Complete genomic characterization of milk vetch dwarf virus isolates from cowpea and broad bean in Anhui province, China

Occurrence, distribution, and genetic diversity of faba bean viruses in China

With worldwide cultivation, the faba bean (Vicia faba L.) stands as one of the most vital cool-season legume crops, serving as a major component of food security. China leads global faba bean production in terms of both total planting area and yield, with major production hubs in Yunnan, Sichuan, Jiangsu, and Gansu provinces. The faba bean viruses have caused serious yield losses in these production areas, but previous researches have not comprehensively investigated this issue. In this study, we collected 287 faba bean samples over three consecutive years from eight provinces/municipalities of China. We employed small RNA sequencing, RT-PCR, DNA sequencing, and phylogenetic analysis to detect the presence of viruses and examine their incidence, distribution, and genetic diversity. We identified a total of nine distinct viruses: bean yellow mosaic virus (BYMV, Potyvirus), milk vetch dwarf virus (MDV, Nanovirus), vicia cryptic virus (VCV, Alphapartitivirus), bean common mosaic virus (BCMV, Potyvirus), beet western yellows virus (BWYV, Polerovirus), broad bean wilt virus (BBWV, Fabavirus), soybean mosaic virus (SMV, Potyvirus), pea seed-borne mosaic virus (PSbMV, Potyvirus), and cucumber mosaic virus (CMV, Cucumovirus). BYMV was the predominant virus found during our sampling, followed by MDV and VCV. This study marks the first reported detection of BCMV in Chinese faba bean fields. Except for several isolates from Gansu and Yunnan provinces, our sequence analysis revealed that the majority of BYMV isolates contain highly conserved nucleotide sequences of coat protein (CP). Amino acid sequence alignment indicates that there is a conserved NAG motif at the N-terminal region of BYMV CP, which is considered important for aphid transmission. Our findings not only highlight the presence and diversity of pathogenic viruses in Chinese faba bean production, but also provide target pathogens for future antiviral resource screening and a basis for antiviral breeding.

The nanovirus U2 protein suppresses RNA silencing via three conserved cysteine residues

Nanoviruses have multipartite, circular, single-stranded DNA genomes and cause huge production losses in legumes and other crops. No viral suppressor of RNA silencing (VSR) has yet been reported from a member of the genus Nanovirus. Here, we demonstrate that the nanovirus U2 protein is a VSR. The U2 protein of milk vetch dwarf virus (MDV) suppressed the silencing of the green fluorescent protein (GFP) gene induced by single-stranded and double-stranded RNA, and the systemic spread of the GFP silencing signal. An electrophoretic mobility shift assay showed that the U2 protein was able to bind double-stranded 21-nucleotide small interfering RNA (siRNA). The cysteine residues at positions 43, 79 and 82 in the MDV U2 protein are critical to its nuclear localization, self-interaction and siRNA-binding ability, and were essential for its VSR activity. In addition, expression of the U2 protein via a potato virus X vector induced more severe necrosis symptoms in Nicotiana benthamiana leaves. The U2 proteins of other nanoviruses also acted as VSRs, and the three conserved cysteine residues were indispensable for their VSR activity.

Genome-wide analysis of milk vetch dwarf virus and related alphasatellites from garlic and aphids in Shandong Province, China

In 2019 and 2020, symptoms of dwarfing, yellowing, and reddening were observed in garlic in open fields in Shandong Province, China. Milk vetch dwarf virus (MDV) was detected in aphids and symptomatic garlic plants using polymerase chain reaction analysis. Furthermore, it was demonstrated using an aphid transmission test that garlic is a natural host of MDV. Rolling-circle amplification was combined with the use of specific primers to amplify the complete genomes of MDV and its related alphasatellites. This is the first report of complete genome sequences of MDV and related alphasatellites from garlic and aphid samples.

