1 Introduction

Input data:

  • File name: ~/share/anastasiaHIVTest/Total dataset Anastasia.csv
  • Filter on diagnosis year applied: [2009, 2018]

Adjustments:

  • Multiple Imputation using Chained Equations - MICE
    • Number of imputations: 2
    • Number of mice iterations: 2
    • Number of degrees of freedom for spline of diagnosis calendar year: 4
    • Impute reporting delays inputs: TRUE
  • Reporting Delays
    • Diagnosis start year: 2000
    • Notification end year: 2017
    • Notification end quarter (integer between 1 and 4): 1
    • Gender: TRUE
    • Transmission: TRUE
    • Migration: TRUE

Report options:

  • Correction of count of cases for reporting delay.
  • Smoothed version of calendar time.
  • CD4 plots without inter-quartile range.

2 Comparison of data by Gender

2.1 Number of diagnoses per year

Data stratified by gender is shown only for unadjusted data since there were no missing data on gender after pre-processing, which takes place before adjustments.

2.1.1 Before and after adjustments

Year of diagnosis Male [N (%)] Female [N (%)] Total [N (%)]
2009 21181 (70) 8932 (30) 30113 (100)
2010 21019 (71) 8754 (29) 29773 (100)
2011 21774 (72) 8547 (28) 30321 (100)
2012 23292 (72) 8901 (28) 32193 (100)
2013 21987 (73) 8119 (27) 30106 (100)
2014 24130 (73) 9046 (27) 33176 (100)
2015 25041 (74) 8880 (26) 33921 (100)
2016 33835 (69) 15388 (31) 49223 (100)
2017 34741 (69) 15892 (31) 50633 (100)
2018 33590 (68) 15525 (32) 49115 (100)
Total 260590 (71) 107984 (29) 368574 (100)

2.2 Median CD4 cell count (cells/µL)

2.2.1 Before adjustments

Year of diagnosis Male [Median (IQR)] Female [Median (IQR)] Overall [Median (IQR)]
2009 362 (176, 545) 334 (160, 531) 353 (170, 541)
2010 365 (180, 550) 331 (160, 525) 354 (172, 544)
2011 369 (180, 553) 343 (168, 535) 360 (176, 549)
2012 370 (180, 556) 338 (162, 535) 360 (175, 550)
2013 383 (190, 571) 353 (180, 554) 374 (187, 567)
2014 384 (191, 575) 350 (173, 549) 374 (187, 569)
2015 383 (195, 573) 357 (174, 555) 376 (189, 569)
2016 349 (171, 531) 336 (168, 525) 344 (170, 529)
2017 336 (155, 523) 323 (150, 510) 332 (154, 520)
2018 331 (151, 518) 325 (146, 510) 329 (150, 515)
Overall 360 (175, 548) 337 (161, 529) 352 (170, 542)

2.2.2 After adjustments

Year of diagnosis Male [Median (IQR)] Female [Median (IQR)]
2009 368 (188, 551) 337 (165, 533)
2010 366 (185, 550) 339 (168, 533)
2011 366 (184, 552) 343 (171, 535)
2012 372 (189, 559) 349 (177, 542)
2013 384 (200, 572) 358 (186, 553)
2014 391 (208, 578) 362 (191, 559)
2015 384 (204, 569) 357 (186, 551)
2016 368 (192, 552) 347 (175, 536)
2017 353 (179, 538) 336 (163, 521)
2018 346 (168, 533) 329 (154, 514)

