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Abstract
Double stranded RNA, isolated from 44 pooled randomly selected vines from a diseased
South African vineyard, has been used in a deep sequencing analysis to build a census
of the viral population. The dsRNA was sequenced in an unbiased manner using the sequencing-by-synthesis
technology offered by the Illumina Genome Analyzer II and yielded 837 megabases of
metagenomic sequence data. Four known viral pathogens were identified. It was found
that Grapevine leafroll-associated virus 3 (GLRaV-3) is the most prevalent species,
constituting 59% of the total reads, followed by Grapevine rupestris stem pitting-associated
virus and Grapevine virus A. Grapevine virus E, a virus not previously reported in
South African vineyards, was identified in the census. Viruses not previously identified
in grapevine were also detected. The second most prevalent virus detected was a member
of the Chrysoviridae family similar to Penicillium chrysogenum virus. Sequences aligning
to two other mycoviruses were also detected.
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