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Table 1 Study participants’ demographic data

From: Deep sequencing of the HIV-1 polymerase gene for characterisation of cytotoxic T-lymphocyte epitopes during early and chronic disease stages

 

Baseline sequencing

Follow-up sequencing

Sample ID

Sex

Age (years)

HIV Stage

HIV VL

Total reads

HIV reads

Sequencing depth (x)

FU interval (weeks)

Total reads

HIV reads

Sequencing depth (x)

261

M

33

E

8.4 × \({10}^{7}\)

415,560

198,157

17,408

No FU

   

2504

F

24

E

3.7 × \({10}^{4}\)

396,640

288,841

25,452

2

483,620

308,253

27,268

3469

F

20

E

3.3 × \({10}^{4}\)

79,948

38,927

3139

9

181,956

104,874

9169

5041

M

23

E

2.2 × \({10}^{7}\)

146,352

108,572

10,023

No FU

   

6512

F

23

E

1.7 × \({10}^{3}\)

155,222

114,138

10,269

2

246,184

181,098

16,380

6727

F

28

E

4.8 × \({10}^{3}\)

91,218

60,365

5230

2

202,824

127,955

11,522

6638

F

28

E

1.9 × \({10}^{5}\)

167,878

108,348

9913

6

309,802

222,628

20,221

6582

F

24

E

6.2 × \({10}^{3}\)

311,276

201,897

17,355

6

857,888

602,248

49,753

9498

F

34

E

5.0 × \({10}^{5}\)

145,514

100,637

8871

No FU

   

9049

F

20

E

1.6 × \({10}^{4}\)

363,168

226,752

19,829

3

1,724,070

1,406,644

65,497

8575

F

27

E

9.3 × \({10}^{4}\)

355,040

238,087

21,126

8

   

8047

M

31

E

1.2 × \({10}^{6}\)

386,426

308,249

28,180

2

559,602

452,725

41,274

7084

F

28

E

3.3 × \({10}^{8}\)

199,022

113,257

9843

4

100,980

81,776

7168

6743

F

26

E

2.7 × \({10}^{4}\)

87,982

43,575

3928

7

223,468

149,257

78,503

6737

F

24

E

2.2 × \({10}^{3}\)

270,528

192,684

16,793

No FU

   

639

F

30

C

6.5 × \({10}^{3}\)

851,104

651,917

60,785

7

408,144

293,996

25,994

641

F

30

C

7.0 × \({10}^{4}\)

1,334,058

969,199

45,128

4

153,448

113,391

10,062

843

F

21

C

2.9 × \({10}^{4}\)

328,480

278,706

16,615

5

1,458,950

1,250,697

58,236

921

F

44

C

9.7 × \({10}^{3}\)

919,452

599,019

49,637

No FU

   

1121

F

27

C

8.0 × \({10}^{4}\)

126,868

90,889

8203

2

394,752

283,697

25,273

1213

F

36

C

3.2 × \({10}^{4}\)

279,080

228,046

14,505

No FU

   

1475

F

32

C

4.4 × \({10}^{4}\)

1,165,614

772,938

35,990

9

276,200

186,658

16,450

2340

F

22

C

1.4 × \({10}^{4}\)

3,144,374

2,260,428

119,694

No FU

   

2678

F

30

C

2.2 × \({10}^{5}\)

406,036

291,734

16,510

4

1,300,644

1,060,811

49,394

2696

F

18

C

3.9 × \({10}^{2}\)

2,426,068

1,624,274

137,760

No FU

   

3253

F

28

C

8.9 × \({10}^{4}\)

1,342,710

893,218

41,590

3

2,060,282

1,337,210

115,839

3387

F

37

C

7.9 × \({10}^{4}\)

1,769,858

1,107,226

95,026

No FU

   

3474

F

21

C

1.6 × \({10}^{4}\)

241,256

164,637

14,848

12

289,220

194,533

17,234

9986

F

28

C

9.7 × \({10}^{4}\)

187,066

116,633

9830

2

90,100

57,543

4772

3606

F

24

C

1.5 × \({10}^{4}\)

558,718

186,290

19,453

No FU

   

3869

F

32

C

2.1 × \({10}^{5}\)

1,413,006

905,554

42,165

4

1,678,940

1,181,291

98,302

3880

F

30

C

7.5 × \({10}^{3}\)

1,569,698

1,138,834

101,974

3

2,339,288

1,600,920

132,141

3910

F

33

C

2.8 × \({10}^{4}\)

929,580

715,365

33,309

3

2,858,950

1,977,216

157,648

3912

F

27

C

3.2 × \({10}^{4}\)

167,708

120,889

10,826

8

364,208

270,552

23,731

3920

F

20

C

6.6 × \({10}^{4}\)

558,718

186,290

16,933

8

741,498

533,342

44,809

3935

F

33

C

2.4 × \({10}^{5}\)

1,733,492

1,367,261

63,663

8

3,256,998

1,870,279

130,685

4351

F

35

C

2.6 × \({10}^{3}\)

1,091,330

855,414

39,830

3

114,350

71,708

5819

4198

F

19

C

1.7 × \({10}^{3}\)

1,523,160

925,214

77,596

No FU

   

5054

F

26

C

2.7 × \({10}^{4}\)

392,770

294,322

26,607

2

323,594

241,595

21,969

6380

F

25

C

1.1 × \({10}^{4}\)

354,870

254,132

23,050

4

229,160

156,127

13,011

6565

F

28

C

5.6 × \({10}^{3}\)

1,827,778

1,280,993

76,473

3

121,716

95,006

8145

6671

F

35

C

1.4 × \({10}^{4}\)

935,030

676,975

40,433

No FU

   

6649

F

32

C

2.1 × \({10}^{4}\)  

1,163,568

755,545

65,939

2

1,482,096

998,909

83,275

6640

F

37

C

3.0 × \({10}^{3}\)

376,388

248,289

21,017

5

1,471,394

1,041,570

93,224

6596

F

31

C

3.8 × \({10}^{3}\)

1,318,526

1,082,538

50,406

8

1,346,566

910,739

78,503

6509

M

36

C

1.0 × \({10}^{5}\)

655,472

520,480

23,577

No FU

   

9915

F

30

C

1.4 × \({10}^{4}\)

489,752

372,610

21,830

No FU

   

9895

F

31

C

4.8 × \({10}^{3}\)

458,108

328,446

18,433

No FU

   

9854

F

20

C

1.2 × \({10}^{4}\)

393,220

336,159

20,018

No FU

   

8828

F

27

C

4.1 × \({10}^{4}\)

1,331,066

985,767

45,900

14

94,018

59,609

5106

7959

F

40

C

1.4 × \({10}^{5}\)

538,128

453,795

23,053

No FU

   

6990

F

26

C

1.7 × \({10}^{4}\)

143,560

101,490

9056

6

179,342

136,949

12,630

  1. ID – identity, M = male; F = female; HIV = human immunodeficiency virus; E = early HIV infection; C = chronic HIV infection; VL = viral load; x = times; FU = follow-up