TABLE 3.
Pipeline validation by RT-PCR.
| Virus1 | Season2 | Virus detection3 | Samples |
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| L1 | L2 | S1 | S2 | |||
| ACLSV | SD | PCR (external) | − | − | − | − |
| Viroscope | − | − | − | − | ||
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| SS | PCR (internal) | − | − | − | − | |
| Viroscope | − | − | − | − | ||
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| ApMV | SD | PCR (external) | − | − | − | − |
| Viroscope | + | − | + | + | ||
|
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| SS | PCR (internal) | − | − | − | − | |
| Viroscope | − | − | − | − | ||
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| CGRMV | SD | PCR (external) | − | − | + | + |
| Viroscope | − | − | + | + | ||
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| SS | PCR (internal) | − | − | + | + | |
| Viroscope | − | − | + | + | ||
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| CNRMV | SD | PCR (external) | + | + | + | + |
| Viroscope | + | + | + | + | ||
|
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| SS | PCR (internal) | + | + | + | − | |
| Viroscope | + | + | + | + | ||
|
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| CVA | SD | PCR (external) | + | + | + | + |
| Viroscope | + | + | + | + | ||
|
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| SS | PCR (internal) | + | + | + | + | |
| Viroscope | + | + | + | + | ||
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| LChV−1 | SD | PCR (external) | − | − | − | + |
| Viroscope | − | − | − | + | ||
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| SS | PCR (internal) | − | − | − | + | |
| Viroscope | − | − | − | + | ||
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| LChV−2 | SD | PCR (external) | − | − | − | − |
| Viroscope | − | − | − | − | ||
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| SS | PCR (internal) | − | − | − | − | |
| Viroscope | − | − | − | − | ||
|
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| PBNSPaV | SD | PCR (external) | − | − | − | − |
| Viroscope | − | − | − | − | ||
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|
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| SS | PCR (internal) | − | − | − | − | |
| Viroscope | − | − | − | − | ||
| PDV | SD | PCR (external) | + | + | + | + |
| Viroscope | + | + | + | + | ||
|
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| SS | PCR (internal) | + | + | + | − | |
| Viroscope | + | + | − | − | ||
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| PNRSV | SD | PCR (external) | + | + | + | + |
| Viroscope | + | + | + | + | ||
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| SS | PCR (internal) | + | + | + | + | |
| Viroscope | + | − | + | + | ||
|
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| PPV | SD | PCR (external) | − | − | − | − |
| Viroscope | − | − | − | − | ||
|
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| SS | PCR (internal) | − | − | − | − | |
| Viroscope | − | − | − | − | ||
|
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| PDS-1 | Internal control | + | + | + | + | |
PDS-1, Phytoene desaturase 1, as internal control gene.
1Virus: ACLSV, apple chlorotic leaf spot virus; ApMV, apple mosaic virus; CGRMV, cherry green ring mottle virus; CNRMV, cherry necrotic rusty mottle virus; CVA, cherry virus A; LChV-1, little cherry virus 1; LChV-2, little cherry virus 2; PBNSPaV, plum bark necrosis stem pitting associated virus; PDV, prune dwarf virus; PNRSV, prunus necrotic ringspot virus; PPV, plum pox virus.
2Season: corresponding to Shoot Development (SD) and Senescence (SS) stages at spring or end of summer season, respectively.
3Virus detection by RT-PCR method corresponds to this study and external lab. NGS data was obtained by Illumina sequencing.
(−) no amplification was observed by two step RT-PCR analysis when visualized the PCR products by eletroforesis in agarose gel (3%) in TBE buffer.
(+) signal on PCR products when visualized by eletroforesis in agarose gel (3%) in TBE buffer.