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 |