SciELO - Scientific Electronic Library Online

vol.72 issue3Controlled traffic and soil physical quality of an Oxisol under sugarcane cultivation author indexsubject indexarticles search
Home Pagealphabetic serial listing  

Services on Demand



  • text new page (beta)
  • English (pdf)
  • Article in xml format
  • How to cite this article
  • SciELO Analytics
  • Curriculum ScienTI
  • Automatic translation


Related links


Scientia Agricola

Print version ISSN 0103-9016

Sci. agric. (Piracicaba, Braz.) vol.72 no.3 Piracicaba May/June 2015 


Survey of viruses belonging to different genera and species in noble garlic in Brazil

Tatiana Mituti1 

Mônika Fecury Moura1 

Julio Massaharu Marubayashi1 

Milena Leite Oliveira1 

Vitor Massami Imaizumi1 

Renate Krause Sakate1 

Marcelo Agenor Pavan1  * 

1São Paulo State University/FCA – Dept. of Plant Protection, R. José Barbosa de Barros, 1780 – 18610-307 – Botucatu, SP – Brazil.


Garlic (Allium sativumL.) is a host to several viruses, most commonly those belonging to theAllexivirus,Carlavirus, orPotyvirusgenera. Nine species distributed among these three genera have been reported in Brazil: two species within carlaviruses, two within potyviruses, and five within allexiviruses. To quantify the prevalence of these viruses, young leaves from 520 plants (plants either symptomatic or asymptomatic) were collected from commercial fields grown in four Brazilian states and analyzed using universal and species-specific primers via the reverse transcription polymerase chain reaction (RT-PCR). Potyvirus presence was positive in 306 samples (81 %), 151 of them (38 %) in mixed infections with other viruses. The most frequent potyviruses wereOnion yellow dwarf virus(OYDV, 56 %) andLeek yellow stripe virus(LYSV, 55 %). 187 samples (49 %) were positive for allexivirus, with 33 (9 %) showing single infections and 154 (41 %) showing mixed infections withGarlic virus A (GarV-A),Garlic virus B(GarV-B),Garlic virus C(GarV-C),Garlic virus D(GarV-D), and species belonging to theCarlavirus andPotyvirusgenera. The predominant species in which allexiviruses were found were GarV-A and GarV-D. Only 15 samples (4 %) were infected solely by a carlavirus, and 63 (17 %) showed mixed infections with viruses from different genera. The dominant species of carlavirus wasGarlic commom latent virus(GarCLV). Carlaviruses and allexiviruses are frequently associated with mixed infections with potyviruses, whereas mixed infections with carlaviruses and allexiviruses are rare. About 70 % of the plants collected were positive for at least one species of virus.

Key words: Allexivirus; Allium sativum; Carlavirus; Potyvirus; occurrence


Garlic (Allium sativumL.) is propagated vegetatively. This procedure allows for the accumulation of pathogens (especially viruses), which are perpetuated by bulbs from one production cycle to the next. Typically, garlic is infected by several viruses belonging to theAllexivirus, Carlavirus, andPotyvirusgenera (Barg et al., 1994;Sumi et al., 1993), which significantly reduce crop yield.

Potyvirusspecies are the most common and damage more garlic when plants are mix-infected with other genera of viruses (Salomon, 2002). They are represented by theOnion yellow dwarf virus (OYDV) andLeek yellow stripe virus (LYSV) species (Chen et al., 2001;Maeso et al., 1997). As regards theCarlavirus genus, the most common species found is theGarlic common latent virus(GarCLV) (Fajardo et al., 2001), andShallot latent virus (SLV) was recently reported in Brazil (Mituti et al., 2011).

