Table 3. Comparison of RT-qPCR, RT-dPCR and RT-PCR array assays.
Characteristics of standard curves based on the RT-qPCR assays and limit of detection (LOD) of viral targets by RT-qPCR, by RT-dPCR and RT-PCR array assays. The differences between relative quantification (by RT-qPCR) and absolute quantification (by RT-dPCR) were indicated.
| Virus | Sample | RT-qPCR (CFX96) | RT-dPCR (FLUIDIGM) | RT-PCR Array (FLUIDIGM) | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Genome | Type of sample | Slope | E | R2 | Range of detection (Ct value) | LOD a | LOD a | log10(qPCR)-log10(dPCR) | Difference between quantification type b | LOD a | log10(qPCR)-log10(PCR array) | |
| Bocavirus | DNA ss | Plasmidic DNA | -3.20 ± 0.20 | 106% | 0.966 | 16.90–37.36 | 0.20 | 0.80 | -0.60 | 0.17 | 1.00 | -0.70 |
| Parvovirus B19 | DNA ss | Plasmidic DNA | -3.05 ± 0.14 | 113% | 0.980 | 15.22–36.35 | 0.10 | 4.00 | -1.60 | -0.31 | 1.00 | -1.00 |
| Sapovirus | RNA+ ss | Transcript RNA | -3.55 ± 0.29 | 91% | 0.963 | 20.21–36.01 | 1.00E+01 | 4.00E+01 | -0.60 | 0.89 | 1.00E+02 | -1.00 |
| Hepatitis E virus | RNA+ ss | Transcript RNA | -3.49 ± 0.23 | 93% | 0.972 | 19.91–38.15 | 1.00E+01 | 4.00E+01 | -0.60 | 1.25 | 1.00E+02 | -1.00 |
| TBEV | RNA+ ss | Transcript RNA | -3.10 ± 0.21 | 110% | 0.970 | 21.66–37.54 | 1.00E+01 | 7.90E+01 | -0.90 | 1.03 | 1.00E+04 | -3.00 |
| Aichi virus | RNA+ ss | Transcript RNA | -3.34 ± 0.46 | 99% | 0.933 | 27.18–36.53 | 1.00E+03 | 7.89E+02 | 0.10 | 1.32 | 1.00E+05 | -2.00 |
| 229E | RNA+ ss | Transcript RNA | -3.05 ± 0.37 | 113% | 0.934 | 25.97–36.89 | 2.00E+01 | 3.95E+02 | -1.30 | 1.64 | 1.00E+03 | -1.70 |
| HKU1 | RNA+ ss | Transcript RNA | -3.41 ± 0.22 | 97% | 0.982 | 25.84–36.34 | 2.00E+01 | 7.90E+01 | -0.60 | 1.57 | 1.00E+04 | -2.70 |
| Cosavirus | RNA+ ss | Transcript RNA | -3.16 ± 0.27 | 107% | 0.978 | 24.26–31.41 | 1.00E+03 | 7.90E+01 | 1.10 | 1.35 | 1.00E+04 | -1.00 |
| Norovirus GGI | RNA+ ss | Transcript RNA | -3.37 ± 0.28 | 98% | 0.973 | 26.97–38.43 | 1.00E+02 | 7.90E+01 | 0.10 | 1.44 | 1.00E+03 | -1.00 |
| Norovirus GGIV | RNA+ ss | Transcript RNA | -3.53 ± 0.35 | 92% | 0.952 | 22.7–37.92 | 2.00E+03 | 7.90E+01 | 1.40 | 1.51 | 1.00E+03 | 0.30 |
| Norovirus GGII | RNA+ ss | Transcript RNA | -3.44 ± 0.32 | 95% | 0.954 | 23.01–38.53 | 1.00E+02 | 7.90E+01 | 0.10 | 1.64 | 1.00E+03 | -1.00 |
| OC43 | RNA+ ss | Transcript RNA | -3.39 ± 0.31 | 97% | 0.952 | 22.84–37.70 | 1.00E+01 | 3.95E+02 | -1.60 | 1.67 | 1.00E+04 | -3.00 |
| NL63 | RNA+ ss | Transcript RNA | -3.31 ± 0.83 | 100% | 0.851 | 28.59–36.63 | 2.00E+02 | 3.95E+02 | -0.30 | 1.97 | 1.00E+04 | -1.70 |
| Hepatitis A virus | RNA+ ss | Transcript RNA | -3.27 ± 0.46 | 102% | 0.916 | 26.03–39.80 | 1.00E+02 | 3.95E+02 | -0.60 | 2.14 | 1.00E+03 | -1.00 |
| Adenovirus 41 | DNA ds | Stool | -3.00 ± 0.16 | 115% | 0.986 | 23.43–35.08 | 1.00E+02 | 7.90E+01 | 0.10 | 1.47 | 1.00E+02 | 0.00 |
| Astrovirus | RNA+ ss | Stool | -3.65 ± 0.54 | 88% | 0.943 | 32.88–42.23 | 2.00E+02 | 7.89E+03 | -1.60 | 3.40 | 1.00E+05 | -2.70 |
| Rotavirus Wa | RNA+ ds | Cell production | -3.51 ± 0.79 | 93% | 0.812 | 22.05–36.45 | 1.00E+02 | 7.89E+02 | -0.90 | 1.56 | 1.00E+04 | -2.00 |
| MNV-1 | RNA+ ss | Cell production | -3.01 ± 0.32 | 115% | 0.947 | 28.33–38.14 | 1.00E+02 | 3.95E+02 | -0.60 | 1.95 | 1.00E+04 | -2.00 |
| Enterovirus | RNA+ ss | Cell production | -3.36 ± 0.59 | 98% | 0.894 | 25.28–36.79 | 1.00E+03 | 3.95E+02 | 0.40 | 1.97 | 1.00E+03 | 0.00 |
| Mengovirus | RNA+ ss | Cell production | -3.21 ± 0.20 | 105% | 0.983 | 26.77–38.00 | 1.00E+02 | 7.89E+02 | -0.90 | 2.05 | 1.00E+04 | -2.00 |
a LOD expressed as number of genome copies/μl of nucleic acids.
b formula = [log10(OD)-log10(digital)].