Genome analysis and detection of a Chilean isolate of Grapevine leafroll associated virus-3

Abstract

The complete genome of the Chilean isolate Cl-766 of Grapevine leafroll-associated virus-3 (GLRaV-3) has been sequenced. This is the first genome sequence obtained from a GLRaV-3 isolate of the Southern hemisphere. The genomic RNA of 17,919 nucleotides contains 13 open reading frames (ORFs) with 5' and 3' untranslated regions (UTR) of 158 and 277 nucleotides, respectively. Comparison with NY1, the only isolate with complete genomic sequence available today, shows 97.6% nucleotide identity between the two isolates. Examination of the genome variability shows that most of the genetic diversity is concentrated in ORF1a. Three additional isolates from different geographic regions of Chile were partially sequenced as well, one which showed sequence divergence with respect to the other local and foreign isolates, indicative of different evolutionary constrains. Immunodetection systems were developed using monoclonal and polyclonal antibodies produced against the recombinant major coat protein of GLRaV-3, providing sensitive and specific detection using a triple antibody sandwich-enzyme linked immunosorbent assay (TAS-ELISA) and an immunocapture-reverse transcription-polymerase chain reaction (IC-RT-PCR) assay.

Genetic diversity analyses reveal novel recombination events in Grapevine leafroll-associated virus 3 in China

“…The coat protein gene sequences of GLRaV-3 studied were distributed in four well defined phylogenetic groups, which were supported by high bootstrap values and inter-group genetic distances. The four groups (1, 2, 3, and 5) were in accordance with those reported, previously (Fajardo et al, 2007;Engel et al, 2008;Jooste et al, 2010;Gouveia et al, 2011). Two new sub-groups (1B and 3B), were identified in the Chinese GLRaV-3 isolates for the first time.…”

“…However, information on the genetic diversity within GLRaV-3 populations is limited compared to other plant viruses. To date, nine complete and near complete genomes for isolates of GLRaV-3 are available (Ling et al, 2004;Engel et al, 2008;Maree et al, 2008;Jarugula et al, 2010;Jooste et al, 2010;Bester et al, 2012). Since GLRaV-3 has a large genome of ca.…”

Development of an immunocapture–reverse transcription–polymerase chain reaction (IC-RT-PCR) using modified viral RNA release protocol for the detection of Grapevine leafroll-associated virus 3 (GLRaV-3)

“…2B). (Engel et al 2008;Sefc et al 2000). In earlier studies of IC-RT-PCR, single buffer for virus extraction and single buffer/condition for the release of viral nucleic acid were used.…”

Rapid detection of Grapevine leafroll-associated virus type 3 using a reverse transcription loop-mediated amplification method

“…Primers for LAMP on GLRaV-3 were designed using the 6 available GLRaV-3 whole genomes; GP18 (EU259806) (Maree et al, 2008), 621 , 623, PL-20 (GQ352631, GQ352632 and GQ352633) (Jooste et al, 2010), Cl-766 (EU344893) (Engel et al, 2008) and NY-1 (AF037268) (Ling et al 1998). The genomes were aligned ClustalW in Bioedit (Version 7.0.8, Ibis Bioscience, Carlsbad) and areas with high similarity (> 90%) were used as targets.…”