Detection and classification of allexiviruses from garlic in China

Whole genome sequence analysis of shallot virus X from India reveals it to be a natural recombinant with positive selection pressure

BACKGROUND

Shallots are infected by various viruses like Onion yellow dwarf virus (OYDV), Leek yellow stripe virus (LYSV), Shallot latent virus (SLV) and Shallot virus X (ShVX). In India, they have been found to be persistently infected by ShVX. ShVX also infects onion and garlic in combination with other carlaviruses and potyviruses. ShVX is a member of genus Allexivirus of family Alphaflexiviridae. ShVX has a monopartite genome, which is represented by positive sense single-stranded RNA. Globally, only six complete and 3 nearly complete genome sequences of ShV X are reported to date. This number is insufficient to measure a taxon's true molecular diversity. Moreover, the complete genome sequence of ShVX from Asia has not been reported as yet. Therefore, this study was undertaken to generate a complete genome sequence of ShVX from India.

RESULTS

Shallot virus X (ShVX) is one of the significant threats to Allium crop production. In this study, we report the first complete genome sequence of the ShVX from India through Next-generation sequencing (NGS). The complete genome of the ShVX (Accession No. OK104171), from this study comprised 8911 nucleotides. In-silico analysis of the sequence revealed variability between this isolate and isolates from other countries. The dissimilarities are spread all over the genome specifically some non-coding intergenic regions. Statistical analysis of individual genes for site-specific selection indicates a positive selection in NABP region. The presence of a recombination event was detected in coat protein region. The sequence similarity percentage and phylogenetic analysis indicate ShVX Indian isolate is a distinctly different isolate. Recombination and site-specific selection may have a function in the evolution of this isolate. This is the first detailed study of the ShVX complete genome sequence from Southeast Asia.

CONCLUSION

This study presents the first report of the entire genome sequence of an Indian isolate of ShVX along with an in-depth exploration of its evolutionary traits. The findings highlight the Indian variant as a naturally occurring recombinant, emphasizing the substantial role of recombination in the evolution of this viral species. This insight into the molecular diversity of strains within a specific geographical region holds immense significance for comprehending and forecasting potential epidemics. Consequently, the insights garnered from this research hold practical value for shaping ShVX management strategies and providing a foundation for forthcoming studies delving into its evolutionary trajectory.

An Inexpensive System for Rapid and Accurate On-site Detection of Garlic-Infected Viruses by Agarose Gel Electrophoresis Followed by Array Assay

Garlic can be infected by a variety of viruses, but mixed infections with leek yellow stripe virus, onion yellow dwarf virus, and allexiviruses are the most damaging, so an easy, inexpensive on-site method to simultaneously detect at least these three viruses with a certain degree of accuracy is needed to produce virus-free plants. The most common laboratory method for diagnosis is multiplex reverse transcription polymerase chain reaction (RT-PCR). However, allexiviruses are highly diverse even within the same species, making it difficult to design universal PCR primers for all garlic-growing regions in the world. To solve this problem, we developed an inexpensive on-site detection system for the three garlic viruses that uses a commercial mobile PCR device and a compact electrophoresis system with a blue light. In this system, virus-specific bands generated by electrophoresis can be identified by eye in real time because the PCR products are labeled with a fluorescent dye, FITC. Because the electrophoresis step might eventually be replaced with a lateral flow assay (LFA), we also demonstrated that a uniplex LFA can be used for virus detection; however, multiplexing and a significant cost reduction are needed before it can be used for on-site detection.

