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T*
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ET
247.124 172.97 35.206 .34015 re
f
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T*
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T*
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9.2314 0 TD
()Tj
/F5 1 Tf
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[(2)-328.3(contingency)-334.1(tables)-337.9(by)-331.3(Fishers)-332.6(exact)]TJ
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T*
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T*
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0 -1.2266 TD
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T*
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[(method)-184.1(was)-179.5(applied)-182.9(to)-180.3(control)-183.6(the)-187.1(per)-179(family)-186.1(error)-181.8(rate)-183.9(\(PFER,)]TJ
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T*
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T*
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(gag)Tj
/F5 1 Tf
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[(sequence)-420.4(analysis)-408.5(of)-414.2(plasma)-413.8(virus)-412.3(from)-412.5(201)-415.8(HIV-1)]TJ
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[(vertically)-255.9(infected)-256.5(pediatric)-257.9(patients)-262.9(showed)-258.6(a)-252.4(high)-255(degree)-260.7(of)]TJ
0 -1.2203 TD
[(diversity,)-317.7(as)-310.6(can)-312(be)-314.1(observed)-316.2(in)-316.7(the)-313.6(Logos)-317.8(graphic)-315.7(represen-)]TJ
T*
[(tation)-326.3(of)-325.7(the)-326.2(alignment)-325.5(\(Fig.)-325.6(1a\).)-324.9(Numerous)-327.4(insertions,)-326.7(dele-)]TJ
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0 -1.2203 TD
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T*
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[(of)-370(conservance)-383.2(in)-373.6(amino)-373.5(acids)-373.4(was)-375.5(observed.)-376.1(To)-372.5(determine)]TJ
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[(polymorphic)-393.7(differences)-397.5(between)-395.3(subtype)-398.9(F)-390.1(and)-391.6(subtype)-398.9(B)]TJ
T*
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0 -1.2266 TD
[(composition)-436.1(with)-432.7(two)-434.8(sample)-433.1(logos.)-435(Figure)-431.6(1b)-427.6(shows)-434.1(that)]TJ
0 -1.2203 TD
[(subtype)-247.2(F)-238.4(sequences)-244.7(are)-246.7(enriched)-247(in)-240.9(certain)-247.1(amino)-240.7(acids)-246.9(at)-240.2(11)]TJ
T*
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6.7246 0 0 5.9768 422.929 362.6645 Tm
(gag)Tj
/F5 1 Tf
8.9663 0 0 8.9663 435.7983 364.1385 Tm
[(protein,)-362.8(differing)-360.8(from)-361.9(those)]TJ
-13.9357 -1.2203 TD
[(prevalent)-325.6(in)-323.1(subtype)-323.1(B)-319.1(sequences:)-329.8(N)]TJ
6.7246 0 0 5.9768 455.981 357.1653 Tm
(3)Tj
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.3254 Tc
(,A)Tj
6.7246 0 0 5.9768 471.4014 357.1653 Tm
0 Tc
(12)Tj
8.9663 0 0 8.9663 478.1479 353.1967 Tm
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(,G)Tj
6.7246 0 0 5.9768 490.0534 357.1653 Tm
0 Tc
(16)Tj
8.9663 0 0 8.9663 496.7999 353.1967 Tm
.3191 Tc
(,I)Tj
6.7246 0 0 5.9768 504.9069 357.1653 Tm
0 Tc
(21)Tj
8.9663 0 0 8.9663 511.6534 353.1967 Tm
.3191 Tc
(,P)Tj
6.7246 0 0 5.9768 522.0849 357.1653 Tm
0 Tc
(26)Tj
8.9663 0 0 8.9663 528.8314 353.1967 Tm
.3191 Tc
(,Q)Tj
6.7246 0 0 5.9768 540.9636 357.1653 Tm
0 Tc
(30)Tj
8.9663 0 0 8.9663 547.7101 353.1967 Tm
(,)Tj
-26.4171 -1.2266 TD
(K)Tj
6.7246 0 0 5.9768 317.2534 346.2235 Tm
(31)Tj
8.9663 0 0 8.9663 323.9999 342.1983 Tm
.376 Tc
(,E)Tj
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0 Tc
(33)Tj
8.9663 0 0 8.9663 341.7448 342.1983 Tm
.376 Tc
(,G)Tj
6.7246 0 0 5.9768 354.1605 346.2235 Tm
0 Tc
(34)Tj
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.376 Tc
(,A)Tj
6.7246 0 0 5.9768 373.4361 346.2235 Tm
0 Tc
(39)Tj
8.9663 0 0 8.9663 380.1826 342.1983 Tm
[(,)-376(and)-372.6(K)]TJ
6.7246 0 0 5.9768 410.6266 346.2235 Tm
(42)Tj
8.9663 0 0 8.9663 417.3731 342.1983 Tm
[(.)-369.6(Next,)-378.5(we)-374.6(looked)-376.8(for)-377(changes)-377.9(in)]TJ
