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Table 3 Sequence coverage of rotavirus genome segments using viral capture and random amplification

From: A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection

Sample ID GP type Genome Coverage (%) VP7 VP4 VP6 VP1 VP2 VP3 NSP1 NSP2 NSP3 NSP4 NSP5
Segment length and coverage (%)
VN-0002 G1P[8] 98.49 1062 (100) 2362 (100) 1356 (100) 3302 (100) 2690 (100) 2591 (100) 1497 (92.9) 1041 (98.3) 1104 (100) 701 (93.3) 567 (85.0)
VN-0006a G1P[8] 91.95 1012 (95.3) 2338 (99.0) 988 (72.9) 3302 (100) 2488 (92.5) 2548 (98.3) 1597 (99.1) 919 (86.8) 1104 (100) 465 (61.9) 300 (45.0)
VN-0013 G1P[8] 99.61 1062 (100) 2359 (99.9) 1332 (98.2) 3302 (100) 2690 (100) 2591 (100) 1579 (98.0) 980 (92.5) 1101 (99.7) 714 (95.1) 606 (90.9)
VN-0057 G1P[8] 97.54 978 (92.1) 2328 (98.6) 1294 (95.4) 3302 (100) 2690 (100) 2575 (99.4) 1514 (94.0) 982 (92.7) 1121 (101.5) 626 (83.4) 606 (90.9)
VN-0030 G1P[8] 95.98 912 (85.9) 2312 (97.9) 1340 (98.8) 3302 (100) 2592 (96.4) 2585 (99.8) 1519 (94.3) 814 (76.9) 1104 (100) 749 (99.7) 579 (86.8)
VN-0062 G1P[8] 91.79 919 (86.5) 2345 (99.3) 913 (67.3) 3205 (97.1) 2690 (100) 2555 (98.6) 1500 (93.1 835 (78.8) 1104 (100) 589 (78.4) 375 (56.2
VN-0324 G1P[8] 94.57 1062 (100) 2359 (99.9) 1356 (100) 3302 (100) 2686 (99.9) 2591 (100) 1328 (82.4) 563 (53.2 1049 (95.0) 714 (95.1) 537 (80.5)
VN-0365 G1P[8] 93.87 961 (90.5) 2359 (99.9) 1204 (88.8) 3302 (100) 2690 (100) 2591 (100) 1539 (95.5) 976 (92.2 1041 (94.3) 530 (70.1) 184 (27.6)
VN-0299 G1P[8] 94.44 948 (89.3) 2314 (98.0) 1181 (87.1) 3215 (97.4) 2690 (100) 2591 (100) 1393 (86.5) 962 (90.8) 1008 (91.3) 440 (58.6) 0 (0)
VN-0172a G1P[8] 88.00 956 (90.0) 2141 (90.6) 1043 (76.9) 3233 (97.9) 2629 (97.7) 2535 (97.8) 1416 (87.9) 570 (53.8) 1041 (94.3) 252 (33.6) 340 (51.0)
VN-0341a G1P[8] 82.54 1012 (95.3) 2338 (99.9) 988 (72.9) 3302 (100) 2488 (92.5) 2548 (98.3) 1009 (62.6) 741 (70.0) 943 (85.4) 72 (9.6) 0 (0)
VN-0221a UT 79.00 867 (81.6) 1945 (82.3) 950 (70.1) 3154 (95.5) 2137 (79.4) 2308 (89.1) 1483 (92.1 539 (50.9) 700 (63.4) 461 (61.4) 0 (0)
VN-0186 UT 99.07 1062 (100) 2359 (99.9) 1356 (100) 3302 (100) 2690 (100) 2591 (100) 1556 (96.6) 1059 (100) 1041 (94.3) 699 (93.1) 667 (100)
VN-0175 UT 91.01 950 (89.5) 2362 (100) 1123 (82.8) 3302 (100) 2690 (100) 2591 (100) 1350 (83.8) 717 (67.7) 1049 (95.0) 675 (89.9) 64 (9.6)
VN-0181a UT 81.64 780 (73.4) 1678 (71.0) 1170 (86.3) 3123 (94.6) 2142 (79.6) 2436 (94.0) 1418 (88.0) 827 (78.1 935 (84.7) 432 (57.5) 667 (100)
VN-0222 G2P[4] 94.80 1031 (97.1) 2362 (100) 1324 (97.6) 3302 (100) 2690 (100) 2591 (100) 1455 (90.3) 898 (84.8) 1036 (93.8) 655 (87.2 210 (31.5)
VN-0321 G2P[4] 91.40 1044 (98.3) 2330 (98.6) 1144 (84.4) 3302 (100) 2637 (98.0) 2591 (100) 1466 (91.0) 860 (81.2 1058 (95.8) 350 (46.6) 176 26.4)
VN-0326 G2P[4] 90.63 952 (89.6) 2335 (98.9) 1083 (79.9) 3302 (100) 2690 (100) 2591 (100) 1263 (78.4) 649 (61.3) 960 (87.0) 589 (78.4) 362 (54.3)
VN-0058a G26P[19] 82.00 800 (75.3) 2359 (99.9) 853 (62.9) 3302 (100) 2400 (89.2) 2490 (96.1) 304 (18.9) 890 (84.0) 709 (64.2) 641 (85.4) 331 (49.6)
VN-0132a G3P[4] 81.00 953 (89.7) 1704 (72.1) 666 (49.1) 3300 (99.9) 2731 (101.5) 2504 (96.6) 1312 (81.4) 478 (45.1 1026 (92.9) 307 (40.9) 0 (0)
VN-1221 G2P[4] 93.83 1020 (96.0) 2334 (98.8) 1356 (100) 3290 (99.6) 2596 (96.5) 2471 (95.4) 1374 (85.3) 1040 (98.2 988 (89.5) 751 (100) 191 (28.6)
VN-0074 G1P[8] 92.09 1007 (94.8) 2062 (87.3) 1356 (100) 3067 (92.9) 2735 (101.7) 2093 (80.8) 1566 (97.2 1058 (99.9) 1074 (97.3) 574 (76.4) 495 (74.2)
VN-0140 G1P[8] 94.78 990 (93.2) 2193 (92.8) 1356 (100) 3302 (100) 2649 (98.5) 2452 (94.6) 1375 (85.4) 1059 (100) 985 (89.2 565 (75.2 660 (99.0)
VN-0196 G9P[4] 91.12 997 (93.9) 2281 (96.6) 1356 (100) 3237 (98.0) 2707 (100) 1925 (74.3) 1502 (93.2 966 (91.2 1012 (91.7) 481 (64.0) 444 (66.6)
VN-3096 G1P[4] 95.51 1029 (96.9) 2334 (98.8) 1356 (100) 3302 (100) 2641 (98.2) 2505 (96.7) 1390 (86.3) 1059 (100) 966 (87.5) 478 (63.6) 662 (99.3)
VN-1604 G2P[4] 92.49 1034 (97.4) 2334 (98.8) 1356 (100) 3252 (98.5) 2619 (97.4) 2347 (90.6) 1150 (71.4) 1056 (99.7) 1005 (91.0) 749 (99.7) 260 (38.9)
  1. aSamples with low coverage chosen for resequencing using both random and specific primers (results shown in Table 5)