. Amplicons of ZTMV (600 bp) from all positive samples were sequenced (OP090160 to OP090169), and were 84.8-85.5% identical with ZTMV-TW (LC371337). Recombinant of ZTMV was detected in one T. anguina with primers mentioned above and was sequenced (OP090173), which had 96.2% nt identity with ZTMV-KF17. To our knowledge, this is the first report of ZTMV infecting ridge gourd, Chieh-qua, T. anguina and sponge gourd. The results implied that ZTMV had a potential risk to more cucurbit crops in the field.

First report of bean common mosaic virus naturally infecting yam bean (Pachyrhizus erosus) in China

Yam bean (Pachyrhizus erosus), a high-yielding leguminous root crop with good nutritional value, is widely cultivated in southern China. In 2020, P. erosus (cv. Mumashan) plants exhibiting irregular yellow leaves and malformed seed pods (Supplementary Fig S1) were observed at Ningbo city, Zhejiang Province, China. To determine the causal agent(s) of the disease, symptomatic leaves (n=4) were collected for electron microscopy negative staining. Virus particles with a length of about 700nm, similar to viruses in the genus Potyvirus, were observed via transmission electron microscope (TEM), suggesting the presence a potyvirus(es). To further confirm which potyvirus(es) infected yam bean, total RNA was extracted from leaf samples of a total of six plants, including four symptomatic plants and two asymptomatic plants using TRIzol reagent (Invitrogen Carlsbad, CA, USA) according to the manufacturer's instructions. RNA was reverse-transcribed into cDNA with M4-T as the 3'-anchoring primer by ReverTra Ace® kit (Toyobo, Japan). Sprimer/M4 Potyviridae specific primers (Chen et al., 2001) were used for PCR analysis. A ~1,700-bp-long product was amplified from four symptomatic plants using KOD FX enzyme (Toyobo, Japan). No such band was amplified from the two asymptomatic plants. The PCR product (~1.7kb) amplified from a single symptomatic plant was ligated into the pEASY®-Blunt Zero vector (TransGen Bio, Beijing, China) and sequenced (Sangon Bio, Shanghai, China). The amplicon showed 99% nucleotide sequence identities with bean common mosaic virus (BCMV) isolate NKY021 (KJ807819). Subsequently, the complete nucleotide sequences of this BCMV isolate (referred as BCMV-NB) was amplified by overlapping RT-PCR and rapid amplification of cDNA ends with primers (Supplementary Table S1) designed from the sequence of BCMV isolate NKY021. The BCMV-NB full genome (Accession No. OL871237) consists of 10,053 nucleotides excluding the poly(A) tail and contains a large open reading frame encoding a polyprotein of 3222 amino acids. BLASTn analysis showed that BCMV-NB shared a sequence identity of 96.4% with BCMV isolate HZZB011 (KJ807815). Phylogenetic tree generated by Neighbour-Joining method revealing the BCMV-NB isolate was grouped together with Chinese isolates from Glycine max (Supplementary Fig S1). To test the infectivity of BCMV-NB, virus-free yam bean (cv. Mumashan) and Nicotiana benthamiana seedlings were mechanically inoculated with sap extracted from the symptomatic leaves of a BCMV-NB-infected yam bean plant. The inoculated yam bean plants developed typical BCMV mosaic and chlorotic symptoms at 16 days post inoculation (dpi), while Nicotiana benthamiana had no obvious symptoms at 10 or 20 dpi (Supplementary Fig S1). BCMV infections were confirmed in yam bean plants (infection rate 6/6) and N. benthamiana plants (infection rate 8/8) by RT-PCR at 16 dpi and 10 dpi, respectively. Twelve further P. erosus plants (cv. Mumashan) were collected from a field in Ningbo city and tested by RT-PCR with BCMV-specific primer pair BCMV CP (+)/(-) (Supplementary Table 1). Eight out of the 12 samples tested positive for BCMV by PCR-gel electrophoresis (Supplementary Fig S1) and Sanger sequencing, suggesting a high incidence of BCMV infection in this field. BCMV infection in yam bean has been reported from Indonesia (Damayanti et al., 2008) and Peru (Fuentes et al., 2012). To the best of our knowledge, this is the first report of BCMV naturally infecting yam bean in China. Thus, special attention and appropriate management strategies are needed to minimize the damage caused by BCMV to yam bean crops in China.