Species in theAllexivirus genus include theGarlic mite-borne filamentous virus(GarMbFV),Garlic virus A(GarV-A),Garlic virus B (GarV-B),Garlic virus C (GarV-C),Garlic virus D(GarV-D),Garlic virus E (GarV-E),Garlic virus X (GarV-X), andShallot virus X(ShVX) (Kanyuka et al., 1992;Sumi et al., 1993;Yamashita et al., 1996). Species reported in Brazil include the GarMbFV, GarV-A, GarV-B, GarV-C, GarV-D, and GarV-X (Melo Filho et al., 2004;Oliveira et al., 2013).

The mid-western and southeastern regions of Brazil are currently the most important areas which produce noble garlic in Brazil, and no prior surveys in commercial fields indicating the prevalence of viruses in these areas exist. Thus, the goal of the authors in this study was to evaluate the occurrence of viruses belonging to theAllexivirus,Carlavirus, andPotyvirusgenera.

Materials and Methods

Sample collection

520 samples of garlic (both from symptomatic and asymptomatic plants) presenting mosaic and chlorotic streaking were collected in commercial fields approximately 70 days after planting in four Brazilian states and seven municipalities, including the following: Goiás (Campo Alegre 9° 46' 46'' latitude S, 36° 21’ 1” longitude W, and Ipameri 17° 43’ 29” latitude S, 48° 9’ 35” longitude W) , Minas Gerais (Santa Juliana 19º 18’ 32” latitude S, 47º 31’27”, longitude W and São Gotardo 19° 18' 27'' latitude S, 46° 3’ 22'' longitude W), Paraná (Bandeirantes 23º 06’ 36” latitude S, 50º 22’ 0” longitude W, Piraquara 25º 26’ 30” latitude S, 49º 03' 48” longitude W, and Guarapuava 25º 23’ 43” latitude S, 51º 27’ 29” longitude W), and São Paulo (São Manuel 22º 43’ 52” latitude S, 48º 34’ 14” longitude W). Collections were made from May 2007−Oct 2011, for a total of 34 collections. Samples collected in Guarapuava were cultivated in a greenhouse, where samples that were free of the garlic virus were propagated.

Genera and species-specific primer development and analysis

Multiple alignments of the main species described in garlic around the world were done using the MEGA 4.0 (Tamura et al., 2007) program. Universal and specific primers were synthesized to detect genera and different species and to partially amplify the region of coat protein (CP) except for LYSV, of which the primers amplified the partial region of the P1 gene (Table 1).

Table 1 – Primer sequences used to detect various viruses in garlic. 

Genus or species Sequence Reference
Carlavirus 5’-GGNTKKGAAWCTGGGAGDCC-3’ Designed for this work
Potyvirus 5'-GAT TTA GGT GAC ACT ATA GT16-3' Gibbs et al., 1997
5'-ATG GTT TGG TGY ATY GAR AAT-3' Mota et al., 2004
Allexivirus 5’ CTACCACAATGGTTCCTC 3’ Oliveira et al., 2013
OYDV 5’ CRCCARTTCTGGATAAYGC 3’ Designed for this work
LYSV 5’ CTTCMTCRCASTCATGKTCC 3’ Designed for this work
5’ AATCTCAACACAACTTATRC 3’ Yoshida et al., 2011
SLV 5’-CTTTTGGTTCACTTTAGG-3’ Mituti et al., 2011
GarCLV 5’-GGSTTTGARACTGGGAGGCC-3’ Designed for this work
GarV-B 5’ GCAGAATAARCCCCCYTC 3’ Oliveira et al., 2013

OYDV=Onion yellow dwarf virus; LYSV=Leek yellow stripe virus ; SLV=Shallot latent virus; GarCLV=Garlic commom latent virus; GarV-A=Garlic virus A; GarV-B=Garlic virus B; GarV-C=Garlic virus C; GarV-D =Garlic virus D.

