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Xin hpv infection process by tdm32 · Pull Request #1860 · UCL/TLOmodel · GitHub

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Xin hpv infection process #1860

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Xin hpv infection process #1860

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6af9c18
This is the first draft of HPV model
Liuxinac Mar 2, 2026
8a7bb49
Add 3 HPV groups, simple sexual mixing, and self-clearance
Liuxinac Mar 25, 2026
8d221b9
add group-specific HPV self-clearance timing and annual logging
Liuxinac Apr 1, 2026
bb183fc
Update HPV module: add natural immunity, HIV/age/vaccination modifier…
Liuxinac Apr 14, 2026
b535f42
Add HPV resource files
Liuxinac Apr 14, 2026
3ccf652
Update HPV module: add natural immunity, HIV/age/vaccination modifier…
Liuxinac Apr 15, 2026
42bfc28
Update HPV self-clearance process
Liuxinac Apr 15, 2026
68dbf74
Refine HPV self-clearance logic
Liuxinac Apr 27, 2026
f465f10
HPV Transmission Model Version 1.0
Liuxinac Apr 30, 2026
4e540d6
HPV Transmission Model Version 1.0
Liuxinac May 5, 2026
48216f9
HPV Transmission Model Version 2.0
Liuxinac May 21, 2026
20c99c1
HPV Transmission Model 4-HPV groups Version
Liuxinac Jun 30, 2026
9f6bf7d
HPV Transmission Model 6-HPV groups Version
Liuxinac Aug 14, 2026
247e5a0
HPV Transmission Model Flexible for different timestep
Liuxinac Sep 22, 2026
5241fb3
HPV Transmission Model Flexible for different timestep
Liuxinac Sep 22, 2026
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2 changes: 1 addition & 1 deletion resources/ResourceFile_Cervical_Cancer/parameter_values.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -52,4 +52,4 @@ months_to_next_appt_treated_less_than_12_mo_ago,3,local,1,36,vague prior,Missing
months_to_next_appt_treated_12_to_36_mo_ago,6,local,1,36,vague prior,Missing
months_to_next_appt_treated_36_to_60_mo_ago,12,local,1,36,vague prior,Missing
palliative_care_interval_months,1,local,0.5,12,vague prior,Missing
main_polling_frequency_months,1,undetermined,1,12,design decision,N/A
main_polling_frequency_months,1,undetermined,1,12,design decision,N/A
40 changes: 40 additions & 0 deletions resources/ResourceFile_HPV/parameter_values.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,40 @@
parameter_name,value,param_label,prior_min,prior_max,prior_note,reference
hiv_pos_init_prev_hpv_hr1,0.05,undetermined,0,1,calibration,"Cubie HA, Morton D, Kawonga E, Mautanga M, Mwenitete I, Teakle N, Ngwira B, Walker H, Walker G, Kafwafwa S, Kabota B, Ter Haar R, Campbell C. HPV prevalence in women attending cervical screening in rural Malawi using the cartridge-based Xpert® HPV assay. J Clin Virol. 2017 Feb;87:1-4. doi: 10.1016/j.jcv.2016.11.014. "
hiv_pos_init_prev_hpv_hr2,0.044,undetermined,0,1,calibration,"Cubie HA, Morton D, Kawonga E, Mautanga M, Mwenitete I, Teakle N, Ngwira B, Walker H, Walker G, Kafwafwa S, Kabota B, Ter Haar R, Campbell C. HPV prevalence in women attending cervical screening in rural Malawi using the cartridge-based Xpert® HPV assay. J Clin Virol. 2017 Feb;87:1-4. doi: 10.1016/j.jcv.2016.11.014. "
hiv_pos_init_prev_hpv_hr3,0.01,undetermined,0,1,calibration,"Cubie HA, Morton D, Kawonga E, Mautanga M, Mwenitete I, Teakle N, Ngwira B, Walker H, Walker G, Kafwafwa S, Kabota B, Ter Haar R, Campbell C. HPV prevalence in women attending cervical screening in rural Malawi using the cartridge-based Xpert® HPV assay. J Clin Virol. 2017 Feb;87:1-4. doi: 10.1016/j.jcv.2016.11.014. "
hiv_pos_init_prev_hpv_hr4,0.075,undetermined,0,1,calibration,"Cubie HA, Morton D, Kawonga E, Mautanga M, Mwenitete I, Teakle N, Ngwira B, Walker H, Walker G, Kafwafwa S, Kabota B, Ter Haar R, Campbell C. HPV prevalence in women attending cervical screening in rural Malawi using the cartridge-based Xpert® HPV assay. J Clin Virol. 2017 Feb;87:1-4. doi: 10.1016/j.jcv.2016.11.014. "
hiv_pos_init_prev_hpv_hr5,0.085,undetermined,0,1,calibration,
hiv_pos_init_prev_hpv_hr6,0.055,undetermined,0,1,calibration,
hiv_neg_init_prev_hpv_hr1,0.022,undetermined,0,1,calibration,
hiv_neg_init_prev_hpv_hr2,0.018,undetermined,0,1,calibration,
hiv_neg_init_prev_hpv_hr3,0.006,undetermined,0,1,calibration,
hiv_neg_init_prev_hpv_hr4,0.03,undetermined,0,1,calibration,
hiv_neg_init_prev_hpv_hr5,0.036,undetermined,0,1,calibration,
hiv_neg_init_prev_hpv_hr6,0.03,undetermined,0,1,calibration,
b_hpv,0.75,undetermined,0,1,calibration,N/A