3 Comparison of data by Transmission

3.1 Number of diagnoses per year

3.1.1 Before adjustments

Year of diagnosis Hetero [N (%)] IDU [N (%)] MSM [N (%)] MTCT [N (%)] Nosocomial [N (%)] Transfusion [N (%)] Missing [N (%)] Overall [N (%)]
2009 12161 (40) 3355 (11) 9413 (31) 357 (1) 55 (0) 79 (0) 4693 (16) 30113 (100)
2010 12112 (41) 3011 (10) 9824 (33) 380 (1) 28 (0) 91 (0) 4327 (15) 29773 (100)
2011 12005 (40) 3208 (11) 9920 (33) 352 (1) 67 (0) 78 (0) 4691 (15) 30321 (100)
2012 12428 (39) 3275 (10) 10919 (34) 372 (1) 104 (0) 86 (0) 5009 (16) 32193 (100)
2013 11179 (37) 2724 (9) 10815 (36) 318 (1) 24 (0) 79 (0) 4967 (16) 30106 (100)
2014 12754 (38) 2521 (8) 11515 (35) 354 (1) 42 (0) 92 (0) 5898 (18) 33176 (100)
2015 12524 (37) 2620 (8) 11647 (34) 333 (1) 28 (0) 76 (0) 6693 (20) 33921 (100)
2016 23617 (48) 6591 (13) 11240 (23) 320 (1) 38 (0) 90 (0) 7327 (15) 49223 (100)
2017 25034 (49) 6844 (14) 10697 (21) 341 (1) 33 (0) 73 (0) 7611 (15) 50633 (100)
2018 25155 (51) 6196 (13) 9868 (20) 336 (1) 19 (0) 80 (0) 7461 (15) 49115 (100)
Overall 158969 (43) 40345 (11) 105858 (29) 3463 (1) 438 (0) 824 (0) 58677 (16) 368574 (100)

3.1.2 After adjustments

Year of diagnosis Hetero [N (%)] IDU [N (%)] MSM [N (%)] MTCT [N (%)] Nosocomial [N (%)] Transfusion [N (%)] Overall [N (%)]
2009 14418 (48) 3940 (13) 11195 (37) 413 (1) 62 (0) 96 (0) 30124 (100)
2010 14303 (48) 3533 (12) 11425 (38) 411 (1) 37 (0) 116 (0) 29825 (100)
2011 14344 (47) 3819 (13) 11692 (38) 395 (1) 82 (0) 97 (0) 30429 (100)
2012 14901 (46) 3862 (12) 12976 (40) 425 (1) 113 (0) 103 (0) 32382 (100)
2013 13682 (45) 3262 (11) 13000 (43) 358 (1) 33 (0) 92 (0) 30427 (100)
2014 15824 (47) 3089 (9) 14210 (42) 413 (1) 51 (0) 114 (0) 33701 (100)
2015 16313 (47) 3388 (10) 14494 (42) 401 (1) 34 (0) 95 (0) 34725 (100)
2016 29435 (56) 8013 (15) 14331 (27) 410 (1) 44 (0) 117 (0) 52350 (100)
2017 32136 (58) 8461 (15) 14115 (26) 447 (1) 37 (0) 91 (0) 55287 (100)
2018 29413 (60) 7213 (15) 11922 (24) 443 (1) 21 (0) 103 (0) 49115 (100)
Overall 194769 (51) 48580 (13) 129361 (34) 4117 (1) 514 (0) 1025 (0) 378366 (100)

