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Garlic common latent virus
Virus classification
(unranked):	Virus
Realm:	Riboviria
Kingdom:	Orthornavirae
Phylum:	Kitrinoviricota
Class:	Alsuviricetes
Order:	Tymovirales
Family:	Betaflexiviridae
Genus:	Carlavirus
Species:	Garlic common latent virus

Garlic common latent virus (GarCLV) is a plant virus member of the genus Carlavirus that has been found infecting garlic globally.^[1]^[2] Detection of the virus in leek and onion has also been reported.^[3]^[4]

Epidemiology

GarCLV main transmission is through propagation material.^[5] 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) or onion yellow dwarf virus (OYDV, Potyvirus) could form ‘garlic viral complex’ which increases severity of the other viruses infection.^[6] Other Allium spp. such as Allium caeruleum, Allium cristophii, Allium cyathophorum, Allium nutans, Allium schoenoprasum, Allium scorodoprasum, Allium senescens subsp. montanum, and Allium sphaerocephalon had also been reported to be infected by GarCLV.^[7]

Genome

The virus complete genome, excluding poly-(A) tail, is 8,353 nt long, and contains six open reading frame (ORFs).^[8] ORFs 2, 3, 4 are triple gene block (TGB) which encodes movement protein, while ORF5 is the viral coat protein (CP) encoding sequence.^[9]

Phylogeny

Earlier phylogenetic analyses based on capsid (CP) gene suggested that global GarCLV isolates were highly similar and can be divided into two major groups only.^[1] However, the latest Phylogenetic trees 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 suggested that both genes were under negative selection pressure, 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.^[10]

References

^ ^a ^b PARRANO, Leonardo; AFUNIAN, Mohammad; PAGLIACCIA, Deborah; DOUHAN, Greg; VIDALAKIS, Georgios (2012). "Characterization of viruses associated with garlic plants propagated from different reproductive tissues from Italy and other geographic regions". Phytopathologia Mediterranea. 51 (3): 549–565. ISSN 0031-9465. JSTOR 43872342.
^ Nam, Moon; Lee, Yeong-Hoon; Park, Chung Youl; Lee, Min-A; Bae, Yang-Soo; Lim, Seungmo; Lee, Joong Hwan; Moon, Jae Sun; Lee, Su-Heon (1 March 2015). "Development of Multiplex RT-PCR for Simultaneous Detection of Garlic Viruses and the Incidence of Garlic Viral Disease in Garlic Genetic Resources". The Plant Pathology Journal. 31 (1): 90–96. doi:10.5423/PPJ.NT.10.2014.0114. PMC 4356611. PMID 25774116.
^ Shahraeen, N.; Lesemann, D. E.; Ghotbi, T. (2008). "Survey for viruses infecting onion, garlic and leek crops in Iran". EPPO Bulletin. 38 (1): 131–135. doi:10.1111/j.1365-2338.2008.01198.x.
^ Santosa, Adyatma Irawan; Ertunc, Filiz (August 2020). "Identification, molecular detection and phylogenetic analysis of four viruses infecting Allium cepa in Ankara Province, Turkey". Journal of Plant Diseases and Protection. 127 (4): 561–569. doi:10.1007/s41348-020-00347-5. S2CID 225488130.
^ Lunello, P; Ducasse, DA; Helguera, M; Nome, SF; Conci, VC (2002). "An Argentinean isolate of Leek yellow stripe virus from leek can be transmitted to garlic". J. Plant Pathol. 84 (1): 11-17. doi:10.4454/jpp.v84i1.1082 (inactive 1 November 2024).{{cite journal}}: CS1 maint: DOI inactive as of November 2024 (link)
^ Fajardo, Thor V. M.; Nishijima, Marta; Buso, José A.; Torres, Antônio C.; Ávila, Antônio C.; Resende, Renato O. (September 2001). "Garlic viral complex: identification of Potyviruses and Carlavirus in Central Brazil". Fitopatologia Brasileira. 26 (3): 619–626. doi:10.1590/S0100-41582001000300007.
^ Mansouri, Faten; Krahulec, František; Duchoslav, Martin; Ryšánek, Pavel (21 May 2021). "Newly identified host range of viruses infecting species of the genus Allium and their distribution in six habitats in the Czech Republic". Plant Pathology. 70 (6): 1496–1507. doi:10.1111/ppa.13391. S2CID 235584351.
^ Song, Sang Ik; Choi, Jin Nam; Song, Jong Tae; Ahn, Ji-Hoon; Lee, Jong Seob; Kim, Minkyun; Cheong, Jong-Joo; Choi, Yang Do (31 October 2002). "Complete genome sequence of garlic latent virus, a member of the carlavirus family". Molecules and Cells. 14 (2): 205–213. doi:10.1016/S1016-8478(23)15094-1. ISSN 1016-8478. PMID 12442892.
^ Yadav, Vineeta; Majumder, Shahana (June 2019). "The first complete genome sequence of garlic common latent virus occurring in India". VirusDisease. 30 (2): 311–314. doi:10.1007/s13337-018-0505-x. PMC 6531568. PMID 31179372.
^ Santosa, Adyatma Irawan; Ertunc, Filiz (10 June 2021). "Phylogenetic and diversity analyses of Garlic common latent virus based on the TGB and CP gene sequence". Plant Protection Science. 57 (3): 179–187. doi:10.17221/149/2020-PPS. S2CID 236311849.