An Annotated List of Legume-Infecting Viruses in the Light of Metagenomics

Legumes, one of the most important sources of human food and animal feed, are known to be susceptible to a plethora of plant viruses. Many of these viruses cause diseases which severely impact legume production worldwide. The causal agents of some important virus-like diseases remain unknown. In recent years, high-throughput sequencing technologies have enabled us to identify many new viruses in various crops, including legumes. This review aims to present an updated list of legume-infecting viruses. Until 2020, a total of 168 plant viruses belonging to 39 genera and 16 families, officially recognized by the International Committee on Taxonomy of Viruses (ICTV), were reported to naturally infect common bean, cowpea, chickpea, faba-bean, groundnut, lentil, peas, alfalfa, clovers, and/or annual medics. Several novel legume viruses are still pending approval by ICTV. The epidemiology of many of the legume viruses are of specific interest due to their seed-transmission and their dynamic spread by insect-vectors. In this review, major aspects of legume virus epidemiology and integrated control approaches are also summarized.

Rapid and visual detection of milk vetch dwarf virus using recombinase polymerase amplification combined with lateral flow strips

Background

Milk vetch dwarf virus (MDV) is an important ssDNA virus which causes yellowing, stunting and leaf rolling symptoms on legumes. In China, the virus causes great economic losses and has recently been found to infect tobacco. The expansion of its host range and its ability to spread rapidly has given rise to the urgent need for a sensitive, specific and rapid diagnostic assay that can assist in effective disease control.

Methods

Assays based on the polymerase chain reaction combined with lateral flow strip detection (PCR-LFS) and recombinase polymerase amplification combined with LFS (RPA-LFS) were developed targeting the coat protein (CP) gene of MDV.

Results

The PCR and RPA assays could detect respectively 10³ copies or 10¹ copies of MDV by agarose gel electrophoresis. The PCR-LFS and RPA-LFS assays developed could both detect as few as 10¹ copies per reaction at 37 °C. Both methods could detect MDV in crude leaf extracts.

Conclusions

The RPA-LFS assay developed is a rapid, sensitive and specific method for detecting MDV, which is convenient and has great potential for use in the field.

Identification of a novel nanovirus in parsley

Using next-generation sequencing to characterize agents associated with a severe stunting disease of parsley from Germany, we identified a hitherto undescribed virus. We sequenced total RNA and rolling-circle-amplified DNA from diseased plants. The genome sequence of the virus shows that it is a member of the genus Nanovirus, but it lacks DNA-U4. In addition to the seven genomic DNAs of the virus, we identified a second DNA-R and seven distinct alphasatellites associated with the disease. We propose the name "parsley severe stunt associated virus" (PSSaV) for this novel nanovirus.

Full genome sequence analysis and putative host-shifting of Milk vetch dwarf virus infecting tobacco (Nicotiana tabacum) in China

BACKGROUND

Tobacco production in China has been affected by plant viruses with Milk vetch dwarf virus (MDV) as a recent invader posing serious concern. According to most of the studies, MDV mainly infects hosts from Fabaceae family but in our previous study we reported its infection in tobacco plant (Nicotiana tabacum L.) in Shandong province.

FINDINGS

In current study (2016-2017), tobacco plants (Nicotiana tabacum) with severe stunting, yellowing and axillary bunch of new leaves were observed in Zhengning, Gansu province. Isolate GSZN yielded into eight genomic circular single-stranded DNA components while no alphasatellite DNA was obtained. High percent identity of this isolate was recorded in overall nucleotide and amino acid assembly with reported MDV isolates worldwide. Phylogenetic analysis fetched into a separate sub-clade comprising of new isolate along with other tobacco infecting isolates of MDV. While recombination was predicted in DNA-C encoding Clink protein and DNA-U1, which may attribute towards the potential host-shifting phenomenon and ability of this virus to expand its host range.

CONCLUSION

To our knowledge this is the first full genome annotation of a Nanovirus, infecting tobacco in natural field conditions, also this is the first extended analysis on host-shifting behavior of MDV.

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.