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Table 1 Summary of patient data and latency results based on 3 rd codon positions

From: Reduced evolutionary rates in HIV-1 reveal extensive latency periods among replicating lineages

Patient ID Patient type Gene L Time points No. taxa H R No. (%) latent taxa detected
         Total Plasma Reservoir FP
K-B U env 714 3 49 1 0 43 (87.8) 24 (85.7) 19 (90.5) 0.7
K-G U env 729 3 49 0 0 38 (77.6) 18 (62.1) 20 (100) 1.0
O-1 E gag 1386 3 20 0 0 16 (80.0) 2 (40.0) 14 (93.3) 0.8
O-7 E gag 1271 9 53 1 3 27 (50.9) 26 (55.3) 1 (16.7) 0.8
O-8 E gag 1298 7 101 0 0 60 (59.4) 15 (27.8) 45 (95.7) 4.7
O-9 E gag 1271 5 50 2 0 32 (64.0) 3 (15.0) 29 (97.0) 0.6
M-1 F pol 985 1 22 0 0 12 (54.5) 6 (60.0) 6 (50.0) 0.1
M-96 F pol 637 2 19 0 0 0 (0.0) 0 (0.0) 0 (0.0) 0
M-100 F pol 637 1 16 0 0 4 (25.0) 2 (40.0) 2 (18.2) 0.3
M-102 F pol 637 3 108 0 1 59 (54.6) 12 (42.8) 47 (58.8) 0.9
M-105 F pol 637 3 54 0 0 48 (87.3) 24 (82.8) 24 (92.3) 0.1
M-110 F pol 637 1 12 0 0 11 (91.7) 5 (83.3) 6 (100) 0.1
M-112 F pol 637 1 25 0 0 18 (72.0) 5 (55.6) 13 (81.3) 0.1
M-122 F pol 637 1 14 0 0 7 (50.0) 0 (0.0) 7 (87.5) 0.7
M-126 F pol 637 1 18 0 0 5 (27.8) 4 (66.7) 1 (0.08) 0.5
M-127 F pol 985 1 14 0 0 8 (57.1) 4 (100) 4 (40.0) 0.1
M-137 F pol 637 2 33 0 0 17 (51.5) 1 (0.06) 16 (94.1) 0.1
M-138 F pol 985 1 11 0 0 0 (0.0) 0 (0.0) 0 (0.0) 0
B-113 T pol 546 10 47 0 0 33 (70.2) 11 (47.8) 22 (91.7) 0.1
B-134 T pol 546 5 76 0 0 54 (71.1) 1 (14.3) 53 (76.8) 1.6
B-136 T pol 546 10 110 0 0 50 (45.5) 5 (11.4) 45 (68.2) 20
B-139 T pol 546 10 126 0 0 88 (69.8) 18 (41.9) 70 (84.3) 4.9
B-147 T pol 546 10 132 0 0 112 (84.8) 28 (65.1) 84 (94.4) 2.5
B-148 T pol 546 4 152 0 0 129 (84.9) 7 (50.0) 122 (88.4) 4.5
B-154 T pol 546 18 337 0 0 154 (45.7) 77 (35.2) 77 (65.3) 5.9
B-154 T env 306 3 64 3 0 50 (78.1) 30 (71.4) 20 (90.9) 1.3
  1. Footnotes: Patient type, U = untreated, E = elite controller, F = failed treatment, T = successful treatment; L = original sequence length of all codon positions; H = number of hypermutants removed; R = number of recombinants removed; No. taxa = number of taxa after H and R removal; FP = estimated number of false positives. Additional results in Additional file 1: Tables S1 and S2.