Complete genome sequence of a new virus from Allium sativum L in China

The complete genome of a new virus belonging to the family Betaflexiviridae was identified in garlic and sequenced by next-generation sequencing and reverse transcription PCR. The complete RNA genome (GenBank accession number OP021693) is 8191 nucleotides in length, excluding the 3' poly(A) tail, and contains five open reading frames (ORFs). These open reading frames encode the viral replicase, triple gene block, and coat protein, and the genome organization is typical of members of the subfamily Quinvirinae. The virus has been tentatively named "garlic yellow curl virus" (GYCV). Phylogenetic analysis suggested that it represents an independent evolutionary lineage in the subfamily, clustering with the currently unclassified garlic yellow mosaic associated virus (GYMaV) and peony betaflexivirus 1 (PeV1). Differences between the phylogenies inferred for the replicase and coat protein indicate that the new virus does not belong to any established genus of the family Betaflexiviridae. This is the first report of GYCV in China.

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.

Identification and Characterization of a Garlic Virus E Genome in Garlic (Allium sativum L.) Using High-Throughput Sequencing from India

Garlic (Allium sativum L.) plants exhibiting mosaics, deformation, and yellow stripes symptoms were identified in Meerut City, Uttar Pradesh, India. To investigate the viruses in the garlic samples, the method of high-throughput sequencing (HTS) was used. Complete genome of the garlic virus E (GarV-E) isolate (NCBI accession No. MW925710) was retrieved. The virus complete genome comprises 8450 nucleotides (nts), excluding the poly (A) tail at the 3' terminus, with 5' and 3' untranslated regions (UTRs) of 99 and 384 nts, respectively, and ORFs encoding replicase with a conserved motif for RNA-dependent RNA polymerase (RdRP), TGB1, TGB2, TGB3, serine-rich protein, coat protein, and nucleic acid binding protein (NABP). The sequence homology shared 83.49-90.40% and 87.48-92.87% with those of GarV-E isolates available in NCBI at the nucleotide and amino acid levels, respectively. Phylogenetic analysis showed a close relationship of this isolate from India (MW925710) with GarV-E isolate YH (AJ292230) from Zhejiang, China. The presence of GarV-E was also confirmed by RT-PCR. The present study is the first report of GarV-E in garlic cultivar Yamuna Safed-3 grown in northern India. However, further studies are needed to confirm its role in symptom development, nationwide distribution, genetic diversity, and potential yield loss to the garlic in India.

Complete genome sequence of a novel foveavirus isolated from Allium sativum L. in China

The complete genome sequence of a novel foveavirus identified in garlic (Allium sativum L.) in China was determined using RNA-seq, reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) PCR. The entire genomic RNA (GenBank accession MT981417) is 8748 nucleotides long excluding the 3'-terminal poly(A) tail and contains five open reading frames (ORFs). These ORFs encode the viral replicase, a triple gene block, and a coat protein. The virus was tentatively named "garlic yellow stripe associated virus" (GarYSaV). Pairwise comparisons of protein sequences show that GarYSaV encodes proteins that share less than 47% identity with those of other foveaviruses, suggesting that it represents a new species in the genus. Phylogenetic analysis of amino acid sequences of the replicase and CP confirm that GarYSaV is a member of the genus Foveavirus. To our knowledge, this is the first report of a foveavirus in a monocot plant.

Molecular identification, incidence and phylogenetic analysis of seven viruses infecting garlic in Ethiopia

Little information exists on the type and incidence of viruses infecting garlic (Allium sativum L) in Ethiopia. Attempts were made to identify the viruses using molecular techniques from 95 composite leaf samples collected from 44 farmers' fields and 51 germplasm accessions. Reverse transcription (RT-) PCR using genus and/or virus specific primers was used to amplify partial genome sequences of potyviruses, allexiviruses, carlaviruses and a tospovirus followed by sequencing of PCR products. Results indicated that ~73.7% of the samples are infected with at least one virus. Onion yellow dwarf virus (OYDV, genus Potyvirus, family Potyviridae) is the most common virus detected followed by Garlic virus C (genus Allexivirus) and Shallot latent virus (SLV, genus Carlavirus). Other viruses detected at lower frequency include Garlic virus X and Garlic virus D (genus Allexivirus), Leek yellow stripe virus (genus Potyvirus) and Iris yellow spot virus (IYSV, genus Tospovirus). Mixed infection of two or more viruses was detected in 65.7% of the samples. Phylogenetic analysis suggested that the different viruses may have been introduced to Ethiopia from Europe or Asia. This is the first report of Garlic virus X, Garlic virus D, IYSV and SLV in garlic in Ethiopia. The high incidence of OYDV and IYSV which cause severe yield loss alone or in mixed infection with allexiviruses and carlaviruses is a cause of concern to growers.

