Thembisa version 4.3: A model for evaluating the impact of HIV/AIDS in South Africa June 2020 Leigh Johnson1 and Rob Dorrington2 1. Centre for Infectious Disease Epidemiology and Research, University of Cape Town 2. Centre for Actuarial Research, University of Cape Town Correspondence to: Leigh Johnson Centre for Infectious Disease Epidemiology and Research University of Cape Town Faculty of Health Sciences Anzio Road Observatory 7925 Tel: +27 21 406 6981 Fax: +27 21 406 6764 Email: [email protected] 1 Table of contents 1. Introduction ............................................................................................................................ 6 2. Model of sexual behaviour..................................................................................................... 9 2.1 Age at sexual debut ........................................................................................................ 11 2.2 Rates at which non-marital partnerships are formed ...................................................... 11 2.3 Marriage and divorce ..................................................................................................... 13 2.4 Commercial sex .............................................................................................................. 14 2.5 Preferences regarding partner risk group ....................................................................... 15 2.6 Preferences regarding partner age .................................................................................. 16 2.7 Coital frequencies ........................................................................................................... 16 2.8 Condom usage ................................................................................................................ 17 2.8.1 Condom use in women (excluding commercial sex)............................................... 17 2.8.2 Condom use in men (excluding commercial sex) ................................................... 21 2.8.3 Condom use in sex worker-client relationships ....................................................... 21 2.9 Effect of CD4 count on level of sexual activity ............................................................. 22 2.10 Effect of knowledge of HIV status on sexual behaviour ............................................. 23 2.11 The effect of ART on sexual behaviour ....................................................................... 25 2.12 Same-sex relationships ................................................................................................. 26 3. Model of HIV disease progression and mortality in adults ................................................. 27 3.1 HIV disease progression and mortality prior to ART initiation ..................................... 28 3.2 HIV testing and diagnosis .............................................................................................. 29 3.3 Adult ART initiation ...................................................................................................... 31 3.3.1 Linkage to ART after diagnosis during pregnancy ................................................. 32 3.3.2 Linkage to ART after HIV diagnosis in OI patients ................................................ 33 3.3.3 Linkage to ART after HIV diagnosis in non-pregnant, asymptomatic adults ......... 33 2 3.3.4 ART initiation in previously-diagnosed adults who did not link to ART soon after diagnosis, up to mid-2019 ................................................................................................ 34 3.3.5 ART initiation in previously-diagnosed adults who did not link to ART soon after diagnosis, after mid-2019 ................................................................................................. 35 3.4 Mortality after ART initiation in adults ......................................................................... 36 3.5 ART interruptions and switches to second-line ART .................................................... 37 4. Model of sexual transmission of HIV .................................................................................. 38 4.1 The effect of sex and relationship type .......................................................................... 38 4.2 The effect of risk group .................................................................................................. 38 4.3 The effect of HIV stage and antiretroviral treatment ..................................................... 39 4.4 Condom effectiveness .................................................................................................... 41 4.5 Age and year effects ....................................................................................................... 42 4.6 Mathematical model of heterosexual transmission ........................................................ 42 4.7 Extensions to represent effect of male circumcision ...................................................... 48 4.7.1 Male circumcision prior to the promotion of MMC as an HIV prevention strategy .......................................................................................................................................... 48 4.7.2 Male circumcision in the MMC campaign era ........................................................ 50 4.8 Extensions to represent effect of pre-exposure prophylaxis (PrEP) .............................. 52 4.8.1 Effectiveness of PrEP .............................................................................................. 52 4.8.2 Risk compensation ................................................................................................... 52 4.8.3 PrEP discontinuation ............................................................................................... 53 4.8.4 Adoption of PrEP..................................................................................................... 53 5. Model of mother-to-child transmission and paediatric HIV ................................................ 55 5.1 Perinatal transmission .................................................................................................... 55 5.1.1 Short-course antiretroviral prophylaxis ................................................................... 55 5.1.2 Effectiveness of long-term maternal ART ............................................................... 56 5.1.3 HIV incidence in pregnancy and retesting in late pregnancy .................................. 58 5.2 Postnatal HIV transmission ............................................................................................ 58 3 5.2.1 Infant feeding practices up to 2011 ......................................................................... 58 5.2.2 Infant feeding practices after 2011 .......................................................................... 59 5.2.3 Postnatal transmission probabilities ........................................................................ 59 5.3 Paediatric HIV survival .................................................................................................. 60 5.3.1 Untreated disease progression and mortality ........................................................... 61 5.3.2 Survival after ART initiation ................................................................................... 62 5.3.3 HIV diagnosis and ART initiation ........................................................................... 63 5.3.4 Transition from paediatric to adult HIV staging ..................................................... 66 6. Demographic assumptions ................................................................................................... 67 6.1 Base population .............................................................................................................. 67 6.2 Fertility ........................................................................................................................... 67 6.3 Non-HIV mortality ......................................................................................................... 70 6.4 Migration ........................................................................................................................ 71 7. Statistical analysis ................................................................................................................ 72 7.1 Prior distributions ........................................................................................................... 72 7. 2 Likelihood definition ..................................................................................................... 73 7.2.1 Likelihood definition for antenatal clinic survey data ............................................. 73 7.2.2 Likelihood definition for household survey prevalence data .................................. 75 7.2.3 Likelihood definition for antiretroviral metabolite data .......................................... 75 7.2.4 Likelihood definition for recorded death data ......................................................... 76 7.3 Posterior simulation........................................................................................................ 78 7.4 Combining uncertainty from different analyses ............................................................. 78 8. Results of model calibration ................................................................................................ 79 8.1 Comparison of prior and posterior distributions ...........................................................