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Institute of Human Virology Division of Epidemiology and Prevention. Development of a Database for Caribbean HIV Molecular Diversity: Relevance to HIV Vaccines & Therapy. Farley R. Cleghorn MD, MPH Division of Epidemiology and Prevention Institute of Human Virology University of Maryland

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Development of a database for caribbean hiv molecular diversity relevance to hiv vaccines therapy l.jpg

Institute of Human Virology

Division of Epidemiology and Prevention

Development of a Database for Caribbean HIV Molecular Diversity:Relevance to HIV Vaccines & Therapy

Farley R. Cleghorn MD, MPH

Division of Epidemiology and Prevention

Institute of Human Virology

University of Maryland

March 6, 2004

Santo Domingo

Cleghorn 20020349


Slide2 l.jpg

A, B, AB recombinant

CRF02_AG, other recombinants

A

Insufficient data

B

CRF01_AE, B

C

B, BF recombinant

F,G,H,J,K,CRF01 other recombinants

D

B, C, BC recombinant

GLOBAL DISTRIBUTION OF HIV-1 SUBTYPES AND RECOMBINANTS

F. McCutchan & J. Carr, 2003


Slide3 l.jpg

Institute of Human Virology

Division of Epidemiology and Prevention

A Distinctive Clade B HIV-1 is Heterosexually Transmitted in Trinidad & Tobago:Epidemiologic Characterization of Trinidad Isolates Characterized for Phylogenetic Analysis

N.A. = North American; STD = Sexually Transmitted Disease; GUD = Genital Ulcerative Disease

Cleghorn et al, Proc Natl Acad Sci USA, 27 (19); 10532-10537, 2000.


Slide4 l.jpg

A Distinctive Clade B HIV-1 is Heterosexually Transmitted in Trinidad & Tobago:

Comparison of Trinidad Consensus V3 loop sequence to Prototypic B

Results I

Institute of Human Virology

Division of Epidemiology and Prevention

B-subtype CTRPNNNTRK SIHIGPGRAF YTTGEIIGDI RQAHC

RH0011 .......... .......Q.. .-........ .....

QZ2226 .........R ..P.....V. .-........ .....

QZ2269 .......... .V.....K.. .-........ .....

QZ2291 .......... ...L...A.. F-........ .....

QZ2313 .......... G.P....SV. .-........ .....

QZ2432 .......... G......G.. .T..D..... .K...

QZ2551 .I........ ........T. .-........ .....

QZ2704 .......... .......SV. .-........ .....

QZ4734 .......... ..N....... .-........ .....

QZ6698 ....S....R ...F...A.. .-........ .....

QH0016 .......... .....A.K.L .-........ .....

QH0020 .......... ..P....SV. .-........ .....

QH0060 .........R ...M...KV. .-........ .....

QH0065 .......... G.T....SV. .-........ .....

QH0132 .........R G..M...K.Y F-........ .....

QH0136 .........R D.T.....V. .-........ .....

QH0515 .......... ....EA.K.L .-........ .....

QH0550 .........R D.A....KV. .-......N. .....

QH0605 .......... G......KV. C-....V... .....

QH0679 .......... .......... .A......N. .....

QH0692 ....G..... .......... .A..D..... .....

QH0705 .......... ...L.A...L .-........ .....

QH0788 .........E ..N....... .Y........ .....

QH0791 .......... G.T.....VS .-....V... ..V..

QH0850 .......... ...L.A.K.L .-........ .....

QH0864 .........R ...M...K.L F-........ .....

QH0865 .......... ..P....... .A......N. .....

QH0908 .........R GVT.....V. .-...VT... .....

QH0944 .I........ .......... .-..D..... .....

QH1116 .......... ...M.....L .-........ .....

QH1420 .......... ...L.A...L .-........ .....

Trinidad .......... .......... .-........ .....

Consensus

Cleghorn et al, Proc Natl Acad Sci USA, 27 (19); 10532-10537, 2000.