Pest categorisation of Apium virus Y

Following a request from the EU Commission, the EFSA Panel on Plant Health conducted a pest categorisation of Apium virus Y (ApVY) for the EU territory. The identity of the ApVY, a member of the genus Potyvirus (family Potyviridae), is well established and reliable detection methods are available. The pathogen is not included in EU Commission Implementing Regulation 2019/2072. ApVY, considered endemic in Australia, was reported also in New Zealand and USA. In the EU, the virus was identified in Germany and Slovenia. No information on adoption of official control measures is available. In natural conditions, ApVY infects plant species of the family Apiaceae (i.e. celery, coriander, dill, parsley, bishop's weed) in which it generally induces leaf symptoms and/or stunting. In some hosts (i.e. parsley and poison hemlock), ApVY may be asymptomatic. The virus is transmitted in a non-persistent manner by the aphid Myzus persicae which is widespread in the EU. Although ApVY transmission through seeds has been experimentally excluded for some hosts (i.e. poison hemlock and celery), uncertainty exists for the other hosts because seed transmission is not uncommon for potyvirids. Plants for planting, including seeds for sowing, were identified as potential pathways for entry of ApVY into the EU. Cultivated and wild hosts of ApVY are distributed across the EU. Economic impact on the production of the cultivated hosts is expected if further entry and spread in the EU occur. Phytosanitary measures are available to prevent further entry and spread of the virus. Currently, ApVY does not fulfil the criterion of being absent or present with restricted distribution and under official control to be regarded as a potential Union quarantine, unless official control is implemented. This conclusion is associated with high uncertainty regarding the current virus distribution in the EU.

Complete genome sequence of a putative novel ilarvirus isolated from Eleocharis dulcis

The complete genomic sequence of a novel ilarvirus from Eleocharis dulcis, tentatively named "water chestnut virus A" (WCVA), was determined using next-generation sequencing (NGS) combined with reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) PCR. The three genomic RNA components of WCVA were 3578 (RNA1), 2873 (RNA2), and 2073 (RNA3) nucleotides long, with four predicted open reading frames containing conserved domains and motifs typical of ilarviruses. Phylogenetic analysis of each predicted protein consistently placed WCVA in subgroup 4 of the genus Ilarvirus, together with prune dwarf virus, viola white distortion associated virus, Fragaria chiloensis latent virus, and potato yellowing virus. The genetic distances and lack of serological reaction to antisera against other ilarviruses suggest that WCVA is a novel member of the genus.

Complete Genome Sequence of Mirabilis Crinkle Mosaic Virus Isolated from Pokeweed in Japan

The complete genome sequence of a pokeweed (Phytolacca americana L.) isolate of mirabilis crinkle mosaic virus (MiCMV) in Japan was determined.

Detection and Distribution of Viruses Infecting Garlic Crops in Australia

The distribution of viruses in eastern Australian field garlic was evaluated. Detection assays were developed that involved generic RT-PCR for viruses in the Allexivirus, Carlavirus and Potyvirus genera followed by virus-specific colorimetric dot-blot hybridization. Assays targeted the potyviruses (onion yellow dwarf virus (OYDV), shallot yellow stripe virus (SYSV), and leek yellow stripe virus (LYSV)), the carlaviruses (garlic common latent virus (GCLV) and shallot latent virus (SLV)), and the allexiviruses (garlic viruses A, B, C, X (GarVA, -B, -C, -X) and shallot virus X (ShVX)). Virus incidence in crops was consistently high, with most plants infected with at least one virus from each genus. OYDV, LYSV, SLV, and GCLV were commonly detected. Three of the four allexiviruses were in all districts surveyed but varied in incidence, whereas ShVX and SYSV were not detected. There was no association between virus species complement and bulb size, indicating size is not a good predictor of the virus status of planting material. The variation of virus incidence across different Australian growing districts and in different cultivars implies multiple introductions of viruses rather than spread within the country. The genetic diversity observed within coat protein sequences of some virus species also supports multiple separate introductions.

Complete genome sequence of pleioblastus mosaic virus, a distinct member of the genus Potyvirus

Pleioblastus mosaic virus (PleMV) is a tentative member of the genus Potyvirus in the family Potyviridae and was discovered in bamboo with mosaic symptoms in Tokyo, Japan. Since no information on the genome sequence of PleMV has been reported, its taxonomic position has long been uncertain. Here, we report the first complete genome sequences of two distinct PleMV isolates. Excluding the 3'-terminal poly(A) tail, their genomic RNA sequences consist of 9,634 and 9,643 nucleotides (nt); both contain a large open reading frame (ORF) encoding a polyprotein and a small ORF termed PIPO. The large ORFs of the two isolates share 79.2% and 87.6% sequence identity at the nucleotide (nt) and amino acid (aa) level, respectively, and were found to have the highest nt and aa sequence identity (69.0% and 69.9%) to the potyvirus johnsongrass mosaic virus (JGMV). Phylogenetic analysis showed that PleMV is most closely related to JGMV but forms its own clade. These results suggest that PleMV is a distinct member of the genus Potyvirus.

Complete genome sequence of a new achyranthes virus A isolate from Achyranthes bidentata in China

We have determined the complete genomic sequence of a potyvirus from Achyranthes bidentata in Zhejiang, China, using reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) PCR. The genomic RNA is 9482 nucleotides (nt) long excluding the 3'-terminal poly(A) tail and encodes a putative large polyprotein with 3073 amino acids (aa). It has 75.4-53.5% nt sequence identity and 84.0-49.1% polyprotein sequence identity to other potyviruses and is probably a distantly related isolate of the same species as the recently reported achyranthes virus A isolate from South Korea (AcVA-SK). This is the first report of the occurrence of a potyvirus infecting A. bidentata in China.