3.2 Median CD4 cell count (cells/µL)

3.2.1 Before adjustments

Year of diagnosis Hetero [Median (IQR)] IDU [Median (IQR)] MSM [Median (IQR)] MTCT [Median (IQR)] Nosocomial [Median (IQR)] Transfusion [Median (IQR)] Missing [Median (IQR)] Overall [Median (IQR)]
2009 304 (130, 496) 377 (210, 568) 413 (247, 584) 552 (252, 979) 246 (111, 481) 338 (145, 453) 241 (61, 437) 353 (170, 541)
2010 300 (130, 488) 380 (196, 553) 417 (250, 596) 620 (332, 1160) 181 (120, 320) 318 (192, 541) 224 (61, 450) 354 (172, 544)
2011 307 (131, 490) 384 (195, 588) 420 (253, 600) 550 (280, 1030) 322 (258, 470) 341 (161, 568) 248 (67, 457) 360 (176, 549)
2012 310 (130, 500) 327 (165, 534) 427 (260, 600) 592 (312, 1194) 422 (248, 547) 361 (247, 507) 224 (62, 424) 360 (175, 550)
2013 320 (144, 512) 331 (147, 540) 443 (270, 619) 612 (341, 1194) 528 (413, 673) 302 (146, 498) 270 (82, 469) 374 (187, 567)
2014 323 (144, 517) 320 (143, 503) 446 (276, 625) 580 (294, 1111) 325 (77, 677) 370 (176, 590) 252 (84, 490) 374 (187, 569)
2015 323 (146, 518) 343 (151, 536) 440 (271, 626) 681 (330, 1194) 364 (232, 574) 359 (200, 528) 306 (110, 520) 376 (189, 569)
2016 312 (144, 501) 319 (156, 502) 430 (265, 604) 590 (278, 1089) 279 (80, 621) 327 (200, 571) 298 (100, 507) 344 (170, 529)
2017 297 (128, 489) 321 (149, 504) 425 (254, 608) 589 (217, 1266) 310 (120, 540) 277 (123, 482) 287 (94, 502) 332 (154, 520)
2018 297 (122, 492) 332 (160, 505) 407 (243, 589) 527 (206, 1079) 328 (161, 508) 268 (123, 500) 302 (112, 505) 329 (150, 515)
Overall 308 (134, 500) 337 (162, 522) 429 (260, 606) 590 (277, 1138) 322 (147, 580) 328 (171, 529) 270 (83, 483) 352 (170, 542)

3.2.2 After adjustments

Year of diagnosis Hetero [Median (IQR)] IDU [Median (IQR)] MSM [Median (IQR)] MTCT [Median (IQR)] Nosocomial [Median (IQR)] Transfusion [Median (IQR)]
2009 304 (132, 495) 367 (194, 547) 414 (246, 593) 567 (277, 955) 375 (194, 594) 318 (141, 509)
2010 305 (132, 494) 360 (185, 546) 415 (248, 594) 564 (291, 1003) 384 (237, 594) 319 (152, 513)
2011 307 (133, 495) 354 (177, 546) 418 (251, 597) 565 (302, 1048) 390 (264, 593) 322 (165, 516)
2012 313 (138, 501) 349 (171, 544) 423 (256, 602) 573 (308, 1085) 392 (249, 589) 329 (178, 521)
2013 322 (147, 513) 347 (169, 542) 432 (264, 611) 591 (308, 1113) 386 (190, 584) 341 (192, 528)
2014 329 (154, 521) 345 (169, 538) 438 (272, 618) 613 (309, 1143) 374 (132, 584) 350 (197, 540)
2015 329 (155, 519) 342 (168, 532) 439 (275, 620) 633 (319, 1183) 358 (105, 594) 349 (188, 557)
2016 322 (150, 509) 339 (167, 524) 435 (273, 616) 633 (322, 1197) 335 (101, 597) 335 (167, 566)
2017 313 (141, 500) 338 (166, 518) 428 (266, 608) 597 (300, 1142) 306 (110, 568) 309 (139, 547)
2018 303 (130, 497) 338 (166, 515) 419 (255, 598) 520 (248, 1005) 273 (127, 499) 273 (110, 496)

4 Comparison of data by Migration

4.1 Number of diagnoses per year

4.1.1 Before adjustments

Year of diagnosis OTHER [N (%)] REPCOUNTRY [N (%)] Missing [N (%)] Overall [N (%)]
2009 10112 (34) 16384 (54) 3617 (12) 30113 (100)
2010 10258 (34) 15844 (53) 3671 (12) 29773 (100)
2011 9998 (33) 16705 (55) 3618 (12) 30321 (100)
2012 10491 (33) 18128 (56) 3574 (11) 32193 (100)
2013 9451 (31) 17228 (57) 3427 (11) 30106 (100)
2014 10345 (31) 17830 (54) 5001 (15) 33176 (100)
2015 10633 (31) 19306 (57) 3982 (12) 33921 (100)
2016 9907 (20) 35177 (71) 4139 (8) 49223 (100)
2017 9642 (19) 36724 (73) 4267 (8) 50633 (100)
2018 9687 (20) 35541 (72) 3887 (8) 49115 (100)
Overall 100524 (27) 228867 (62) 39183 (11) 368574 (100)

