HIV Diversity in East Africa

Transcription

1 HIV Diversity in East Africa Kayvon Modjarrad, M.D., Ph.D. 16 March 2015 The views expressed are those of the authors and should not be construed to represent the positions of the U.S. Army or the Department of Defense.

2 Outline Viral Diversity Public Data RV 217 (Uganda, Kenya, Tanzania) Study Design Basic Demographics Predictors CD4, VL

3 Causes of HIV-1 Diversity Rapid turnover rate ~10 10 virions/day Half life of virions in blood (~2h) & infected cells (~2d) No RT proof-reading mutations per genome per replication cycle Multiple ways of generating variants Accumulation of base substitutions Insertions and deletions Addition and loss of glycosylation sites Recombination

4 Mean pairwise diversity (%) Mean pairwise diversity (%) MHRP HIV-1 Relative Sequence Diversity HIV-1 subtype B, US, env-gp120, 652 sequences Influenza A, H3N2, US, HA, 1460 sequences 1960s 1970s 1980s 1990s 2000s 2010s r 2 = r 2 =

5 Circulating HIV-1 sequences in sub-saharan Africa Phylogenetic analyses of all sequences available in LANL (28 Feb 2015, M. Rolland) full-length genomes reverse transcriptase (RT) envelope gp120 genes Subtype distribution analysis from (Hemelaar et al) and S. Tovanabutra ( ) The real proportion of recombinants likely higher than reported Analysis of independent sequences: one sequence per subject Number of independent sequences genome RT gp120 East Africa Southern Africa Central Africa West Africa All

6 MHRP contribution to circulating HIV-1 sequences Number of genome sequences coming from MHRP Africa Central Africa East Africa Southern Africa West Africa From MHRP MHRP %age Else All Number of RT sequences coming from MHRP Africa Central Africa East Africa Southern Africa West Africa From MHRP MHRP %age Else All Number of gp120 sequences coming from MHRP Africa Central Africa East Africa Southern Africa West Africa From MHRP MHRP %age Else All * Note: it is not all MHRP-derived sequences since only one sequence from a given individual is retained.

7 Most Prevalent HIV-1 Subtypes ( ) B, and other recombinants(recs.) CRF02_AG, A, and C CRF02_AG, G, and high proportion of their recombinants A, C, D, F, G, H, J, K, CRF01_AE, CRF02_AG, and high proportion of their recombinants A, D, and high proportion of their recombinants A, D, C, and high proportion of their recombinants A, C, and high proportion of their recombinants C, and low proportion of recombinants Insufficient data

8 East Africa HIV-1 Sequence Diversity A B C D F G CRF01_AE CRF02_AG OTHER CRF URF genome 230 sequences East Africa gp sequences

9 Large Proportion of Recombinants in East African MHRP Sites 30% A1/D Uganda MHRP, % A1 38% D 6% C/D 1% A1/C 0.8% A1/C/D 0.4% C C 29% A1/D 9% A1/C/D 36% A1 Kenya MHRP, % A1/A2/D 5% A1/C 5% C 4% A2/D 3% A1/A2/C/D 2% G A, D A, D +recs. +recs. A, C +recs. Tanzania MHRP, % A1/C 40% C 17% A1 11% A1/C 8% C/D 3% A1/D 1% A1/A2/ 1% D

10 Subtype A1 is 3/4 th of published sequences in Rwanda Subtypes Rwanda 16% A1/C 74% A1 5% C 3% D 2% A1/D Kemal et al, AIDS Res Hum Retroviruses, 2013 Rusine et al, PLOS One, 2012

11 RV217 Background Early Capture HIV Cohort (ECHO) Define HIV prevalence, incidence, risk and retention in very high risk participants Exchange goods for sex Unprotected sex w/ HIV+ partner Unprotected sex w/ >3 partners Report STI symptoms Capture 150 acute HIV infections 2,926 screened 1,605 enrolled 2 x week finger sticks (600 μl) Qualitative HIV PCR in real time 62 acute HIV-1 infections Uganda Kenya Tanzania Screened Enrolled Incident Cases

12 Age (Years) MHRP RV217 (East Africa) Age Consistent Across Cohorts Uganda Kenya Tanzania Prevalent (N=134) Incident (N=62) Nega ve (N=2552)