Molecular Characterization of Hovenia Dulcis-Associated Virus 1 (HDaV1) and 2 (HDaV2): New Tentative Species within the Order Picornavirales

In a systematic field survey for plant-infecting viruses, leaf tissues were collected from trees showing virus-like symptoms in Brazil. After viral enrichment, total RNA was extracted and sequenced using the MiSeq platform (Illumina). Two nearly full-length picorna-like genomes of 9534 and 8158 nucleotides were found associated with Hovenia dulcis (Rhamnaceae family). Based upon their genomic information, specific primers were synthetized and used in RT-PCR assays to identify plants hosting the viral sequences. The larger contig was tentatively named as Hovenia dulcis-associated virus 1 (HDaV1), and it exhibited low nucleotide and amino acid identities with Picornavirales species. The smaller contig was related to insect-associated members of the Dicistroviridae family but exhibited a distinct genome organization with three non-overlapping open reading frames (ORFs), and it was tentatively named as Hovenia dulcis-associated virus 2 (HDaV2). Phylogenetic analysis using the amino acid sequence of RNA-dependent RNA polymerase (RdRp) revealed that HDaV1 and HDaV2 clustered in distinct groups, and both viruses were tentatively assigned as new members of the order Picornavirales. HDaV2 was assigned as a novel species in the Dicistroviridae family. The 5′ ends of both viruses are incomplete. In addition, a nucleotide composition analysis (NCA) revealed that HDaV1 and HDaV2 have similarities with invertebrate-infecting viruses, suggesting that the primary host(s) of these novel virus species remains to be discovered.

Pest categorisation of non-EU viruses and viroids of potato

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of those viruses and viroids (hereafter referred to as viruses) of Solanum tuberosum and other tuber-forming Solanum spp. (hereafter referred to as potato) which are considered to be either non-EU or of undetermined standing based on a previous EFSA opinion. These viruses belong to different families and genera and either have an established identity or produce consistent symptoms. Plants for planting is the main pathway for entry for all categorised viruses as they can all be transmitted by vegetative propagation. Several categorised viruses have a relatively wide host range and/or are vector-transmitted, increasing the potential for entry. The information currently available on geographical distribution, biology, epidemiology, impact and potential entry pathways has been evaluated with regard to the criteria to qualify as potential Union quarantine pest or as Union regulated non-quarantine pest (RNQP). Since this opinion addresses specifically the non-EU potato viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as potential Union regulated non-quarantine pests. The following viruses meet the criteria to qualify as potential Union quarantine pest: APLV, APMMV, APMoV, ChiLCV, CYSDV, PAMV, PBRSV, PVH, PVP, PVT, PYDV, PYMV, PYV, PYVV, RCVMV, SALCV, SB26/29, ToCV, ToLCNDV, ToMHaV, ToMoTV, ToSRV and ToYVSV. With the exception of the criterion regarding the potential for consequences in the EU territory, for which the Panel is unable to conclude because of lack of information, AVB, CPSbV, PaLCrV, PapMV, PVB, PVU, SB41 and TVBMV meet all the other criteria to qualify as potential Union quarantine pest. PotLV and WPMV do not qualify as potential Union quarantine pest, since they are not reported to have any impact. For most of the categorised viruses, the conclusions of the Panel have inherent uncertainties, due to the lack of quantitative data on their impact and/or absence or limited availability of information on the biology, epidemiology and geographical distribution.

Phylodynamics of sunflower chlorotic mottle virus, an emerging pathosystem

Distribution and epidemiological patterns of sunflower chlorotic mottle virus (SCMoV) in sunflower (Helianthus annuus L.) growing areas in Argentina were studied from 2006 to 2017. The virus was detected exclusively in the Pampas region (Entre Ríos, Santa Fe, Córdoba, La Pampa and Buenos Aires provinces). Phylodynamic analyses performed using the coat protein gene of SCMoV isolates from sunflower and weeds dated the most recent common ancestor (MRCA) back to 1887 (HPD95% = 1572-1971), which coincides with the dates of sunflower introduction in Argentina. The MRCA was located in the south of Buenos Aires province and was associated with sunflower host (posterior probability for the ancestral host, ppah = 0.98). The Bayesian phylodynamic analyses revealed the dispersal patterns of SCMoV, suggesting a link between natural host diversity, crop displacement by human activities and virus spread.

Complete nucleotide sequence of a new potexvirus, 'Cnidium virus X', isolated from Cnidium officinale in Japan

A flexuous virus was detected in a Cnidium officinale plant in Japan showing mosaic symptoms. The virus was assigned to the genus Potexvirus based on analysis of its complete nucleotide sequence. The genomic RNA of the virus was 5,964 nucleotides in length, excluding the 3'-terminal poly(A) tail. It contained five open reading frames (ORFs), consistent with other members of Potexvirus. The ORF sequences differ from those of previously reported potexviruses. Phylogenetic analysis indicated that the polymerase of the virus is closely related to that of strawberry mild yellow edge virus; and the CP, to those of both yam virus X and vanilla virus X. We propose that this virus be designated as "cnidium virus X" (CnVX).

