Table 2 Concentration of rotavirus in samples at each step of the capture and amplification process
Sample ID | GP type | Initial input | Post-viral capture | Double-stranded cDNA | Random amplification | Genome sequencing | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
Ct value | Target copies | Ct value | Target copies | Ct value | Target copies | Ct value | Target copies | Total reads | RoV reads (% output) | ||
VN-0002 | G1P[8] | 13.25 | 4 × 108 | 22.75 | 7 × 105 | 28.25 | 2 × 104 | 16.3 | 5 × 107 | 1,009,250 | 951,969 (94.3) |
VN-0006 | G1P[8] | 15.28 | 1 × 108 | 24.78 | 2 × 105 | 30.28 | 4 × 103 | 18.02 | 2 × 107 | 1,102,774 | 932,674 (84.6) |
VN-0013 | G1P[8] | 14.07 | 2 × 108 | 23.57 | 4 × 105 | 29.07 | 9 × 103 | 23.18 | 5 × 105 | 1,172,366 | 1,087,933 (93.0) |
VN-0057 | G1P[8] | 10.31 | 3 × 109 | 19.81 | 5 × 106 | 25.31 | 1 × 105 | 16.92 | 4 × 107 | 1,269,282 | 910,567 (71.7) |
VN-0030 | G1P[8] | 11.66 | 1 × 109 | 21.16 | 2 × 106 | 26.66 | 5 × 104 | 18.45 | 1 × 107 | 1,064,026 | 78,217 (7.4) |
VN-0062 | G1P[8] | 8.3 | 1 × 1010 | 20.45 | 3 × 105 | 35.65 | 1 × 102 | 20.55 | 3 × 106 | 1,037,480 | 778,628 (75.1) |
VN-0324 | G1P[8] | 17.54 | 2 × 107 | 27.04 | 4 × 104 | 32.54 | 9 × 102 | 20.12 | 4 × 106 | 1,279,046 | 1,042,325 (81.5) |
VN-0365 | G1P[8] | 13.82 | 3 × 108 | 23.32 | 5 × 105 | 28.82 | 1 × 104 | 15.89 | 7 × 107 | 1,305,760 | 1,271,769 (97.4) |
VN-0299 | G1P[8] | 14.22 | 2 × 108 | 23.72 | 4 × 105 | 29.22 | 8 × 103 | 27.8 | 2 × 104 | 1,266,286 | 1,149,123 (90.8) |
VN-0172 | G1P[8] | 14.3 | 1 × 1010 | 23.80 | 3 × 105 | 29.3 | 8 × 103 | 19.63 | 6 × 106 | 1,816,574 | 1,298,619 (71.5) |
VN-0341 | G1P[8] | 12.14 | 9 × 108 | 21.64 | 1 × 106 | 27.14 | 3 × 104 | 20.61 | 3 × 106 | 1,668,438 | 1,514,101 (90.8) |
VN-0221 | UT | 18.38 | 1 × 107 | 27.88 | 2 × 104 | 33.38 | 5 × 102 | 30.63 | 3 × 103 | 1,479,948 | 336,552 (22.7) |
VN-0186 | UT | 17.7 | 2 × 107 | 27.20 | 3 × 104 | 32.7 | 8 × 102 | 24.78 | 2 × 105 | 1,459,470 | 1,440,853 (98.7) |
VN-0175 | UT | 24.25 | 2 × 105 | 33.75 | 4 × 102 | 39.25 | 9 × 101 | 29.96 | 5 × 103 | 1,306,208 | 1,138,961 (87.2) |
VN-0181 | UT | 25 | 1 × 105 | 34.50 | 2 × 102 | 40 | 5 × 101 | 30.44 | 4 × 103 | 1,285,912 | 140,328 (10.9) |
VN-0222 | G2P[4] | 18.76 | 1 × 107 | 28.26 | 2 × 104 | 33.76 | 4 × 102 | 23 | 6 × 105 | 1,289,724 | 1,204,896 (93.4) |
VN-0321 | G2P[4] | 21.62 | 1 × 106 | 31.12 | 2 × 103 | 36.62 | 5 × 101 | 26 | 7 × 104 | 1,113,180 | 724,701 (65.1) |
VN-0326 | G2P[4] | 13.5 | 4 × 108 | 23.00 | 6 × 105 | 28.5 | 1 × 104 | 27.48 | 3 × 104 | 426,240 | 347,019 (81.4) |
VN-0058 | G26P[19] | 17 | 1 × 1010 | 26.50 | 5 × 104 | 32 | 1 × 103 | 28.98 | 1 × 104 | 1,434,422 | 739,222 (51.5) |
VN-0132 | G3P[4] | 16.66 | 4 × 107 | 26.16 | 7 × 104 | 31.66 | 2 × 103 | 23.68 | 4 × 105 | 1,316,574 | 743,642 (56.5) |
VN-1221 | G2P[4] | 13.25 | 4 × 108 | 22.75 | 7 × 105 | 28.25 | 1 × 103 | 16.26 | 1 × 104 | 700,632 | 555,195 (79.2) |
VN-0074 | G1P[8] | 14.8 | 2 × 108 | 24.30 | 2 × 105 | 29.8 | 6 × 103 | 16.87 | 4 × 107 | 991,014 | 153,654 (15.5) |
VN-0140 | G1P[8] | 13.21 | 4 × 108 | 22.71 | 7 × 105 | 28.21 | 1 × 103 | 15.7 | 1 × 104 | 665,478 | 578,601 (87.0) |
VN-0196 | G9P[4] | 16.18 | 6 × 107 | 25.68 | 9 × 104 | 31.18 | 2 × 103 | 17.28 | 3 × 107 | 743,184 | 66,378 (8.9) |
VN-3096 | G1P[4] | 13.52 | 4 × 108 | 23.02 | 6 × 105 | 28.52 | 1 × 103 | 15.78 | 1 × 104 | 567,266 | 381,270 (67.2) |
VN-1604 | G2P[4] | 15.31 | 1 × 108 | 24.81 | 2 × 105 | 30.31 | 4 × 103 | 17.55 | 2 × 107 | 670,404 | 330,173 (49.3) |