13 Weight (kilograms) MHRP RV217 (East Africa) Weight Lower in AHI 70 Uganda Kenya 65 Tanzania Prevalent (N=134) Incident (N=62) Nega ve (N=2552)

14 RV217 Clinical Symptoms During AHI Africa (n=25) Thailand (n=17) All (n=42) Symptom: N(%) N(%) N(%) Fever 14 (56%) 7 (41%) 21 (50%) Headache 12 (48%) 6 (35%) 18 (43%) Feeling of Illness 11 (44%) 5 (29%) 16 (38%) Abnormality: Lymph* 2 (8%) 16 (94%) 18 (43%) HEENT** 3 (12%) 15 (88%) 18 (43%) Cardiovascular 12 (48%) 5 (29%) 17 (40%) *Fisher s Exact p-value < **Fisher s Exact p-value <0.001

15 RV217 AHI Summary VL Statistics All East Africa (EA) Thailand (TH) Mean, Median (IQR) Mean, Median (IQR) Mean, Median (IQR) Peak VL 6.76, 6.74 ( ) 6.78, 6.76 ( ) 6.73, 6.66 ( ) Peak Day 12.6, 13 (11-14) 12.3, 13 (11-14) 13.1, 14 (11-15) Nadir VL 4.11, 4.31 ( ) 3.78, 3.65 ( ) 4.60, 4.62 ( ) Nadir Day 41.1, 42 (29-50) 41.5, 43 (36-49) 40.4, 41 (29-52) Set-Point VL 4.25, 4.38 (3.68, 4.93) 3.92, 3.84 (3.47,4.46) 4.72, 4.81 ( ) VL=Viral Load IQR=Interquartile Range

16 RV217 Sequencing Project Log 10 VL 8 25 participants with longitudinal sequence data: Sequencing of HIV-1 near-full-length genomes (~8.8 Kb) 10 HIV-1 genomes per time point for each participant 3 time points: 1 week, 1 month, 6 months 20 additional participants with only the first time point sequenced Days from first HIV-positive RNA test Kenya Tanzania Uganda

17 0.06 MHRP RV 217 HIV-1 Subtypes 18 subjects from Kenya: 7 subtype A1 1 subtype C B D 2 A1/C recombinants 5 A1/D recombinants 3 A1/C/D recombinants A1 18 subjects from Tanzania: 3 subtype A1 7 subtypes C 4 A1/C recombinants 1 A1/D recombinant CRF02_AG 1 C/D recombinant 2 A1/C/D recombinant 9 subjects from Uganda: C A2 CRF01_AE 3 subtype A1 5 A1/D recombinants 1 A1/C/D recombinant F1 F2 K H J G

18 Mean CD4 Tcell counts Log 10 VL MHRP HIV-1 Subtype and markers of disease progression Individuals infected with HIV-1 subtype C showed lower CD4 counts and higher VL setpoint than those infected with HIV-1 subtype A A1 C REC. 0 A1 C REC.

19 Mean CD4 T cell count Log 10 VL MHRP Most participants infected by single founder variant 18 of 27 participants HIV-1 infections with multiple founder variants associated with higher VL setpoint, lower CD4 counts Multiple Single Single Multiple 0 Peak Nadir Setpoint

20 Conclusions The HIV-1 epidemic is continuously becoming more heterogeneous. Increasing proportion of intra- and inter-subtype recombinants, making subtype delineation becoming more difficult. Sequence analyses show extensive interconnections with adjacent countries. There is a need to publish more sequences. Identifying, following, and intervening in early acute HIV infection will help characterize viral evolution and corresponding immunity.

21 Acknowledgments MHRP-WRAIR Merlin L. Robb Nelson L. Michael Jerome H. Kim Leigh Anne Eller Julie Ake Sheila Peel Linda Jagodzinski Shelly Krebs RV217 Sequencing Morgane Rolland Sodsai Tovanabutra David Chang Erik Billings Eric Sanders-Buell Meera Bose Gustavo Kijak Anne Marie O'Sullivan Shana Miller Kultida Poltavee Jenica Lee Grace Ibitamuno Sevan Muhammad Bahar Ahani Steven LePore Elizabeth Harbolick Celina Oropeza Joey Patterson Adam Bates Michelle Lazarro Kalpana Dommaraju MHRP DCAC Rory Deshano Nan Wang Mark Milazzo Michelle Liu Jun Tian WRP-Kericho Kathleen Rono Fred Sawe Doug Shaffer Kibet Shikuku Samoel Khamadi MMRP-Tanzania Lucas Maganga Leonard Maboko Phillip Mann Erica Sanga Michael Hoelscher Cornelia Lueer MUWRP-Uganda Hannah Kibuukaa Arthur Sekiziyivu Fatim Cham Jallow Lillian Mutengu Ali Taylor Britta Flach

