High prevalence of polymorphism in HIV1 variants ... · 2 Infectology Center of Latvia 1890 Riga...
Transcript of High prevalence of polymorphism in HIV1 variants ... · 2 Infectology Center of Latvia 1890 Riga...
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High prevalence of polymorphism in HIV1 variants circulating
in Latvia
High prevalence of polymorphism in HIV1 variants circulating
in Latvia
D.Dusacka, L.Guseva, T.Kolupajeva, J.Vrublevska, I.Januskevica, J.Storozenko, B.Rozentale
Infectology Center of Latvia, Riga, Latvia
D.Dusacka, L.Guseva, T.Kolupajeva, J.Vrublevska, I.Januskevica, J.Storozenko, B.Rozentale
Infectology Center of Latvia, Riga, Latvia
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Infectology Center of Latvia
1890 Riga City Council decided to build a leper hospital in Riga. The founder initiator –surgeon, Dr.med. Adolf von Bergman.
1891-1937 Riga Leper Hospital for 40-80 patients
1941-1945 Riga Hospital for Special Infectious Diseases with 240 beds.
1945-1982 Riga Hospital for Infectious Diseases
1982 Republic’s Hospital for Clinical Infectious Diseases
1996 State Infectology Center, restructured later as state company “Infectology Center of Latvia”
2004 State agency “Infectology Center of Latvia” under the supervision of the Ministry of Health• 200 beds and more than 35 000 outpatient visits per year• Reference laboratory for microbiology including HIV/AIDS
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1987 – 2009 Cumulative number of known HIV cases is 4401, 665 patients are on AIDS stage, 428 patients died (217 – on AIDS stage)2939 patients registered at the ICL (67%)
HIV/AIDS in Latvia (by 31.03.2009)
Public Health Agency
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1990 - AZT monotherapy was started, 1996 – HAART, 336 patients are currently getting treatment2003 - Resistance testing– by hybridization-based kit (Versant HIV1 Inno-LiPa,
InnoGenetics)– since 2006 - by sequencing – based kit (TRUGENE
HIV1 BayerHealthCare-diagnostics )
2006 - Resistance testing before starting therapy and in case of treatment failures
(HIV Treatment Guidelines, ICL, Riga, 2006)
HIV/AIDS in Latvia (by 01.03.2009)
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To detect subtypes circulating in Latvia in 2006-2008to detect prevalence of HIV drug resistance associated mutations (RAMs) – in treatment – naïve– treatment- experienced patients
to analyze the susceptibility of HIV circulating in treatment – naïve and treatment-experienced patients to different drugs groups
Aim of study
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Methods: population
Data of HIV genotyping, performed in 2006-2008 for clinical reason:– 126 treatment-experienced individuals with
treatment failures– 99 treatment-naïve individuals were tested before
starting therapy Data of HIV genotyping, performed in 2007-2008 in the frame of the EHR (European HIV Resistance ) project :– 34 treatment-naïve individuals
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Characteristics of the study population
Characteristics Treatment naïve
Treatment experienced Total
Number 133 126 259Age 2 - 66 y. 1 - 79 y. 1 - 79 y.Sex 92♂ / 41♀ 80♂ / 46♀ 172♂ / 87♀Heterosexual 46 30 76MSM 11 28 39IDU 75 59 134Vertical transm. 1 7 8Unknown 0 2 2
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Methods: TRUGENE HIV-1
Sequencing of pol genes:PR codons 4-99RT codons 38-247Interpretation according to TRUGEN expert
BayerHealthCare-diagnostics
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Subtyping was performed by using Rega 2.0. data base
Phylogenetic analyses were conducted using MEGA version 4 (Tamura, Dudley, Nei, and Kumar 2007)
References sequences from the HIV sequence database at Los Alamos
RAMs (Resistance Associated Mutations) inclusion criteria for estimation of prevalence:
– IAS (International AIDS Society) mutation list (2008),that is used often in surveillance studies in Europe
– according to R.W. Shafer et al. (2007)
Methods
