Characterisation of the Viral Community Associated with the Alfalfa Weevil (Hypera postica) and Its Host Plant, Alfalfa (Medicago sativa)

Advances in viral metagenomics have paved the way of virus discovery by making the exploration of viruses in any ecosystem possible. Applied to agroecosystems, such an approach opens new possibilities to explore how viruses circulate between insects and plants, which may help to optimise their management. It could also lead to identifying novel entomopathogenic viral resources potentially suitable for biocontrol strategies. We sampled the larvae of a natural population of alfalfa weevils (Hypera postica), a major herbivorous pest feeding on legumes, and its host plant alfalfa (Medicago sativa). Insect and plant samples were collected from a crop field and an adjacent meadow. We characterised the diversity and abundance of viruses associated with weevils and alfalfa, and described nine putative new virus species, including four associated with alfalfa and five with weevils. In addition, we found that trophic accumulation may result in a higher diversity of plant viruses in phytophagous pests compared to host plants.

RNA-seq reveals plant virus composition and diversity in alfalfa, thrips, and aphids in Beijing, China

Viruses are widespread in alfalfa (Medicago sativa L.), representing a key limitation to the production of this important forage plant. Understanding the diversity of plant viruses in alfalfa and their potential vectors will play an important role in management to minimize the emergence, transmission, and impact of viruses. Next-generation sequencing (NGS) targeting the transcriptome was applied to monitor the virus communities in alfalfa and its two main pests, thrips (Odontothrips loti Haliday and Frankliniella intonsa Trybom) and aphids (Acyrthosiphon pisum Mordvilko and Therioaphis trifolii Monell). A comparison of transcriptome datasets with reference databases revealed the presence of eight candidate viruses. Five out of the eight viruses, alfalfa mosaic virus (AMV), Medicago sativa alphapartitivirus 1 (MsAPV1), Medicago sativa deltapartitivirus 1 (MsDPV1), Medicago sativa amalgavirus 1 (MsAV1), and bean yellow mosaic virus (BYMV), were confirmed by RT-PCR. We identified and determined the presence of four RNA viruses from alfalfa samples, two viruses (AMV and MsAPV1) from thrips samples, and one virus (BYMV) from T. trifolii. All sequences isolated from the insect samples were more than 95% identical to the sequences from the alfalfa samples or to sequences from the National Center for Biotechnology Information (NCBI) reference database. The RNA-seq results of this study suggest that AMV and MsAPV1 are the predominant RNA plant viruses infecting alfalfa and that they are carried by the major pests. This lays the foundation for future research on the vectors and transmission of these viruses. In addition, the sequence data have enabled the assembly of the first complete genome sequence of MsDPV1 from alfalfa.

Alfalfa leaf curl virus is efficiently acquired by its aphid vector Aphis craccivora but inefficiently transmitted

Alfalfa leaf curl virus (ALCV) is the first geminivirus for which aphid transmission was reported. Transmission by Aphis craccivora was determined previously to be highly specific and circulative. Using various complementary techniques, the transmission journey of ALCV was monitored from its uptake from infected plant tissues up to the head of its vector. ALCV was shown to be restricted to phloem tissues using fluorescence in situ hybridization (FISH) and electropenetrography (EPG) monitoring of virus acquisition. Furthermore, the virus is heterogeneously distributed in phloem tissues, as revealed by FISH and quantitative PCR of viral DNA acquired by EPG-monitored aphids. Despite the efficient ingestion of viral DNA, about 106 viral DNA copies per insect in a 15 h feeding period on ALCV-infected plants, the individual maximum transmission rate was 12 %. Transmission success was related to a critical viral accumulation, around 1.6×107 viral DNA copies per insect, a threshold that generally needed more than 48 h to be reached. Moreover, whereas the amount of acquired virus did not decrease over time in the whole aphid body, it declined in the haemolymph and heads. ALCV was not detected in progenies of viruliferous aphids and did not affect aphid fitness. Compared to geminiviruses transmitted by whiteflies or leafhoppers, or to luteoviruses transmitted by aphids, the transmission efficiency of ALCV by A. craccivora is low. This result is discussed in relation to the aphid vector of this geminivirus and the agroecological features of alfalfa, a hardy perennial host plant.