22 APPENDIX

23 Southern Africa A B C D G J CRF02_AG OTHER CRF URF C genome 399 sequences Southern Africa 0.06 B D Sequences in black are recombinants

24 Central Africa Central Africa A B C D F G H J K CRF01_AE CRF02_AG OTHER CRF URF A1 CRF02_AG G F D RT 290 sequences N 0.2 P Sequences in black are recombinants O

25 West Africa West Africa A B C D F G H J K CRF01_AE CRF02_AG OTHER CRF URF A1 G CRF02_AG C B D RT 251 sequences O D G A1 CRF02_AG gp sequences O Sequences in black are recombinants 0.3

26 RV subjects Examples of recombination patterns Uganda Uganda Tanzania Subtype A1 Subtype B Subtype C Subtype D Subtype F1 Subtype G Subtype H Subtype J Subtype K nucleotide position nucleotide position nucleotide position Kenya Kenya Kenya nucleotide position nucleotide position nucleotide position

27 Mean pairwise diversity (%) Mean pairwise diversity (%) MHRP RV217 HIV-1 diversification over the first six months of infection for 17 subjects infected with single HIV-1 founders. 1.5 pol 1.5 env Days from first HIV-positive RNA test Days from first HIV-positive RNA test Differences across the HIV-1 genome: gag, pol < env, or nef. Variability among individuals First month of infection: demographic processes dominate negative deviations from neutral evolution with Tajima s D and Fu and Li s D* tests, but no sign of selective adaptation with the Hudson-Kreitman-Aguadé tests Afterwards: evidence of selection, both CTL- and antibody-driven

28 Substitution rate per site per year x10-3 Substitution rate per site per year x10-3 MHRP RV217 HIV-1 diversification over the first six months of infection for 17 subjects infected with single HIV-1 founders. 30 pol 30 env A1 C REC. 0 A1 C REC. Differences across the HIV-1 genome: gag, pol < env, or nef. Variability among individuals Heterotachy between subtypes Average rate in env (8.30x10-3 ) comparable to previously published data: 9.20x10-3 (Shankarappa et al., 1999), 11.1x10-3 (Herbeck et al, 2011)

29 DRM identified in 2 of 45 RV217 subjects No DRM identified in protease sequences. NRTI- and NNRTI-associated mutations found in RT sequences from 2 subjects The mutations are identified in sequences from the first week of infection and are stable over six months of follow up. Kenyan subject 20631: NNRTI: K101E Subject with average VL setpoint log 10 = 3.73 (median for Kenyans = 3.95) and high mean CD4 = 1,148 (median for Kenyans = 708) Ugandan subject 10502: NRTI: K65R, M184V NNRTI: L100I, K103N Subject with low VL setpoint log 10 = 2.71 (median for Ugandans = 4.7) and high mean CD4 = 988 (median for Thais = 595) This subject had a positive Aptima test, and his next visit was 24 days later: at that time, his VL was 9,120 copies/ml, it was 832 copies at day 34, and remained between 240 and 1,230 copies until day 386 (last date available), suggesting that the combination of mutations seen in this subject have an impact on HIV s replicative capacity.

30 VL (log10 cps/ml) MHRP RV 217: The Early Capture HIV Cohort / ECHO Median interval: last negative to first positive = 5 days (range 2-32) Nadir VL Min VL Prior to Day 60 Set-Point Average VL Day 80 and Day 360 minimum two measurements Upslope Day 0 = Last Negative if Last Negative < 10 days prior to VL days to peak day to EIA days to Nadir 2 Day 0 = 1 st pos RNA Days From First RNA Positive The views expressed are those of the authors and should not be construed to represent the positions of the U.S. Army or the Department of Defense.

31 Log Viral Load (mean ± SEM) MHRP Viral Load by region (days) 7 6 VL > in males: Reported in US populations: NEJM (2001): 344 (10): p720 Reported in Africa: JID (2004): 189: p p= Early Nadir 2 1 Africa (n=19) Asia (n=15) Days From First RNA Positive