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Phylogenetic analyses by MEGA v.4
References sequences from the HIV sequence database at Los Alamos:
A1.RU.2003.03RU200613A1.RU.2000.RU00051A1.BY.1997.97BL006AF193275A1.UA.2000.RU98UA0116
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03AB.RU.97.KAL1532.AF19327603.AB.RU.1998.RU9800103.AB.BY.2000.98BY1044306_cpxRU.2005.04RU001
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Results of HIV subtyping
83%
15% 2%
Treatment naïve group Treatment experienced group
Most common HIV-1 subtypes in our study were subtypes A -77.2% and B – 20.8%Rare subtypes:- treatment naïve: CRF02AG, CRF03AB, CRF06CPX- treatment experienced: C
72%
26%2%
Subtype A Subtype B Others
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Transmission ways
Treatment naïve(n=133)
Treatment experienced (n=126)
HIV-1 subtypes HIV-1 subtypesA1 B others A1 B others
IDU 71 3 - 59 0 0MSM 1 7 - 2 25 -Hetero 36 7 3 22 6 2Bisexual - 3 - - 1 -Vertical 1 - - 7 - -Unknown 1 - - - 2 -Total 110/83% 20/15% 3/2% 90/71% 34/27% 2/2%
Results of HIV subtyping
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94.7%
5.3% 30%
70%
RAMs Prevalence in Treatment naïve GroupAccording to IAS
mutation list (2008)According to R.W. Shafer
et al. (2007)
Class RAMs n Predicted drug resistance
NRTI M184V 2 Lamivudine (3TC)
A62V 40 Cause only in combination with Q151M
NNRTI K103N 2
Nevirapine (NVP), Efavirence (EFV)K103N+G190S 1
K103N+P225H 1
NRTI+NNRTI M184N+K101E+G190S 1 Lamivudine (3TC) and Nevirapine (NVP), Efavirence (EFV)
MutantWild
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Prevalence of polymorphic mutations among treatment naïve patients (n=133)
RAMsA subtype
(n=110/83%)B subtype
(n=20/15%)Others
(n=3/2%)n % n % n %
Only A62V 5 4,5 1 5 0 0
Only V77I 3 3 8 40 1 2
A62V + V77I 34 31 0 0 0 0
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RAMsA subtype
(n=91/72%)B subtype
(n=33/26%)Others
(n=2/2%)
n % n % n %
Only A62V 1 1 1 3 0 0
Only V77I 5 6 10 29 0 0
A62V + V77I 23 26 0 0 0 0
Prevalence of polymorphic mutations among treatment experienced patients (n=126)
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LV.0
825.
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135.
IDU.
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532.
IDU.
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068.
HE.t.
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IDU.
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.t.A
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62V.V77 I
LV .2554.IDU.tn
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77I
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62V.V77I
LV.251 7.IDU.t.A
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LV .11 22. IDU.t.A
62 V.V 77I
L V.154 2. IDU .tn .A 62V .V7 7 I
L V .1028 .ID U .t .V 77 I
L V .10 35 . ID U . tn .A 62 V.V 77 I
L V .2 3 1 7 .H E . tn .A 6 2 .V 7 7 I
L V .2 3 6 1 .H E . tn .A 6 2 V .V 7 7 I
L V .2 6 8 2 . H E .t n. A 6 2 V
L V .2 8 3 0 .H E . tn .A 6 2 V .V 7 7 I
L V .1 1 3 9 .H E .t .A 6 2 V .V 7 7 IL V .2 6 9 3 .H E .t n .A 6 2 V .V 7 7 IL V .1 6 3 8 . ID U . tn .A 6 2 V . V 7 7 IL V .2 6 1 1 .H E . tn .A 6 2 V .V 7 7 I
L V .2 3 9 6 .N E Z . t.A 6 2 V . V 7 7 I
L V .0 7 2 8 . ID U . t.A 6 2 V .V 7 7 I
L V .1 7 7 6 .ID U .t n .A 6 2 V .V 7 7 I
L V .0 7 71 . ID U . t.A 6 2 V .V 7 7 I
L V .2 537 .H E . tn .A 62V .V7 7 I
L V.066 7. ID U .t.A 62V .V7 7I
LV.267 8.HE .tn.A6 2V .V 77I
LV .1059 .IDU .tn .A 62V .V 77 I
LV.268 5.HE .tn.A6 2V .V77I
LV .0716 .IDU .t .A 62V .V77 I
LV.2127.IDU.t.A 62V .V77I
LV.2677 .IDU .tn.A62V.V77 I
LV.1045.IDU.tn.A62V
A1.RU.2000 .RU00051
A1.UA.2000.98UA0116
A1.BY.1997.97BL006 AF193275
LV.0389.IDU.tn.A62V
LV.2227.HE.t.A62V
LV.0128.IDU.t.V77I
LV.2453.HE.tn.V77I
LV.1
080.
IDU
.tn.A
62V.
V77I
LV.2
659.
IDU.
tn.A
62V.
V77I
LV.1
022.
IDU.
tn.A
62V.
V77I
LV.2
271.
IDU.
tn.A
62V.
V77I
LV.1
160.
IDU
.t.A
62V.
V77I
LV.2
056.
IDU.
t.A62
V.V7
7ILV
.071
2.ID
U.tn
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V
LV.1
042.
