From 82589313a382ad1484bafb627f61a24a1466438d Mon Sep 17 00:00:00 2001 From: andrew-phillips-1 <39617310+andrew-phillips-1@users.noreply.github.com> Date: Thu, 26 Sep 2024 12:28:43 +0100 Subject: [PATCH] adding transmission through breastfeeding --- hiv_synthesis.sas | 41 +++++++++++++++++++++++++++++++++-------- 1 file changed, 33 insertions(+), 8 deletions(-) diff --git a/hiv_synthesis.sas b/hiv_synthesis.sas index f1adb2df..119ad33c 100644 --- a/hiv_synthesis.sas +++ b/hiv_synthesis.sas @@ -185,7 +185,7 @@ newp_seed = 7; * prob_pregnancy_base; r=rand('uniform'); prob_pregnancy_base=0.06 + r*0.05; * rate_birth_with_infected_child; %sample(rate_birth_with_infected_child, 0.3 0.4 0.5 0.6, 0.05 0.25 0.6 0.1); - +* rate_trans_breastfeeding; %sample_uniform(rate_trans_breastfeeding, 0.05 0.1); * Nduati et al. 2000; * this is rate per 3 months with vl between 4 and 5; * prob_stop_breastfeeding_yr1; *JAS Apr2023; prob_stop_breastfeeding_yr1 = 0.02;*73; * 3-monthly probability of stopping breastfeeding in first year after birth; * dependent_on_time_step_length ; *ts1m - switch to 1-month probabilities; @@ -9872,6 +9872,29 @@ if t ge 2 then cd4=cd4_tm1+cc_tm1; if onart_birth_with_inf_child=1 and child_with_resistant_hiv=1 then onart_birth_with_inf_child_res=1; + +* TRANSMISSION TO CHILD DURING BREASTFEEDING ; * andrew sep 24; + + onart_breastfeeding=0; child_infected_breastfeeding=0; + + if breastfeeding=1 and hiv=1 and (date_last_birth_with_inf_child =. or caldate{t} - date_last_birth_with_inf_child > 1.5) + and (date_last_child_inf_bf = . or caldate{t} - date_last_child_inf_bf > 1.5) then do; * checking that if mtct ever occurred that this is a new child; + if onart=1 then onart_breastfeeding=1; + u=rand('uniform'); + if . < vl <= 3 then u=u*1000; + if 3 < vl <= 4 then u=u*2; + if 4 < vl <= 5 then u=u*1; + if 5 < vl then u=u/2; + if u < rate_trans_breastfeeding then do; + child_infected_breastfeeding=1; ever_child_inf_breastfeeding=1; date_last_child_inf_bf = caldate{t}; + end; + end; + + + + + + * NEW RESISTANCE MUTATIONS ARISING (and dominating) - if resistance appears between t-1 and t it doesnt affect the viral load until t+1; @@ -11959,7 +11982,7 @@ res_cost=0;t_adh_int_cost =0; cost_test=0; cost_prep_oral=0; cost_prep_inj =0; c * low cost partially is to take account of possibility of child dying ; * dependent_on_time_step_length ; -cost_child_hiv = 0; if ever_birth_with_inf_child=1 then cost_child_hiv = cost_child_hiv_a; +cost_child_hiv = 0; if ever_birth_with_inf_child=1 or ever_child_inf_breastfeeding=1 then cost_child_hiv = cost_child_hiv_a; cost_child_hiv_mo_art = 0; if ev_birth_with_inf_ch_onart=1 then cost_child_hiv_mo_art = cost_child_hiv_mo_art_a; @@ -16142,7 +16165,7 @@ end; *live dalys for the mother due to having given birth to a child with hiv; daly_mtct=0; ddaly_mtct=0; -if ever_birth_with_inf_child=1 then do; +if ever_birth_with_inf_child=1 or ever_child_inf_breastfeeding=1 then do; daly_mtct=0.025; ddaly_mtct = daly_mtct*discount; end; @@ -17238,6 +17261,8 @@ if 15 <= age and (death = . or caldate&j = death ) then do; s_birth_with_inf_child + birth_with_inf_child ; s_child_with_resistant_hiv + child_with_resistant_hiv ; s_give_birth_with_hiv + give_birth_with_hiv ; s_onart_birth_with_inf_child_res + onart_birth_with_inf_child_res ; s_onart_birth_with_inf_child + onart_birth_with_inf_child ; s_breastfeeding + breastfeeding ; s_plw + plw; + s_onart_breastfeeding + onart_breastfeeding; s_child_infected_breastfeeding + child_infected_breastfeeding; + /*circumcision*/ @@ -18839,7 +18864,7 @@ s_want_no_more_children s_pregnant_ntd s_pregnant_vlg1000 s_pregnant_o_dol s_pregnant_onart_vl_vhigh s_pregnant_onart_vl_vvhigh s_birth_with_inf_child s_child_with_resistant_hiv s_give_birth_with_hiv s_onart_birth_with_inf_child_res s_onart_birth_with_inf_child -s_breastfeeding s_plw +s_breastfeeding s_plw s_breastfeeding s_onart_breastfeeding s_child_infected_breastfeeding /*circumcision*/ s_mcirc s_mcirc_1519m s_mcirc_2024m s_mcirc_2529m s_mcirc_3034m s_mcirc_3539m s_mcirc_4044m s_mcirc_4549m @@ -18893,7 +18918,7 @@ prob_lossdiag_adctb prob_lossdiag_non_tb_who3e higher_newp_less_engagement fo rate_test_startprep_any rate_choose_stop_prep_oral prob_prep_oral_b circ_inc_rate circ_red_10_14 circ_inc_15_19 circ_red_20_30 circ_red_30_50 p_hard_reach_w hard_reach_higher_in_men p_hard_reach_m inc_cat base_rate_sw prob_prep_any_restart_choice add_prep_any_uptake_sw cd4_monitoring base_rate_stop_sexwork rred_a_p higher_newp_with_lower_adhav -rr_int_tox rate_birth_with_infected_child incr_mort_risk_dol_weightg +rr_int_tox rate_birth_with_infected_child rate_trans_breastfeeding incr_mort_risk_dol_weightg greater_disability_tox greater_tox_zdv rel_dol_tox dol_higher_potency prop_bmi_ge23 pr_res_dol cab_time_to_lower_threshold_g ntd_risk_dol oth_dol_adv_birth_e_risk ntd_risk_dol double_rate_gas_tox_taz zdv_potency_p75 sw_program sw_higher_int rel_sw_lower_adh sw_higher_prob_loss_at_diag rate_engage_sw_program rate_disengage_sw_program @@ -19805,7 +19830,7 @@ s_want_no_more_children s_pregnant_ntd s_pregnant_vlg1000 s_pregnant_o_dol s_pregnant_onart_vl_vhigh s_pregnant_onart_vl_vvhigh s_birth_with_inf_child s_child_with_resistant_hiv s_give_birth_with_hiv s_onart_birth_with_inf_child_res s_onart_birth_with_inf_child -s_breastfeeding s_plw +s_breastfeeding s_plw s_onart_breastfeeding s_child_infected_breastfeeding /*circumcision*/ s_mcirc s_mcirc_1519m s_mcirc_2024m s_mcirc_2529m s_mcirc_3034m s_mcirc_3539m s_mcirc_4044m s_mcirc_4549m @@ -20663,7 +20688,7 @@ s_want_no_more_children s_pregnant_ntd s_pregnant_vlg1000 s_pregnant_o_dol s_pregnant_onart_vl_vhigh s_pregnant_onart_vl_vvhigh s_birth_with_inf_child s_child_with_resistant_hiv s_give_birth_with_hiv s_onart_birth_with_inf_child_res s_onart_birth_with_inf_child -s_breastfeeding s_plw +s_breastfeeding s_plw s_breastfeeding s_onart_breastfeeding s_child_infected_breastfeeding /*circumcision*/ s_mcirc s_mcirc_1519m s_mcirc_2024m s_mcirc_2529m s_mcirc_3034m s_mcirc_3539m s_mcirc_4044m s_mcirc_4549m @@ -20719,7 +20744,7 @@ prob_lossdiag_adctb prob_lossdiag_non_tb_who3e higher_newp_less_engagement fo rate_test_startprep_any rate_choose_stop_prep_oral prob_prep_oral_b circ_inc_rate circ_red_10_14 circ_inc_15_19 circ_red_20_30 circ_red_30_50 p_hard_reach_w hard_reach_higher_in_men p_hard_reach_m inc_cat base_rate_sw prob_prep_any_restart_choice add_prep_any_uptake_sw cd4_monitoring base_rate_stop_sexwork rred_a_p higher_newp_with_lower_adhav -rr_int_tox rate_birth_with_infected_child nnrti_res_no_effect double_rate_gas_tox_taz incr_mort_risk_dol_weightg +rr_int_tox rate_birth_with_infected_child rate_trans_breastfeeding nnrti_res_no_effect double_rate_gas_tox_taz incr_mort_risk_dol_weightg greater_disability_tox greater_tox_zdv rel_dol_tox dol_higher_potency prop_bmi_ge23 pr_res_dol cab_time_to_lower_threshold_g ntd_risk_dol oth_dol_adv_birth_e_risk zdv_potency_p75 death_r_iris_pop_wide_tld sw_program sw_higher_int rel_sw_lower_adh sw_higher_prob_loss_at_diag rate_engage_sw_program rate_disengage_sw_program