rr_hpv_hiv_no_art,2.6,undetermined,0,1,calibration,"Liu G, Sharma M, Tan N, Barnabas RV. HIV-positive women have higher risk of human papilloma virus infection, precancerous lesions, and cervical cancer. AIDS. 2018 Mar 27;32(6):795-808. doi: 10.1097/QAD.0000000000001765. PMID: 29369827; PMCID: PMC5854529."
rr_hr1_vaccinated,0.1,undetermined,0,1,calibration,"Basu P, et al. Vaccine efficacy against persistent human papillomavirus (HPV) 16/18 infection at 10 years after one, two, and three doses of quadrivalent HPV vaccine in girls in India: a multicentre, prospective, cohort study. Lancet Oncol. 2021 Nov;22(11):1518-1529. doi: 10.1016/S1470-2045(21)00453-8. Epub 2021 Oct 8. Erratum in: Lancet Oncol. 2022 Jan;23(1):e16. doi: 10.1016/S1470-2045(21)00700-2. "
rr_hr2_vaccinated,0.1,undetermined,0,1,calibration,N/A
rr_hr3_vaccinated,0.9,undetermined,0,1,calibration,N/A
rr_hr4_vaccinated,0.9,undetermined,0,1,calibration,N/A
rr_hr5_vaccinated,0.9,undetermined,0,1,calibration,
rr_hr6_vaccinated,0.9,undetermined,0,1,calibration,
rr_hpv_age50plus,0.5,undetermined,0,1,calibration,"Mchome B, Linde DS, Manongi R, Waldstroem M, Lftner T, Wu C, Mwaisalage J, Rasch V, Kjaer SK. Incident detection of human papillomavirus - a prospective follow-up study among Tanzanian women with a focus on HIV status. Int J Infect Dis. 2021 Sep;110:165-170. doi: 10.1016/j.ijid.2021.07.011. "
median_clear_hr1,14,undetermined,0,1,calibration,"Muñoz N, Méndez F, Posso H, Molano M, van den Brule AJ, Ronderos M, Meijer C, Muñoz A; Instituto Nacional de Cancerologia HPV Study Group. Incidence, duration, and determinants of cervical human papillomavirus infection in a cohort of Colombian women with normal cytological results. J Infect Dis. 2004 Dec 15;190(12):2077-87. doi: 10.1086/425907. Epub 2004 Nov 22. PMID: 15551205."
median_clear_hr2,12,undetermined,0,1,calibration,"Muñoz N, Méndez F, Posso H, Molano M, van den Brule AJ, Ronderos M, Meijer C, Muñoz A; Instituto Nacional de Cancerologia HPV Study Group. Incidence, duration, and determinants of cervical human papillomavirus infection in a cohort of Colombian women with normal cytological results. J Infect Dis. 2004 Dec 15;190(12):2077-87. doi: 10.1086/425907. Epub 2004 Nov 22. PMID: 15551205."
median_clear_hr3,12,undetermined,0,1,calibration,"Muñoz N, Méndez F, Posso H, Molano M, van den Brule AJ, Ronderos M, Meijer C, Muñoz A; Instituto Nacional de Cancerologia HPV Study Group. Incidence, duration, and determinants of cervical human papillomavirus infection in a cohort of Colombian women with normal cytological results. J Infect Dis. 2004 Dec 15;190(12):2077-87. doi: 10.1086/425907. Epub 2004 Nov 22. PMID: 15551205."
median_clear_hr4,12,undetermined,0,1,calibration,"Muñoz N, Méndez F, Posso H, Molano M, van den Brule AJ, Ronderos M, Meijer C, Muñoz A; Instituto Nacional de Cancerologia HPV Study Group. Incidence, duration, and determinants of cervical human papillomavirus infection in a cohort of Colombian women with normal cytological results. J Infect Dis. 2004 Dec 15;190(12):2077-87. doi: 10.1086/425907. Epub 2004 Nov 22. PMID: 15551205."
median_clear_hr5,12,undetermined,0,1,calibration,
median_clear_hr6,12,undetermined,0,1,calibration,
clear_shape,0.7,undetermined,0,1,calibration,N/A
rr_clear_hiv_no_art,0.72,undetermined,0,1,calibration,"Liu G, Sharma M, Tan N, Barnabas RV. HIV-positive women have higher risk of human papilloma virus infection, precancerous lesions, and cervical cancer. AIDS. 2018 Mar 27;32(6):795-808. doi: 10.1097/QAD.0000000000001765.
"
age_mixing_within,0.7,undetermined,0,1,calibration,"Reed DM. Age-disparate and intergenerational sex partnerships and HIV: the role of gender norms among adolescent girls and young women in Malawi. BMC Public Health. 2024 Feb 22;24(1):575. doi: 10.1186/s12889-024-17868-5.
"
age_mixing_adjacent,0.23,undetermined,0,1,calibration,"Reed DM. Age-disparate and intergenerational sex partnerships and HIV: the role of gender norms among adolescent girls and young women in Malawi. BMC Public Health. 2024 Feb 22;24(1):575. doi: 10.1186/s12889-024-17868-5.
"
age_mixing_distant,0.07,undetermined,0,1,calibration,"Reed DM. Age-disparate and intergenerational sex partnerships and HIV: the role of gender norms among adolescent girls and young women in Malawi. BMC Public Health. 2024 Feb 22;24(1):575. doi: 10.1186/s12889-024-17868-5.
"
hpv_event_frequency_months,1,undetermined,0,1,calibration,N/A
hpv_logging_frequency_months,6,undetermined,0,1,calibration,N/A
persistent_threshold_months,12,undetermined,0,1,calibration,N/A
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