Characterization of alfalfa virus F, a new member of the genus Marafivirus

Viral infections of alfalfa are widespread in major cultivation areas and their impact on alfalfa production may be underestimated. A new viral species, provisionally named alfalfa virus F (AVF), was identified using a virion-associated nucleic acid (VANA) metagenomics-based approach in alfalfa (Medicago sativa L.) samples collected in Southern France. The nucleotide sequence of the viral genome was determined by de-novo assembly of VANA reads and by 5'/3' RACE with viral RNA extracted from enriched viral particles or with total RNA, respectively. The virus shares the greatest degree of overall sequence identity (~78%) with Medicago sativa marafivirus 1 (MsMV1) recently deduced from alfalfa transcriptomic data. The tentative nucleotide sequence of the AVF coat protein shares ~83% identity with the corresponding region of MsMV1. A sequence search of the predicted single large ORF encoding a polyprotein of 235kDa in the Pfam database resulted in identification of five domains, characteristic of the genus Marafivirus, family Tymoviridae. The AVF genome also contains a conserved "marafibox", a 16-nt consensus sequence present in all known marafiviruses. Phylogenetic analysis of the complete nucleotide sequences of AVF and other viruses of the family Tymoviridae grouped AVF in the same cluster with MsMV1. In addition to 5' and 3' terminal extensions, the identity of the virus was confirmed by RT-PCRs with primers derived from VANA-contigs, transmission electron microscopy with virus-infected tissues and transient expression of the viral coat protein gene using a heterologous virus-based vector. Based on the criteria demarcating species in the genus Marafivirus that include overall sequence identity less than 80% and coat protein identity less than 90%, we propose that AVF represents a distinct viral species in the genus Marafivirus, family Tymoviridae.

Endosymbionts Differentially Alter Exploratory Probing Behavior of a Nonpersistent Plant Virus Vector

Insect endosymbionts (hereafter, symbionts) can modify plant virus epidemiology by changing the physiology or behavior of vectors, but their role in nonpersistent virus pathosystems remains uninvestigated. Unlike propagative and circulative viruses, nonpersistent plant virus transmission occurs via transient contamination of mouthparts, making direct interaction between symbiont and virus unlikely. Nonpersistent virus transmission occurs during exploratory intracellular punctures with styletiform mouthparts when vectors assess potential host-plant quality prior to phloem feeding. Therefore, we used an electrical penetration graph (EPG) to evaluate plant probing of the cowpea aphid, Aphis craccivora Koch, an important vector of cucurbit viruses, in the presence and absence of two facultative, intracellular symbionts. We tested four isolines of A. craccivora: two isolines were from a clone from black locust (Robinia pseudoacacia L.), one infected with Arsenophonus sp. and one cured, and two derived from a clone from alfalfa (Medicago sativa L.), one infected with Hamiltonella defensa and one cured. We quantified exploratory intracellular punctures, indicated by a waveform potential drop recorded by the EPG, initiation speed and frequency within the initial 15 min on healthy and watermelon mosaic virus-infected pumpkins. Symbiont associations differentially modified exploratory intracellular puncture frequency by aphids, with H. defensa-infected aphids exhibiting depressed probing, and Arsenophonus-infected aphids an increased frequency of probing. Further, there was greater overall aphid probing on virus-infected plants, suggesting that viruses manipulate their vectors to enhance acquisition-transmission rates, independent of symbiont infection. These results suggest facultative symbionts differentially affect plant-host exploration behaviors and potentially nonpersistent virus transmission by vectors.