Slide5 l.jpg

Institute of Human Virology

Division of Epidemiology and Prevention

A Distinctive Clade B HIV-1 is Heterosexually Transmitted in Trinidad & Tobago: Mean Pairwise Genetic Distances of Trinidad HIV-1 “Signature” C2-V5 Sequences by Year

Only those samples with the threonine deletion (N=25) were used for this analysis, which

calculates a summary measure per annum of inter-case sequence variability.

Cleghorn et al, Proc Natl Acad Sci USA, 27 (19); 10532-10537, 2000.


Slide6 l.jpg

Institute of Human Virology

Division of Epidemiology and Prevention

A Distinctive Clade B HIV-1 is Heterosexually Transmitted in Trinidad & Tobago:

HIV-1 in Trinidad: A significant subcluster within the B subtype

QH0132

QH0791

QZ6698

QH0908

QH0944

QZ2291

QH0020

QZ4734

QH0065

QZ2704

RH0011

QZ2313

QH1420

QH0550

QH0705

QH0864

QZ2551

QZ2226

QH0850

QZ2269

QH0136

QH0016

QH0605

QH0515

93

QH0060

QH1116

QH0865

QH0679

QH0788

QH0692

Trinidad

QZ2432

Trinidad*

100

Thailand

SFMHS

Envelope, C2-V5

.10

Cleghorn et al, Proc Natl Acad Sci USA, 27 (19); 10532-10537, 2000.


Slide7 l.jpg

A

E

C

A_Q2317

A_UG037

AE_CAR402

AE_CM240

C_C2220

C_BR025

G

G_HH8793

100

F

G_SE6165

100

F_F9363

100

F_BZ126

100

J

J_SE9280

100

100

J_SE9173

D

100

D_ELI

B_OYI

D_NDK

B_SF2

100

B_MN

QH0692

86

100

QH0788

QH0865

QZ4734

100

QH0550

QH0679

QH0060

QH0908

QH0605

QH1420

QH0016

Whole Envelope

QH1116

QH0864

QH0850

QH0136

QH0944

QH0515

QH0132

QH0065

QH0705

QH0020

B

QH0791

Institute of Human Virology

Division of Epidemiology and Prevention

.10

A Distinctive Clade B HIV-1 is Heterosexually Transmitted in Trinidad & Tobago:Phylogenetic Analysis of Whole Envelope Sequences from 22 Trinidad HIV-1 Isolates

Cleghorn et al, Proc Natl Acad Sci USA, 27 (19); 10532-10537, 2000.


A distinctive clade b hiv 1 is heterosexually transmitted in trinidad tobago conclusions l.jpg

Institute of Human Virology

Division of Epidemiology and Prevention

A Distinctive Clade B HIV-1 is Heterosexually Transmitted in Trinidad & Tobago:Conclusions

These results demonstrated that:

  • Clade B HIV-1 is circulating in Trinidad & Tobago

  • Distinguished only by genetic marker from prototypic strains, but phenotypically identical

  • Strong founder effect from North American HIV-1

  • Relatively stable V3 loop

  • Diversity occurring at standard rate

  • Canonical clade B HIV-1 can generate a typical heterosexual epidemic

Cleghorn et al, Proc Natl Acad Sci USA, 27 (19); 10532-10537, 2000.


Slide9 l.jpg

Institute of Human Virology

Division of Epidemiology and Prevention

New Testing Strategy to Detect Early HIV-1 Infection for Use in Incidence Estimates and for Clinical and Prevention Purposes

Robert S. Janssen; Glen A. Satten; Farley R. Cleghorn; Susan L. Stramer; Bhupat D. Rawal; Thomas R. O'Brien; Barbara J. Weiblen; Frederick M. Hecht; Noreen Jack; James O. Kahn; Margaret A. Chesney; Michael P. Busch

Plot of standardized 3A11-LS optical density (OD) values of specimens obtained since estimated day of seroconversion on 3A11 assay.

