Novel nanovirus and associated alphasatellites identified in milk vetch plants with chlorotic dwarf disease in Iran

Members of the family Nanoviridae are multi-component single-stranded DNA viruses that infect a variety of plant species. Using a combination of conventional PCR and high throughput sequencing-based approach, we identified a novel nanovirus infecting two symptomatic milk vetch plants (Astragalus myriacanthus Boiss.; family Fabaceae) showing marginal leaf chlorosis, little leaves and dwarfing in Iran. All eight segments (DNA-C, DNA-M, DNA-N, DNA-R, DNA-S, DNA-U1, DNA-U2 and DNAU4) were recovered and Sanger sequenced. The genome of this new nanovirus, hereby referred to as milk vetch chlorotic dwarf virus (MVCDV), shares 62.2-74.7 % nucleotide pairwise identity with the genomes of other nanoviruses. DNA-C, DNA-M, DNA-N, DNA-S components are most closely related to those of black medic leaf roll virus (BMLRV), sharing between 67.8-81.2 % identity. We also identified three nanoalphasatellites (family Alphasatellitidae) associated with the nanovirus which belong to species Faba bean necrotic yellows alphasatellite 1 (genus Subclovsatellite), Faba bean necrotic yellows alphasatellite 2 (genus Fabenesatellite) and Sophora yellow stunt alphasatellite 5 (genus Clostunsatellite). Given the significant diversity of Astragalus spp. in Iran, it is likely that there could be more nanoviruses circulating in these plants and that these may play a role in the spread of these nanovirus to cultivated fabaceous hosts.

Rapid detection of milk vetch dwarf virus by loop-mediated isothermal amplification

Milk vetch dwarf virus (MDV) is a member of the genus Nanovirus, and its genome is composed of multiple circular 1-kb ssDNA components. In this study, we first determined that the diseased tobacco samples obtained in Zhucheng, Shandong Province were naturally infected with MDV using a polymerase chain reaction (PCR) assay. Subsequently, loop-mediated isothermal amplification (LAMP) was developed for the detection of MDV for the first time. The Mg2+ and dNTP concentrations and the reaction temperature and time of the LAMP were optimized to 8 mM, 1.8 mM, 65 °C, and 60 min, respectively. The best ratio of the inner primers (FIP and BIP) to the outer primers (F3 and B3) was 2:1. The LAMP detection limit was 100 times greater than that of PCR. The nucleotide amplification could be clearly observed by adding SYBR Green I. The positive and negative reactions exhibit distinctly different colors in daylight; however, the positive reactions exhibit green fluorescence under a UV lamp. Therefore, the method is stable, sensitive and specific.

Two distinct nanovirus species infecting faba bean in Morocco

Using monoclonal antibodies raised against a Faba bean necrotic yellows virus (FBNYV) isolate from Egypt and a Faba bean necrotic stunt virus (FBNSV) isolate from Ethiopia, a striking serological variability among nanovirus isolates from faba bean in Morocco was revealed. To obtain a better understanding of this nanovirus variability in Morocco, the entire genomes of two serologically contrasting isolates referred to as Mor5 and Mor23 were sequenced. The eight circular ssDNA components, each identified from Mor5- and Mor23-infected tissues and thought to form the complete nanovirus genome, ranged in size from 952 to 1,005 nt for Mor5 and from 980 to 1,004 nt for Mor23 and were structurally similar to previously described nanovirus DNAs. However, Mor5 and Mor23 differed from each other in overall nucleotide and amino acid sequences by 25 and 26%, respectively. Mor23 was most closely related to typical FBNYV isolates described earlier from Egypt and Syria, with which it shared a mean amino acid sequence identity of about 94%. On the other hand, Mor5 most closely resembled a FBNSV isolate from Ethiopia, with which it shared a mean amino acid sequence identity of approximately 89%. The serological and genetic differences observed for Mor5 and Mor23 were comparable to those observed earlier for FBNYV, FBNSV, and Milk vetch dwarf virus. Following the guidelines on nanovirus species demarcation, this suggests that Mor23 and Mor5 represent isolates of FBNYV and FBNSV, respectively. This is the first report not only on the presence of FBNSV in a country other than Ethiopia but also on the occurrence and complete genome sequences of members of two nanovirus species in the same country, thus providing evidence for faba bean crops being infected by members of two distinct nanovirus species in a restricted geographic area.