Identification of novel RNA viruses in alfalfa (Medicago sativa): an Alphapartitivirus, a Deltapartitivirus, and a Marafivirus

Genomic RNA molecules of plant RNA viruses are often co-isolated with the host RNAs, and their sequences can be detected in plant transcriptome datasets. Here, an alfalfa (Medicago sativa) transcriptome dataset was analyzed and three new RNA viruses were identified, which were named Medicago sativa alphapartitivirus 1 (MsAPV1), Medicago sativa deltapartitivirus 1 (MsDPV1), and Medicago sativa marafivirus 1 (MsMV1). The RNA-dependent RNA polymerases of MsAPV1, MsDPV1, and MsMV1 showed about 68%, 58%, and 46% amino acid sequence identity, respectively, with their closest virus species. Sequence similarity and phylogenetic analyses indicated that MsAPV1, MsDPV1, and MsMV1 were novel RNA virus species that belong to the genus Alphapartitivirus of the family Partitiviridae, the genus Deltapartitivirus of the family Partitiviridae, and the genus Marafivirus of the family Tymoviridae, respectively. The bioinformatics procedure applied in this study may facilitate the identification of novel RNA viruses from plant transcriptome data.

Alfalfa virus S, a new species in the family Alphaflexiviridae

A new species of the family Alphaflexiviridae provisionally named alfalfa virus S (AVS) was discovered in alfalfa samples originating from Sudan. A complete nucleotide sequence of the viral genome consisting of 8,349 nucleotides excluding the 3' poly(A) tail was determined by high throughput sequencing (HTS) on an Illumina platform. NCBI BLAST searches revealed that the virus shares the greatest degree of sequence identity with members of the family Alphaflexiviridae, genus Allexivirus. The AVS genome contains six computationally-predicted open reading frames (ORF) encoding viral replication protein, triple gene block protein 1 (TGB1), TGB2, TGB3-like protein, unknown 38.4 kDa protein resembling serine-rich 40 kDa protein characteristic for allexiviruses, and coat protein (CP). AVS lacks a clear 3' proximal ORF that encodes a nucleic acid-binding protein typical for allexiviruses. The identity of the virus was confirmed by RT-PCR with primers derived from the HTS-generated sequence, dot blot hybridization with DIG-labeled virus-specific RNA probes, and Western blot analysis with antibodies produced against a peptide derived from the CP sequence. Transmission electron microscopic observations of the infected tissues showed the presence of filamentous particles similar to allexiviruses in their length and appearance. To the best of our knowledge, this is the first report on the identification of a putative allexivirus in alfalfa (Medicago sativa). The genome sequence of AVS has been deposited in NCBI GenBank on 03/02/2016 as accession № KY696659.

The Effects of Bean Leafroll Virus on Life History Traits and Host Selection Behavior of Specialized Pea Aphid (Acyrthosiphon pisum, Hemiptera: Aphididae) Genotypes

Intraspecific specialization by insect herbivores on different host plant species contributes to the formation of genetically distinct "host races," but the effects of plant virus infection on interactions between specialized herbivores and their host plants have barely been investigated. Using three genetically and phenotypically divergent pea aphid clones (Acyrthosiphon pisum L.) adapted to either pea (Pisum sativum L.) or alfalfa (Medicago sativa L.), we tested how infection of these hosts by an insect-borne phytovirus (Bean leafroll virus; BLRV) affects aphid performance and preference. Four important findings emerged: 1) mean aphid survival rate and intrinsic rate of population growth (Rm) were increased by 15% and 14%, respectively, for aphids feeding on plants infected with BLRV; 2) 34% of variance in survival rate was attributable to clone × host plant interactions; 3) a three-way aphid clone × host plant species × virus treatment significantly affected intrinsic rates of population growth; and 4) each clone exhibited a preference for either pea or alfalfa when choosing between noninfected host plants, but for two of the three clones tested these preferences were modestly reduced when selecting among virus-infected host plants. Our studies show that colonizing BLRV-infected hosts increased A. pisum survival and rates of population growth, confirming that the virus benefits A. pisum. BLRV transmission affected aphid discrimination of host plant species in a genotype-specific fashion, and we detected three unique "virus-association phenotypes," with potential consequences for patterns of host plant use by aphid populations and crop virus epidemiology.