Molecular characterization of a new potyvirus infecting passion fruit

A potyvirus (isolate PFV-FJ) infecting passion fruit in China was identified by small-RNA sequencing. The complete genome sequence of PFV-FJ was determined to be 9974 nucleotides, excluding the poly(A) tail. PFV-FJ shares 70-72% nucleotide and 69-74% amino acid sequence identity at the polyprotein level with seven reported potyviruses, but 89% nucleotide and 91% amino acid sequence identity with an unreported potyvirus, tentatively named "passionfruit Vietnam potyvirus" (PVNV-DakNong). This suggests that PFV-FJ and PVNV-DakNong should belong to the same potyvirus species and that PFV-FJ is a new member of the genus Potyvirus. This new potyvirus was tentatively named "passion fruit severe mottle-associated virus".

Polyvalent Detection of Members of the Genus Potyvirus by Molecular Hybridization Using a Genus-Probe

The use of a unique riboprobe named polyprobe, carrying partial sequences of different plant viruses or viroids fused in tandem, has permitted the polyvalent detection of up to 10 different pathogens by using a nonradioactive molecular hybridization procedure. In the present analysis, we have developed a unique polyprobe with the capacity to detect all members of the genus Potyvirus, which we have named genus-probe. To do this, we have exploited the capacity of the molecular hybridization assay to cross-hybridize with related sequences by reducing the hybridization temperature. We observed that sequences showing a percentage similarity of 68% or higher could be detected with the same probe by hybridizing at 50 to 55°C, with a detection limit of picograms of viral RNA comparable to the specific individual probes. According to this, we developed several polyvalent polyprobes, containing three, five, or seven different 500-nucleotide fragments of a conserved region of the NIb gene. The polyprobe carrying seven different conserved regions was able to detect all the 32 potyviruses assayed in the present work with no signal in the healthy tissue, indicating the potential capacity of the polyprobe to detect all described, and probably uncharacterized, potyviruses being then considered as a genus-probe. The use of this technology in routine diagnosis not only for Potyvirus but also to other viral genera is discussed.

Maize Dwarf Mosaic Virus: From Genome to Disease Management

Maize dwarf mosaic virus (MDMV) is a serious maize pathogen, epidemic worldwide, and one of the most common virus diseases for monocotyledonous plants, causing up to 70% loss in corn yield globally since 1960. MDMV belongs to the genus Potyvirus (Potyviridae) and was first identified in 1964 in Illinois in corn and Johnsongrass. MDMV is a single stranded positive sense RNA virus and is transmitted in a non-persistent manner by several aphid species. MDMV is amongst the most important virus diseases in maize worldwide. This review will discuss its genome, transmission, symptomatology, diagnosis and management. Particular emphasis will be given to the current state of knowledge on the diagnosis and control of MDMV, due to its importance in reducing the impact of maize dwarf mosaic disease, to produce an enhanced quality and quantity of maize.

Comparison of genus-specific primers in RT-PCR for the broad-spectrum detection of viruses in the genus Potyvirus by plant diagnostic laboratories

The Potyvirus genus is one of the largest genera of plant viruses and encompasses many economically important pathogens. While a number of degenerate primers for use in broad spectrum RT-PCR assays have been published, it is not clear which of these primers would be the most useful for use by plant diagnostic laboratories. Twelve sets of primers were tested for their ability to detect nine potyviruses in a two-step RT-PCR. Viruses were extracted from different host backgrounds and were selected to represent eight clades plus one species between clades (sensu Gibbs and Ohshima, 2010). Results of this study indicated that the primers CIFor/CIRev produced easily detectable amplicons from all nine potyviruses without non-specific amplification, false positives, or false negatives. CIFor/CIRev produced single amplicons from potyvirus-infected tissues which could be sequenced directly without gel purification to identify the virus to species.

Complete genome sequence of yam chlorotic necrosis virus, a novel macluravirus infecting yam

The complete genome sequence of a novel member of the genus Macluravirus was determined from yam plants with chlorotic and necrotic symptoms in China. The genomic RNA consists of 8,261 nucleotides (nt) excluding the 3'-terminal poly(A) tail, containing one long open reading frame (ORF) encoding a large putative polyprotein of 2,627 amino acids. Its genomic structure is typical of macluraviruses, which lack the P1 protein, N-terminal HC-Pro, and D-A-G motif for aphid transmission that are found in potyviruses. The virus shares 56.3-63.8% sequence identity at the genome sequence level and 49.7-63.9% at the polyprotein sequence level with other members of the genus Macluravirus. Phylogenetic analysis based on the complete polyprotein sequence of representative members of the family Potyviridae clearly places the virus within the genus Macluravirus. These results suggest that the virus, tentatively named "yam chlorotic necrosis virus" (YCNV), should be considered a member of a novel species in the genus Macluravirus.

Complete genome sequence and construction of an infectious full-length cDNA clone of a German isolate of celery mosaic virus

The complete genome sequence of a German isolate of celery mosaic virus (CeMV, a potyvirus) from Quedlinburg (DSMZ PV-1003) was determined (MF962880). This represents the second fully sequenced genome of this virus, along with a Californian isolate (HQ676607.1). The positive-sense single-stranded RNA is 10,000 nucleotides in length and shows the typical organization of potyviruses but has a shorter PIPO than CeMV California. In comparison to CeMV isolates from different origins, CeMV-Quedlinburg and isolates from the Netherlands (AF203531.1) and Aschersleben, Germany (AJ271087.1) show a NAG instead of DAG in the region of the coat protein responsible for aphid transmission. In this study the first infectious full-length clone of celery mosaic virus was obtained and the infectivity confirmed by Rhizobium radiobacter infiltration of Apium species.

