This repository holds the code for two papers, described below. Both used the same EpiModelHIV engine.
Jones J, Le Guillou A, Gift TL, Chesson H, Bernstein KT, Delaney KP, Lyles C, Berruti A, Sullivan PS, Jenness SM. Effect of Screening and Treatment for Gonorrhea and Chlamydia on HIV Incidence Among Men Who Have Sex With Men in the United States: A Modeling Analysis. Sex Transm Dis. 2022; 49(10): 669-676. doi:10.1097/OLQ.0000000000001685
Jones J, Jenness SM, Le Guillou A, Sullivan PS, Gift TL, Delaney KP, Chesson H. Estimated Number of Incident HIV Infections in Men Who Have Sex With Men Attributable to Gonorrhea and Chlamydia, Per Gonococcal or Chlamydial Infection, in the United States. Sex Transm Dis. 2023; 50(2): 83-85. doi:10.1097/OLQ.0000000000001724
The engine is release GCCT-STD of EpiModel/EpiModelHIV. Install it with:
remotes::install_github("EpiModel/EpiModelHIV@GCCT-STD")The supplements to both papers name the CombPrevNet branch, but the code here was run on the engine in this release.
ARTnetData is a private package. It is needed only to re-estimate the networks. The paper's networks were estimated with ARTnet 2.5.0, which is no longer public, so renv.lock installs ARTnet 2.9.3, the first version in the public ARTnet repository. Networks re-estimated with it may not match the paper's exactly.
Effect of Screening and Treatment for Gonorrhea and Chlamydia on HIV Incidence among Men who Have Sex with Men in the United States: A Modeling Analysis
This repository holds the source code to reproduce our analysis estimating the effect of increased screening for gonorrhea and chlamydia among men who have sex with men on downstream HIV incidence.
Jones J, Le Guillou A, Gift TL, Chesson H, Bernstein KT, Delaney KP, Lyles C, Berruti A, Sullivan PS, Jenness SM. Effect of Screening and Treatment for Gonorrhea and Chlamydia on HIV Incidence Among Men Who Have Sex With Men in the United States: A Modeling Analysis. Sex Transm Dis. 2022 Oct 1;49(10):669-676. doi: 10.1097/OLQ.0000000000001685. Epub 2022 Jul 29. PMID: 35921635; PMCID: PMC9481699.
Background
Previous models have estimated the total population attributable fraction of Neisseria gonorrhoeae and Chlamydia trachomatis (NG/CT) on HIV incidence among men who have sex with men (MSM), but this does not represent realistic intervention effects. We estimated the potential impact of screening for NG/CT on downstream incidence of HIV among MSM.
Methods
Using a network model, we estimated the effects of varying coverage levels for sexually transmitted infection screening among different priority populations: all sexually active MSM regardless of HIV serostatus, MSM with multiple recent (past 6 months) sex partners regardless of serostatus, MSM without HIV, and MSM with HIV. Under the assumption that all screening events included a urethral test, we also examined the effect of increasing the proportion of screening events that include rectal screening for NG/CT on HIV incidence.
Results
Increasing annual NG/CT screening among sexually active MSM by 60% averted 4.9% of HIV infections over a 10-year period (interquartile range, 2.8%-6.8%). More HIV infections were averted when screening was focused on MSM with multiple recent sex partners: 60% coverage among MSM with multiple recent sex partners averted 9.8% of HIV infections (interquartile range, 8.1%-11.6%). Increased sexually transmitted infection screening among MSM without HIV averted more new HIV infections compared with the transmissions averted because of screening MSM with HIV, but fewer NG/CT tests were needed among MSM with HIV to avert a single new HIV infection.
Conclusions
Screening of NG/CT among MSM is expected to lead to modest but clinically relevant reductions in HIV incidence among MSM.
Estimated Number of Incident HIV Infections in Men Who Have Sex With Men Attributable to Gonorrhea and Chlamydia, Per Gonococcal or Chlamydial Infection, in the United States
Jones J, Jenness SM, Le Guillou A, Sullivan PS, Gift TL, Delaney KP, Chesson H. Estimated Number of Incident HIV Infections in Men Who Have Sex With Men Attributable to Gonorrhea and Chlamydia, Per Gonococcal or Chlamydial Infection, in the United States. Sex Transm Dis. 2023 Feb 1;50(2):83-85. doi: 10.1097/OLQ.0000000000001724. Epub 2022 Oct 29. PMID: 36630415.
Using a network modeling approach, we estimate that the probability of a sexually transmitted infection–attributable HIV infection among men who have sex with men is 0.44% per gonococcal or chlamydial infection.
Using a network model, we simulated transmission of HIV, gonorrhea, and chlamydia among men who have sex with men to estimate the number of HIV infections that can be attributed to gonorrhea and chlamydia, per gonococcal and chlamydial infection. This metric can inform future modeling and health economic studies.