Reconstitution of authentic nanovirus from multiple cloned DNAs

We describe a new plant single-stranded DNA (ssDNA) virus, a nanovirus isolate originating from the faba bean in Ethiopia. We applied rolling circle amplification (RCA) to extensively copy the individual circular DNAs of the nanovirus genome. By sequence analyses of more than 208 individually cloned genome components, we obtained a representative sample of eight polymorphic swarms of circular DNAs, each about 1 kb in size. From these heterogeneous DNA populations after RCA, we inferred consensus sequences of the eight DNA components of the virus genome. Based on the distinctive molecular and biological properties of the virus, we propose to consider it a new species of the genus Nanovirus and to name it faba bean necrotic stunt virus (FBNSV). Selecting a representative clone of each of the eight DNAs for transfer by T-DNA plasmids of Agrobacterium tumefaciens into Vicia faba plants, we elicited the development of the typical FBNSV disease symptoms. Moreover, we showed that the virus thus produced was readily transmitted by two different aphid vector species, Aphis craccivora and Acyrthosiphon pisum. This represents the first reconstitution of a fully infectious and sustainably insect-transmissible nanovirus from its cloned DNAs and provides compelling evidence that the genome of a legume-infecting nanovirus is typically comprised of eight distinct DNA components.

Arabidopsis thaliana is a host of the legume nanovirus Faba bean necrotic yellows virus

We report infection of Arabidopsis thaliana with the legume nanovirus Faba bean necrotic yellows virus (FBNYV) by its insect vector Aphis craccivora. Symptoms of FBNYV infection on A. thaliana include stunting and reduced apical dominance, and are rather mild, compared to the severe necrosis and early plant death induced by the virus in the natural host Vicia faba. An inoculation access period of 6h is sufficient to transmit FBNYV to A. thaliana. FBNYV is readily transmitted back from A. thaliana to V. faba, where it induces the characteristic severe disease symptoms. Hence, passage through A. thaliana does not affect FBNYV pathogenicity. FBNYV accumulates to the highest levels in roots and stems, compared to cauline and rosette leaves. In cauline leaves, the kinetics of virus accumulation correlates with the amount of master Rep protein accumulation.

A PCR-Based Method, With Internal Control, for the Detection of Banana Bunchy Top Virus in Banana

Banana bunchy top disease is a major constraint to banana production in most regions where this crop is grown. The disease is caused by Banana bunchy top virus (BBTV), a multicomponent, single-stranded DNA virus of the family Nanoviridae. We have designed primers to a conserved region of the master replication-associated protein that are useful for the polymerase chain reaction (PCR)-mediated detection of BBTV. In addition, primers to banana genomic sequence are used as an internal control, overcoming the uncertainty (owing to false-negatives) inherent in PCR diagnostics. Together these primer sets are a valuable tool in the effort to control BBTV, particularly in screening micropropagated banana plantlets for the absence of virus before release to farmers.

[Specific amplification of the coding sequences of BBTV III, IV, I and their application in BBTV detection]

Banana bunchy top virus disease (BBTD) is a disastrous disease in bananas, and it is spreading in the world (including China) by the banana bunchy top virus(BBTV). At present, virus-free plantlets are used to prevent BBTD in banana production, therefore, it is very important to establish a method to detect BBTV quickly, sensitively and specifically. ELISA is now popularly used to detect BBTV. The sensitivity of this method is not high enough, and needs specific antiserum, otherwise, pseudo-positive results often occur. According to DNA coding sequences of component III, IV and I of BBTV isolates from Zhangzhou, China, three pairs of primers are designed to establish a PCR method to specifically amplify parts of coding sequences of the BBTV coat protein, movement protein and replicase-association. This method is also applicable to detect BBTV of bananas or cultured banana seedlings in other regions.