Total RNA was extracted (Bertheau et al., 1998) and used in a one-step reverse transcription polymerase chain reaction (RT-PCR) assay. A total volume of 25 µL, 12.5 µL of 2X PCR master mix, 1 µM of each primer, one unit of AMV (Avian Mieloblastosis virus) reverse transcriptase, 2.5 µL of total RNA, and nuclease-free water were used. The reaction consisted of the following: 30 min at 42 °C; 1 min at 95 °C; 40 cycles of 94 °C for 40 s, 50 °C for 60 s, and 72 °C for 60 s; and a final extension for 10 min at 72 °C. The same reaction cycle was used to detect the species of theCarlavirusgenus, GarCLV, OYDV, and LYSV. For the other primers, the reaction cycle was performed in accordance with the bibliographic references cited inTable 1. Amplicons of five samples of each genus and species were sequenced to evaluate the efficiency of primers.

Results and Discussion

Potyvirus was the most common genus identified in 306 samples (81 %), of which 155 (41 %) were infected only by potyviruses (Table 2). Mixed infections between OYDV and LYSV were found in 61 samples (16 %). 94 samples (25 %) had potyviruses and allexiviruses; 23 (6 %) were infected with potyviruses plus carlaviruses, and 34 (9 %) were infected with potyviruses, allexiviruses, and carlaviruses, indicating that approximately half of the collected samples had mixed infections of viruses belonging to the three different genera tested.

Table 2 – Detection of genera and species ofAllexivirus,Carlavirus andPotyvirusby the reverse transcription polymerase chain reaction (RT-PCR), using universal and specific primers. 

Genus (no. positive samples) No. of species No. of samples (%)
Potyvirus only (155) One species 94 (25 %)
Two species 61 (16 %)
Carlavirus only (15) One species 13 (3 %)
Two species 2 (1 %)
Allexivirus only (53) One species 33 (9 %)
Two species 13 (3 %)
More than three species 7 (2 %)
Potyvirus + Carlavirus (23) Two species 11 (3 %)
More than three species 12 (3 %)
Potyvirus + Allexivirus (94) Two species 54 (14 %)
More than three species 40 (11 %)
Carlavirus + Allexivirus (6) Two species 6 (2 %)
Potyvirus + Allexivirus+ Carlavirus (34) Three species 4 (1 %)
Four species 9 (2 %)
Five species 16 (4 %)
Six species 5 (1 %)
Total of positive samples 380

LYSV and OYDV were found with the same frequency in noble garlic from Brazil. Our results differ from previous studies byFayad-Andre et al. (2011), which showed LYSV to be predominant compared to OYDV. In this study, only noble garlic was analyzed, whileFayad-Andre et al. (2011) collected garlic from different production systems. Noble garlic has the higher commercial price compared to tropical garlic, which produces lower quality and smaller bulbs over a shorter cycle (Filgueira, 2007).

Followed by potyviruses, allexiviruses were found with high incidence, being detected in 187 samples collected (49 %). GarV-D and GarV-A can be considered the predominant species, with 109 (29 %) and 107 (28 %) positive samples, respectively. 41 samples (11 %) were positive for GarV-C, while GarV-B (the rarest) was found only in 18 samples (5 %).

The transmission of allexiviruses can easily occur because the mite is a pest commonly found in bulbs, which facilitates the transmission of viruses (Cafrune et al., 2006). Our results also differed from those obtained byFayad-Andre et al. (2011), because GarV-C was seen to be the prevalent species in all production systems, while GarV-D was limited to the Cerrado region.

Carlaviruses were detected in 78 samples (21 %), indicating relatively low prevalence, with GarCLV being the predominant species. SLV was detected only in 11 samples (3 %). In Brazil, the occurrence of carlaviruses is low, with GarCLV being the prevalent species. This genus can cause crop losses which are somewhat limited, but it can cause significant yield losses when plants are co-infected with potyviruses as a result of synergistic effects (Takaichi et al., 1998).

