The Rakai Health Sciences Program (RHSP) in Uganda provides a unique setting for implementation science and operational research related to HIV/AIDS. The RHSP oversees HIV services in Rakai District and has conducted several studies evaluating different models of service delivery. Some examples included a trial of a demand generation approach to increase uptake of HIV/family planning services and studies examining determinants and impact of scaling up medical male circumcision. The RHSP also utilizes longitudinal cohort data to evaluate the impact of combination HIV prevention approaches and quantify HIV care cascades over time. This provides opportunities for collaborative research on improving health services and outcomes in the region.

1. Rakai District

2. Rakai Health Sciences Program
- Initiated by Ugandan colleagues (Drs.
D Serwadda and N Sewankambo) in
1987
- Researchers at:
- Makerere University
- Uganda Virus Research Institute
- Johns Hopkins
- Columbia University, Karolinska,
University of Toronto,
University College London,
etc…
- NIH/NIAID (International Center
for Excellence in Research)
- Registered independent legal entity in
Uganda
- ~ 350 Ugandan colleagues and staff

3. Rakai Community Cohort Study: core of the RHSP
Observational research
(Quantitive / Qualitative)
- Community demography
- HIV epi/dynamics and spacial dynamics
- HIV/STI risk factors (biological and behavioral)
- Use of services
- STIs, OIs, malaria, NCD
- Social (Intimate partner violence, alcohol…)
- Time trends …. And much more
Randomized Trials
-STD control for HIV prevention& pregnancy
outcomes
- Male circ for HIVI prevention in men
- Male circ for HIV prevention in women
partners
- HSV-2 suppression for HIV progression
- Prevention of IPV and HIV (SHARE trial)
-Trial of demand generation (Stylish Man &
Woman)
Implementation
Science/Operations Research
P-MTCT, condoms, VCT, ART/HIV care
provision, male circumcision, family planning,
adolescent health, prevention of intimate partner
violence
Methods of improving service uptake and
adherence (peer programs, communication
technologies)
Service provision
-Combined HIV prevention, HIV/STI care and
treatment, family planning, some general health
care
Basic science (with an epi
flavor)
- Mucosal immunology, microbiology,
pathology, immunohistochemistry, HSV-2,
drug resistance, HSV-2, HPV
Molecular epi
- HIV Subtypes, HIV superinfection
- HIV phylogentics
- ART resistance
Clinical studies:
HIV related neurological outcomes
Liver fibrosis, CVD, kidney disease, etc…

4. Presentation of RHSP studies and resources
• Kate Grabowski:
– Cohort and key nested studies
• Aaron Tobian
– Lab studies and resources
• Larry Chang
– Clinical and HIV prevention studies, and
implementation science
• Maria Wawer
– Mop up

5. What we hope will come of this presentation
• Opportunities for you
– Secondary data analyses
– New setting for your current research interests and
ideas
– New research ideas
– Grants (!)
• Opportunities for RHSP
– New research ideas
– New collaborations (and grants )
– New expertise (substance abuse research, etc…)

6. The Rakai Community Cohort Study:
Overview and opportunities for population-based
HIV research and beyond in Rakai, Uganda

7. Rakai Community Cohort Study
(RCCS)
• Open population-based HIV
incidence cohort in 40-50 agricultural,
trading, and fishing communities in
Rakai District, Uganda
• ~15-17,000 study participants are
surveyed on an ~annual basis.
• Surveys ongoing since 1994.
• 16 survey rounds completed
• Fish communities surveyed beginning in
survey round 15
• N=4 fish landing sites (Dimu and Kansensero)
• Each survey includes household
census and individual interviews for
adults aged 15-49.

8. RCCS data overview
• Census
• Household membership
• Family relationships
• In/out migration
• Deaths and births
• GPS
• Socio-demographic and
behavioral survey
• Basic demographics
• Relationship history
• Egocentric Sexual networks
• Family planning
• Uptake of prevention interventions
• HIV/STI Testing
• Biological samples stored
• Qualitative data
• Focus groups, in-depth interviews
Survey Subject
Areas Captured
72,962
Total RCCS
Subjects
Research Data
16 Rounds of Study + Lab Data
Over 1,800 Questions
55,664 Households in Census

9. Prevalence
(%)
Incidence (per
100py)
General
Population
11 0.8
Fish Landing Sites 34 3.2
Table 1. Male HIV prevalence and incidence, 2012-2013
HIV incidence and prevalence in
the RCCS
Prevalence
(%)
Incidence (per
100py)
General
Population
17 1.0
Fish Landing Sites 49 3.7
Table 2. Female HIV prevalence and Incidence, 2012-2013

10. Large Spatial heterogeneity in HIV
burden

11. 0
2
4
6
8
10
12
14
16
18
R1 R2 R3 R4 R6 R7 R8 R9 R10 R11 R12 R13 R14
1.6
0.2
HIVprevalence,%
HIVIncidence/100py
1.0
1.4
Longitudinal trends in the RCCS
0.6
1995 2002 2013

12. High viral diversity in RCCS
communities
• High viral diversity.
• Subtypes A and D predominate, both heterosexually
transmitted.
• Incidence declines in both subtypes, but rapid decline
in D.

