SnoB SnoB INI-resistance in non-B Subtypes Stefan Esser, Saleta - - PowerPoint PPT Presentation

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SnoB SnoB INI-resistance in non-B Subtypes Stefan Esser, Saleta - - PowerPoint PPT Presentation

Jun 30, 2023 674 likes •1.06k views

SnoB SnoB INI-resistance in non-B Subtypes Stefan Esser, Saleta Sierra-Aragn, Melanie Balduin, Andre Altmann, Hauke Walter, Rolf Kaiser SnoB SnoB SnoB Study Impact of HIV-1 integrase subtype-specific polymorphisms in therapy nave non-B

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SnoB SnoB

INI-resistance in non-B Subtypes

Stefan Esser, Saleta Sierra-Aragón, Melanie Balduin, Andre Altmann, Hauke Walter, Rolf Kaiser

SnoB SnoB

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SLIDE 2

SnoB SnoB

  • Dr. Stefan Esser

Department of Dermatology and Venerology, University Hospital Essen, Germany

SnoB Study

Impact of HIV-1 integrase subtype-specific polymorphisms in therapy naïve non-B infected patients

  • n the activity of Raltegravir

(RAL, MK-0518, Isentress)

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SnoB SnoB

Why an HIV Subtype Non-B study in Germany?

  • HIV Non-B subtypes spread in different regions in the world
  • Migrants from different geographic regions, countries and

continents migrate to Germany

  • Migrants in Germany do not migrate mainly from ancient colonies

like in some other European countries

  • Many migrants come from regions with high HIV prevalence
  • Germans like to travel all over the world also in high prevalence

regions

  • In Germany HIV centres have the chance to sequenze blood

samples with many different HIV-subtypes

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SLIDE 4

SnoB SnoB

SnoB Study: Design

  • National pilot multicenter cohort-study to investigate the

polymorphisms in the integrase genes of non-B-subtypes in respect to INI resistance.

  • Cooperating HIV-centres in Germany collect blood-samples
  • f 100 ART naïve HIV-positive patients with clinical

expected or known non-B subtype infection before initiating antiretroviral therapy.

  • Blood samples be sent to the investigators for sequencing

integrase genes and constructing an interpretation system.

  • Special genotypes will be additionally analyzed in

phenotypic assays.

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SLIDE 5

SnoB SnoB

Protocol: SnoB Study

  • Primary Endpoint:

– To investigate the natural polymorphisms in the integrase genes of HIV non-B subtypes

  • Secondary Endpoints:

– To compare non-B subtypes polymorphisms with HIV-1 subtype B and known genotypic integrase resistance mutations – To examine the impact of non-B subtypes polymorphisms on RAL activity in vitro – To determine whether non-B subtypes carry natural resistance to the INI Raltegravir

  • Patient Inclusion Criteria

– Therapy-naïve HIV-positive patients with known or expected non-B subtype infection independent of transmitted resistance – Signed an informed consent prior to any study procedures

  • Patient Exclusion Criteria

– Therapy-experienced HIV-positive patients

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SnoB SnoB

Einsender n B non-B Ø To do MX01, Uniklinik Düsseldorf 121 60 36 22 3

  • Med. I, Uniklinik Köln

115 65 26 14 10

  • Dr. Markus Bicke l, Frankfu rt

53 2 44 7

  • Dr. Esser, Uniklinik Essen

45 17 21 7 Klinikum Osnabrück GmbH 24 14 5 2 3

  • Dr. Oette, Krankenhau s der Augustinerinnen

13 7 1 3 2 Labor Lad emannbogen, Hamburg 13 8 5 Charité, Berlin 9 6 3

  • Prof. Rockstro h, Uniklinik Bonn

5 1 4 Uniklinik Freiburg 5 1 2 2 Poliklinik, Uniklinik München 4 1 3 Uniklink Hamburg-Eppendorf 4 4

