Table 7. Comparison between RT-qPCR assays in detecting citrus tatter leaf virus inoculated and non-inoculated citrus plants.
| Sample | Experiment | RNA Concentration (ng/μL) |
260 / 280 Ratio |
RT-qPCR Cq Value | ||||
|---|---|---|---|---|---|---|---|---|
| COX (n = 4) |
CTLV This study Lab A1 (n = 4) |
CTLV This study Lab B2 (n = 2) |
CTLV Liu et al. 2011 (n = 4) |
CTLV Cowell et al. 2017 (n = 4) |
||||
| CTLV Isolates (True Positive) | ||||||||
| IPPN122 | TH2986-48 | 165.60 | 1.92 | 12.91 ± 0.04 | 22.16 ± 0.05 | 25.16 ± 0.03 | 27.82 ± 0.26 | 32.54 ± 0.37 |
| TL100 | 1713–1 | 86.24 | 2.24 | 14.83 ± 0.13 | 24.20 ± 0.14 | 26.66 ± 0.58 | 27.11 ± 0.23 | 21.77 ± 0.28 |
| TL100A | 94.88 | 2.07 | 15.05 ± 0.05 | 24.14 ± 0.06 | 24.92 ± 1.48 | 28.54 ± 0.20 | 22.07 ± 0.11 | |
| TL100B | 46.80 | 2.31 | 15.43 ± 0.06 | 22.55 ± 0.02 | 25.95 ± 1.35 | 26.49 ± 0.23 | 22.55 ± 0.04 | |
| TL101 | 1713–2 | 38.72 | 2.60 | 15.98 ± 0.04 | 20.80 ± 0.08 | 23.61 ± 2.39 | 25.24 ± 0.26 | 22.61 ± 0.05 |
| TL101A | 115.04 | 2.09 | 14.76 ± 0.07 | 21.85 ± 0.10 | 24.09 ± 0.00 | 26.41 ± 0.22 | 21.98 ± 0.08 | |
| TL101B | 41.76 | 2.18 | 15.48 ± 0.26 | 21.62 ± 0.18 | 23.04 ± 1.21 | 25.89 ± 0.24 | 23.00 ± 0.15 | |
| TL101-ND | 130.32 | 2.06 | 14.63 ± 0.22 | 21.78 ± 0.13 | 21.27 ± 0.00 | 26.11 ± 0.14 | 20.75 ± 0.09 | |
| TL102 | 2-8-92 | 129.76 | 2.18 | 14.77 ± 0.20 | 22.66 ± 0.27 | 25.14 ± 0.21 | 27.26 ± 0.28 | 21.90 ± 0.04 |
| TL103 | 3288–1 | 139.76 | 2.14 | 14.51 ± 0.10 | 24.71 ± 0.10 | 26.25 ± 0.23 | 28.54 ± 0.02 | - |
| 3288–2 | 161.04 | 2.27 | 14.51 ± 0.39 | 22.40 ± 0.14 | 24.18 ± 0.26 | 26.20 ± 0.48 | - | |
| TL104 | 1855–12 | 73.44 | 2.24 | 15.80 ± 0.09 | 25.62 ± 0.11 | 22.92 ± 1.22 | 28.07 ± 0.20 | - |
| 2881–1 | 104.72 | 2.05 | 15.19 ± 0.17 | 28.94 ± 0.21 | 26.44 ± 0.11 | 32.76 ± 0.40 | - | |
| 1855–13 | 148.40 | 2.15 | 14.25 ± 0.06 | 27.18 ± 0.09 | 24.64 ± 0.38 | 31.91 ± 0.28 | - | |
| TL110 | 3288–3 | 88.64 | 2.06 | 15.26 ± 0.12 | 22.90 ± 0.10 | 22.21 ± 0.06 | 31.01 ± 0.20 | 21.97 ± 0.05 |
| 3288–4 | 120.64 | 2.11 | 14.81 ± 0.09 | 20.97 ± 0.06 | 23.47 ± 0.41 | 26.89 ± 0.10 | 20.35 ± 0.08 | |
| TL111 | 3288–6 | 189.60 | 2.03 | 14.01 ± 0.07 | 24.49 ± 0.08 | 28.22 ± 0.84 | 29.87 ± 0.34 | 21.09 ± 0.15 |
| TL112 | 3291–9 | 140.08 | 2.15 | 14.64 ± 0.17 | 22.75 ± 0.10 | 24.53 ± 0.62 | 28.97 ± 0.21 | 22.66 ± 0.07 |
| TL113 | 3291–10 | 119.12 | 2.24 | 14.75 ± 0.11 | 22.42 ± 0.06 | 23.72 ± 0.13 | 27.91 ± 0.16 | 26.34 ± 0.03 |
| TL114 | 3291–11 | 197.28 | 2.11 | 13.88 ± 0.04 | 23.48 ± 0.09 | 24.54 ± 0.06 | 29.30 ± 0.17 | 24.31 ± 0.12 |
| TL115 | 3170–1 | 221.20 | 2.09 | 13.68 ± 0.18 | 23.22 ± 0.10 | 26.12 ± 0.00 | 26.57 ± 0.13 | - |
| 3170–2 | 176.00 | 2.22 | 14.06 ± 0.09 | 23.08 ± 0.06 | 27.17 ± 0.30 | 27.55 ± 0.09 | - | |
| CTLV-Non-inoculated (True Negative) | ||||||||
| Murcott Mandarin | 1005674 | 44.24 | 2.12 | 16.41 ± 0.11 | - | - | - | - |
| Fortune Mandarin | 3014073 | 57.84 | 2.01 | 16.91 ± 0.10 | - | - | - | - |
