''Garlic common latent virus'' (GarCLV) is a plant virus member of the genus ''

Carlavirus ''Carlavirus'', formerly known as the "Carnation latent virus group", is a genus of viruses in the order ''Tymovirales'', in the family ''Betaflexiviridae''. Plants serve as natural hosts. There are 53 species in this genus. Diseases associated w ...

'' that has been found infecting

garlic Garlic (''Allium sativum'') is a species of bulbous flowering plant in the genus ''Allium''. Its close relatives include the onion, shallot, leek, chive, Allium fistulosum, Welsh onion and Allium chinense, Chinese onion. It is native to South A ...

globally. Detection of the virus in

leek The leek is a vegetable, a cultivar of ''Allium ampeloprasum'', the broadleaf wild leek ( syn. ''Allium porrum''). The edible part of the plant is a bundle of leaf sheaths that is sometimes erroneously called a stem or stalk. The genus ''Alli ...

and

onion An onion (''Allium cepa'' L., from Latin ''cepa'' meaning "onion"), also known as the bulb onion or common onion, is a vegetable that is the most widely cultivated species of the genus ''Allium''. The shallot is a botanical variety of the onion ...

has also been reported.

Epidemiology

GarCLV main transmission is through propagation material. As a result, it is often widespread among garlic crop. The virus single infection in garlic is usually symptomless, but in mixed infections with leek yellow stripe virus (LYSV, ''

Potyvirus ''Potyvirus'' is a genus of positive-strand RNA viruses in the family ''Potyviridae''. Plants serve as natural hosts. The genus is named after member virus ''potato virus Y''. Potyviruses account for about thirty percent of the currently known ...

'') or onion yellow dwarf virus (OYDV, ''

'') could form ‘garlic viral complex’ which increases severity of the other viruses infection. Other

Allium ''Allium'' is a genus of monocotyledonous flowering plants that includes hundreds of species, including the cultivated onion, garlic, scallion, shallot, leek, and chives. The generic name ''Allium'' is the Latin word for garlic,Gledhill, Davi ...

spp. such as Allium caeruleum, Allium cristophii,

Allium cyathophorum ''Allium cyathophorum'' is a Chinese (杯花韭, bei hua jiu) species of flowering plant in the onion genus ''Allium'' of the family Amaryllidaceae. It grows at elevations from 2700 metres up to 4600 metres. Description This bulbous herbaceous p ...

, Allium nutans,

Allium schoenoprasum Chives, scientific name ''Allium schoenoprasum'', is a species of flowering plant in the family Amaryllidaceae that produces edible leaves and flowers. Their close relatives include the common onions, garlic, shallot, leek, scallion, and ...

Allium scorodoprasum The sand leek (''Allium scorodoprasum''), also known as rocambole and Korean pickled-peel garlic, is a Eurasian species of wild onion with a native range extending across much of Europe, Middle East, and Korea. The species should not be confused ...

, Allium senescens subsp. montanum, and Allium sphaerocephalon had also been reported to be infected by GarCLV.

Genome

The virus complete genome, excluding poly-(A) tail, is 8,353 nt long, and contains six

open reading frame In molecular biology, open reading frames (ORFs) are defined as spans of DNA sequence between the start and stop codons. Usually, this is considered within a studied region of a prokaryotic DNA sequence, where only one of the six possible readin ...

(ORFs). ORFs 2, 3, 4 are triple gene block (TGB) which encodes

movement protein In order for a virus to infect a plant, it must be able to move between cells so it can spread throughout the plant. Plant cell walls make this moving/spreading quite difficult and therefore, for this to occur, movement proteins must be present. A ...

, while ORF5 is the

viral coat protein A capsid is the protein shell of a virus, enclosing its genetic material. It consists of several oligomeric (repeating) structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or may ...

(CP) encoding sequence.

Phylogeny

Earlier phylogenetic analyses based on

capsid A capsid is the protein shell of a virus, enclosing its genetic material. It consists of several oligomeric (repeating) structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or may ...

(CP) gene suggested that global GarCLV isolates were highly similar and can be divided into two major groups only. However, the latest

Phylogenetic trees A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...

constructed using complete nucleotide sequences of each of TGB and CP gene clustered global isolates available in NCBI GenBank into three major clades. Isolates in the third group have high genetic variability among themselves and to isolates in the two other groups, and also seems to be more rarely found in the nature. The subsequent

population study Population study is an interdisciplinary field of scientific study that uses various statistical methods and models to analyse, determine, address, and predict population challenges and trends from data collected through various data collection m ...

suggested that both genes were under negative

selection pressure Any cause that reduces or increases reproductive success in a portion of a population potentially exerts evolutionary pressure, selective pressure or selection pressure, driving natural selection. It is a quantitative description of the amount of ...

, with pressure on CP were more intense than on TGB. As consequences, TGB gene has higher genetic variations than CP gene. The high variations on TGB gene sequences probably reduced vitality of some isolates, especially those belong to highly variable Clade 3, which could be one of reasons for the rarity of Clade 3 isolates in the nature.

References

{{Taxonbar, from=Q18965548 Carlaviruses Viral plant pathogens and diseases