p15 encoded by Garlic virus X is a pathogenicity factor and RNA silencing suppressor

Garlic virus X (GarVX) encodes a 15 kDa cysteine-rich protein (CRP). To investigate the function(s) of p15, its subcellular localization, role as a symptom determinant and capacity to act as a viral suppressor of RNA silencing (VSR) were analysed. Results showed that GFP-tagged p15 was distributed in the cytoplasm, nucleus and nucleolus. Expression of p15 from PVX caused additional systemic foliar malformation and led to increased accumulation of PVX, showing that p15 is a virulence factor for reconstructed PVX-p15. Moreover, using a transient agro-infiltration patch assay and a Turnip crinkle virus (TCV) movement complementation assay, it was demonstrated that p15 possesses weak RNA silencing suppressor activity. Removal of an amino acid motif resembling a nuclear localization signal (NLS) prevented p15 from accumulating in the nucleus but did not abolish its silencing suppression activity. This study provides the first insights into the multiple functions of the GarVX p15 protein.

Allexiviruses may have acquired inserted sequences between the CP and CRP genes to change the translation reinitiation strategy of CRP

Allexiviruses are economically important garlic viruses that are involved in garlic mosaic diseases. In this study, we characterized the allexivirus cysteine-rich protein (CRP) gene located just downstream of the coat protein (CP) gene in the viral genome. We determined the nucleotide sequences of the CP and CRP genes from numerous allexivirus isolates and performed a phylogenetic analysis. According to the resulting phylogenetic tree, we found that allexiviruses were clearly divided into two major groups (group I and group II) based on the sequences of the CP and CRP genes. In addition, the allexiviruses in group II had distinct sequences just before the CRP gene, while group I isolates did not. The inserted sequence between the CP and CRP genes was partially complementary to garlic 18S rRNA. Using a potato virus X vector, we showed that the CRPs affected viral accumulation and symptom induction in Nicotiana benthamiana, suggesting that the allexivirus CRP is a pathogenicity determinant. We assume that the inserted sequences before the CRP gene may have been generated during viral evolution to alter the termination-reinitiation mechanism for coupled translation of CP and CRP.

The unfolded protein response and programmed cell death are induced by expression of Garlic virus X p11 in Nicotiana benthamiana

Garlic virus X (GarVX) ORF3 encodes a p11 protein, which contributes to virus cell-to-cell movement and forms granules on the endoplasmic reticulum (ER) in Nicotiana benthamiana. Expression of p11 either from a binary vector, PVX or TMV induced ER stress and the unfolded protein response (UPR), as demonstrated by an increase in transcription of the ER luminal binding protein (BiP) and bZIP60 genes. UPR-related programmed cell death (PCD) was elicited by PVX : p11 or TMV : p11 in systemic infected leaves. Examination of p11 mutants with deletions of two transmembrane domains (TM) revealed that both were required for generating granules and for inducing necrosis. TRV-based VIGS was used to investigate the correlation between bZIP60 expression and p11-induced UPR-related PCD. Less necrosis was observed on local and systemic leaves of bZIP60 knockdown plants when infected with PVXp11, suggesting that bZIP60 plays an important role in the UPR-related PCD response to p11 in N. benthamiana.

