Data






Patient id Time point (years) CD4 count Viral load HIV diversity (pi) AB diversity (pi) AB divergence HIV synonymous divergence HIV non-synonymous divergence HIV selection (dN/dS) AbR baseline mean sigma CDR AbR baseline mean sigma FWR
1 3.134246575 650 10921 0.962883074 31.42784051 0.025343316 0.003431918 0.009771407 0.897678174 -0.267096465 -0.626047382
1 3.597260274 638 10953 0.923537102 30.58687734 0.017401099 0.004464967 0.010485998 0.665737803 -0.424897436 -0.634765338
1 4.038356164 588 6776 1.030236894 33.34546146 0.033766187 0.010967445 0.008186044 0.587132954 0.067016208 -0.647559682
1 4.509589041 594 8282 1.664950215 30.62854942 0.03072828 0.02144313 0.013908429 0.668481704 -0.051294197 -0.497362125
1 4.939726027 504 8180 2.359579284 31.45303203 0.022937954 0.013804519 0.021766889 1.329512927 -0.259059035 -0.670731385
1 5.37260274 480 11219 1.013113077 33.06618029 0.041278368 0.02753884 0.022165023 0.892786492 0.109878325 -0.781401594
1 6.339726027 527 10369 3.336719573 33.06845236 0.03916407 0.032236368 0.034268363 1.241403925 -0.005876142 -0.580941297
1 6.761643836 530 12393 2.386692622 32.49247074 0.032470667 0.029811622 0.050361987 1.788219409 -0.035170866 -0.586913318
1 7.775342466 553 3748 1.420556338 30.9622112 0.025423737 0.029438954 0.043389359 1.537030342 -0.296303235 -0.509235234
1 8.78630137 462 3985 2.312157877 30.19324967 0.028966396 0.043628562 0.050026131 1.312444272 -0.005679978 -0.510372316
1 9.043835616 462 2513 4.980656284 32.89510597 0.024732189 0.057028981 0.042658621 1.05908435 -0.235467482 -0.683055702
1 9.632876712 400 9174 3.908967923 31.71970856 0.028645347 0.063160135 0.050499447 0.853462554 -0.207488574 -0.717251318
1 10.05205479 422 7655 4.109722179 32.99668486 0.046175176 0.070027695 0.061830139 0.943240244 -0.065406573 -0.775309244
1 10.49315068 469 6998 6.243090511 33.1681666 0.034083624 0.077590675 0.069690991 0.996994107 -0.078837026 -0.541306118
1 11 407 6351 5.241385215 31.31501605 0.034829487 0.04563295 0.049390097 1.651579772 -0.034298244 -0.573489768
1 11.46027397 354 8034 5.106067329 32.40244583 0.035162056 0.073951615 0.076666888 1.104567981 -0.13853098 -0.55418999
1 11.88219178 463 8576 NA NA NA NA NA NA NA NA
1 12.32328767 NA 6074 2.429638373 31.38306512 0.024938877 0.08366321 0.080737896 0.986944971 -0.222589876 -0.624221247
1 12.76712329 377 10732 1.717734914 32.15417293 0.024681057 0.116208691 0.0929822 0.804067117 -0.131803255 -0.659684416
1 13.43287671 361 5551 4.302853265 31.9195419 0.032727179 0.050587386 0.077495352 1.649461183 -0.02063332 -0.600621653
1 14.36986301 NA NA NA 33.55786864 0.043449362 NA NA NA 0.05229394 -0.606128091
2 2.745205479 520 8828 1.316956761 30.63020186 0.05074184 0.029787229 0.008508336 0.285900939 -0.003463204 -0.77783611
2 3.145205479 391 9934 1.148209349 33.00126006 0.026016124 0.028081865 0.021967405 0.852368239 -0.091579265 -0.685207046
2 4.024657534 567 11900 1.787466782 33.39781293 0.033760821 0.018193731 0.03095216 1.700962169 0.1012852 -0.626537558
2 4.509589041 368 7026 1.790802817 32.22950985 0.024295536 0.030678953 0.041818922 1.415825804 0.053358696 -0.641258488
2 5.005479452 351 3565 2.06066574 32.16383597 0.019586797 0.033814167 0.068577922 2.242408836 -0.186683821 -0.717242142
2 5.449315068 317 6220 3.928410266 33.22997869 0.027391557 0.047406467 0.061760019 1.369855977 0.073454088 -0.635910267
2 5.945205479 350 12279 3.785100571 33.31775315 0.033616307 0.047198098 0.069764406 1.566392472 0.131170993 -0.616544825