4.1.2 After adjustments

Year of diagnosis OTHER [N (%)] REPCOUNTRY [N (%)] Overall [N (%)]
2009 11539 (38) 18586 (62) 30124 (100)
2010 11772 (39) 18054 (61) 29825 (100)
2011 11396 (37) 19033 (63) 30429 (100)
2012 11942 (37) 20440 (63) 32382 (100)
2013 10953 (36) 19474 (64) 30427 (100)
2014 12504 (37) 21197 (63) 33701 (100)
2015 12277 (35) 22447 (65) 34725 (100)
2016 11651 (22) 40699 (78) 52350 (100)
2017 11699 (21) 43588 (79) 55287 (100)
2018 10602 (22) 38513 (78) 49115 (100)
Overall 116334 (31) 262032 (69) 378366 (100)

4.2 Median CD4 cell count (cells/µL)

4.2.1 Before adjustments

Year of diagnosis OTHER [Median (IQR)] REPCOUNTRY [Median (IQR)] Missing [Median (IQR)] Overall [Median (IQR)]
2009 306 (140, 495) 385 (198, 569) 388 (182, 600) 353 (170, 541)
2010 318 (144, 503) 390 (203, 575) 308 (140, 492) 354 (172, 544)
2011 322 (147, 505) 389 (200, 580) 342 (156, 513) 360 (176, 549)
2012 320 (148, 510) 389 (200, 574) 352 (155, 549) 360 (175, 550)
2013 345 (170, 535) 393 (200, 585) 375 (181, 540) 374 (187, 567)
2014 354 (171, 550) 388 (197, 579) 377 (190, 569) 374 (187, 569)
2015 371 (180, 563) 379 (196, 570) 392 (191, 610) 376 (189, 569)
2016 369 (179, 562) 337 (168, 519) 375 (186, 573) 344 (170, 529)
2017 364 (182, 566) 322 (146, 508) 388 (216, 600) 332 (154, 520)
2018 357 (177, 553) 321 (142, 506) 383 (185, 593) 329 (150, 515)
Overall 340 (162, 536) 357 (174, 544) 364 (175, 560) 352 (170, 542)

4.2.2 After adjustments

Year of diagnosis OTHER [Median (IQR)] REPCOUNTRY [Median (IQR)]
2009 320 (150, 509) 384 (202, 569)
2010 323 (151, 510) 381 (199, 568)
2011 328 (155, 512) 381 (198, 568)
2012 336 (162, 521) 385 (202, 574)
2013 348 (173, 536) 394 (211, 583)
2014 361 (185, 552) 396 (215, 584)
2015 369 (191, 561) 381 (205, 567)
2016 371 (191, 563) 359 (186, 542)
2017 367 (188, 559) 342 (169, 524)
2018 356 (183, 551) 338 (157, 521)

5 Comparison of the reported and estimated number of diagnoses per year

Diagnosis
year
Reported
 
Weight
estimated
Weight
not estimated
Estimated
unreported
[N (95% CI)]
Estimated
total
[N (95% CI)]
2009 30113 10100 20013 11 (-8, 31) 30124 (30105, 30144)
2010 29773 22792 6982 52 (-89, 194) 29825 (29684, 29967)
2011 30321 28328 1993 108 (-451, 666) 30429 (29870, 30987)
2012 32193 30378 1816 191 (-2108, 2490) 32384 (30085, 34683)
2013 30106 29624 482 321 (263, 379) 30427 (30369, 30485)
2014 33176 32786 390 525 (452, 599) 33701 (33628, 33775)
2015 33921 33685 236 804 (708, 901) 34725 (34629, 34822)
2016 49223 49168 56 3123 (2984, 3262) 52346 (52207, 52485)
2017 50633 13046 37586 4651 (4480, 4822) 55284 (55113, 55455)
2018 49115 0 49115 0 (0, 0) 49115 (49115, 49115)
Total 368574 249906 118668 9786 (6230, 13343) 378360 (374804, 381917)