First report of garlic virus E in Australia

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.

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First report of garlic virus D in garlic from D.R. Congo

Journal of Plant Pathology ◽

10.1007/s42161-018-0033-y ◽

2018 ◽

Vol 100 (1) ◽

pp. 143-143

Author(s):

Shahana Majumder ◽

Kate Mbay ◽

Jyoti Singh

Keyword(s):

First Report ◽

Garlic Virus

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First report of garlic virus D in Allium stracheyi from India

Journal of Plant Pathology ◽

10.1007/s42161-020-00632-0 ◽

2020 ◽

Vol 102 (4) ◽

pp. 1347-1347

Author(s):

Shahana Majumder ◽

Sneha Singh ◽

Jyoti Singh

Keyword(s):

First Report ◽

Garlic Virus

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First Report of Garlic virus A in Garlic From India

Plant Disease ◽

10.1094/pdis-11-14-1210-pdn ◽

2015 ◽

Vol 99 (9) ◽

pp. 1288-1288 ◽

Cited By ~ 3

Author(s):

S. J. Gawande ◽

V. S. Gurav ◽

A. A. Ingle ◽

J. Gopal

Keyword(s):

First Report ◽

Garlic Virus

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First Report of Garlic virus B infecting Garlic in India

Plant Disease ◽

10.1094/pdis-01-20-0156-pdn ◽

2020 ◽

Author(s):

Praveen Baliram Roylawar ◽

Kiran S Khandagale ◽

Pragati Randive ◽

Gorakshnath E. Atre ◽

Suresh Janardhan Gawande ◽

...

Keyword(s):

Consensus Sequence ◽

Sandwich Elisa ◽

Rna Extraction ◽

Enzyme Linked Immunosorbent Assay ◽

Experimental Plot ◽

Rt Pcr ◽

First Report ◽

The Impact ◽

Garlic Virus ◽

Germplasm Accessions

Garlic (Allium sativum L.) is an economically important spice and vegetable crop grown throughout the world. Garlic viral disease complex caused by multiple virus infections is an important constraint in exploiting the potential yield of garlic. Among these viral pathogens, allexivirus (family Alphaflexiviridae) is the genus of viruses known for their degenerative effect on garlic yield. Their coexistence with other viruses, particularly potyviruses, has an adverse effect on garlic yield and quality (Perotto et al. 2010). During Sept 2018, while screening garlic germplasm accessions for the presence of allexiviruses, symptoms like foliar mosaic and curling were observed on accession G-204, planted at an experimental plot of ICAR-DOGR, Pune, India. A total of five samples comprised of five randomly selected G-204 garlic plants were collected from the experimental plot. Each sample contained leaves from the top, middle, and bottom portion of the individual garlic plants. These samples were subjected to RNA extraction using the RNeasy Plant Mini Kit (Qiagen, Germany) followed by reverse transcription (RT) using the Transcriptor cDNA synthesis kit (Roche Diagnostics, GmbH, Germany). The extracted RNA was then tested for allexiviruses such as garlic virus A (GarV-A), garlic virus B (GarV-B), garlic virus C (GarV-C), garlic virus D (GarV-D), and garlic virus X (GarV-X) by polymerase chain reaction (PCR) (Gawande et al. 2015; Roylawar et al. 2019; Baranwal et al. 2011; Gieck et al. 2009). Leaf samples tested through RT-PCR were found positive for garlic viruses GarV-A, GarV-B, GarV-C, GarV-D, and GarV-X. Allexiviruses other than GarV-B had been previously reported in India and hence further tests were conducted to confirm GarV-B infection. RT-PCR using primers, CF 5’- ATGGGAGACAGGTCGCAA-3’ and CR5’- CTAAAATGTAAGCATGAGCGGT-3’ designed specific to the coat protein yielded a 735-bp amplicon from all five G-204 plants. The amplified product was purified using QIAquick PCR Purification Kit (Qiagen, Germany) and cloned in pJET1.2 vector (Thermo Scientific, Lithuania). Two clones containing the CP gene were bidirectionally sequenced, and a consensus sequence was submitted to GenBank (MN650206). BLASTn results indicated that this consensus sequence showed 97.96% nucleotide (KP657919.1) and 100% amino acid sequence (AKN19940.1) identity with the CP sequence of GarV-B isolate from Poland. The presence of GarV-B was confirmed by enzyme-linked immunosorbent assay (ELISA) using a double-antibody sandwich ELISA kit (Arsh Biotech, Delhi, India) as per the manufacturer’s protocol. An absorbance of reaction was read using a microplate reader at 405 nm. The mean OD values of negative and positive controls were 0.034 and 0.373, respectively. The OD values of five samples tested ranged from 0.210 to 0.296 indicating a positive reaction for GarV-B. To assess the presence of GarV-B in the available genetic stock, we tested 30 garlic germplasm accessions for GarV-B using RT-PCR. Out of these, 17 accessions were found positive for GarV-B. GarV-B has been reported from many countries (Gieck et al. 2009). This is the first report of GarV-B from India. Globally, allexiviruses are known for their adverse impact on garlic production (Oliveira et al. 2014). GarV-B together with other viruses can be a potential threat to garlic production in India. Further, detailed evaluations are needed to study the impact of GarV-B on garlic production in India.