2 6.964383562 336 15292 2.753306128 33.09033122 0.026094255 0.049463788 0.081525156 1.76573255 -0.007704933 -0.749593583
2 7.397260274 360 6322 2.350467311 32.56348663 0.023278955 0.054751754 0.089084306 1.822180658 -0.055608864 -0.798462486
2 7.750684932 340 5625 1.121208048 31.25649906 0.016967131 0.050760733 0.094362017 2.026559287 -0.123303977 -0.689944554
2 8.210958904 176 4734 2.205531425 31.74555522 0.02578669 0.054486073 0.100099013 1.974405769 0.1269517 -0.600845896
2 8.682191781 237 9101 0.148174358 31.37915793 0.020522666 0.053611645 0.106013731 2.060367691 -0.080693979 -0.676488696
2 9.301369863 189 11593 1.584406456 32.86482228 0.035537331 0.067149577 0.105428996 1.675328744 0.176757798 -0.591647614
2 10.50410959 176 39454 1.363059734 32.67917686 0.038789594 0.083094849 0.109266258 1.367922853 0.09302012 -0.668206682
2 10.96438356 139 29596 3.054054317 32.48181141 0.025192463 0.081434576 0.108395173 1.42436792 0.056207524 -0.705078075
2 11.43287671 110 103761 3.410130119 31.48490636 0.029114285 0.088192815 0.111931043 1.381522668 0.118806226 -0.408076769
2 12.75616438 NA NA NA 31.27132389 0.024495479 NA NA NA 0.022679057 -0.892745548
3 0.265753425 468 2221 0.047449332 29.47460691 0.014242464 0.000282585 0.000207769 0 -0.357771594 -0.624391373
3 0.734246575 448 3231 0.042142137 29.36624759 0.012599267 0.013644318 0.000204011 0.015066734 -0.432444182 -0.751816309
3 1.194520548 NA 1613 0.061852863 28.63114301 0.008329784 0.013842149 0.004012099 0.292305783 -0.662083794 -0.694745704
3 2.032876712 624 2109 0.743863572 NA NA 0.026394386 0.001857208 0.061252022 NA NA
3 2.589041096 476 6664 1.129648696 30.04415296 0.012903019 0.021229446 0.008442182 0.404289707 -0.494846196 -0.875943618
3 3.471232877 409 6549 1.150376726 29.13738406 0.011304102 0.040226297 0.008682105 0.261668371 -0.549365975 -0.616802045
3 3.947945205 403 3667 0.674232164 28.82893615 0.011571662 0.030484467 0.008995857 0.328854139 -0.462970982 -0.777494664
3 4.868493151 363 4932 1.811972999 28.55817962 0.012411633 0.035614685 0.016886386 0.550634013 -0.585655447 -0.612835723
3 5.731506849 384 7303 1.27073511 29.05499991 0.018074113 0.020002489 0.022864405 1.293578705 -0.315942979 -0.799855179
3 7.189041096 299 2585 2.366997304 30.61573159 0.016332178 0.027196213 0.040154759 1.892235443 -0.494823232 -0.816107691
4 0.197260274 950 1723 NA 33.60841293 0.04552731 NA NA NA -0.03646416 -0.456966967
4 0.479452055 1116 1984 0.058345895 31.36586155 0.026122568 0.000390052 0.000269228 0.008019673 -0.194815728 -0.58890989
4 1.169863014 828 4813 0.305460468 31.80475096 0.030721244 0.026640714 0.01625455 0.608655559 -0.062243265 -0.610559828
4 2.093150685 713 20446 1.169835931 32.06802556 0.026445265 0.037462615 0.015289173 0.428712666 0.064507736 -0.486473972
4 2.495890411 707 2813 1.030319695 32.3559103 0.035076064 0.048370938 0.023252046 0.497725135 -0.011722417 -0.496007499
4 3.468493151 578 7710 1.440200983 32.16179555 0.031314085 0.041660105 0.034853006 0.892496439 -0.020633173 -0.538196995
4 4.424657534 692 6278 2.153188247 31.22325927 0.017334451 0.059304571 0.042936624 0.760283138 -0.257733638 -0.619946775
4 4.868493151 467 2944 2.356668756 33.01436461 0.038746636 0.077734484 0.051085287 0.66978532 0.080584945 -0.477979153
4 5.353424658 525 1849 0.064181983 31.83308039 0.03937085 0.105722779 0.060380244 0.552741169 -0.015193539 -0.638685016
4 6.232876712 446 4507 0.06106054 32.44487091 0.029330093 0.079297017 0.064148582 0.80084683 -0.008676885 -0.530346169
