Vineyards in the Atacama region in Chile were surveyed from 2007 to 2009 for the presence of viruses. This region is an important area of table grape production, supplying international markets with its fruits in the off season of the Northern Hemisphere. Reverse transcription‐polymerase chain reaction (RT‐PCR) assay was used to detect the most economically important grapevine viruses in 1000 samples, including symptomatic and asymptomatic plants. The rate of positive samples was 8.8% for Grapevine leafroll‐associated virus 1 (GLRaV‐1), 46.8% for Grapevine leafroll‐associated virus 2 (GLRaV‐2), 9.1% for Grapevine leafroll‐associated virus 3 (GLRaV‐3), 12.3% for Grapevine virus A (GVA), 30.7% for Grapevine fleck virus (GFkV) and 9.6% for Grapevine fanleaf virus (GFLV). Overall virus infection was 68.7%. DNA sequencing confirmed the identification of viruses in selected samples, and comparative analysis indicated that Chilean isolates have moderate‐to‐high molecular identities with corresponding virus reference strains selected from GenBank. The high level of viral infection observed indicates that viruses are involved in decreasing table grape production in the region. This is the first extensive virus survey performed in the Atacama region, is also the first study of genetic comparison of grapevine viruses developed in South America with a wide spectrum of viruses and isolates and provides an assessment of grapevine viruses on table grape.
Tomato ringspot virus (ToRSV) has been detected in Chile, causing economically important diseases in a wide range of hosts. A ToRSV isolate was obtained from raspberry cv Heritage (Rasp-CL) showing leaf yellowing and stunting. The complete genome of Rasp-CL was sequenced by deep sequencing. The Rasp-CL RNA1 sequence shared 97.4 % nucleotide sequence identity with divergent RNA1 of isolate Rasp1-2014, while Rasp-CL RNA2 showed high divergence from all four isolates available in the database, sharing only 63.9-72.7 % nucleotide sequence identity. This difference was mainly based on the X4 coding region, which has been reported to be a high-variability region. Moreover, based on differences in the X4 region, three Rasp-CL RNA2 variants of different length were identified in the same host. One putative recombination event was identified between the Rasp-CL and GYV-2014 X4 genes. Phylogenetic analysis suggested that ToRSV isolates with currently available sequences form three distinct groups. Our results suggest that, for an accurate phylogenetic classification of ToRSV, it is necessary to obtain sequences of both RNAs. This is the first report of a complete ToRSV genome sequence from South America.
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