Occurrence and Phylogenetic Analysis of Potyviruses, Carlaviruses and Allexiviruses in Garlic in <scp>S</scp>udan

Mohammed, H. S.; Zicca, Stefania; Manglli, Ariana; Mohamed, M. I.; Siddig, Marmar Abdel Rahman El; Hussein, A. M.; Tomassoli, L.

doi:10.1111/jph.12115

Cited by 12 publications

(9 citation statements)

References 22 publications

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“…The genetic diversity of allexivirus populations has been reported when comparing the CP and the replicase sequences, indicating population differentiation (Chen et al, 2001;Melo-Filho et al, 2004;Mohammed et al, 2013). Our data indicates that phylogenetic clustering among allexivirus isolates was independent of geographical area (Figure 1B).…”

Section: Phylogenetic Analyses and Taxonomic Impactsupporting

confidence: 66%

Allexivirus: review and perspectives

Mansouri

Ryšánek

2021

Phytopathol. Mediterr.

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Allexivirus (Alphaflexiviridae) was first described in 1970 by Razvjazkina. Since then, Allexivirus species have been detected in many countries. Although this genus primarily infects plants in the Amaryllidaceae, other hosts include plants in the Fabaceae, Rosaceae and Orchidaceae. Thirteen Allexivirus species have been assigned. Eight of these infect Allium hosts, and these include: shallot virus X (ShVX), 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), and garlic-mite filamentous virus (GarMbFV). Five have been described from non-Allium hosts, including blackberry virus E (BVE), vanilla latent virus (VLV), alfalfa virus S (AVS), Arachis pintoi virus (ApV), and Senna severe yellow mosaic virus (SSYMV). This review analyzes the taxonomic positions of the thirteen recognized species and four unassigned species (Allexivirus DS-2013/CZE isolate, shallot mite-borne latent virus (SMbLV), cassia mild mosaic virus (CaMMV), and papaya virus A (PaVA)). Based on the inspection of data, we have concluded that PaVA is an Allexivirus, DS-2013/CZE is an isolate of GarV-D, and SMbLV is an isolate of ShVX. Current knowledge of the host ranges, symptoms, genome structure and modes of transmission of these viruses is also summarized, and control measures employed against them are outlined.

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Section: Phylogenetic Analyses and Taxonomic Impactsupporting

confidence: 66%

Allexivirus: review and perspectives

Mansouri

Ryšánek

2021

Phytopathol. Mediterr.

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“…Overall, phylogenetic studies showed that Ethiopian garlic virus isolates are in most cases clustered together and their geographical origin and phylogenetic relatedness are often not correlated. Several studies conducted in other countries indicated similar evolutionary phenomena and attributed it to the fact that international exchange of vegetative planting materials between countries contributing to high diversity and rapid evolution of garlic viruses (Bereda et al 2017;Koo et al 2002;Mohammed et al 2013;Taglienti et al 2018;Wylie et al 2012). Historically, Ethiopia has been actively involved in trade and germplasm exchange of horticultural spices including Allium crops with Asian, Middle East, European and North African countries.…”

Section: Discussionmentioning

confidence: 90%

Molecular identification, incidence and phylogenetic analysis of seven viruses infecting garlic in Ethiopia

2019

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Little information exists on the type and incidence of viruses infecting garlic (Allium sativum L) in Ethiopia. Attempts were made to identify the viruses using molecular techniques from 95 composite leaf samples collected from 44 farmers' fields and 51 germplasm accessions. Reverse transcription (RT-) PCR using genus and/or virus specific primers was used to amplify partial genome sequences of potyviruses, allexiviruses, carlaviruses and a tospovirus followed by sequencing of PCR products. Results indicated that 73.7% of the samples are infected with at least one virus. Onion yellow dwarf virus (OYDV, genus Potyvirus, family Potyviridae) is the most common virus detected followed by Garlic virus C (genus Allexivirus) and Shallot latent virus (SLV, genus Carlavirus). Other viruses detected at lower frequency include Garlic virus X and Garlic virus D (genus Allexivirus), Leek yellow stripe virus (genus Potyvirus) and Iris yellow spot virus (IYSV, genus Tospovirus). Mixed infection of two or more viruses was detected in 65.7% of the samples. Phylogenetic analysis suggested that the different viruses may have been introduced to Ethiopia from Europe or Asia. This is the first report of Garlic virus X, Garlic virus D, IYSV and SLV in garlic in Ethiopia. The high incidence of OYDV and IYSV which cause severe yield loss alone or in mixed infection with allexiviruses and carlaviruses is a cause of concern to growers.

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“…Serological detection such as DAS-ELISA has limitations in the production of specific antibodies against virus species from mixed infection (Pramesh et al, 2012). Nucleotidebased detection or molecular techniques such as Reverse Transcription -Polymerase Chain Reaction (RT-PCR) proved more highly specific, reliable and sensitive than ELISA for viral diagnostics (Mohammed et al, 2013;Jones et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Double Infection of Onion yellow dwarf virus and Shallot latent virus in Garlic from Several Regions in Indonesia

Nurenik

Hartono

Sulandari

et al. 2021

JPTI

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Viruses have been a problem on garlic cultivations in various countries. There are several viruses reported infecting garlic. Genera Potyvirus and Carlavirus are the most common viruses found infecting garlic. Mixed infection on garlic is often designated as a “garlic viral complex”. These viruses can be transmitted through imported garlic seeds. Therefore, it is necessary to conduct early detection of garlic seeds to prevent the epidemic of these viruses. This study aimed to detect Onion yellow dwarf virus (OYDV) and Shallot latent virus (SLV) on garlic. Garlic samples were obtained from Enrekang, Magelang, Temanggung, Tawangmangu, and Yogyakarta. Total RNA was extracted from the samples and subsequently used for RT-PCR using two pairs of specific primers SLV-F/SLV-R and OYDV-F/OYDV-R. Primary pair SLV-F/SLV-R in amplicons sized 276 bp, while OYDV-F/OYDV-R in amplicons sized 112 bp. RT-PCR results showed that OYDV was found in all samples tested in this study. Meanwhile, double infections (OYDV and SLV) were found in eight out of ten samples tested. These results indicated that double infections on garlic were common in Indonesia.

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Occurrence and Phylogenetic Analysis of Potyviruses, Carlaviruses and Allexiviruses in Garlic in Sudan

Cited by 12 publications

References 22 publications

Allexivirus: review and perspectives

Allexivirus: review and perspectives

Molecular identification, incidence and phylogenetic analysis of seven viruses infecting garlic in Ethiopia

Double Infection of Onion yellow dwarf virus and Shallot latent virus in Garlic from Several Regions in Indonesia

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