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First Report of Garlic virus X Infecting Garlic in India

Plant Disease ◽

10.1094/pdis-03-11-0198 ◽

2011 ◽

Vol 95 (9) ◽

pp. 1197-1197 ◽

Cited By ~ 7

Author(s):

V. K. Baranwal ◽

P. Singh ◽

R. K. Jain ◽

S. Joshi

Keyword(s):

Nucleotide Sequence ◽

Coat Protein ◽

Agricultural Research ◽

Indian Agricultural Research Institute ◽

Latent Virus ◽

Onion Yellow Dwarf Virus ◽

Rt Pcr ◽

First Report ◽

Blast Analysis ◽

Garlic Virus

Garlic (Allium sativum) is an important crop in several states of India. Filamentous viruses such as Onion yellow dwarf virus (OYDV), Shallot latent virus (SLV), and Garlic common latent virus (GarCLV) have been reported previously in different garlic cultivars from India (4). These viruses are transmitted from generation to generation through cloves and cause severe reduction in yield and quality. During December 2010, garlic plants were observed with mosaic leaf symptoms and stunting in an experimental field at the Indian Agricultural Research Institute, Delhi. Cloves and leaves from 3-month-old symptomatic plants of five different cultivars (G-282, IC-375416, Ruag, Yamuna Safed, and ACC-40), originally from different regions of India, were collected from the field in Delhi and total RNA was extracted using an RNeasy Plant Mini Kit (Qiagen, Valencia, CA). The presence of OYDV and GarCLV was confirmed by reverse transcription (RT)-PCR in all cultivars, while the presence of SLV was only confirmed in cv. G-282 by RT-PCR. Since Allexiviruses are common in garlic, their detection in cloves was confirmed by RT-PCR using primers ALLEX 1 and ALLEX 2 (2). An ~200-bp amplification product was observed in all five cultivars. To further characterize the Allexivirus in these cultivars, an amplicon of ~900 bp was amplified with Allex-CP (1) and ALLEX 2 (2) primers and cloned and sequenced. BLAST analysis of the nucleotide sequences from five garlic cultivars showed identity with different allexiviruses, Garlic virus A (GarV-A) (74 to 83%), Garlic virus E (GarV-E) (74 to 80%), Garlic virus D (GarV-D) (76 to 79%), and Garlic virus X (GarV-X) (75 to 78%). Since species demarcation in the genus Allexivirus is based on the coat protein (CP) gene (3), another set of primers, 5′-MYT KGA GTG GCT VAC ACA YAT-3′ and 5′-ATT RAA GTC GTG RGG ATG CAT-3′ was designed. These primers were derived from conserved regions of ORF4 and ORF5 (CP) sequences of allexiviruses available in the NCBI database and used in RT-PCR to obtain the complete CP. An ~1.5-kb amplicon was obtained only in cv. G-282 that originated from the southern part of India. A similar amplicon was obtained from Chenopodium amaranticolor mechanically inoculated with leaf sap from cv. G-282. Sequences (1,422 bp) obtained from three clones each from garlic cv. G-282 and C. amaranticolor were identical and BLAST analysis of the consensus nucleotide sequence showed maximum identity of 75 to 81% with isolates of GarV-X. The 1,422 nucleotide sequence was comprised of 690 bp of ORF4 (partial) and 732 bp of the CP. The coat protein sequence (GenBank Accession No. HQ822272) shared a 79.6 to 81.1% identity in nucleotide and 89.3 to 90.9% in amino acid sequence with different isolates of GarV-X (GenBank Accession Nos. AJ292229, U89243, and GQ475426). To our knowledge, this is the first report of GarV-X in a garlic cultivar from India. The characterization and identification of allexiviruses is important for production of virus-free garlic plants through tissue culture in India. References: (1) J. Chen et al. Arch. Virol. 149:435, 2004. (2) C. I. Dovas et al. J. Phytopathol.149:731, 2001. (3) C. M. Fauquet et al. Virus Taxonomy-VIIIth Report of the ICTV, Academic Press, London, 2005. (4) S. Majumder and V. K. Baranwal. Plant Dis. 93:106, 2009.