Complete genome sequence and integrated protein localization and interaction map for alfalfa dwarf virus, which combines properties of both cytoplasmic and nuclear plant rhabdoviruses

We have determined the full-length 14,491-nucleotide genome sequence of a new plant rhabdovirus, alfalfa dwarf virus (ADV). Seven open reading frames (ORFs) were identified in the antigenomic orientation of the negative-sense, single-stranded viral RNA, in the order 3'-N-P-P3-M-G-P6-L-5'. The ORFs are separated by conserved intergenic regions and the genome coding region is flanked by complementary 3' leader and 5' trailer sequences. Phylogenetic analysis of the nucleoprotein amino acid sequence indicated that this alfalfa-infecting rhabdovirus is related to viruses in the genus Cytorhabdovirus. When transiently expressed as GFP fusions in Nicotiana benthamiana leaves, most ADV proteins accumulated in the cell periphery, but unexpectedly P protein was localized exclusively in the nucleus. ADV P protein was shown to have a homotypic, and heterotypic nuclear interactions with N, P3 and M proteins by bimolecular fluorescence complementation. ADV appears unique in that it combines properties of both cytoplasmic and nuclear plant rhabdoviruses.

Genetic Diversity, Reassortment, and Recombination in Alfalfa mosaic virus Population in Spain

The variability and genetic structure of Alfalfa mosaic virus (AMV) in Spain was evaluated through the molecular characterization of 60 isolates collected from different hosts and different geographic areas. Analysis of nucleotide sequences in four coding regions--P1, P2, movement protein (MP), and coat protein (CP)--revealed a low genetic diversity and different restrictions to variation operating on each coding region. Phylogenetic analysis of Spanish isolates along with previously reported AMV sequences showed consistent clustering into types I and II for P1 and types I, IIA, and IIB for MP and CP regions. No clustering was observed for the P2 region. According to restriction fragment length polymorphism analysis, the Spanish AMV population consisted of seven haplotypes, including two haplotypes generated by reassortment and one involving recombination. The most frequent haplotypes (types for P1, MP, and CP regions, respectively) were I-I-I (37%), II-IIB-IIB (30%), and one of the reassortants, II-I-I (17%). Distribution of haplotypes was not uniform, indicating that AMV population was structured according to the geographic origin of isolates. Our results suggest that agroecological factors are involved in the maintenance of AMV genetic types, including the reassortant one, and in their geographic distribution.

Complete nucleotide sequence of Alfalfa mosaic virus isolated from alfalfa (Medicago sativa L.) in Argentina

The complete nucleotide sequence of an Alfalfa mosaic virus (AMV) isolate infecting alfalfa (Medicago sativa L.) in Argentina, AMV-Arg, was determined. The virus genome has the typical organization described for AMV, and comprises 3,643, 2,593, and 2,038 nucleotides for RNA1, 2 and 3, respectively. The whole genome sequence and each encoding region were compared with those of other four isolates that have been completely sequenced from China, Italy, Spain and USA. The nucleotide identity percentages ranged from 95.9 to 99.1 % for the three RNAs and from 93.7 to 99 % for the protein 1 (P1), protein 2 (P2), movement protein and coat protein (CP) encoding regions, whereas the amino acid identity percentages of these proteins ranged from 93.4 to 99.5 %, the lowest value corresponding to P2. CP sequences of AMV-Arg were compared with those of other 25 available isolates, and the phylogenetic analysis based on the CP gene was carried out. The highest percentage of nucleotide sequence identity of the CP gene was 98.3 % with a Chinese isolate and 98.6 % at the amino acid level with four isolates, two from Italy, one from Brazil and the remaining one from China. The phylogenetic analysis showed that AMV-Arg is closely related to subgroup I of AMV isolates. To our knowledge, this is the first report of a complete nucleotide sequence of AMV from South America and the first worldwide report of complete nucleotide sequence of AMV isolated from alfalfa as natural host.