Potyviruses, allexiviruses, and carlaviruses were found in most regions, except for the state of Goiás, where GarV-B, GarV-C, and GarV-D were not detected. Also, SLV was not found in Paraná (Table 3). 141 samples were negative for the three genera. Most of them were found in Paraná (34 %), where garlic seed free of viruses is maintained in greenhouses, and Minas Gerais (27 %), where the same seed is multiplied in fields (Table 3).

Table 3 – Occurrence of species of Potyvirus (Leek yellow stripe virus -LYSV andOnion yellow dwarf virus -OYDV), Carlavirus (Garlic common latent virus -GarCLV andShallot latent virus -SLV) and Allexivirus (Garlic virus A -GarV-A;Garlic virus B -GarV-B;Garlic virus C -GarV-C andGarlic virus D -GarV-D) in Brazil, analyzed from April 2007 to Oct 2011. 

Genera Species Collection Site (number of collected samples)
Minas Gerais (228 samples) Goiás (49 samples) Paraná (149 samples) São Paulo (94 samples)
Potyvirus LYSV 98 (43 %) 21 (43 %) 42 (28 %) 47 (50 %)
OYDV 91 (40 %) 24 (49 %) 47 (32 %) 49 (52 %)
Carlavirus GarCLV 33 (14 %) 5 (10 %) 3 (2 %) 37 (39 %)
SLV 5 (2 %) 1 (2 %) 0 5 (5 %)
Allexivirus GarV-A 45 (20 %) 2 (4 %) 20 (13 %) 40 (43 %)
GarV-B 3 (1 %) 0 7 (5 %) 8 (9 %)
GarV-C 9 (4 %) 0 5 (3 %) 27 (29 %)
GarV-D 40 (2 %) 0 39 (26 %) 30 (32 %)
Virus Free - 62 (27 %) 9 (18 %) 50 (34 %) 19 (20 %)

Infected bulbs seem to be common in commercial fields, and the occurrence of two or more viruses of different taxonomic groups is also common. There was no correlation between the occurrence of species with producing regions of the country, probably as a result of the exchange of garlic seed in the southern, southeastern, and mid-western regions of Brazil.


This research was supported by FAPESP (São Paulo State Foundation for Research Support), Fellowship number 2010/16148-9, CNPq (Brazilian National Council for Scientific and Technological Development), Fellowship number 472032/2010-0, and the first author was supported by a fellowship from CAPES PDSE 5279/11-9 (Coordination for the Improvement of Higher Level Personnel).


Barg, E.; Lesemann, D.E.; Vetten, H.J. 1994. Identification, partial characterization, and distribution of viruses infecting allium crops in South and Southeast Asia. Acta Horticulturae 358: 251-258. [ Links ]

Bertheau, Y.; Frechon, D.; Toth, I.K.; Hyman, L.J. 1998. DNA amplification by polymerase chain reaction (PCR). p. 38-48. In: Perombelon, M.V.M.; Wolff, J.M. (eds.). Methods for the detection and quantification ofErwinia carotovora subsp.atroseptica on potatoes. Scottish Crop Research Institute, Dundee, Scotland. [ Links ]

Cafrune, E.E.; Balzarini, M.; Conci, V. 2006. Changes in the concentration of anAllexivirusduring the crop cycle of two garlic cultivars. Plant Disease 90: 1293-1296. [ Links ]

Chen, J.; Chen, J.; Adams, M.J. 2001. Molecular characterization of a complex mixture of viruses in garlic with mosaic symptoms in China. Archives of Virology 146: 1841-1853. [ Links ]

Fajardo, T.V.M.; Nishijima, M.; Buso, J.A.; Torres, A.C.; Avila, A.C.; Resende, R.O. 2001. Garlic viral complex: identification of potyviruses and carlaviruses in Central Brasil. Fitopatologia Brasileira 26: 619-626. [ Links ]

Fayad-Andre, M.S.; Dusi, A.N.; Resende, R.O. 2011. Spread of viruses in garlic fields cultivated under different agricultural production systems in Brazil. Tropical Plant Pathology 36: 341-349. [ Links ]