13. Nested studies – examples and
possibilities
• Risk assessment
• Evaluation of prevention
interventions and service utilization
• Male circumcision
• Community randomized trials
• Mobility and migration analyses
• Sexual network studies
• High risk populations
• Couples analyses
• Family planning and health studies
• Demographics and household
structure
• HIV transmission dynamics

14. Multidisciplinary research: HIV
transmission dynamics in the RCCS
Background:
The extent to which continued HIV
transmission in sub-Saharan Africa is driven
by intra-community sexual networks versus
viral introductions from outside of
communities remains unknown.
Methods:
Data: RCCS (2008-2009)
46 communities, 11 geographic regions
Spatial dependence between HIV cases
(n=1,786)
14,594 participants total, HIV prevalence ~
12%
189 incident cases
>8000 geo-located households
Genetic relatedness of infecting viruses with
respect to spatial location (env, gag genes)
Transmission model
Attributable fractions from intra-household,
intra-community, and extra-community
sexual contacts (self-reported locations)
Grabowski et al., Plos Med, 20

15. Multidisciplinary research: HIV
transmission dynamics in the RCCS
Grabowski et al., Plos Med, 20
• Household transmission is common.
• Strong genetic and spatial clustering in
households.
• Transmission model: 39% (95% CI: 32-44%)
of transmissions occurred within stable
household partnerships.
• Extra-household HIV acquisition is more
common from non-stable partners outside of
the local community
• High viral diversity and weak spatial
clustering at the community scale
• 44% of incident cases clustered with
another participant in one or both
gene regions.
• 60% of incident cases that did not
cluster with a household partner,
clustered exclusively with extra-
community participants
• Transmission model: 62% (95%CI: 58-66%)
infected outside household were infected

16. Linkage of disparate community-based
HIV epidemics in Rakai
• R01 NIAID, Gates Foundation
(PANGEA-HIV)
• Timeframe: 2014-2018
• What? Elucidation of community
sexual network structures and
quantification of the extent to
which fishing communities drive
endemic HIV transmission in
Rakai, District
• How? RCCS observational data
on migration, geography of
sexual partnerships, and whole
genome HIV sequencing
• Opportunities?
– Data analysis
Ron Gray (PI), Kate Grabowski

17. Rakai Lab Studies
(Not just an HIV support laboratory)
International Collaborators:
NIH International Centers of Excellence in Research (ICER)
Thomas Quinn Lab Group (NIH/JHU)
University of Toronto
George Washington University
Karolinska Institute

18. Randomised Trials Showed Male
Circumcision Reduces HIV Infection
Rakai, Uganda
Gray et. al. (2007) Lancet; 657 – 66
Kisumu, Kenya
Bailey et. al. (2007) Lancet; 643 – 56
Orange Farm, South Africa
Auvert et. al. (2005) PLoS Med; e298

19. Rakai Laboratory Assays
• ELISA/Serology
– HIV Detection
– HIV Incidence
– HSV-2
– CMV
– HBV
– HCV
• PCR/Nucleic Acid Testing
– HIV Detection
– HIV viral load
– HSV-2
– HPV
– CMV
– Malaria
• Complete Blood Count
• Flow cytometry
• Histology processing
• Microscopy
– Bacterial vaginosis
– Malaria
• Bacterial culture
– Trichomonas vaginalis
• 454 Pyrosequencing
– HIV-superinfection
– Microbiome
• Other Infections to be assessed
– Dengue?
– Influenza?

20. Male Circumcision (MC): Why the foreskin is
our window to viruses and immunology
• 3 male circumcision trials showed the foreskin
is the site of entry for 50-60% of HIV
• Serum samples, genital swabs and foreskin
tissues provide insight into virology,
immunology and the microbiome
• All studies presented today are from archived
samples to give you examples of types of
studies that can be performed with the RHSP
archive.