Survival of murine norovirus, Tulane virus, and hepatitis A virus on alfalfa seeds and sprouts during storage and germination

Human norovirus (huNoV) and hepatitis A virus (HAV) have been involved in several produce-associated outbreaks and identified as major food-borne viral etiologies. In this study, the survival of huNoV surrogates (murine norovirus [MNV] and Tulane virus [TV]) and HAV was investigated on alfalfa seeds during storage and postgermination. Alfalfa seeds were inoculated with MNV, TV, or HAV with titers of 6.46 ± 0.06 log PFU/g, 3.87 ± 0.38 log PFU/g, or 7.01 ± 0.07 log 50% tissue culture infectious doses (TCID50)/g, respectively. Inoculated seeds were stored for up to 50 days at 22°C and sampled during that storage period on days 0, 2, 5, 10, and 15. Following storage, virus presence was monitored over a 1-week germination period. Viruses remained infectious after 50 days, with titers of 1.61 ± 0.19 log PFU/g, 0.85 ± 0.21 log PFU/g, and 3.43 ± 0.21 log TCID50/g for MNV, TV, and HAV, respectively. HAV demonstrated greater persistence than MNV and TV, without a statistically significant reduction over 20 days (<1 log TCID50/g); however, relatively high levels of genomic copies of all viruses persisted over the testing time period. Low titers of viruses were found on sprouts and were located in all tissues as well as in sprout-spent water sampled on days 1, 3, and 6 following seed planting. Results revealed the persistence of viruses in seeds for a prolonged period of time, and perhaps of greater importance these data suggest the ease of which virus may transfer from seeds to sprouts and spent water during germination. These findings highlight the importance of sanitation and prevention procedures before and during germination.

Protective lactogenic immunity conferred by an edible peptide vaccine to bovine rotavirus produced in transgenic plants

Vaccines produced in transgenic plants constitute a promising alternative to conventional immunogens, presenting the possibility of stimulating secretory and systemic immunity against enteric pathogens when administered orally. Protection against enteric pathogens affecting newborn animals requires, in most cases, the stimulation of lactogenic immunity. Here, the group presents the development of an experimental immunogen based on expression of an immunorelevant peptide, eBRV4, of the VP4 protein of bovine rotavirus (BRV), which has been described as harbouring at least one neutralizing epitope as well as being responsible for the adsorption of the virus to epithelial cells. The eBRV4 epitope was efficiently expressed in transgenic alfalfa as a translational fusion protein with the highly stable reporter enzyme β-glucuronidase (βGUS), which served as a carrier, stabilized the synthesized peptide and facilitated screening for the higher expression levels in plants. Correlation of expression of the eBRV4 epitope in plants with those presenting the highest βGUS activities was confirmed by a Western blot assay specific for the BRV peptide. The eBRV4 epitope expressed in plants was effective in inducing an anti-rotavirus antibody response in adult female mice when administered either intraperitoneally or orally and, more importantly, suckling mice born from immunized female mice were protected against oral challenge with virulent rotavirus. These results demonstrate the feasibility of inducing lactogenic immunity against an enteric pathogen using an edible vaccine produced in transgenic plants.

The complete nucleotide sequence of apple mosaic virus (ApMV) RNA 1 and RNA 2: ApMV is more closely related to alfalfa mosaic virus than to other ilarviruses

The complete nucleotide sequences of apple mosaic virus RNA 1 and 2 have been characterized. Apple mosaic virus RNA 1 is 3476 nucleotides in length and encodes a single large open reading frame (ORF), whereas apple mosaic virus RNA 2 is 2979 nucleotides in length and also encodes a single ORF. The amino acid sequences encoded by RNA 1 and 2 show similarity to all of the other ilarviruses for which sequence data are available, but both are more closely related to alfalfa mosaic virus (AMV) than to other ilarviruses. Points of similarity include the absence of ORF 2b, present on the RNA 2 of all previously characterized ilarviruses. The close relationship to AMV also occurs in the movement protein, encoded by RNA 3, but not with the coat protein. These data suggest that the present taxonomy should be revised, and that AMV should be considered an aphid-transmissible ilarvirus.