| Ponkan Mandarin | 1005802 | 28.48 | 2.34 | 17.08 ± 0.11 | - | - | - | - |
| Cleopatra Mandarin | 1005683 | 40.56 | 2.12 | 17.89 ± 0.06 | - | - | - | - |
| Parson Special Mandarin | 3014062 | 35.44 | 2.00 | 16.52 ± 0.07 | - | - | - | - |
| Tango Mandarin | 1005668 | 39.76 | 2.00 | 15.71 ± 0.12 | - | - | - | - |
| Primosole Mandarin | 1005924 | 17.36 | 2.31 | 15.92 ± 0.04 | - | - | - | - |
| Macetera Sweet Orange | 3014130 | 52.88 | 1.99 | 15.65 ± 0.10 | - | - | - | - |
| Pehrson #3 Valencia | 1005873 | 40.48 | 2.07 | 15.33 ± 0.21 | - | - | - | - |
| Pehrson #4 Valencia | 3014051 | 44.96 | 2.10 | 15.98 ± 0.02 | - | - | - | - |
| Rocky Hill Navel | 1005796 | 47.92 | 2.07 | 16.26 ± 0.07 | - | - | - | - |
| Rio Grande Navel | 1005810 | 53.44 | 2.10 | 15.64 ± 0.10 | - | - | - | - |
| Skaggs Bonanza Navel | 1005797 | 49.92 | 2.02 | 16.19 ± 0.10 | - | - | - | - |
| Autumn Gold Navel | 1005884 | 58.96 | 2.21 | 15.91 ± 0.05 | - | - | - | - |
| China S-9 Satsuma | 1005895 | 61.68 | 2.02 | 15.61 ± 0.10 | - | - | - | - |
| China S-18 Satsuma | 3015105 | 29.92 | 2.38 | 17.05 ± 0.04 | - | - | - | - |
| China S-1 Satsuma | 3015102 | 39.52 | 2.01 | 16.61 ± 0.10 | - | - | - | - |
| China S-17 Satsuma | 3014074 | 12.48 | 3.18 | 15.96 ± 0.09 | - | - | - | - |
| Minneola Tangelo | 1005678 | 56.24 | 2.20 | 17.88 ± 0.04 | - | - | - | - |
| Schaub Rough Lemon | 1005710 | 22.32 | 2.23 | 17.06 ± 0.11 | - | - | - | - |
| Marumi Kumquat | 3014132 | 28.40 | 2.40 | 16.51 ± 0.17 | - | - | - | - |
| Australian Finger Lime | 1005608 | 53.28 | 2.32 | 17.05 ± 0.08 | - | - | - | - |
| Eustis Limequat | 1005814 | 28.40 | 2.38 | 16.49 ± 0.02 | - | - | - | - |
| Valentine Pummelo | 3014144 | 47.60 | 2.34 | 16.57 ± 0.09 | - | - | - | - |
| X639 | 3014082 | 33.84 | 2.42 | 18.63 ± 0.09 | - | - | - | - |
| RT-qPCR Controls | ||||||||
| Positive | H11 / UCD* | NT | NT | 13.71 ± 0.08 | 17.96 ± 0.07 | 23.98 ± 0.37* | 24.38 ± 0.32 | 14.95 ± 0.19 |
| No Template | H9 | - | - | - | - | - | - | - |
| Negative | 861-S-1 | NT | NT | 15.45 ± 0.15 | - | - | - | - |
| RT-qPCR Performance | CTLV This study Lab A1 |
CTLV This study Lab B2 |
CTLV Liu et al. 2011 |
CTLV Cowell et al. 2017 |
||||
| Sn | 1.00 | 1.00 | 1.00 | 0.68 | ||||
| Sp | 1.00 | 1.00 | 1.00 | 1.00 | ||||
| LR+ | UN | UN | UN | UN | ||||
| LR- | 0.00 | 0.00 | 0.00 | 0.32 | ||||
| J | 1.00 | 1.00 | 1.00 | 0.68 | ||||
Abbreviations: Cq: quantitative cycle. CTLV: citrus tatter leaf virus. COX: cytochrome oxidase gene of host plants used as positive internal control [27]. NT: not tested. UN: undefined number (denominator equals 0).
1Lab A: Citrus Clonal Protection Program, University of California, Riverside, with ThermoFisher Scientific QuantStudio 12K Flex Real-Time PCR System.
2Lab B: Real-Time PCR Research & Diagnostic Core Facility, University of California, Davis, with ThermoFisher 7900HT FAST Real-time PCR system.
*Different positive control was used at Lab B.