The global trade in fresh produce and the vagility of plant viruses: a case study in garlic

As cuisine becomes globalized, large volumes of fresh produce are traded internationally. The potential exists for pathogens infecting fresh produce to hitchhike to new locations and perhaps to establish there. It is difficult to identify them using traditional methods if pathogens are novel, scarce, and/or unexpected. In an attempt to overcome this limitation, we used high-throughput sequencing technology as a means of detecting all RNA viruses infecting garlic (Allium sativum L.) bulbs imported into Australia from China, the USA, Mexico, Argentina and Spain, and those growing in Australia. Bulbs tested were grown over multiple vegetative generations and all were stably infected with one or more viruses, including two species not previously recorded in Australia. Present in various combinations from 10 garlic bulbs were 41 virus isolates representing potyviruses (Onion yellow dwarf virus, Leek yellow stripe virus), carlaviruses (Shallot latent virus, Garlic common latent virus) and allexiviruses (Garlic virus A, B, C, D, and X), for which 19 complete and 22 partial genome sequences were obtained, including the first complete genome sequences of two isolates of GarVD. The most genetically distinct isolates of GarVA and GarVX described so far were identified from Mexico and Argentina, and possible scenarios explaining this are presented. The complete genome sequence of an isolate of the potexvirus Asparagus virus 3 (AV3) was obtained in Australia from wild garlic (A. vineale L.), a naturalized weed. This is first time AV3 has been identified from wild garlic and the first time it has been identified beyond China and Japan. The need for routine generic diagnosis and appropriate legislation to address the risks to primary production and wild plant communities from pathogens spread through the international trade in fresh produce is discussed.

Viruses of the genus Allium in the Mediterranean region

Allium species are economically important crops in the Mediterranean basin. Viruses are among the most important pathogens affecting their yield and especially those belonging to the genera Potyvirus, Carlavirus, and Allexivirus. Members of the genus Potyvirus are usually the most abundant and cause most of the damage induced. Nevertheless, coinfections with different viruses are not scarce, especially in garlic, and can have synergistic effects that lead to even greater crop losses. Vegetative propagation of alliums and the transmission of most of their viruses by arthropod vectors have significantly contributed to their wide dissemination in the Mediterranean region and elsewhere in the world. Here, we review the general biological and molecular features, the epidemiology, incidence, and methods of diagnosis of the most widespread allium viruses in the basin. Control measures are proposed depending on the mode of propagation of the various alliums, the epidemiology of their viruses and the cultivation procedures adapted by the Mediterranean farmers. The importance of the production and use of virus-free propagative material in order to combat viral diseases of allium crops is especially highlighted. A final discussion focuses on the main shortages identified in the research area of allium viruses, and proposals are made for putative future developments.

Garlic virus X 11-kDa protein granules move within the cytoplasm and traffic a host protein normally found in the nucleolus

The subcellular localization of the 11-kDa protein (p11) encoded by ORF3 of Garlic virus X (GarVX; genus Allexivirus, family Alphaflexiviridae) was examined by confocal microscopy. Granules with intense fluorescence were visible on the endoplasmic reticulum when p11 fused with green or red fluorescent protein (GFP or RFP) was expressed in epidermal cells of Nicotiana benthamiana. Moreover, the p11-RFP granules moved in the cytoplasm, along the cell periphery and through the cell membranes to adjacent cells. A 17-kDa protein (p17) of garlic interacting with p11 was identified by yeast two-hybridization and bimolecular fluorescence complementation assay. When p17 fused to GFP was expressed in epidermal cells of N. benthamiana, it localized to the nucleolus. However, in the presence of GarVX p11, the distribution of p17 changed to that of p11, but did not appear to affect the pattern of movement of p11.