A core promoter hairpin is essential for subgenomic RNA synthesis in alfalfa mosaic alfamovirus and is conserved in other Bromoviridae

The nucleotide sequence immediately in front of the initiation site for subgenomic RNA 4 synthesis on RNA 3 minus strand, which has been proved to function as a core promoter, was inspected for secondary structure in 26 species of the plant virus family Bromoviridae. In 23 cases a stable hairpin could be predicted at a distance of 3 to 8 nucleotides from the initiation site of RNA 4. This hairpin contained several conserved nucleotides that are essential for core promoter activity in brome mosaic virus (R.W. Siegel, S. Adkins and C.C. Kao, Proc. Natl. Acad. Sci. USA 94, 11238-11243, 1997). Phylogenetic evidence and evidence from the effect of artificial mutations reported in the literature (E.A.G. van der Vossen, T. Notenboom and J.F. Bol, Virology 212, 663-672, 1995) indicate that the stem-loop structure is essential for promoter activity in alfalfa mosaic virus and probably in other Bromoviridae. Stability of the hairpin is most pronounced in the genera Alfamovirus and Ilarvirus which display genome activation by coat protein. The hypothesis is put forward that with these viruses the coat protein is needed for the viral RNA polymerase to interact with the core promoter hairpin leading to access for the enzyme to the initiation site of RNA 4.

The structure of alfalfa mosaic virus capsid protein assembled as a T=1 icosahedral particle at 4.0-A resolution

K. Fukuyama, S. S. Abdel-Meguid, J. E. Johnson, and M. G. Rossmann (J. Mol. Biol. 167:873-984, 1983) reported the structure of alfalfa mosaic virus assembled from the capsid protein as a T=1 icosahedral empty particle at 4.5-A resolution. The information contained in the structure included the particle size, protein shell thickness, presence of wide holes at the icosahedral fivefold axes, and a proposal that the capsid protein adopts a beta-barrel structure. In the present work, the X-ray diffraction data of Fukuyama et al. as well as the data subsequently collected by I. Fita, Y. Hata, and M. G. Rossmann (unpublished) were reprocessed to 4.0-A resolution, and the structure was solved by molecular replacement. The current structure allowed the tracing of the polypeptide chain of the capsid protein confirming the beta-sandwich fold and provides information on intersubunit interactions in the particle. However, it was not possible to definitively assign the amino acid sequence to the side chain density at 4-A resolution. The particle structure was also determined by cryoelectron microscopy and image reconstruction methods and found to be in excellent agreement with the X-ray model.

Stability of porcine reproductive and respiratory syndrome virus in the presence of fomites commonly found on farms

OBJECTIVE

To determine the survival of porcine reproductive and respiratory syndrome virus (PRRSV) on nonliving substances (fomites) at 25 to 27 C.

DESIGN

Prospective controlled study.

SAMPLE POPULATION

3 solid, 6 porous, and 7 liquid fomites.

PROCEDURE

The fomites were contaminated with known concentrations of PRRSV. Samples for virus isolation were obtained on day 0 through day 11, assayed in cell cultures, and stained with fluorescent antibody conjugate.

RESULTS

The virus was recovered only on day-0 samples of alfalfa, wood shavings, straw, plastic, boot rubber, and stainless steel. Virus was isolated from city water through day 11, from well water through day 9, and from 2 buffer solutions for 4 and 6 days. The virus was isolated only on day 0 from swine saliva, urine, and fecal slurry.

CLINICAL IMPLICATIONS

Results indicated that PRRSV is a fairly labile virus, but because of its duration of viability in water, contamination of drinking water and lagoons by PRRSV-shedding swine would serve as sources of virus to infect susceptible swine.

Characterization of the alfalfa mosaic virus strain T6

A strain T6 of alfalfa mosaic virus (AlMV) was characterized. It was isolated from field grown lucerne. Purified virus preparations contained four types of particles, B, M, Tb and Ta, containing separately encapsidated ssRNAs 1 to 4. The strain T6 was able to infect 40 different plant species of 9 families, and to develop a systemic infection in most of them. The symptomatology on bean and the RNA mobility of the AlMV strains T6 and 425 were compared. The classical cross-protection experiments on bean have shown that plants inoculated with strain 425 did not develop symptoms of the challenge strain T6.