-11.8807 -1.2203 TD
(p6)Tj
/F6 1 Tf
6.7246 0 0 5.9768 320.655 329.7826 Tm
(gag)Tj
/F5 1 Tf
8.9663 0 0 8.9663 333.1842 331.2566 Tm
[(that)-320(could)-319.8(be)-320.5(associated)-326.8(with)-318.8(ARV)-324.6(treatment,)-321.4(by)-318.7(com-)]TJ
-2.4912 -1.2203 TD
[(paring)-202.6(subtype)-202.9(F)-200.4(sequences)-206.8(from)-203.8(naive)-203.1(and)-201.9(ARV-experienced)]TJ
0 -1.2266 TD
[(individuals)-342.6(\(Fig.)-344.6(1c\).)-343.6(Interestingly,)-346.6(we)-343(found)-346.1(that)-339(subtype)-348.4(F)]TJ
0 -1.2203 TD
[(sequences)-358.5(from)-355.6(ARV-experienced)-363.4(patients)-357.7(were)-362.5(enriched)-354.5(in)]TJ
T*
[(leucine)-453.5(at)-448.9(position)-455.4(5)-454.8(o)0(f)-452.2(p)0(6)]TJ
/F6 1 Tf
6.7246 0 0 5.9768 420.1511 285.9023 Tm
(gag)Tj
/F5 1 Tf
8.9663 0 0 8.9663 429.8456 287.433 Tm
[(,)-451.8(while)-448.3(sequences)-459.7(from)-450.4(naive)]TJ
-13.2718 -1.2266 TD
[(patients)-281.8(were)-274(enriched)-278.6(in)-278.8(proline.)-277.3(The)-278.2(frequency)-279.4(of)-281.5(the)-275.6(P5L/)]TJ
0 -1.2203 TD
[(T/I)-476(mutation)-477(was)-476.7(0%)-475.4(in)-474.8(the)-478(naive)-475(and)-473.8(37%)-474.9(in)-474.8(the)-478(ARV-)]TJ
T*
[(experienced)-291.2(group.)-285.4(For)-286.1(subtype)-291.4(B,)-284.1(this)-286.9(mutation)-293.6(was)-287(similar)]TJ
T*
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0 -1.2266 TD
[(data)-558.9(not)-556.7(shown\))-563.1(despite)-559.6(the)-560.2(small)-561.9(number)-557.4(of)-559.7(sequences)]TJ
0 -1.2203 TD
[(available)-279.8(for)-282.1(comparison.)]TJ
1.1128 -1.2203 TD
[(Next,)-454.4(we)-456.8(analyzed)-461.7(the)-459(frequency)-456.4(of)-458.5(duplications,)-462.2(inser-)]TJ
-1.1128 -1.2267 TD
[(tions,)-368.5(and)-366.3(deletions)-371.9(in)-367.3(the)-370.5(p6)]TJ
/F6 1 Tf
6.7246 0 0 5.9768 428.8818 198.2551 Tm
(gag)Tj
/F5 1 Tf
8.9663 0 0 8.9663 441.8644 199.729 Tm
[(sequences)-371.2(to)-363.6(identify)-372.8(other)]TJ
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[(changes)-283.1(that)-288.4(could)-281.8(be)-282.5(associated)-288.8(with)-287.2(subtype)-285.1(or)-281.7(ARV)-286.7(treat-)]TJ
T*
[(ment)-330.1(\(Table)-333.3(1\).)-331.7(Of)-332.3(the)-332.5(six)-335.8(changes)-333.7(found)-333.5(in)-329.4(our)-333.6(dataset,)-335.9(de-)]TJ
0 -1.2266 TD
[(letion)-215.9(of)-218.2(the)-212.4(amino)-215.4(acid)-220.3(at)-215(position)-215.1(22,)-216.9(duplication)-217.8(of)-218.2(P37,)-212(and)]TJ
0 -1.2203 TD
[(premature)-191.1(stop)-189.3(codon)-194.6(at)-189.7(position)-196.2(50)-188.7(were)-185.5(present)-196.7(in)-190.3(almost)-188.5(all)]TJ
T*
[(subtype)-392.6(F)-396.4(sequences)-396.5(from)-393.5(the)-395.8(naive)-392.8(and)-397.9(ARV)-394.1(group,)-392.9(indi-)]TJ
0 -1.2266 TD
[(cating)-295.1(subtype-specic)-299.6(polymorphisms)-293.5(independent)-299.4(of)-294.1(ARV)]TJ
0 -1.2203 TD
[(exposure.)-549.8(In)-555.6(subtype)-550.7(B,)-549.7(these)-555.1(changes)-555(were)-552.2(observed)-550.2(in)]TJ
T*
[(030%)-284.2(of)-281.5(the)-288.3(sequences,)-285.6(and)-284.1(mainly)-283.8(in)-285.1(the)-282(ARV-experienced)]TJ
T*
[(group,)-298.1(although)-297.1(differences)-296.4(were)-299.3(not)-297.5(statistically)-299.1(signicant.)]TJ
0 -1.2266 TD
[(Of)-281.7(the)-288.3(remaining)-281.5(three)-288.9(changes,)-286(insertions)-285.9(in)-285.1(the)-288.3(KQE)-280.7(motif,)]TJ
0 -1.2203 TD
[(and)-214.6(between)-224.6(amino)-221.7(acids)-215.3(S25)-218.8(and)-220.9(P26,)-218.3(were)-223.4(present)-222(in)-215.6(011%)]TJ
T*
[(of)-275.1(the)-275.6(sequences,)-272.9(and)-277.8(mainly)-271.2(in)-272.5(the)-275.6(ARV-experienced)-281.2(group.)]TJ
0 -1.2267 TD
[(Interestingly,)-416.2(duplications)-421.4(in)-411.6(the)-421.1(PTAPP)-413.1(motifpreviously)]TJ
/F1 1 Tf
-28.0042 77.228 TD
[(VARIABILITY)-338.8(IN)]TJ
6.4556 0 0 6.4556 131.0173 749.7069 Tm
(P)Tj
8.9663 0 0 8.9663 135.3259 749.7069 Tm
(6)Tj
/F13 1 Tf
6.4556 0 0 6.4556 143.2629 749.7069 Tm
(GAG)Tj
/F1 1 Tf
8.9663 0 0 8.9663 160.5543 749.7069 Tm
[(OF)-331.2(HIV-1)-333.3(SUBTYPE)-338(F)-30943.6(1057)]TJ
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