  • Dres. Carl s und Hube r, Düsseldorf

2 2

  • Dres. Mauss, Athmann, Hegene r, Schmutz

2 1 1 Medizinische Hochschul e Hannover 2 1 1 Studien und Projekte GmbH, Hamburg 2 2

  • Dr. Arbter, Krefeld

1 1

  • Dr. Becker-Boost, Duisburg

1 1

  • Dr. Kwirant, Duisburg

1 1

  • Dr. Stechel, Köln

1 1

  • Dres. Gippert, Hatman, Quaing, Münster

1 1

  • Dres. Rei th, Gottstein, Düsseldo rf

1 1 Klinikum Dortmund gGmbH 1 1 Labor Dr . Quade, Köln 1 1 427 175 168 66 18

24 collaborating centres 24 collaborating centres

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SnoB SnoB

n = 427

Female Male Unknown Gender 113

(26.4%)

274

(64.2%)

40

(9.4%)

Median Max. Min. Unknown1 Age 36 years 77 years 0 years 22

(5.2%)

Time to analysis1 4 months 19 years 0 months 198

(46.4%)

VL 48282 5100000 <40 166

(38.9%)

CD4+-T-cell counts 320 1056 3 296

(69.3%)

Africa Asia+ Middle East

America + EU Warshau Treaty Unknown

Nationality 75

(17.6%)

13

(3.0%)

265

(62.1%)

15

(3.5%)

59

(13.8%)

1Time-span from first HIV+ diagnosis to IN analysis

(All) patients characteristics (All) patients characteristics

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SnoB SnoB

n=427 Nationality Subtype Africa Asia + Middle East

America + EU Warsaw Treaty

Unknown

Unknown

(n=84)

14

(16.7%)

  • 47

(56.0%)

2

(2.4%)

21

(25.0%)

B

(n=175)

3

(1.7%)

4

(2.3%)

148

(84.6%)

2

(1.1%)

18

(10.3%)

non-B

(n=168)

58

(34.5%)

9

(5.4%)

70

(41.7%)

11

(6.5%)

20

(11.9%)

dataset: subtypes distribution dataset: subtypes distribution

Samples: Current Status

  • 343 samples with sequence
  • 66 samples negative
  • 18 currently being processed
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SLIDE 9

SnoB SnoB

n = 175

Female Male Unknown Gender 14

(8.0%)

156

(89.1%)

5

(2.9%)

Median Max. Min. Unknown1 Age 37 years 77 years 0 months 3

(1.7%)

Time to analysis1 1 month 14 years 5 days 83

(47.4%)

VL 74488 5100000 <40 74

(42.3%)

CD4+-T-cell counts 295 989 3 108

(61.7%)

Africa Asia + Middle East America + EU Warshau Treaty Unknown Nationality 3

(1.7%)

4

(2.3%)

148

(84.6%)

2

(1.1%)

18

(10.3%)

1Time-span from first HIV+ diagnosis to IN analysis

Subtype B: patients´ characteristics Subtype B: patients´ characteristics

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SnoB SnoB

n=427 Nationality Subtype Africa Asia + Middle East

America + EU Warsaw Treaty

Unknown

Unknown

(n=84)

14

(16.7%)

  • 47

(56.0%)

2

(2.4%)

21

(25.0%)

B

(n=175)

3

(1.7%)

4

(2.3%)

148

(84.6%)

2

(1.1%)

18

(10.3%)

non-B

(n=168)

58

(34.5%)

9

(5.4%)

70

(41.7%)

11

(6.5%)

20

(11.9%)

dataset: subtypes distribution dataset: subtypes distribution

Samples: Current Status

  • 343 samples with sequence
  • 66 samples negative
  • 18 currently being processed
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SLIDE 11

SnoB SnoB

n = 168

Female Male Unknown Gender 82

(48.8%)

70

(41.7%)

16

(9.5%)

