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INTRODUCTION
The genus Allium, family Amaryllidaceae, includes several plant species that are native to the northern hemisphere and are distributed through Europe, Asia, North America, and the north of Africa (Li et al., 2010; Phillips, 2010). Most Amaryllidaceae species grow in temperate zones, some can grow in the tropics and a few, like A. schoenoprasum, may grow in the arctic (Pastor and Valdes, 1983). Plants within this family are characterized by the uniformity of their floral structures despite the variability present in the morphology of other plant parts. Among the 2800 species belonging to the family Amaryllidaceae, only species within the Allium and Asparagus genera have agronomical importance (García et al., 2011). Onion (A. cepa), garlic (A. sativum), shallot (A. cepa var. ascalonicum) and leek (A. ampeloprasum var. porrum) are the most widely consumed Allium species worldwide (Rabinowitch, 2017). They have several medicinal uses, including treatment for diabetes, fever, jaundice, spleen enlargement, etc. (Sujitha et al., 2016). In South America these crops are planted in tempered valleys and Andean territories with moderately cold climates, close to distribution centers (Ministerio de Agricultura, Ganadería y Pesca-MAGAP, 2013). In the Andean region, Allium crops are socio-economically important due to the direct or indirect workforce associated with their production.
Allium vegetables are the fourth most abundant group of commercially produced non-leguminous vegetables (FAO, 2016). The worldwide demand for bulb onion has been growing constantly showing a 70 % increase from 2000, when 50 million ton were produced, to 2014, when production reached 85 million ton (Boon, 2015). The leading exporters include The Netherlands, China, Mexico, India, USA, Egypt, Spain, New Zealand and Argentina. The main importers are USA, United Kingdom, Malaysia, Germany, Saudi Arabia, Japan, Canada, Czech Republic, Republic of Korea, and Brazil (Galmarini, 2018). United Kingdom and Germany are the main onion export market for Argentina and Chile, the largest exporters in South America, although their product also reaches United States, Canada, Japan and Malaysia. In countries like Peru and Chile, sweet onions are produced to export to the United States market from January to May. Onion and garlic production is economically important in other Latin American countries such as Mexico and Ecuador, where shallot production is also significant.
As a result of the great scale production and the vegetative nature of Allium propagation, pathogens that affect these crops abound. Shallot virus X (ShVX), from the Flexiviridae family and genus Allexivirus, is one of the several viruses infecting Allium (Howitt et al., 2006; Zavriev and Vishnichenko, 2005). When infecting garlic, Allexivirus causes yield losses as the bulb size of infected plants is smaller compared to healthy plants (Cafrune et al., 2006).
DISTRIBUTION AND SYMPTOMS
Shallot virus X was firts reported in Russia (Vishnichenko et al., 1993; Kanyuka et al., 1992; Zavriev and Vishnichenko, 2005). The sequence contains six open reading frames (ORFs). The virus has also been reported in the Netherlands (van Dijk and van der Vlugt, 1994), India (Majumder et al., 2008), New Zealand (Perez-Egusquiza et al., 2009), Sudan (Hamed et al., 2012), Italy (Taglienti et al., 2015) and Poland (Bereda and Paduch-Cichal, 2016). Recently, the virus was discovered in South America (Granda et al., 2017), and it is presumed that it is distributed worldwide.
Plants infected by ShVX may be asymptomatic or display mild mosaic and chlorotic symptoms. In Argentina, a study showed a 14 to 32 % decrease in bulb weight and a 6 to 32 % decrease in bulb diameter, related to Allexivirus infection in garlic (Cafrune et al., 2006), resulting in significant yield losses. Nevertheless, it has been observed that, in natural conditions, viruses from the Allexivirus, Carlavirus, and Potyvirus genera can form viral complexes, making it difficult to relate symptomatology with a specific virus (Katiset al., 2012). These viral complexes are common among plants from the Amaryllidaceae family (Mituti et al., 2015; Song et al., 1998).
TRANSMISSION
The only known vector of ShVX is the dry bulb mite (Aceria tulipae) (Van Dijk et al., 1991; Sang Gu et al., 2007), a pathogen that can persist in plant material destined for propagation (Van Dijk et al., 1991; Adams et al., 2004). It has been observed that the pathogen employs unconventional routes to overcome the plant viral defenses, which may be related with a increase in the fitness of the virus (Arkhipov et al., 2017).
Mechanical sap inoculation has been proved effective for transmitting all members of the Allexivirus genus (Adams et al., 2004). In the other hand, virus transmission vectored by aphids has not been reported for any Allexivirus (Zavriev and Vishnichenko, 2005).
MORPHOLOGY AND GENOME
The first structural analysis of ShVX revealed similarities with the genomic organization of Carlavirus but lack ORF6 (Chen et al., 2004; Kanyuka et al., 1992). Later, as the number of available viral genomes increased, it was determined that ShVX together with other viruses detected in the genus Allium (Garlic virus A, -B, -C, -D) belongs to the genus Allexivirus (Song et al., 1998; Sumi et al, 1999). Furthermore, comparative genome and protein analyses, indicate that the Allexivirus are part of the Flexiviridae family (Adams et al., 2004; Zavriev and Vishnichenko, 2005). The Flexiviridae includes viruses with filamentous virions, polyadenylated genome, and a triple gene block of movement proteins which are known to infect plants and plant-pathogenic fungi (Martelli et al., 2007).