JAMA Vol. 280, pp. 42-48, Jul. 1, 1998


Stages of early hiv infection l.jpg

Stages of early HIV infection

N

I

P*

POS

WB

Ab

RNA

  • LS EIA defined stages

LS-Ab

p24 Ag

0 I II III IV V VI VII

0

25

50

75

100

125

150

175

200

Days from HIV Exposure

M. Busch et al

2001


Slide11 l.jpg

Determination of Tdt for OTDV at SOD of 0.4

1.00

Lowness extrapolation

.80

.60

OTDV SOD

.40

.20

0.00

0

10

20

30

40

50

60

70

80

90

100

Cleghorn, 2000

DAYS POST SEROCONVERSION


Ls eia window period estimates organon teknika corporation s vironostika less sensitive eia l.jpg

Standardized Optical Density Cut-off Value

Days

95% C.I.

& AIDS Misclassified

0.50

97

93, 103

1.5

0.75

133

127, 140

4.2

1.00

170

162, 183

5.0

1.25

210

199, 227

6.9

1.50

249

230, 277

7.6

2.00

336

314, 400

8.4

LS-EIA Window Period EstimatesOrganon Teknika Corporation’s Vironostika Less-Sensitive EIA

*

CDCApril 2001


Calculating incidence using s ls data l.jpg

Institute of Human Virology

Division of Epidemiology and Prevention

Calculating Incidence using S/LS data

Idt = ndt/N (Ts/Tdt) 100

Idt = Incidence per annum

ndt= number detuned as recent

N = number of detuned plus negatives

Ts = Calendar time in days of sampling

Tdt = Estimate of time (#days) between Sensitive

and Less Sensitive Assays

I = Pdt x 365/Tdt

I = Incidence

Pdt = prevalence of detuned (recent samples)

Tdt = average time to detune sample in days


Cleghorn et al international aids meeting barcelona 2002 l.jpg

Institute of Human Virology

Division of Epidemiology and Prevention

Cleghorn et al, International AIDS Meeting,Barcelona, 2002

  • A serological 2 stage detuned algorithm can accurately

  • ascertain recent seroconverters for pathogenesis studies;

  • 2) Loss to follow-up of recent cases is significantly reduced;

  • 3) Incidence estimates suitable for program planning and

  • vaccine trials can be generated;

  • 5) Technology transfer allows local ownership of methodology,

  • allowing application to other activities such as sentinel studies

  • for program planning and interventions.


Slide15 l.jpg

BF Recombinants

Subtype F

Subtype B

BF Recombinants

.10

Institute of Human Virology

Division of Epidemiology and Prevention

Schematic Representation of the evolution

Of BF recombinants in South America

J. Carr et al, 2002


Slide16 l.jpg

CRF12_BF

Other

BF

Recombinants

F

B

Genes

Reverse Transciptase

Protease

Institute of Human Virology

Division of Epidemiology and Prevention

The ProRT amplicon as a screening tool-Latin America

J. Carr et al, 2001


Put these together l.jpg

Put these together:

  • Use detuned (S/LS) assay to identify recent infections (current force of epidemic)

  • Generate incidence estimates, initially focusing on Vaccine Trial Sites

  • Recover RNA amplicons from recently infected serum suitable for sequencing

  • Focus on parts of genome (RT/Pro) which delivers data on circulating resistance patterns

  • Track Molecular diversity of regional epidemic

  • Expert interpretation of resistance mutations and their significance.

NIAID R21 AI057084

2003-2005


Slide18 l.jpg

5 Caribbean sites (200 “confirmed” seropos. samples/site)

1,000 seropositive samples

DV-SOD 1.0 (IHV)

=150

Incidence Estimation

85%

15%

N= 850 Established

N= 150 Recents

Rapid UG S/LS (N=150)

NIAID R21 AI057084

2003-2005

10% unconfirmed

90% confirmed recents

15 non-confirmed 135 Recents

recents

Increase PPV

to 100% for

true recents

Viral

genotyping

(HJF)

DV-SOD 0.4

26%

74%

Select 50

SOD > 0.4 SOD < 0.4

(N=99)

(N=26)

(N=24/73)

26% (N=26) 0-35 days post-SC

74% (N=73) 35-170 days post-SC

EPT


Slide19 l.jpg

Institute of Human Virology

Division of Epidemiology and Prevention

~300 ProRT Sequences from South America & 12 Caribbean (Jam & TT)