Median Max. Min. Unknown1 Age 35 years 71 years 0 months 12

(7.1%)

Time to analysis1 6 months 11 years 8 days 71

(42.3%)

VL 46100 163000 88 42

(25.0%)

CD4+-T-cell counts 309 859 8 113

(67.3%)

Africa Asia + Middle East America + EU Warshau Treaty Unknown Nationality 58

(34.5%)

9

(5.4%)

70

(41.6%)

11

(6.6%)

20

(11.9%)

1Time-span from first HIV+ diagnosis to IN analysis

Subtype Non-B: patients´ characteristics Subtype Non-B: patients´ characteristics

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SLIDE 12

SnoB SnoB

n=168

Nationality Subtype # of samples Africa Asia + Middle East America + EU Warsaw Treaty Unknown

02_AG 44

(26.2%)

20

(45.5%)

  • 11

(25.0%)

2

(4.5%)

11

(25.0%)

A 42

(25.0%)

10

(23.8%)

2

(4.8%)

18

(42.9%)

7

(16.7%)

5

(11.9%)

C 23

(13.7%)

8

(34.8%)

1

(4.3%)

11

(64.7%)

  • 2

(8.7%)

01_AE 17

(10.1%)

1

(5.9%)

5

(29.4%)

9

(60.0%)

  • D

15

(8.9%)

6

(40%)

  • 8

(60.0%)

  • G

11

(6.6%)

4

(36.4%)

1

(9.1%)

4

(36.4%)

2

(18.2%)

  • F

7

(4.2%)

3

(42.9%)

  • 4

(57.1%)

  • 06_CPX

3

(1.8%)

3

(100%)

  • 11_CPX

3

(1.8%)

1

(33.3%)

  • 1

(33.3%)

  • 1

(33.3%)

12_BF 2

(1.2%)

  • 1

(50%)

  • 1

(50%)

10_CD 1

(0.6%)

1

(100%)

  • Subtype Non-B:

subtype distribution Subtype Non-B: subtype distribution

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SnoB SnoB

Thanks to

  • the collaborating centres
  • The patients
  • MSD
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SLIDE 14

SnoB SnoB

  • Dr. Saleta Sierra-Aragón

Institute of Virology, University of Cologne, Germany

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SnoB SnoB

Hazuda et al. 2007; Lataillade et al. 2007; Malet et

  • al. 2008; Miller et al. 2008; Sichtig et al 2009

N155H Q148R/H/K Y143R

Primary mutations Secondary mutations

E138A/K G140S/A L74M T97A E92Q L74M T97A V151I Y143H G163R

INI-resistance associated mutations INI-resistance associated mutations

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SLIDE 16

SnoB SnoB

N155H Q148R/H/K Y143R

Primary mutations Secondary mutations

E138A/K G140S/A L74M T97A E92Q L74M T97A V151I Y143H G163R

Detected INI-resistance associated mutations Detected INI-resistance associated mutations

Hazuda et al. 2007; Lataillade et al. 2007; Malet et

  • al. 2008; Miller et al. 2008; Sichtig et al 2009

Secondary mutations with a prevalence of 0.3 - 2.6 %, and limited to ≤ 1 per genome.

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SnoB SnoB

Accessory mutations: Detected in cell culture under RAL / EVG. In vivo importance unknown. H51Y, T66AK, V72I, L74I, S119GPRT, T112I, F121Y, T125AK, A128T, Q146K, S147G, S153AY, M154I, K156N, E157Q, V165I, V201I, I203M, T206S, S230RN, V249I, R263K, C280Y

INI-resistance associated mutations INI-resistance associated mutations

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SLIDE 18

SnoB SnoB

Accessory mutations: Detected in cell culture under RAL / EVG. In vivo importance unknown. H51Y, T66AK, V72I, L74I, S119GPRT, T112I, F121Y, T125AK, A128T, Q146K, S147G, S153AY, M154I, K156N, E157Q, V165I, V201I, I203M, T206S, S230RN, V249I, R263K, C280Y