Complete genome sequence of Paris mosaic necrosis virus, a distinct member of the genus Potyvirus

The complete genomic sequence of a novel potyvirus was determined from Paris polyphylla var. yunnanensis. Its genomic RNA consists of 9,660 nucleotides (nt) excluding the 3'-terminal poly (A) tail, containing the typical open reading frame (ORF) of potyviruses and encoding a putative large polyprotein of 3030 amino acids. The virus shares 53.9-70.1% nt sequence identity and 43.9-73.2% amino acid sequence identity with other viruses classified within the genus Potyvirus. Proteolytic cleavage sites and conserved motifs of the potyviruses were identified in the polyprotein and within individual proteins. Phylogenetic analysis indicated that the virus is most closely related to members of the BCMV subgroup. The results suggest that the virus should be classified as a novel species within the genus Potyvirus, which we tentatively name "Paris mosaic necrosis virus".

Plant viruses and viroids in the United Kingdom: An analysis of first detections and novel discoveries from 1980 to 2014

This review covers 35 years (1980-2014) representing a period of changing land use and agricultural practices in the United Kingdom (UK), which have also witnessed a marked change in the availability and application of new diagnostic technologies. During this period there have been 53 first records of viruses and viroids, of which 36 were first UK findings and a further 17 previously undescribed viruses. Given the challenges in detection and diagnosis of plant viruses, the field of plant virology has been an early adopter of new diagnostic technologies and these data highlight the transition from a reliance on biological, morphological, and serological based identification to the increased application of nucleic acid based detection methods and latterly the emergence of Next-Generation Sequencing. This review presents a comprehensive record of these findings and an analysis of how the potential drivers of change such as commodity based research, trade, as well as the application of diagnostic technology, could have influenced the frequency and type of findings.

Identification of a New Cotton Disease Caused by an Atypical Cotton Leafroll Dwarf Virus in Argentina

An outbreak of a new disease occurred in cotton (Gossypium hirsutum) fields in northwest Argentina starting in the 2009-10 growing season and is still spreading steadily. The characteristic symptoms of the disease included slight leaf rolling and a bushy phenotype in the upper part of the plant. In this study, we determined the complete nucleotide sequences of two independent virus genomes isolated from cotton blue disease (CBD)-resistant and -susceptible cotton varieties. This virus genome comprised 5,866 nucleotides with an organization similar to that of the genus Polerovirus and was closely related to cotton leafroll dwarf virus, with protein identity ranging from 88 to 98%. The virus was subsequently transmitted to a CBD-resistant cotton variety using Aphis gossypii and symptoms were successfully reproduced. To study the persistence of the virus, we analyzed symptomatic plants from CBD-resistant varieties from different cotton-growing fields between 2013 and 2015 and showed the presence of the same virus strain. In addition, a constructed full-length infectious cDNA clone from the virus caused disease symptoms in systemic leaves of CBD-resistant cotton plants. Altogether, the new leafroll disease in CBD-resistant cotton plants is caused by an atypical cotton leafroll dwarf virus.

Further characterization of Maize chlorotic mottle virus and its synergistic interaction with Sugarcane mosaic virus in maize

Maize chlorotic mottle virus (MCMV) was first reported in maize in China in 2009. In this study we further analyzed the epidemiology of MCMV and corn lethal necrosis disease (CLND) in China. We determined that CLND observed in China was caused by co-infection of MCMV and sugarcane mosaic virus (SCMV). Phylogenetic analysis using four full-length MCMV cDNA sequences obtained in this study and the available MCMV sequences retrieved from GenBank indicated that Chinese MCMV isolates were derived from the same source. To screen for maize germplasm resistance against MCMV infection, we constructed an infectious clone of MCMV isolate YN2 (pMCMV) and developed an Agrobacterium-mediated injection procedure to allow high throughput inoculations of maize with the MCMV infectious clone. Electron microscopy showed that chloroplast photosynthesis in leaves was significantly impeded by the co-infection of MCMV and SCMV. Mitochondria in the MCMV and SCMV co-infected cells were more severely damaged than in MCMV-infected cells. The results of this study provide further insight into the epidemiology of MCMV in China and shed new light on physiological and cytopathological changes related to CLND in maize.

The complete sequence and genome organization of ligustrum virus A, a novel carlavirus

The complete genome sequence of ligustrum virus A (LVA) from a Ligustrum obtusifolium Sieb. & Zucc. plant was determined. The genomic RNA has 8,525 nucleotides, excluding the poly(A) tail, and consists of six open reading frames typical of members of the genus Carlavirus, family Betaflexiviridae. Phylogenetic analysis of the viral replicase and coat protein (CP) indicated that LVA is closely related to daphne virus S and helenium virus. The replicase and CP of LVA shared 44.73-52.35 % and 25.39-62.46 % amino acid identity, respectively, with those of other carlaviruses. These results suggest that LVA is a member of a distinct carlavirus species.