Molecular variability and genetic structure of the population of Onion yellow dwarf virus infecting garlic in Iran

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

A biomarker for the identification of four Phaeoacremonium species using the beta-tubulin gene as the target sequence

A real-time polymerase chain reaction (PCR) was developed for the rapid detection and identification of Phaeoacremonium species, the fungi associated with severe diseases in grapevines. A degenerate primer pair (F2bt-R1bt) with homology to the beta-tubulin gene was designed to be used in the amplification of 11 species of Phaeoacremonium. Four species-specific probes labelled with three different fluorescent dyes were designed to be used with the degenerate primers in a real-time PCR for the identification of Phaeoacremonium aleophilum, P. parasiticum, P. viticola and P. mortoniae. Combinations of two probes in a duplex real-time PCR allowed to detect and identify a mixture of Phaeoacremonium species and cross-amplifications were not detected. This method was applied to detect Phaeoacremonium species in eight wood fragments from grapevine plants naturally infected, and results were compared with those obtained with nested PCR and culturing on growth media. Real-time PCR detected Phaeoacremonium in 100% of the analysed fragments, whereas nested PCR did only in the 62% of them and requiring subsequent restriction fragment-length polymorphism analysis to identify the species. This method is a sensitive tool to detect and identify Phaeoacremonium species in infected grapevine wood. Real-time PCR assay defined here can be used in a plant nursery program to identify pathogen-free plants in order to manage Petri disease of grapevines.

Yield Loss in Garlic Caused by Leek yellow stripe virus Argentinean Isolate

Garlic plants (Allium sativum) are naturally infected by a complex of viruses in the genera Potyvirus, Carlavirus, and Allexivirus. The yield of virus-free garlic plants (noninoculated control) was compared with that of plants infected with an Argentinean isolate of Leek yellow stripe virus (LYSV; L treatment) and garlic plants infected with the virus complex (VC). Evaluations were conducted in the field and in anti-aphid cages during two crop cycles after planting three sizes of cloves (categories). The percent plant emergence in the noninoculated control and in the L treatments (between 80 and 100%) did not differ statistically, but the percent emergence for these two treatments was double that for the VC treatment (25 to 62%). Plant height and leaf number in the L treatment were lower than in the noninoculated control during the first evaluation (year 1), but they did not differ during the second evaluation (year 2). However, both treatments produced taller plants with more leaves than those of VC in both years. The L treatment decreased bulb weight up to 28% and perimeter up to 9% when compared with those in the noninoculated control maintained in the anti-aphid cages until the end of the experiment. However, differences between these treatments were higher in the field experiments where plants were exposed to infection by other viruses (up to 36% in bulb weight and 13% in perimeter). Bulbs of the VC-infected plant treatment were reduced up to 74% in weight and 37% in perimeter. In field evaluations, a high percentage of plants were infected with Onion yellow dwarf virus (58 to 100%), whereas fewer were infected with LYSV (15 to 68%). Garlic virus A infection was high in plants previously infected with LYSV (96 and 97%), but lower in the noninoculated control (12 and 68%). These results show the high impact of the virus complex on garlic yield and the effect of LYSV as a component of the garlic virus complex.

Effect of Two Allexivirus Isolates on Garlic Yield

Garlic (Allium sativum) is infected by numerous viruses forming a viral-complex, which is widely distributed in the garlic production regions of Argentina. This work is the first report of the effect of two Allexivirus isolates, Garlic virus A (GarV-A) and Garlic virus C (GarV-C), on garlic yield. Garlic cvs. Morado-INTA and Blanco-IFFIVE were used in the experiments, and four treatments were evaluated: plants inoculated with GarV-A only, GarV-C only, virus-free plants (negative control), and plants infected with the virus-complex. Assays were performed in anti-aphid cages and in the field during 2002 and 2003. GarV-A caused significant reductions in bulb weight (14 to 32%) and diameter (6 to 11%) compared with the negative control in the two cultivars under both assay conditions. GarV-C caused less damage than GarV-A (15% in weight and 5% in diameter) with respect to the negative control in cv. Blanco-IFFIVE, and did not produce significant yield losses in cv. Morado-INTA in either year or under either assay condition.