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First report of garlic viruses A, B and C on garlic (Allium sativum L.) in Tunisia

Plant Disease ◽

10.1094/pdis-08-21-1706-pdn ◽

2021 ◽

Author(s):

Chadha Ayed ◽

Imen Hamdi ◽

Asma Najar ◽

Armelle Marais ◽

Chantal Faure ◽

...

Keyword(s):

Synergistic Effects ◽

Direct Sequencing ◽

Germplasm Collection ◽

Rt Pcr ◽

Serological Tests ◽

First Report ◽

Three Samples ◽

Pcr Assays ◽

Virus C ◽

Garlic Virus

Mite-borne viruses belonging to the genus Allexivirus (family Alphaflexiviridae) commonly occur on garlic in many parts of the world. There are usually asymptomatic and cause small damage to the plants, but often occur in mixed infection with potyviruses and carlaviruses, with synergistic effects reducing crop quality and leading to higher losses (Taglienti et al. 2017). Their occurrence on Tunisian garlic crops was studied here in the same garlic germplasm collection mentioned in a previous first report (Ayed et al. 2019). Leaf samples from a total of 66 garlic accessions were tested by DAS-ELISA using specific antibodies (DSMZ, Germany) against garlic virus A (GarV-A), garlic virus B (GarV-B) and garlic virus C (GarV-C). These serological tests showed individual virus incidence of respectively 56.4%, 67.7% and 10%. Our findings corroborate with the results of Chodorska et al (2012). In order to confirm the presence of these viruses, RT-PCR assays were performed using total RNAs extracted using two silica-capture extraction procedures according to Foissac et al (2005) and specific primers targeting the coat protein genes of the various viruses. These primers, designed for the present study are (GarV-A-F: 5' YCTYTTCTCHYTDGCHTGGACYTG 3' and GarV-A-R: 5' RCCYTTCCTAGACCARTTRGCRGG 3' for GarV-A; GarV-B-F: 5' TGGGCYTGYTACCACAAYGGATC 3' and GarV-B-R 5' TCTGCGCGVGTGGADACCATRTT 3' for GarV-B; GarV-C-F: 5' ARGAYCTYTTYTCMCTYGCRTGGGC 3' and GarV-C-R: 5' GGAGGYTCRTGAATYTGTTGTTG 3' for GarV-C). The viruses were detected by a two-step RT-PCR as described by Marais et al (2015). PCRs consisted of one cycle at 95 °C for 5 min; followed by 40 cycles of denaturation at 95 °C for 45 s, annealing at 45 °C for 45 s, and elongation at 72 °C for 45s; and a final extension step at 72 °C for 10 min. Products of the expected size (214 bp for GarV-A, 363 bp for GarV-B and 439 bp for GarV-C) were amplified from 58 (88%), 47 (71%) and 56 (85%) accessions, respectively. Forty three samples (65%) were co-infected by the three viruses. Higher numbers of positives revealed by RT-PCR especially in the case of GarV-C may reflect the higher sensitivity and efficiency of this technique compared to ELISA. Direct sequencing of selected amplicons of the expected size obtained for GarV-A, -B, and -C Tunisian isolates was performed and the sequences submitted to GenBank, validating the specificity of the three RT-PCR assays. The two sequenced GarV-A isolates (MK599147 and MN995836) shared 98% nucleotide (nt) sequence identity with each other, and 93-94% identity with the closest isolate in GenBank, the “G118” isolate from China (MN059320). The three sequenced GarV-B isolates (MN995829 to MN995831) shared 88-98% nt identity with each other. For “GarV-B 18.1” (MN995830) and “GarV-B 36.2” (MN995831) the closest isolate was “1109.1” (JX682828) from Spain (92-93% nt identity). For “GarVB 17.2” (MN995829), the closest isolate was “B-Sp-3” (LC97167) from Spain (90% nt identity). The sequenced GarV-C isolate (MN995834) showed the highest sequence nt identity (93%) with the “GarV-9” isolate (HQ724848) from Spain. To our knowledge this is the first report of the presence of GarV-A, -B and -C in Tunisia. The presence of these allexiviruses may pose a threat to the preservation of the Tunisian garlic germplasm and, more broadly, to garlic production in Tunisia. For this reason, the scrupulous identification of viruses occurring in garlic plants will help to use the appropriate strategy to decrease viral incidence in garlic growing area.