Complete Genome Sequence of a South Korean Isolate of Habenaria mosaic virus

Habenaria mosaic virus (HaMV), a member of the genus Potyvirus in the family Potyviridae, was first discovered from Habenaria radiata in Japan. The complete genomic sequence of a South Korean isolate (PA1) of HaMV infecting Plantago asiatica L. was determined with high-throughput RNA sequencing.

Complete genome sequence of tobacco mosqueado virus

We describe the genomic characteristics of a new potyvirus isolated from tobacco plants showing mottling ("mosqueado" in Portuguese) in southern Brazil. The complete genomic sequence consists of 9896 nucleotides, without the poly(A) tail, and shares the highest pairwise nucleotide sequence identities of 68.5 % with pepper yellow mosaic virus and 68.2 % with Brugmansia mosaic virus isolate D437. These identity values are below the level of 76.0 % used as a criterion for species demarcation in the genus Potyvirus based on the complete genome sequence. The viral genomic organization and sequence comparison thus suggest that this virus, tentatively named "tobacco mosqueado virus" (TMosqV), represents a new potyvirus species.

The first complete sequence and genome structure of daphne virus Y

From Daphne odora Thunb., an ornamental shrub in the Republic of Korea, a potyvirus was identified that has an RNA genome of 9,448 nucleotides (excluding the 3'-terminal poly(A) tail) encoding a polyprotein of 3,065 amino acids, with nine putative protease cleavage sites producing ten proteins. Since this potyvirus shared the highest nucleotide sequence identity (91 %; query coverage 5 %) with the available partial sequence of daphne virus Y (DVY) from New Zealand (EU179854), it was considered a Korean isolate of DVY. This is the first molecular characterization of the complete genome sequence of a DVY isolate.

Reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid diagnosis of chilli veinal mottle virus

Chilli veinal mottle virus (ChiVMV) causes significant economic loss to chilli cultivation in northeastern India, as well as in eastern Asia. In this study, we have developed a single-tube one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid, sensitive and specific diagnosis of ChiVMV. Amplification could be visualized after adding SYBR Green I (1000×) dye within 60 min under isothermal conditions at 63 °C, with a set of four primers designed based on the large nuclear inclusion protein (NIb) domain of ChiVMV (isolate KC-ML1). The RT-LAMP method was 100 times more sensitive than one-step reverse transcription polymerase chain reaction (RT-PCR), with a detection limit of 0.0001 ng of total RNA per reaction.

Complete genome sequence of yam chlorotic necrotic mosaic virus from Dioscorea parviflora

The complete genome sequence of yam chlorotic necrotic mosaic virus (YCNMV) was determined. It is a monopartite ssRNA 8208 nucleotides in length (excluding the poly(A) tail) and encoding a polyprotein of 2622 amino acids. Sequence analysis showed that the P1 region and some conserved motifs, such as the typical potyvirus aphid-transmission motifs DAG, PTK and KITC, are absent. Phylogenetic analysis based on the complete polyprotein sequences of YCNMV and selected members of the family Potyviridae clearly showed that this virus should be assigned to the genus Macluravirus and suggest that YCNMV is a new member of the genus Macluravirus.

Development of an agroinoculation system for full-length and GFP-tagged cDNA clones of cucumber green mottle mosaic virus

The complete 6243-nucleotide sequence of a cucumber green mottle mosaic virus (CGMMV) isolate from bottle gourd in Zhejiang province, China, was determined. A full-length cDNA clone of this isolate was constructed by inserting the cDNA between the 35S promoter and the ribozyme in the binary plasmid pCB301-CH. A suspension of an Agrobacterium tumefaciens EHA105 clone carrying this construct was highly infectious in Nicotiana benthamiana and bottle gourd. Another infectious clone containing the green fluorescence protein (GFP) reporter gene was also successfully constructed. This study is the first report of the efficient use of agroinoculation for generating CGMMV infections.

Detection of pepper mild mottle virus in pepper sauce in China

Pepper mild mottle virus (PMMoV) was detected by RT-PCR in all 42 pepper sauce samples from the 10 main manufacturing provinces in China at concentrations ranging from 3.8 to 8.8 (Log10 copies/mL). Their coat protein nucleotide sequences had 97.4 to 100 % identity to each other and 92.4 to 100 % to other published isolates. The samples remained infectious to N. benthamiana, indicating that commercial trade in sauce could contribute to the natural spread of PMMoV.