Filgueira, F.A.R. 2007. New Manual of Vegetable Crops: modern agro-technology in the production and marketing of vegetables. = Novo Manual de Olericultura: agrotecnologia moderna na produção e comercialização de hortaliças. 3ed. Editora UFV, Viçosa, MG, Brazil (in Portuguese). [ Links ]

Gibbs, A.; Mackenzie, A. 1997. A primer pair for amplifying part of the genome of all potyvirids by RT-PCR. Journal of Virological Methods 63: 9-16. [ Links ]

Kanyuka, K.V.; Vishnichenko, V.K.; Levay, K.E.; Kondrikov, D.Y.; Ryabov, E.V.; Zavriev, S.K. 1992. Nucleotide sequence of shallot virus X RNA reveals a 5’-proximal cistron closely related to those of potexviruses and a unique arrangement of the 3’-proximal cistrons. Journal of General Virology 73: 2553-2560. [ Links ]

Maeso, C.; Pagani, C.; Conci, V.C.; Mirabelle, L. 1997. Studies on viruses affecting garlic in Uruguay. Acta Horticulturae 433: 617-622. [ Links ]

Melo Filho, P.A.; Nagata, T.; Dusi, A.N.; Buso, J.A.; Torres, A.C.; Eiras, M.; Resende R.O. 2004. Detection of threeAllexivirusspecies infecting garlic in Brazil. Pesquisa Agropecuária Brasileira 39: 735-740. [ Links ]

Mituti, T.; Marubayashi, J.M.; Moura, M.F.; Krause-Sakate; R.; Pavan, M.A. 2011. First Report ofShallot latent virus in Garlic in Brazil. Plant Disease 95: 227. [ Links ]

Mota, L.D.C.; Della Vecchia, M.G.S.; Gioria, R.; Kitajima, E.W.; Rezende, J.A.M.; Camargo, L.E.A.; Amorim, L. 2004.Pfaffia mosaic virus: a new potyvirus found infectingPfaffia glomerata in Brazil. Plant Pathology 53: 368-37. [ Links ]

Oliveira, M.L.; Hoffmann, M.I.M.; Mituti, T.; Pavan, M.A.; Krause-Sakate, R. 2013. First report ofGarlic virus Xin garlic plants in Brazil. Plant Disease 98: 1013-1013. [ Links ]

Salomon, R. 2002. Virus Diseases in Garlic and the propagation of virus-free plants. p. 311-327. In: Rabinowitch, H.D; Currah, L., eds. Allium Crop Science: Recent Advances, New York, NY, USA. [ Links ]

Sumi, S.; Tsuneyoshi, T.; Furutani, H. 1993. Novel rod-shaped viruses isolated from garlic,Allium sativum, possessing a unique genome organization. Journal of General Virology 74: 1879-1885. [ Links ]

Takaichi, M.; Yamamoto, M.; Nagakubo, T.; Oeda, K. 1998. Four garlic viruses identified by Reverse Transcription-Polymerase Chain Reaction and their regional distribution in Northern Japan. Plant Disease 82: 694-698. [ Links ]

Tamura, K.; Dudley, J.; Nei, M.; Kumar, S. 2007. MEGA 4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599. [ Links ]

Yamashita, K.; Sakai, J.; Hanada, K. 1996. Characterization of a new virus garlic (Allium sativumL.), garlic mite-borne mosaic virus. Annals of the Phytopathological Society of Japan 62: 483-489. [ Links ]

Yoshida, N.; Shimura, H.; Yamashita, K.; Suzuki, M.; Masuta, C. 2011. Variability in the P1 gene helps to refine phylogenetic relationships among Leek yellow stripe virus isolates from garlic. Archives of Virology 157: 147-53. [ Links ]

Received: May 13, 2014; Accepted: September 24, 2014

*Corresponding author <>

Creative Commons License This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.