Phylogenetic and diversity analyses of Garlic common latent virus based on the TGB and CP gene sequence

Garlic common latent virus (GarCLV, Carlavirus), in co-infection, often worsens the severity of other Allium viruses on the garlic (Allium sativum Linnaeus). The nucleotide (nt) and amino acid (aa) sequences of the TGB and CP genes were analysed to get the first deep insight into the genomic variations and population structure of GarCLV. Global recombinant-free isolates were clustered into three clades in both the nt-based phylogenetic trees of TGB and CP. The clade 3 isolates shared low similarity percentages among themselves, as well as to the clade 1 and 2 isolates. Most major aa changes in the CP were observed on its 5' and 3' ends. Clade 2 obtained the lowest S, η, k, and π values for both the TGB and CP, which indicated low variations among its isolates. Both TGB and CP have undergone a negative selection, with CP being under stronger negative pressure than TGB. Neutrality tests estimated the non-significant negative values to all clades for TGB and CP, except Tajima's D for clade 2 of the TGB. The results of the K_s*, K_st*, Z*, and Snn tests suggested that all three phylogroups were divergent to each other for both TGB and CP. The high F_st on all the clade comparisons for both TGB and CP showed a large gene flow among three clades.

Incidence of viruses in cloves and bulbils of garlic ecotypes in Croatia

In a survey on the sanitary status of garlic collection performed in 2016 at the Institute of Agriculture and Tourism in Poreč (Croatia), 24 ecotypes and cultivars were tested by DAS-ELISA test for the presence of four main garlic viruses: Garlic common latent virus (GCLV), Shallot latent virus (SLV), Leek yellow stripe virus (LYSV) and Onion yellow dwarf virus (OYDV). The least frequent virus was SLV, whereas the most frequent was LYSV. In most ecotypes the infection of cloves was lower than infection of bulbils, while for SLV we found higher infection in cloves. Total virus infection of Istrian ecotypes was lower than infection of Dalmatian ones. Total incidence of viruses in Croatian garlic material ranged from 40.6% to 100.0%, depending on ecotype. In imported cultivar ‘Rose de Lautrec’ we found no infection with SLV. A high percentage of mixed infections in garlic cloves was also found and for double infections it ranged from 69% to 88%. Infection with all tested viruses was observed in 78% cloves. The most infected combination was double infections with potyviruses LYSV+OYDV. To the best of our knowledge, this is the first report of SLV infection in garlic in Croatia.

Distribución viral en plantas de cebolla (Allium cepa L.) asintomáticas

Se estudió por medio de DAS- ELISA la distribución del Onion yellow dwarf virus (OYDV, virus del enanismo amarillo de la cebolla), Garlic common latent virus (GarCLV, virus latente común del ajo), Shallot latent v irus (SLV, virus latente del chalote), Leek yellow stripe virus (LYSV: virus de la franja amarilla del puerro), Tobacco etch virus (TEV, virus del jaspeado del tabaco) y Tomato spotted wilt virus (TSWV, virus de la marchitez manchada del jitomate) en hojas, psdeudotallo e inflorescencia de plantas de cebolla asintomáticas colectadas en diferentes épocas de 2010 en tres localidades del estado de Zacatecas, México. Se registró la presencia de esos virus en los órganos mencionados aunque resultó frecuente detectar infecciones mezcladas en hojas individuales donde las interacciones más comunes involucraban dos, tres y cuatro virus. No se encontró una tendencia que relacione la presencia viral con los órganos vegetales analizados o con la edad de las hojas; sin embargo, las infecciones con un solo virus parecen ser menos frecuentes en las hojas de edad intermedia.

Distribution of viruses in the shallot germplasm collection of the Czech Republic – Short Communication

The Czech collection of shallot (Allium cepa var. ascalonicum) genetic resources (122 accessions) was surveyed for the presence of four different viruses, i.e. Onion yellow dwarf virus, Leek yellow stripe virus, Garlic common latent virus (GCLV), and Shallot latent virus, by DAS-ELISA. The shallot seems to be resistant against GCLV because none of the tested plants was infested by this virus. Other three viruses were found with an incidence ranging from 53% to 93% for genotypes and 48% to 87% for plants. Most of the tested shallot genotypes were simultaneously infected with two or three viruses. These results were compared with neighbouring collection of garlic where all four viruses were found widespread with an incidence ranging from 65% to 83% for genotypes and 39% to 61% for plants.

Deteksi Virus pada Bawang Merah (Allium cepa var. ascalonicum) dengan Metode Dot Immuno Binding Assay

<p>Bawang merah umumnya diperbanyak secara vegetatif menggunakan umbi. Bibit unggul bawang merah ditentukan<br />antara lain oleh status kesehatan benihnya termasuk bebas dari infeksi virus. Penyakit yang disebabkan oleh virus yang bersifat<br />tular umbi merupakan salah satu kendala dalam meningkatkan produksi bawang merah. Penelitian bertujuan untuk mengetahui<br />jenis-jenis virus terbawa umbi pada beberapa varietas bawang merah yang berasal dari Jawa Tengah (Brebes) dan Jawa Barat<br />(Cirebon, Kuningan, Majalengka, Bandung), yaitu Bima Curut, Bima Brebes, Sumenep, Jawa, Batu Merah, Batu Putih, Nganjuk,<br />Timur Carwan, Ilokos, dan Jalaksana. Deteksi virus dilakukan dengan metode dot immuno binding assay (DIBA) menggunakan<br />antibodi spesifik. Deteksi virus pada umbi bawang dilakukan dengan dua teknik, yaitu deteksi langsung dari umbi dan deteksi daun<br />muda yang diambil dari umbi yang ditumbuhkan selama 30 hari. Hasil deteksi menunjukkan adanya infeksi onion yellow dwarf<br />virus (OYDV), shallot latent virus (SLV), dan garlic common latent virus (GCLV) dengan infeksi tertinggi OYDV dan SLV. Infeksi <br />virus lebih banyak terdeteksi dari sampel daun muda dibandingkan dengan dari sampel umbi. Infeksi virus tertinggi ditemukan pada <br />sampel umbi varietas Nganjuk, Batu Putih, Jawa, dan Sumenep asal Majalengka, Kuningan, dan Bandung.</p>