21. Male Circumcision Reduces
HSV-2 Acquisition
0
1
2
3
4
5
6
7
8
9
10
Overall 2+ Sexual
Partners
Inconsistent
condom use
Age 20-24
HSV-2Incidence/100py
Control
Circumcision
IRR = 0.72
(0.56-0.96)
IRR = 0.48
(0.31-0.73) IRR = 0.47
(0.30-0.73) IRR = 0.55
(0.36-0.84)
Tobian et al. NEJM 2009

22. Male Circumcision Reduces Human
Papillomavirus (HPV) Prevalence in Men
Tobian et al. NEJM 2009
0.0
10.0
20.0
30.0
40.0
50.0
60.0
High-risk
HPV
Non-high-risk
HPV
All HPV
genotypes
Multiple high-
risk HPV
Prevalence(%)
Control
Intervention
PRR = 0.65
(0.45-0.94)
PRR = 0.66
(0.49-0.91)
PRR = 0.70
(0.53-0.91)
PRR = 0.35
(0.17-0.71)
27.9
18.0
26.2
39.4
4.7
13.7
35.6
51.2

23. 0
10
20
30
40
50
60
Trichomonas BV Severe BV
Prevalence(%)
Control
Circumcision
Male Circumcision Reduces Trichomonas and
Bacterial Vaginosis in Female Partners
PRR 0.53
CI 0.33 – 0.85
PRR 0.80
CI 0.71 – 0.89
PRR 0.31
CI 0.18 – 0.54
Gray et al. Am J Ob Gyn 2009
11.2
5.9
50.6
40.3
6.5
2.0

24. 0.0
10.0
20.0
30.0
40.0
50.0
60.0
All HPV genotypes Low-risk HPV High-risk HPV
Prevalence(%)
Control
Intervention
Male Circumcision Reduces HPV
Prevalence in Women
PRR = 0.82
(0.72-0.92)
PRR = 0.77
(0.66-0.91) PRR = 0.71
(0.60-0.85)
56.5
46.1
42.5
32.9
38.6
27.5
Wawer et al. Lancet 2011

25. Biological Plausibility
CD4+
T Cells
Dendritic Cells
Tobian et al. J Infect Dis. 2013Redd et al, J Infect Dis. 2011
 Foreskins from HSV-2 seropositive
men have high frequency of CD4+
T-cells present in submucosa
 Foreskins from men who have
recently cleared HPV have a sig.
increase in dendritic cells

26. Liu, CM et al MBio 2013
Male Circumcision Reduces Prevalence and
Load of Genital Anaerobic BacteriaPro-inflammatory Anaerobic bacteria are
reduced by circumcision; Rakai Trial
Liu et al Mbio 2013
Species Circumcised
Prevalence %
Uncircumcised
Prevalence %
Absolute
difference (%)
Clostridia 84.4 48.1 -36
Prevotella 90.9 51.9 -39
Finegoldia 79.2 48.1 -31
Dialister 61.0 16.5 -45
Decreased pro-inflammatory anaerobes may reduce HIV target cell recruitment and
reduce HIV risk following MC
Decreased pro-inflammatory anaerobes may reduce HIV target cell recruitment and reduce
the risk of HIV following male circumcision.

27. Flow Cytometry
PBMCs
Foreskin
FSC
SSC
CD3
CD4
IFNγ
IL17a
CCR5
SSC
stimulated

28. HSV-2 infection associated with
increase in CCR5 expression on
foreskin CD4 T cells
0
15
30
45
60
p = 0.024ns
Blood Foreskin
HSV-2 Positive
HSV-2 Negative
%CCR5+ofCD4Tcells
Prodger et al, AIDS, 2012

29. HIV Shedding from MC Wounds

30. Redd et al, JID, 2012
Diagnostic Criteria for Superinfection
Rakai, Uganda
Rate of SI (1.4/100py)

31. Available Archived Samples
• 20 years of consecutive samples among persistently
HIV-negative, HIV-positive and HIV-seroconverters
• 476,000 samples
– 162,000 genital swabs
– 314,000 sera
• Human cellular DNA
– Buffy coat
– Vaginal and penile swabs
• Largest repository of foreskins in the world

32. HIV Implementation Research
in Rakai, Uganda:
Overview & Opportunities
Larry William Chang, MD, MPH
Assistant Professor of Medicine, Epidemiology, & International Health
Johns Hopkins School of Medicine and Bloomberg School of Public Health

33. Overview
• Since 2004, RHSP has provided combination HIV prevention
(CHP) services as a PEPFAR implementer
– pre-antiretroviral therapy (ART) and ART care (with virologic
outcomes)
– prevention of mother to child HIV transmission (PMTCT)
– medical male circumcision (MMC)
– HIV counseling and testing (HCT)
– condoms and promotion of behavioral change
• 2004-2012, most services provided directly through RHSP-
run clinics.
• Currently, a hybrid, RHSP oversees all government provided
HIV services in the entire Rakai District and provides some
services directly.