Full-genome analyses of a Potato Virus Y (PVY) isolate infecting pepper (Capsicum annuum L.) in the Republic of South Africa

Potato Virus Y (PVY) is a pathogen of economic importance in pepper and other major crop species in the family Solanaceae. Three major PVY strain groups: O, C, and N, have been distinguished on the basis of genome sequencing. In this study, the first full-genome sequence of a PVY isolate (JVW-186) infecting pepper from the province of KwaZulu-Natal, Republic of South Africa is reported. The complete genome sequence of JVW-186 was assembled from overlapping RT-PCR clones using MEGA 5 software. Two ORFs were identified at position 186 and 2915 of the sequence encoding the viral polyprotein and the frameshift translated protein P3N-PIPO, respectively. RDP4 software confirmed three recombination breakpoints at position 343, 1365, and 9308 of the sequence. At each recombination event, a 1,021-bp fragment at the 5' end in the region of the P1/HC-Pro protein and a 392-bp fragment in the region of the coat protein shared a high sequence similarity of 91.8 and 98.89 % to the potato borne PVY(C) isolate PRI-509 and the PVY(O) isolate SASA-110, respectively. The non-recombinant fragment 1 (342-bp) clustered within the C clade of PVY isolates; however, the large 7,942-bp fragment 3 did not cluster within any of the clades. This suggests the possibility of a PVY isolate that has evolved due to the dynamics of selection pressure or the likelihood of an ancestral PVY strain.

Complete genome sequence of a South Korean isolate of Brugmansia mosaic virus

We determined the complete genome sequence of a South Korean (SK) isolate of Brugmansia mosaic virus (BruMV), which has recently been proposed to be a member of a new species in the genus Potyvirus. The genomic RNA of BruMV isolate SK is 9781 nucleotides in length (excluding the 3'-terminal poly (A)) and shares complete nucleotide and polyprotein amino acid sequence identities of 85.6 % and 93.1 %, respectively, with the type isolate (D-437) of BruMV described in the USA. To our knowledge, this is the first report providing evidence of considerable sequence variation in BruMV.

Two generic PCR primer sets for the detection of members of the genus Torradovirus

Two degenerate primer pairs were designed for the universal detection of members of the genus Torradovirus. Primer pair Torrado-1F/Torrado-1R was designed based on the RNA-dependent RNA polymerase region located in RNA1 and primer pair Torrado-2F/Torrado-2R based on a region overlapping the two first coat proteins Vp35 and Vp26 in RNA2. The primers were used in two-step and one-step RT-PCR protocols. Both primer pairs were able to detect 14 out of 15 isolates belonging to the two torradovirus species Tomato torrado virus (ToTV) and Tomato marchitez virus (ToMarV) and the two tentative species Tomato chocolate spot virus (ToChSV) and Tomato chocolàte virus (ToChV). Due to poor sample quality, one isolate of ToTV was detected with primer pair Torrado-2F/Torrado-2R and not with primer pair Torrado-1F/Torrado-1R, suggesting that the latter primer pair was less sensitive. Nevertheless, both primer pairs proved to be suitable for the universal RT-PCR detection of torradoviruses and can be deployed for the detection of all currently known torradoviruses and possibly for the detection of new members of this group.

Complete genome sequence of two isolates of pokeweed mosaic virus and its relationship to other members of the genus Potyvirus

The complete genomic sequences of two isolates of pokeweed mosaic virus (PkMV) were determined to be 9512 nucleotides long, excluding the poly(A) tail. Their genomic organization is typical of potyviruses and contains conserved motifs found in members of the genus Potyvirus. Pairwise comparisons showed that PkMV and other members of the genus Potyvirus share 51.0-57.5 % sequence identity at the genome sequence level and 39.8-53.0 % at the polyprotein sequence level. Phylogenetic analysis indicated that PkMV is most closely related to several viruses in the PVY group of the genus Potyvirus. The genomic information obtained for PkMV suggests that this virus is a distinct potyvirus.

Method: a single nucleotide polymorphism genotyping method for Wheat streak mosaic virus

BACKGROUND

The September 11, 2001 attacks on the World Trade Center and the Pentagon increased the concern about the potential for terrorist attacks on many vulnerable sectors of the US, including agriculture. The concentrated nature of crops, easily obtainable biological agents, and highly detrimental impacts make agroterrorism a potential threat. Although procedures for an effective criminal investigation and attribution following such an attack are available, important enhancements are still needed, one of which is the capability for fine discrimination among pathogen strains. The purpose of this study was to develop a molecular typing assay for use in a forensic investigation, using Wheat streak mosaic virus (WSMV) as a model plant virus.

METHOD

This genotyping technique utilizes single base primer extension to generate a genetic fingerprint. Fifteen single nucleotide polymorphisms (SNPs) within the coat protein and helper component-protease genes were selected as the genetic markers for this assay. Assay optimization and sensitivity testing was conducted using synthetic targets. WSMV strains and field isolates were collected from regions around the world and used to evaluate the assay for discrimination. The assay specificity was tested against a panel of near-neighbors consisting of genetic and environmental near-neighbors.

RESULT

Each WSMV strain or field isolate tested produced a unique SNP fingerprint, with the exception of three isolates collected within the same geographic location that produced indistinguishable fingerprints. The results were consistent among replicates, demonstrating the reproducibility of the assay. No SNP fingerprints were generated from organisms included in the near-neighbor panel, suggesting the assay is specific for WSMV. Using synthetic targets, a complete profile could be generated from as low as 7.15 fmoles of cDNA.

CONCLUSION

The molecular typing method presented is one tool that could be incorporated into the forensic science tool box after a thorough validation study. This method incorporates molecular biology techniques that are already well established in research and diagnostic laboratories, allowing for an easy introduction of this method into existing laboratories.