Subtype B

Jamaica

Trinidad & Tobago

BF Recombinants

Subtype F

Other Subtypes

0.10


Slide20 l.jpg

Institute of Human Virology

Division of Epidemiology and Prevention

Trinidad Recently Infected 2001/2002

.10

Early Results: Subtype B Pro/RT only


Slide21 l.jpg

01JAM18920

B_U23487

B_896

B_WR27

B_Bol0122

B_BCSG3C

B_D31

B_YU2

B_JRCSF

B_RL42

B_LAI

B_NY5

CRC08656

B_CAM1

CRC08749

CRC08718

B_HAN

B_3202A12

CRC08683

B_MN

B_OYI

CRC08746

CRC08695

CRC08704

Institute of Human Virology

Division of Epidemiology and Prevention

B_SF2

B_ARCH054

CRC08767

B_RF

B_ARMS008

CRC08794

01JAM22731

CRC08693

.10

Subtype B – recent TT & Jam

72

85

ProRT


Slide22 l.jpg

1 11 21 31

| | | |

1 CTRPNNNTRK SIHIGPGRAF YTTGXIIGDI RQAHC 35 B consensus

1 .I.......R ..A....A.. ..-.EV.... .K.Y. 34 CRC08718 - new

1 .........R G..M...K.Y F.-.E..... ..... 34 QH0132

1 .........R ...M...KV. ..-.E..... ..... 34 QH0060

1 .......... ..P....SV. ..-.E..... ..... 34 QH0020

1 .........R D.T.....V. ..-.E..... ..... 34 QH0136

1 .......... ..N....... ..-.E..... ..... 34 QZ4734

1 .......... .....A.K.L ..-.E..... ..... 34 QH0016

1 .......... G.T....SV. ..-.E..... ..... 34 QH0065

1 .......... ....EA.K.L ..-.E..... ..... 34 QH0515

1 .........R D.A....KV. ..-.E...N. ..... 34 QH0550

1 .......... G......KV. C.-.E.V... ..... 34 QH0605

1 .......... .......... .A..E...N. ..... 35 QH0679

1 ....G..... .......... .A..D..... ..... 35 QH0692

1 .......... ...L.A...L ..-.E..... ..... 34 QH0705

1 .........E ..N....... .Y..E..... ..... 35 QH0788

1 .......... G.T.....VS ..-.E.V... ..V.. 34 QH0791

1 .......... ...L.A.K.L ..-.E..... ..... 34 QH0850

1 .........R ...M...K.L F.-.E..... ..... 34 QH0864

1 .......... ..P....... .A..E...N. ..... 35 QH0865

1 .........R GVT.....V. ..-.EVT... ..... 34 QH0908

1 .I........ .......... ..-.D..... ..... 34 QH0944

1 .......... ...M.....L ..-.E..... ..... 34 QH1116

1 .......... ...L.A...L ..-.E..... ..... 34 QH1420

Institute of Human Virology

Division of Epidemiology and Prevention

CRC08718 V3 Loop


Hiv incidence estimates in trinidad l.jpg

Institute of Human Virology

Division of Epidemiology and Prevention

HIV Incidence Estimates in Trinidad

Cleghorn et al, Amer J Epidemiol 147(9):834-839, 1998


Conclusions l.jpg

Conclusions

  • The (cost-effective) combination of S/LS assay testing and RNA recovery generates both HIV incidence and HIV molecular diversity;

  • RT/Pro analysis allows examination of common resistance mutations;

  • These three critical parameters are at the core of understanding and responding to the HIV/AIDS epidemic in the region;


Collaborators l.jpg

Collaborators

  • HJF: Jean Carr, Francine McCutchan

  • IHV: Niel Constantine, Anne Sill

  • Trinidad: Noreen Jack, Courtenay Bartholomew

  • Haiti: Jean Pape, Marie Deschamps

  • DR: Ernesto Guerrero, Yeycy Donastorg

  • Jamaica: Peter Figueroa, Evadne Williams

  • Puerto Rico: Carmen Zorilla, Y. Yamamura


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