34. Evaluating demand generation (stylish man) for
HIV/family planning services Rakai
• R01 NIAID
• Timeframe: 2014-2018
• What? A novel, demand creation
approach (mass media + community
mobilization) to increasing HIV service
and family planning uptake by
demedicalizing HIV prevention and
care.
• How? Community-randomized trial
• Opportunities?
– Adaptive study design
Maria Wawer (PI) et al.

35. Male Circumcision
• U01 K25 NIAID
• What? Determinants and impact of
male circumcision uptake,
circumcision device safety, task
shifting models, infant circumcision,
role of women in increasing
circumcision uptake.
• How? RCCS, Qualitative
• Opportunities?
– Mixed methods research
understanding health seeking
behaviors
– New behavioral interventions
Xiangrong Kong, Ron Gray

36. Combination HIV Prevention Evaluation
and Treatment Cascades
• Funding: Multiple sources
• Timeframe: 2000-2017
• What? Impact of combination HIV prevention on HIV
incidence, quantification of HIV service cascades over
time
• How? RCCS, time series analysis
• Opportunities
– Analytic input, economic evaluation, modeling
Everyone. Figure courtesy of Veena Billioux.

37. The PeerCARE Study: A Randomized Trial
• Timeframe: 2011-2013
• What? A randomized trial on the impact of peer support
on pre-ART outcomes (n=442).
• Results? Peers improved engagement in care,
cotrimoxazole use, and water vessel use.
• Opportunities
– Secondary data analyses
– Psychometric evaluation of
behavioral model (sIMB)
Larry Chang (PI) et al.

38. Mobile Ecological Momentary Assessment & Intervention
of Unhealthy Behaviors in Rakai, Uganda
• Center for Global Health Award
• Timeframe: 2015-2016
• What? Proof-of-concept study on whether we can use
smartphones to collect near real-time, geo-located
behavioral data (e.g. sex, smoking, alcohol).
• How? N~50, 60 days f/u, process indicators, qualitative
eval, compare to conventional survey
• Opportunities
– Similar study in other settings?
– Novel analyses?
Larry Chang (PI), Kate Grabowski (Co-Investigator/Analyst)

39. CHWs, mHealth, and Combination HIV
Prevention in a Hotspot: A Randomized Trial
• R01 (scored within funding range)
• Timeframe: 2015-2019
• What? A randomized trial on the impact of
CHWs promoting CHP supported by novel
mHealth tools.
• How? Household-level randomization in
Kasensero, a fishing community on Lake
Victoria which qualifies for Treatment as
Prevention (TasP). Primary outcomes are
CHP coverage evaluated via RCCS.
• Opportunities
– Nested studies
– Economic evaluations
Larry Chang (PI) et al.

40. Geospatial HIV Implementation Research
• Funding Source: None yet
• RHSP has collected rich geospatial data on
households, health care facilities,
community, and geographic features.
• The data can be linked to HIV
epidemiologic, service utilization, and
clinical outcomes offering the opportunity
for novel geospatially-informed HIV
implementation research.
Examples/Opportunities:
– Impact of clinic distance and travel time on virologic outcomes
of HIV-infected patients on antiretroviral therapy and on MMC
uptake
– Geospatial analyses of the appropriateness of HIV health facility
and service distribution in Rakai, Uganda
Larry Chang, Kate Grabowski

41. How to start a collaboration
• Most important: contact us to chat
• Secondary data analyses: short proposal to be
shared with US and Ugandan collaborators,
indication of funding for data set creation - if
needed.
• New RCCS module: same as above.
• New study: Discussion with US and Ugandan
colleagues on study goals and potential design;
drafted study aims; ongoing consultation.

42. Contact information
• Kate Grabowski: mgrabows@jhu.edu (cohort, transmission dynamics,
phylogentics)
• Aaron Tobian: atobian1@jhmi.edu (lab, virology, immunology)
• Larry Chang: lchang8@jhmi.edu (implementation sci, clinical)
• Maria Wawer: mwawer1@jhu.edu (a bit of everything)
• Ron Gray: rgray4@jhu.edu (a bit of everything)
• Xiangrong Kong: xkong4@jhu.edu (biostats, epi, health seeking behaviors)
• Tom Quinn: tquinn2@jhmi.edu (lab, virologiy, NIH)
• Oliver Laeyendecker: olaeyen1@jhmi.edu (lab, virology, NIH, )
• Andy Redd: aredd2@jhmi.edu (lab, immunology, NIH)
• Jessica Prodger: jessiprodger@gmail.com (immunology)
• Caitlin Kennedy: caitlinkennedy@jhu.edu (qualitative research)
• Ned Sacktor: sacktor@jhmi.edu (neuro-HIV epidemiology)
• Nandy Pilgrim npilgrim@popcouncil.org (social science, adolescents)
• Lilian Mutesi (Admin): lmutesi1@jhu.edu