5 0.523287671 515 1324 0.065729784 30.70108964 0.015470772 0.000358183 0.000294974 0.002322547 -0.185848929 -0.613419058
5 0.6 601 1896 NA NA NA NA NA NA NA NA
5 0.753424658 575 928 0.075744809 31.10135351 0.017834998 0.013439205 0.004110904 0.309529436 -0.227352118 -0.649760713
5 0.835616438 543 683 NA 31.8797135 0.022026407 NA NA NA -0.11824099 -0.685754995
5 0.989041096 653 6803 0.06897661 33.27452404 0.042345092 0.00037037 0.004083942 0.291849159 0.07854869 -0.646449849
5 1.42739726 582 1229 0.070900994 31.31447234 0.019419985 0.000410947 0.007870202 0.58211336 -0.317151925 -0.704406397
5 1.906849315 308 8022 0.83638132 32.05157353 0.023276904 0.007828745 0.00736192 0.483504149 -0.165227933 -0.654871779
5 2.364383562 344 6489 0.987551553 32.26519443 0.037087242 0.005362904 0.012647952 0.847809328 0.284827546 -0.544443304
5 2.879452055 291 2852 0.423617759 31.84254336 0.020639913 0.001883393 0.015734042 1.239533864 -0.204547953 -0.709016857
5 3.301369863 180 3275 1.50909894 30.72423722 0.020621756 0.013333366 0.022116435 1.567827586 -0.25660189 -0.670602254
5 3.62739726 224 809 0.813276562 30.61352263 0.01548543 0.009316212 0.026738083 1.887868542 -0.463834858 -0.612809437
5 4.608219178 NA NA NA 30.84334399 0.018411575 NA NA NA -0.283366156 -0.593886894
6 0.526027397 315 24721 0.511707487 31.38320433 0.018446474 0.002336586 0.003332664 0.159777215 -0.023768399 -0.544540502
6 1.189041096 364 67552 4.928474788 31.55282593 0.025527465 0.008079277 0.00778936 0.657991561 -0.024610666 -0.658401121
6 2.117808219 374 37108 1.119284472 31.49707466 0.019014375 0.00239226 0.005379747 0.438554345 -0.144879017 -0.665534902
6 3.032876712 275 79115 2.842810086 31.39724331 0.021176967 0.009626846 0.010890642 0.65656998 -0.03721762 -0.564936377
6 3.967123288 267 53101 2.688490269 31.26711719 0.017665401 0.018947888 0.013010371 0.807814382 -0.182680237 -0.560670045
6 4.890410959 159 52693 1.552643471 32.2578296 0.028918897 0.027907844 0.021818079 0.823247489 -0.058503308 -0.57974662
6 5.791780822 159 27492 2.298211764 32.48866906 0.033700188 0.027745711 0.01793108 0.729077709 -0.22541224 -0.386937004
6 6.731506849 103 30525 2.207475167 31.12833381 0.018608727 0.031240944 0.019463641 0.695570539 -0.387771958 -0.636854853
6 7.693150685 166 37537 NA 32.19249926 0.027834685 NA NA NA -0.213171071 -0.467318014
6 8.553424658 151 72101 1.705444496 31.71038152 0.022279003 0.049153804 0.040276855 0.864631697 -0.305156594 -0.462049112
7 0.136986301 676 500000 0.293379715 32.09284542 0.010528102 0.000664597 0.000594011 0.003734733 -0.73101688 -1.059960824
7 0.410958904 1110 46498 0.230973239 31.53425013 0.011548783 0.004037112 0.000294304 0.014403802 0.010379746 -0.697697182
7 1.101369863 1082 4089 0.539997972 31.55667603 0.021379863 0.008956778 0.001603682 0.083714661 -0.096767668 -0.60761054
7 1.6 NA 6623 0.358785212 31.9525837 0.024032882 0.0001237 0.006660407 0.532233893 -0.120563275 -0.571081618
7 2.115068493 780 5267 0.826987662 31.49488659 0.0213341 0.008264741 0.007266776 0.467884766 -0.299146919 -0.686100254
7 2.597260274 726 7738 1.036456061 32.55631428 0.027946659 0.00398767 0.011934059 0.794354039 -0.163490025 -0.611848886
7 2.994520548 792 6641 0.998088226 32.46887089 0.025324223 0.012248546 0.021305264 1.431453539 -0.280161049 -0.630913488
7 3.454794521 786 7451 1.59408391 32.76187696 0.030103769 0.009402638 0.029665085 2.153319618 -0.235574029 -0.791629479
7 5.161643836 711 19298 1.731935981 31.97444057 0.023730205 0.013092254 0.033196866 2.194643323 -0.255377968 -0.747155528