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446.
IDU
.tn.V
77I
LV.1
530.
IDU.
t.V77
I
LV.0
937.
IDU.
t.A62
V.V7
7I
LV.2
308.
IDU.
t.A62
V.V7
7I
LV.0
930.
IDU.
tn.A
62V.
V77I
LV.2
656.
HE.tn
.A62
V
LV.1
129.
IDU.
t.V77
I
LV.25
82.ID
U.tn
.A62
V.V7
7I
LV.2
515.
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.A64
V.V77
I
LV.06
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LV.A003
.06.
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.V77
I
LV.0191.HE.tn
.V77I L
V .1468.IDU.tn
.A62V.V
77I
A 1.UG.98.98UG57136.A
F48 4509
A2 .CD.97.97C DKTB 48.A
F28 6238
A 2.C Y.94 .94 CY 017 41 .A F2862 37
A1 .K E.94.Q 23 17 .A F0048 85
A1 .S E .94 .S E 7253 .A F 0696 70
A 1.U G .92 .92U G 037 .U 5 1190
03 A B .R U .199 7 .K A L 15 3 2
0 3 A B .R U .9 7 .K A L 1 5 3 2 .A F 1 9 3 2 7 6
0 3 A B .B Y .2 0 0 0 .9 8 B Y 1 0 4 4 3
0 3 A B .R U .1 9 9 8 .R U 9 8 0 0 1L V .2 6 3 3 . ID U . tn .A 6 2 VL V . 2 4 3 7 . ID U . tn .V 7 7 IB .R U . 2 0 0 4 .0 4 R U 1 2 8 0 0 5
L V .0 2 4 1 . H O . t. A 6 2 V
L V . 2 0 3 1 .H O .t n .V 7 7 I
L V . 2 3 3 0 .B I. tn . V 7 7 I
B .R U .2 0 0 4 .0 4 R U 1 3 9 0 8 9
B .R U .2 0 0 4 .0 4 R U 1 3 9 0 9 5
L V .2 6 72 . ID U . tn .V 7 7 I
B .R U .20 04 .04R U 129 005
L V .04 86 .B I .t .V 77 I
LV .00 12.HO .t.V 77I
LV .0014 .H O .t .V 77 I
LV.004 2.HO .t.V7 7I
LV.005 0.HO.t.V7 7I
LV.143 2.HE.t .V77I
LV.0113.HO.tn.V77 I
LV.2705.HE.tn.V77 I
LV.2288.HO.t.V77I
LV.2563.BI.tn.V77I
LV.2010.HO.tn.V77I
LV.2269.BI.tn.V77I
06 cpx.RU.2005.04RU
001
N.CM.02.DJO
0131.AY532635
O.CM
.98.98CM
U2901.AY169812
0 . 0 5
Phylogenetic analyses of sequences with A62V and/ or V77I
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Prevalence of polymorphic mutations among treatment naïve patients
15,6
57,0
11,718,8
12,5
87,5
7,8 6,317,2
86,7
35,9
86,7
43,8
0102030405060708090
%
L10I
I13V
I15V
G16
E
K20
R
M36
I
D60
E
I62V
L63P
/T
H69
K
V77I
L89M I93L
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Most frequently occured RAMs in thetreatment experienced group
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23
64
13
5 4 5 64
0
5
10
15
20
25M
184V
A62
V
T21
5Y
K70
R
K10
3N
G19
0S
P225
H
L90
M
M46
I
V82
A
NRTI mutation NNRTI mutation PI mutation
%
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Susceptibility to drugs amongtreatment experienced patients
6%
2%
14%
59%
6% 1% 3%9%
Susceptible NRTI NNRTIPI NRTI+NNRTI NRTI+PINNRTI+PI NRTI+NNRTI+PI
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Conclusions:
1. Most common HIV-1 subtypes in our study were subtypes A -77.2% and B – 20.8%, that agree with previously published data for Latvia.
2. Prevalence of drug resistant virus in treatment-naive HIV1 infected persons was estimated as 5.3 %. These data are comparable with available data for the Europe.
3. Drug resistance was predicted in 31% of treatment experienced individuals.
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4. High frequency of polymorphism in HIV1 subtype A at protease and RT sites was detected in treatment-naïve group: A62V - 35.5%, that occurs mostly in combination with V77I (31%). Sequences with A62V and V77I combination were closely related.
5. In HIV1 subtype B A62V was detected rare (5%), combination A62V and V77I was not observed.
6. Others most frequent polymorphisms in subtypes A and B were M36I – 87,5 %, H69K -86,7 %, L89M -86,7 %, I13V- 57 %.
Conclusions: