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contig integrated 474 reads (0.15% of reads for an average coverage of 10.1×) while the
corresponding values for the contig for #5b are 2185 reads (2.4% of total reads) for a
coverage of 47.2×. The two GRGV contigs showed 91.4% nt sequence identity between
themselves and the closest GRGV full genome sequence in GenBank, MZ451067 from Canada,
shared respectively 98.9 and 91.6% nt identity with them. The near complete genome contigs
were deposited in GenBank (ON603917 and ON603918). Simultaneously, two near-full-length
genomic contigs for GRVFV were identified from #5b and also deposited in GenBank (ON603919
and ON603920). These contigs show 84.4% nt identity to each other and were respectively
assembled from 4,643 (5.2% of total reads) and 5,326 reads (6.0% of total reads) for respective
average coverages of 102.3× and 117.3×. The closest full GRVFV genome in GenBank is
MZ027155 from the United States, with 84.3 to 85.3% nt identity. Confirmation of the presence
of GRGV and GRVFV in the doubly infected #5b was achieved by specific RT-PCR assays. A
published assay (Beuve et al. 2015) was used for GRGV and primers GRVFV-Cp-F 5′
-AAYCCTGTCACHCTCCACTG-3′ and GRVFV-Cp-R 5′-TTCATGGTGGTGCCDGTGAG-3′ (Tm 55°C)
were used for GRVFV. The obtained 447-nt GRGV amplicon showed a single difference with the
HTS contig while the 218-nt GRVFV amplicon showed three mutations as compared to one of
the HTS contigs. The different grapevines had initially been sampled because they showed
relatively poor and stunted growth, but besides GRVFV and/or GRGV the HTS analysis
indicated that they were also infected by hop stunt viroid, grapevine yellow speckle viroid 1,
grapevine rupestris stem pitting virus, a novel nepovirus (#4), and grapevine leafroll-associated
virus 2 and grapevine Pinot gris virus (#5b) so the results reported here do not shed novel
light on the potential pathogenicity of GRGV or GRVFV. To the best of our knowledge, this is
the first report of GRGV and GRVFV in grapevines in Portugal.
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corresponding values for the contig for #5b are 2185 reads (2.4% of total reads) for a
coverage of 47.2×. The two GRGV contigs showed 91.4% nt sequence identity between
themselves and the closest GRGV full genome sequence in GenBank, MZ451067 from Canada,
shared respectively 98.9 and 91.6% nt identity with them. The near complete genome contigs
were deposited in GenBank (ON603917 and ON603918). Simultaneously, two near-full-length
genomic contigs for GRVFV were identified from #5b and also deposited in GenBank (ON603919
and ON603920). These contigs show 84.4% nt identity to each other and were respectively
assembled from 4,643 (5.2% of total reads) and 5,326 reads (6.0% of total reads) for respective
average coverages of 102.3× and 117.3×. The closest full GRVFV genome in GenBank is
MZ027155 from the United States, with 84.3 to 85.3% nt identity. Confirmation of the presence
of GRGV and GRVFV in the doubly infected #5b was achieved by specific RT-PCR assays. A
published assay (Beuve et al. 2015) was used for GRGV and primers GRVFV-Cp-F 5′
-AAYCCTGTCACHCTCCACTG-3′ and GRVFV-Cp-R 5′-TTCATGGTGGTGCCDGTGAG-3′ (Tm 55°C)
were used for GRVFV. The obtained 447-nt GRGV amplicon showed a single difference with the
HTS contig while the 218-nt GRVFV amplicon showed three mutations as compared to one of
the HTS contigs. The different grapevines had initially been sampled because they showed
relatively poor and stunted growth, but besides GRVFV and/or GRGV the HTS analysis
indicated that they were also infected by hop stunt viroid, grapevine yellow speckle viroid 1,
grapevine rupestris stem pitting virus, a novel nepovirus (#4), and grapevine leafroll-associated
virus 2 and grapevine Pinot gris virus (#5b) so the results reported here do not shed novel
light on the potential pathogenicity of GRGV or GRVFV. To the best of our knowledge, this is
the first report of GRGV and GRVFV in grapevines in Portugal.
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