7 6.679452055 515 20282 1.311545677 31.81055511 0.023215218 0.015382226 0.039512522 2.561415001 -0.24591256 -0.717611453
8 0.197260274 655 17185 0.386217015 32.36461921 0.028354276 0.004605104 0.001272277 0.111644573 0.1150189 -0.496095644
8 0.536986301 664 15093 0.880178289 33.00190024 0.035544616 0.004445306 0.009946749 0.718566603 0.005348092 -0.595519498
8 1.205479452 513 18421 1.092483752 33.16803854 0.047079004 0.000116299 0.015733547 1.059029654 0.111861614 -0.554446336
8 1.652054795 689 15697 0.59061237 33.49530454 0.043252021 0.013560605 0.018393672 1.299316641 -0.081099275 -0.5982362
8 2.112328767 439 6950 0.736573403 32.15648506 0.03515476 0.024591851 0.020361374 0.859261301 -0.201378317 -0.66762773
8 2.632876712 575 10120 0.852615333 31.80313185 0.033938679 0.023003459 0.022465792 1.09338332 -0.135891276 -0.541665281
8 3.046575342 529 9577 0.069243295 32.90410288 0.036030895 0.000391812 0.026407657 2.024548482 -0.113463966 -0.676594823
8 3.284931507 363 12231 0.0727297 32.99070303 0.037487924 0.000393498 0.033878959 2.629304762 -0.105038607 -0.61844981
8 3.723287671 418 14672 0.547998221 32.49996792 0.037083103 0.012681685 0.02472727 1.789068474 -0.103734287 -0.658924893
8 4.504109589 321 44503 1.231625208 30.5739057 0.024226973 0.007755678 0.032789105 2.333146846 -0.534094142 -0.866500498
9 0.216438356 574 2219 0.059591526 31.14313914 0.020094005 0.00032336 0.000287384 0.017517426 -0.214518501 -0.693673144
9 0.517808219 579 4375 0.069738129 30.64588308 0.019931541 0.01367974 0.007749255 0.569098678 -0.219761022 -0.530308493
9 1.230136986 503 5303 0.332578806 31.9011365 0.025078578 0.002552625 0.001577746 0.32337459 -0.155923209 -0.561981615
9 1.882191781 484 10119 0.509147706 33.06030842 0.039847582 0.023871073 0.001861089 0.084110608 -0.036450903 -0.626619999
9 2.131506849 519 28644 1.29450848 31.65403552 0.022910219 0.026081953 0.011031233 0.461718894 -0.152676729 -0.696467935
9 2.361643836 465 15767 0.072311027 32.99783229 0.036245786 0.013769473 0.011545796 0.847036098 -0.062917464 -0.636882534
9 2.8 460 26028 1.059759766 30.79606402 0.016620032 0.029650833 0.00901087 0.423789112 -0.385301148 -0.779705556
9 3.147945205 504 26391 1.261654627 30.86873656 0.016058172 0.025817715 0.00676213 0.315031046 -0.418106848 -0.808590829
9 3.509589041 423 22056 0.894860028 31.40652627 0.019681959 0.007562811 0.009155456 0.784317479 -0.363606965 -0.744407425
9 3.739726027 474 18817 0.45677677 30.87509539 0.017142556 0.025657205 0.025437307 1.029721532 -0.440396787 -0.799926598
10 0.065753425 803 41 NA 30.4010054 0.023473996 NA NA NA -0.179140771 -0.564594161
10 0.304109589 1115 40 NA 32.61520026 0.04805921 NA NA NA -0.05777739 -0.597351036
10 0.835616438 1009 40 NA 32.78095787 0.03781498 NA NA NA -0.038566237 -0.580157506
10 1.065753425 1048 40 NA 33.10481989 0.04123612 NA NA NA 0.018570575 -0.610744361
10 1.523287671 959 40 NA 30.14418838 0.014330317 NA NA NA -0.288326454 -0.596232338
10 1.98630137 944 40 NA 33.38391243 0.058418278 NA NA NA 0.036581985 -0.62942434
10 2.446575342 894 51 NA 30.4308189 0.025725826 NA NA NA -0.030031647 -0.588650623
10 2.906849315 840 74 NA 30.22814509 0.027746901 NA NA NA 0.068284531 -0.520502398
10 3.367123288 1013 2977 0.058871495 29.67158476 0.035142618 0.000353231 0.000266206 0.00261076 0.578332896 -0.247450585
10 3.82739726 859 6312 0.291702847 30.13042032 0.025710872 0.000152282 0.006274879 0.472162659 -0.148697094 -0.568715804