KEYWORDS

single nucleotide polymorphisms, genotyping, plant pathology, viruses, microbial forensics, Single base primer extension, SNaPshot Multiplex Kit.

Characterization and Distribution of a Potyvirus Associated with Passion Fruit Woodiness Disease in Uganda

This article describes the incidence and etiology of a viral disease of passion fruit in Uganda. Symptoms, including those characteristic of passion fruit woodiness disease (PWD), were observed on 32% of plants in producing areas. Electron microscopic observations of infected tissues revealed flexuous filaments of ca. 780 nm. Enzymelinked immunosorbent assays indicated a serological relationship with Cowpea aphid-borne mosaic virus (CABMV) and Passion fruit ringspot virus (PFRSV). In host range studies, only species in the families Solanaceae and Chenopodiaceae were susceptible, and neither Vigna unguiculata nor Phaseolus vulgaris became infected. Coat protein (CP) gene sequences of eight isolates exhibited features typical of potyviruses and were highly similar (88 to 100% identity). However, the sequences had limited sequence identity with CP genes of two of the three potyviruses reported to cause PWD: East Asian Passiflora virus and Passion fruit woodiness virus (PWV). Deduced amino acid sequences for the CP of isolates from Uganda had highest identity with Bean common mosaic necrosis virus (BCMNV) (72 to 79%, with evolutionary divergence values between 0.17 and 0.19) and CABMV (73 to 76%, with divergence values between 0.21 and 0.25). Based on these results and in accordance with International Committee for Taxonomy of Viruses criteria for species demarcation in the family Potyviridae, we conclude that a previously unreported virus causes viral diseases on passion fruit in Uganda. The name "Ugandan Passiflora virus" is proposed for this virus.

Complete genome sequence of pepper yellow mosaic virus, a potyvirus, occurring in Brazil

The complete genomic sequence of pepper yellow mosaic virus (PepYMV), a member of the genus Potyvirus, was determined. The sequence was 9745 nucleotides long, excluding the 3' poly(A) tail. The genome contained a large open reading frame encoding a polyprotein of 3085 amino acids, which contained the typically conserved motifs found in members of the genus Potyvirus and an additional P3-PIPO (pretty interesting potyvirus ORF). In a pairwise comparison with other potyvirus sequences, the full genome of PepYMV shared a maximum of 63.84 % nucleotide sequence identity with pepper mottle virus (PepMoV), followed by verbena virus Y (VVY, 62.11 %), potato virus Y (PVY, 62.07 %) and Peru tomato mosaic virus (PTV, 62.00 %). Based upon a phylogenetic analysis, PepYMV was most closely related to PepMoV and PTV, within the PVY subgroup cluster, like most potyviruses isolated in solanaceous hosts in South America.

Complete nucleotide sequence of Cherry leaf roll virus (CLRV), a subgroup C nepovirus

The complete nucleotide sequence of both genomic (+)ss RNAs of a rhubarb isolate of Cherry leaf roll virus (CLRV) was determined. The larger RNA1 is 7918 nucleotides and the shorter RNA2 6360 nucleotides in size, each genome component comprising a single open reading frame (ORF). The RNA1-encoded polyprotein (P1) is 2112 amino acids long (235.6 kDa) containing domains characteristic for a proteinase-cofactor (PCo), nucleotide-binding helicase (Hel), genome-linked protein (VPg), proteinase (Pro), and an RNA-dependent RNA polymerase (Pol). The RNA2-encoded polyprotein (P2) has a molecular mass of 174.9 kDa (1589 aa) encoding the putative movement protein (MP) and the coat protein (CP) of CLRV. The genome region upstream of the MP has a coding capacity of 77 kDa, however processing of P2 by the putative virus-encoded proteinase and protein-function encoded by this region is unknown. Furthermore, it could be demonstrated that the 5'-termini including the N-terminal region (208 aa) of P1 and P2 of the rhubarb isolate of CLRV are nearly identical among the two genome segments. The taxonomic position of CLRV as member of the genus Nepovirus was confirmed by phylogenetic analyses employing the amino acid sequences of the conserved Pro-Pol region of RNA1, the complete P2, and the CP. However, clustering of Nepovirus-species according to allocated subgroups was inconsistent and depended on the compared genome fragment.

Analysis of the tomato mild mottle virus genome indicates that it is the most divergent member of the genus Ipomovirus (family Potyviridae)

The complete genome of a tomato mild mottle virus (ToMMV) isolate was analysed, and some biological features were characterized. The ssRNA genome of ToMMV from Ethiopia encompasses 9283 nucleotides (excluding the 3' poly(A) tail) and encodes a polyprotein of 3011 amino acids. Phylogenetic and pairwise comparisons with other members of the family Potyviridae revealed that ToMMV is the most divergent member of the genus Ipomovirus, with a genome organization similar to that of members of the species Sweet potato mild mottle virus, the type species of the genus. In contrast to earlier reports, ToMMV isolates from Yemen and Ethiopia were not transmitted by the aphid Myzus persicae, but they were transmitted very erratically by the whitefly Bemisia tabaci. A comparison of the 3'-proximal sequences of different isolates provided evidence for geographically associated genetic variation.