Shallot virus X has a monopartite genome represented by a single strand positive RNA with six ORFs and a polyadenilated 3´-end (Kanyuka et al., 1992). The virions of ShVX are highly-flexible, filamentous particles of aproximately 800 nm of length and 12 nm of width, harbouring a 8890 nucleotide genome (Kanyuka et al., 1992; Vishnichenko et al., 1993). The virion length is similar to that of a potyvirus but its flexibility resembles that of a closterovirus (King et al., 2012).
ORF1, located in the 5´ -end of the ShVX genome, codes for a viral replicase of approximately 195 kDa. The proteins coded by ORF2 and ORF3, of 26 and 11 kDA, respectively (Kanyuka et al., 1992), are similar to the triple gene block proteins, TGB1 and TGB2 that are found in diverse plant viruses (Morozov and Solovyev, 2003). ORF4 codes for P42, a serine rich 42 kDa-protein of unknown function and with no orthologous genes found in other Allexivirus nor in closely related genera, such as Potexvirus or Carlavirus. It is likely that P42 function is related to viral movement (Arkhipov et al., 2013). ORF5 codes for the coat protein of 28 kDa, and ORF6 for a small, 15 kDa, cysteine-rich protein which is related to a small protein located close to the 3´end of Carlavirus. Lukhovitskaya et al., 2014) demonstrated that this small protein acts as a viral transcription factor that supresses gene silencing.
Several filamentous and rod-shaped virus genomes contain a triple gene block that codes for three proteins that are essential for viral movement through plasmodesmata and systemic transport (Verchot-Lubicz et al., 2010). Species from the genus Allexivirus contain part of the TGB3 within their genome but it is not expressed by an individual ORF, as it lacks a start codon (Kanyuka et al., 1992; Chen et al., 2001). Nevertheless, the TGB3 protein of ShVX and other Allexivirus may be expressed along with TGB2 from a bicistronic mRNA, requiring a leaky ribosome scanning (Lezzhov et al., 2015).
DIAGNOSIS OF ShVX
ELISA (Enzyme-Linked Immuno Sorbent Assay) and PCR (Polymerase Chain Reaction) are the most common methods for plant pathogenic virus detection worldwide (Boonham et al., 2014). Aditionally, the use of electron microscopy for morphological characterization and of indicator plants to determine alternative hosts and symptoms associated to viral infections, are common use in viral diagnosis. According to Boonham et al. (2014), the choice of diagnosis technique should depend on sensitivity, especificity, repeatibility and reproductibility.
Shallot virus X was first detected with indirect ELISA using horeradish peroxidase (Vishnichenko et al., 1993). Currently, the use of double antibody sandwich ELISA, using ShVX-specific antiserum (DSMZ AS-1042) is common. Nevertheless, low viral titers present in plant samples impede a reproducible detection of the pathogen through ELISA (Ling et al., 2001).
Traditional diagnostics methods based on serology, host range, and symptoms are limited in their ability to differentiate among Allium viruses, owing to the presence of complex viral mixtures exhibiting similar symptoms and possessing restricted host ranges. Reverse transcription coupled with the polymerase chain reaction (RT-PCR) is often used for the diagnosis of RNA viruses (Navot et al., 1992). This is a fast, highly-sensitive method that, when multiplexed, allows the simultaneous identification of several different viruses (Crosslin and Hamlin, 2011). Methods for RT-PCR diagnosis of individual viruses affecting Allium species have been developed and optimized (Bereda and Paduch-Cichal, 2017; Dovas et al., 2001; Perez-Egusquiza et al., 2009; Vishnichenko et al., 1993; Zavriev and Vishnichenko, 2005). However, it is necessary to effectively diagnose various types of Allium viruses at the same time. Multiplex detection assays have been developed for the detection of Onion yellow dwarf virus (OYDV) and Shallot latent virus (SLV)(Majumderet al., 2008), OYDV, SLV, Garlic common latent virus (GarCLV) and allexiviruses in Indian garlic accessions (Majumder and Baranwal, 2014), and for detection of several garlic viruses (Hu et al., 2015).
Recently, next-generation sequencing (NGS) of total RNA from infected plants have been widely adopted to identify all the different viruses that might be present in a sample (Pallás et al., 2018). However, there are no reports about the use of NGS for detection of ShVX.
MANAGEMENT
Vegetatively propagated crops can be infected by different virus species that tend to accumulate over generations resulting in yield losses and varietal degeneration (Pagán et al., 2014; Pramesh and Baranwal, 2015). Therefore, a periodical renovation, using virus-free plant material, is needed.
There is no literature available regarding methods to manage ShVX in the field; however, Perotto et al. (2010) and Shiboleth et al.(2001) reported that Allexivirus-free plants can be vegetatively reproduced using meristems. Garlic virus-free plants produced significantly higher yields compared to infected plants. The stem-disc dome culture method and its combination with thermotherapy could also eliminate Allexivirus in garlic plants (Ayabe and Sumi 2001; Ghaemizadeh et al., 2013).
CONCLUSION
Shallot virus X is a hardly known plant pathogenic virus that infects and causes yield reduction in Allium species. Since symptoms are unconspicuous and they are usually present in complex with other viruses, it is difficult to eliminate them. However, various procedures for controlling ShVX can be implemented depending upon situation. Development of resistant varieties, application of agronomic and biotechnological methods, and adequate plant nutrition and pest control, can be used in an integrated manner to manage this virus which is still a challenge for Allium producers.