Detected INI-resistance associated mutations Detected INI-resistance associated mutations

accessory mutations with a prevalence of 0.6 - 73.5 %

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SnoB SnoB

B

n=175

non B

n=168 n % n % p value (two-tailed) Y143CR 1.000 Q148HKR 1.000 N155H 1.000 T66I 1.000 L74M 3 1.7 5 3.0 0.495 E92Q 1.000 T97A 2 1.1 7 4.2 0.448 E138AK 1.000 G140AS 1.000 Y143H 1 0.6 0.490 V151I 3 1.7 3 1.8 1.000 G163R 1 0.6 0.490

primary secondary

INI-resistance associated mutations: subtypes INI-resistance associated mutations: subtypes

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SnoB SnoB

B

n= 1 7 5

non B

n= 1 6 8 n % n % p value (two-tailed) H51Y 1.000 T66AK 1.000 V7 2 I 1 2 7 7 2.6 90 53.6 p < 0 .0 0 1 L7 4 I 9 5.1 3 3 1 9.6 p < 0 .0 0 1 S1 1 9 GPRT 8 3 4 7.4 48 28.6 p < 0 .0 0 1 T1 1 2 I 16 9.1 2 9 1 7.3 0 3 7 F121Y 1.000 T1 2 5 AK 57 32.6 14 4 8 5.7 p < 0 .0 0 1 A128T 2 1.2 0.239 Q146K 1.000 S147G 1.000 S153AY 1 0.6 0.490 M154I 5 2.9 3 1.8 0.724 K1 5 6 N 1 6 9 .1 1 0.6 p < 0 .0 0 1 E157Q 4 2.3 5 3.0 0.746 V165I 8 4.6 16 9.5 090 V2 0 1 I 93 53.1 15 9 9 4.6 p < 0 .0 0 1 I203M 9 5.1 8 4.8 1.000 T2 0 6 S 28 16.0 7 1 4 2.3 p < 0 .0 0 1 S2 3 0 RN 1 9 1 0.9 2 1.2 p < 0 .0 0 1 V249I 1.000 R263K 1.000 C280Y 1.000

additional

INI-resistance associated mutations: subtypes INI-resistance associated mutations: subtypes

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SnoB SnoB

INI-resistance associated mutations: subtypes INI-resistance associated mutations: subtypes

n V72I L74I T112I S119GPRT T125 K156 V201 T206 S230N Subtype n % n % n % n % n % n % n % n % n % 01_AE 17 4 23,5 1 5,9 1 5,9 2 11,8 17 100 17 100 1 5,9 02_AG 44 33 75,0 9 20,5 8 18,2 8 18,2 41 93,2 42 95,5 42 95,5 06_CPX 3 2 66,7 1 33,3 3 100 3 100 1 33,3 10_CD 1 1 100 1 100 11_CPX 3 2 66,7 1 33,3 3 100 1 33,3 1 33,3 12_BF 2 2 100 2 100 2 100 A1 40 9 22,5 19 47,5 2 5,0 21 52,5 36 90 1 2,5 32 80 4 10 1 2,5 A2 2 1 50 1 50 B 175 127 72,6 9 5,1 16 9,1 83 47,4 57 32,6 16 9,1 85 48,6 28 16,0 19 10,9 C 23 21 91,3 2 8,7 2 8,7 5 21,7 21 91,3 21 91,3 3 13,0 D 15 4 26,7 4 26,7 4 26,7 11 73,3 15 100 4 26,7 1 6,7 F1 3 3 100 2 66,7 1 33,3 3 100 3 100 2 66,7 F2 4 3 75,0 3 75,0 1 25,0 4 100 2 50 G 11 8 72,7 2 18,2 6 54,5 3 27,3 7 63,6 11 100 10 90,9 S 343 217 42 45 131 201 17 238 99 21

