The Incidence Patterns Model to Estimate the Distribution of New HIV Infections in Sub-Saharan Africa: Development and Validation of a Mathematical Model.
Programmatic planning in HIV requires estimates of the distribution of new HIV infections according to identifiable characteristics of individuals. In sub-Saharan Africa, robust routine data sources and historical epidemiological observations are available to inform and validate such estimates.



We developed a predictive model, the Incidence Patterns Model (IPM), representing populations according to factors that have been demonstrated to be strongly associated with HIV acquisition risk: gender, marital/sexual activity status, geographic location, "key populations" based on risk behaviours (sex work, injecting drug use, and male-to-male sex), HIV and ART status within married or cohabiting unions, and circumcision status. The IPM estimates the distribution of new infections acquired by group based on these factors within a Bayesian framework accounting for regional prior information on demographic and epidemiological characteristics from trials or observational studies. We validated and trained the model against direct observations of HIV incidence by group in seven rounds of cohort data from four studies ("sites") conducted in Manicaland, Zimbabwe; Rakai, Uganda; Karonga, Malawi; and Kisesa, Tanzania. The IPM performed well, with the projections' credible intervals for the proportion of new infections per group overlapping the data's confidence intervals for all groups in all rounds of data. In terms of geographical distribution, the projections' credible intervals overlapped the confidence intervals for four out of seven rounds, which were used as proxies for administrative divisions in a country. We assessed model performance after internal training (within one site) and external training (between sites) by comparing mean posterior log-likelihoods and used the best model to estimate the distribution of HIV incidence in six countries (Gabon, Kenya, Malawi, Rwanda, Swaziland, and Zambia) in the region. We subsequently inferred the potential contribution of each group to transmission using a simple model that builds on the results from the IPM and makes further assumptions about sexual mixing patterns and transmission rates. In all countries except Swaziland, individuals in unions were the single group contributing to the largest proportion of new infections acquired (39%-77%), followed by never married women and men. Female sex workers accounted for a large proportion of new infections (5%-16%) compared to their population size. Individuals in unions were also the single largest contributor to the proportion of infections transmitted (35%-62%), followed by key populations and previously married men and women. Swaziland exhibited different incidence patterns, with never married men and women accounting for over 65% of new infections acquired and also contributing to a large proportion of infections transmitted (up to 56%). Between- and within-country variations indicated different incidence patterns in specific settings.



It is possible to reliably predict the distribution of new HIV infections acquired using data routinely available in many countries in the sub-Saharan African region with a single relatively simple mathematical model. This tool would complement more specific analyses to guide resource allocation, data collection, and programme planning.
Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom.|Division of Global Public Health, University of California San Diego, San Diego, California, United States of America.
Annick
0000-0002-6033-9837
A
Bórquez
Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom.
Anne
A
Cori
Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom.
Erica L
EL
Pufall
Rakai Health Sciences Program, Entebbe, Uganda.
Jingo
0000-0002-3793-6350
J
Kasule
Department of Population Health, London School of Hygiene &Tropical Medicine, London, United Kingdom.
Emma
0000-0002-4941-5739
E
Slaymaker
Department of Population Health, London School of Hygiene &Tropical Medicine, London, United Kingdom.
Alison
A
Price
Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom.
Jocelyn
J
Elmes
Department of Population Health, London School of Hygiene &Tropical Medicine, London, United Kingdom.
Basia
B
Zaba
Department of Population Health, London School of Hygiene &Tropical Medicine, London, United Kingdom.
Amelia C
AC
Crampin
Rakai Health Sciences Program, Entebbe, Uganda.
Joseph
0000-0003-4101-3038
J
Kagaayi
Rakai Health Sciences Program, Entebbe, Uganda.
Tom
T
Lutalo
Mwanza Research Centre, National Institute for Medical Research, Mwanza, Tanzania.
Mark
0000-0001-6756-9742
M
Urassa
Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom.
Simon
S
Gregson
Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom.
Timothy B
TB
Hallett
D000328:Adult; D017954:Africa South of the Sahara / Q000453:epidemiology; D001499:Bayes Theorem; D005260:Female; D015658:HIV Infections / Q000453:epidemiology* / Q000209:etiology; D006801:Humans; D015994:Incidence; D008297:Male; D008962:Models, Theoretical; D012307:Risk Factors; D012737:Sex Factors; D012959:Socioeconomic Factors