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First Report of Garlic virus B and Garlic virus D in Garlic in the Pacific Northwest

Plant Disease ◽

10.1094/pdis-93-4-0431a ◽

2009 ◽

Vol 93 (4) ◽

pp. 431-431 ◽

Cited By ~ 6

Author(s):

S. L. Gieck ◽

P. B. Hamm ◽

N. L. David ◽

H. R. Pappu

Keyword(s):

Pacific Northwest ◽

Seed Production ◽

The Other ◽

Rt Pcr ◽

Specific Primers ◽

Sequence Comparisons ◽

First Report ◽

The Pacific ◽

The Impact ◽

Garlic Virus

With the recent report of several viruses infecting garlic (Allium sativum L.) grown in the Pacific Northwest (1–3), studies were initiated on cloves planted in the fall of 2006 to determine the presence of additional viruses infecting plants exhibiting mosaic and/or chlorotic leaves. Cloves from symptomatic plants of the cultivar ‘Early’ from two seed production fields in Benton County, WA and two seed production fields in Morrow County, OR were tested by two-step reverse transcription (RT)-PCR using primers specific to the coat protein (CP) of the allexiviruses (4), since garlic infected with this group had similar symptoms in Asia and South America (4). Of the 87 cloves tested, 84 were positive, and four representative samples of the RT-PCR amplicons from each location were cloned and sequenced. Sequence comparisons indicated that the cloves from both locations were infected with Garlic virus D (GarV-D), also known as Japanese garlic virus (JGV), since they shared 98% identity with known isolates (GenBank Accession Nos. L388922.1, AF519572.1, and AB010303.1). In addition, sequences of isolates from the Oregon cloves shared a 96% identity with a known isolate of Garlic virus B (GarV-B; GenBank Accession No. AF543829.1). Because no antiserum specific to these viruses was available, primers specific to the CP genes of GarV-D (JGV-F2/JGV-R2 5′-GCTCACTCRGATGTGTTAGC-3′ and 5′-CGCGTGGACATAAGTTGTTG-3′) and GarV-B (GVB-F1/GVB-R2 5′-GAGGAGAACTAACGCCACAC-3′ and 5′-ACGACCTAGCTTCCTACTTG-3′) were designed and the cloves were retested by RT-PCR using these virus-specific primers. With the GarV-D specific primers, 98 and 63% of the cloves were positive from Washington and Oregon, respectively, and 52% of the cloves from Oregon were positive using the GarV-B specific primers. None of the cloves tested from Washington were positive for GarV-B. The identity of the amplicons was verified by cloning and sequencing (GarV-D, GenBank Accession No. FJ643476; GarV-B, GenBank Accession No. FJ643475). Incidence of the two viruses differed between Oregon and Washington was likely due to the expansion of the seed lots in two different locations (California and Nevada) prior to planting in 2006. With such high infection rates, studies should be conducted to determine the impact of these viruses on yield when plants are singly infected as well as in combination with the other viruses known to infect garlic in this region. These and the other viruses (1) are likely to impact yield. To our knowledge, this is the first report of GarV-D (JGV) and GarV-B in garlic in the Pacific Northwest. References: (1) S. L. Gieck et al. Plant Dis. 91:461, 2007. (2) H. R. Pappu et al. Plant Dis. 89:205, 2005 (3) H. R. Pappu et al. Online publication. doi:10.1094/PHP-2008-0919-01-RS. Plant Health Progress, 2008. (4) T. Tsuneyoshi et al. Phytopathology 86:253, 1996.

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