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SnoB SnoB

INI-resistance prediction: routine diagnostics INI-resistance prediction: routine diagnostics

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SnoB SnoB

geno2pheno[integrase] geno2pheno[integrase] INI-resistance prediction: routine diagnostics INI-resistance prediction: routine diagnostics

www.genafor.org

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SnoB SnoB

geno2pheno[integrase] geno2pheno[integrase] INI-resistance prediction: routine diagnostics INI-resistance prediction: routine diagnostics

www.genafor.org

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SnoB SnoB

geno2pheno[integrase] geno2pheno[integrase] INI-resistance prediction: routine diagnostics INI-resistance prediction: routine diagnostics

www.genafor.org

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SnoB SnoB

geno2pheno[integrase] geno2pheno[integrase] INI-resistance prediction: routine diagnostics INI-resistance prediction: routine diagnostics

www.genafor.org

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SnoB SnoB

  • mutations
  • subtype
  • alignement
  • pdf

maker

INI-resistance prediction: routine diagnostics INI-resistance prediction: routine diagnostics

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SnoB SnoB

INI-resistance prediction: routine diagnostics INI-resistance prediction: routine diagnostics

Saleta S

SnoB-0354

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SnoB SnoB

HIV grade HIV grade INI-resistance prediction: routine diagnostics INI-resistance prediction: routine diagnostics

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SnoB SnoB

HIV grade HIV grade

  • mutations
  • subtype
  • alignement

INI-resistance prediction: routine diagnostics INI-resistance prediction: routine diagnostics

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SnoB SnoB

INI resistance phenotypic assay INI resistance phenotypic assay

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SnoB SnoB

  • Cell line: CEMx-174
  • Indicator: LTR induced Luciferase activity
  • NL4-3 has been done 6 times independently
  • All others 2-3 times
  • RF are mean values

The lacking isolates did not result in sufficient activity

RAL resistance: preliminary phenotypic data RAL resistance: preliminary phenotypic data

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SnoB SnoB

RAL resistance: preliminary phenotypic data RAL resistance: preliminary phenotypic data

Strain (subtype) IC50 (nM) RF NL4-3 6.6 1 A 5.1 0.8 C 3.8 0.6 D3 20.8 3.2 F1 5.1 0.8 F2 3.4 0.5 G 18.2 2.8 H 4.9 0.7

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SnoB SnoB

Low frequence

  • f (most) INI-resistance mutations prior to RAL /

EVG administration in all subtypes. Differences in INI-resistance mutations prevalence amon g

  • subtypes. Resistance may develop differently.

Phenotypic assay for INI-resistance ongoing in collaboration with Erlangen.

Conclusions Conclusions

  • In vitro data suggest a possible influence of viral subtype
  • n INI susceptibility (D, G lower susceptibility to RAL).
  • Further improvement of geno2pheno[integrase]

.

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SnoB SnoB

All 24 centers and 427 patients MSD

  • Dept. Dermatology, University of Duisburg-Essen

Pia Schenk-Westkamp, Heidi Wiehler, Anja Bunk, Robert Jablonka, Birgit Ross, Melanie Stengl, Ulf Dittmer, Dirk Schadendorf, Stefan Esser Institute of Virology, University of Cologne Nadine Sichtig, Melanie Balduin, Eugen Schülter, Dörte Hammerschmidt, Jens Verheyen, Elena Knops, Maria Neumann-Fraune, Susanna Trapp, Eva Heger, Finja Schweizer, Claudia Müller, Angelika Hergesell, Herbert Pfister, Rolf Kaiser MPI for Informatics, Saarbrücken Andre Altmann, Alexander Thielen, Tobias Sing, Achim Buech, Oliver Sander, Alejandro Pironti, Thomas Lengauer

Acknowledgements Acknowledgements

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SnoB SnoB

Thank you !