First Report of Shallot latent virus in Garlic in Brazil.

Abstract

Garlic (Allium sativum L.) can be infected by several viruses of the genera Allexivirus, Carlavirus, and Potyvirus (3). Garlic common latent virus (GarCLV) and Shallot latent virus (SLV) are the most important Carlavirus species infecting garlic, but only GarCLV has been described on garlic in Brazil. Seven hundred thirty-one samples of garlic showing mosaic symptoms and chlorotic streaking were collected from the states of São Paulo (São Manuel), Minas Gerais (Santa Juliana and São Gotardo), Goiás (Campo Alegre and Ipameri), and Paraná (Guarapuava and Piraquara) from April 2008 to July 2009 and analyzed by double-antibody sandwich (DAS)-ELISA for the presence of GarCLV and SLV using specific antiserum for SLV and GarCLV according to the manufacturer's protocol (Agdia Inc., Elkhart, IN). Cultivars sampled were Caçador, Chonan, Ito, Jonas, Quitéria, and Tropical. Fifty-five samples (7.5% of 731) tested positive for GarCLV, and none of the samples tested positive for SLV. Total RNA was extracted (2) from 15 samples that represented different states of production and used with primers SLV 7044 (5'-CTTTTGGTTCACTTTAGG-3') and SLV 8004 (5'-GCACGCAATAGTCTACGG-3'), designed in this study, to detect SLV in a one-step reverse transcription (RT)-PCR assay. Only 3 of the 15 samples, two from São Paulo and one from Paraná State, produced a 960-bp fragment covering the putative coat protein gene (ORF 5) (1) of SLV. The amplicons of the three isolates were sequenced. A nucleotide sequence identity of 91 to 92% was detected in comparison with two strains of SLV (GenBank Accession Nos. AB004567 and DQ520093), indicating the presence of two isolates of SLV in São Manuel (São Paulo State) and one in Piraquara, Paraná State (submitted to GenBank as Accession Nos. GU120176, HQ128602, and GU120175, respectively). To confirm identity of the virus, another pair of primers was constructed and tested (SLV 6737: 5'-YCCSGCCARGAAYTTCCC-3', and SLV 7060: 5'-TTAGAGCGCTGTWAACC-3'), from which a 340-bp fragment covering a portion of TGB2 (ORF 3) and TGB3 (ORF 4) (1) was amplified using the two isolates from São Paulo (GenBank Accession Nos. HQ123181 and HQ123182, respectively). The amplicon sequences shared 87% identity with that of an SLV isolate (Accession No. AJ292226), which confirmed the presence of SLV. The low titer of SLV in garlic might account for the false negative results by DAS-ELISA. The source of cultivated garlic bulbs in these regions of Brazil is unknown. Garlic cloves have been cultivated in São Manuel for approximately 15 years, indicating that SLV may have been present in Brazil for many years. To our knowledge, this is the first report of SLV in Brazil.