This is a COPASI version of the HIV/HPV coinfection model submitted to PLoS One.

Title: Modeling the mechanisms by which HIV-associated immunosuppression influences HPV persistence at the oral mucosa

Authors: Meghna Verma*, Samantha Erwin*, Vida Abedi, Raque Hontecillas, Stefan Hoops, Andrew Leber, Josep Bassaganya-Riera, Stanca Ciupe

* Contributed equally to the work

Corresponding Authors: Josep Bassaganya-Riera and Stanca Ciupe
 4.0 inactive inactive inactive inactive inactive inactive inactive inactive inactive inactive inactive inactive inactive inactive inactive inactive inactive inactive inactive inactive inactive inactive Sharif Shohan Mohammad Umer msharifshohan@ebi.ac.uk EMBL-EBI Bassaganya-Riera Josep jbassaga@vt.edu VT Hontecillas Raquel rmagarzo@vt.edu VT Hoops Stefan shoops@vbi.vt.edu VT Ciupe Stanca stanca@math.vt.edu VT Abedi Vida abedi@vt.edu VT Verma Meghna meghna89@vt.edu VT Erwin Samantha sherwin@vt.edu VT Leber Andrew ajleber@vt.edu VT 2015-12-16T13:33:59Z 2015-12-16T13:33:59Z Modeling the Mechanisms by Which HIV-Associated Immunosuppression Influences HPV Persistence at the Oral Mucosa 2015-12-16T13:33:59Z msharifshohan@ebi.ac.uk Sharif Shohan Mohammad Umer EMBL-EBI ajleber@vt.edu Leber Andrew VT abedi@vt.edu Abedi Vida VT jbassaga@vt.edu Bassaganya-Riera Josep VT rmagarzo@vt.edu Hontecillas Raquel VT stanca@math.vt.edu Ciupe Stanca VT shoops@vbi.vt.edu Hoops Stefan VT meghna89@vt.edu Verma Meghna VT sherwin@vt.edu Erwin Samantha VT 2015-12-16T13:33:59Z 2016-04-27T12:05:45Z a s13 s16 a s16 s13 2016-05-02T15:49:09Z b omega s13 s16 s4 omega s13 s16 s16 b s4 2016-05-02T14:10:10Z k1 mu s12 mu k1 s12 2019-11-22T10:36:42Z beta e_rt s2 s4 1 e_rt beta s4 s2 2019-11-22T10:36:42Z k2 mu s13 mu k2 s13 2016-04-18T10:29:39Z N2 p phi psi s12 s14 s2 psi s14 1 p s2 N2 s12 phi 1 p s2 N2 s12 2016-04-27T12:03:35Z a s12 s16 a s12 s16 2016-05-02T12:16:37Z N1 delta e_pi s3 1 e_pi N1 delta s3 2019-11-22T10:36:42Z omega s13 s16 omega s13 s16 2016-04-27T12:05:53Z epi r s13 r epi s13 2019-11-22T10:36:29Z v v 2016-02-09T15:04:47Z 
HIV
 inside UNKNOWN HIV 2016-01-20T12:54:05Z 
HIV infected cells
 inside UNKNOWN HIV-Infected 2016-01-20T12:54:26Z 
CD4+ T cells
 inside UNKNOWN T 2016-01-20T12:48:52Z 
HPV
 inside UNKNOWN HPV 2016-01-20T12:50:08Z 
HPV specific CTL
 inside UNKNOWN Effector cells 2015-12-17T10:50:26Z 
HPV self-proliferating cells
 inside UNKNOWN HPV-oncogenic 2016-01-20T12:54:52Z 
HPV infected cells
 inside UNKNOWN HPV-infected 2016-01-20T12:54:46Z 2016-05-02T12:23:16Z 2016-05-02T12:23:11Z 2016-05-02T14:05:23Z 2016-05-02T16:09:06Z 2016-05-02T16:21:25Z 2016-05-02T16:43:18Z 2016-05-02T17:34:28Z 2016-05-02T17:35:55Z 2016-05-02T16:48:09Z 2016-05-02T17:35:54Z beta s4 s2 c1 N1 s4 d s4 beta s4 s2 
N1 - Ciupe MS, Bivort BL, Bortz DM, Nelson PW. Estimating kinetic parameters from HIV primary infection data through the eyes of three different mathematical models. Math Biosci. 2006;200:1-27.

delta - Klatt NR, Shudo E, Ortiz AM, Engram JC, Paiardini M, Lawson B, et al. CD8+ lymphocytes control viral replication in SIVmac239-infected rhesus macaques without decreasing the lifespan of productively infected cells. PLoS Pathog. 2010; 6:1-11.
 STATE_TRANSITION 2015-12-16T13:34:07Z default Rate_Law_for_Production_of_HIV_virion_1 N1 delta e_pi s3 
Ramratnam B, Bonhoeffer S, Binley J, Hurley A, Zhang L, Mittler JE, et al.  Rapid production and clearance of HIV-1 and hepatitis C virus assessed by large volume plasma apheresis. Lancet. 1999;354:1782-5.
 STATE_TRANSITION 2016-01-19T15:02:45Z default c1 s2 STATE_TRANSITION 2016-01-19T15:10:00Z default Rate_Law_for_production_of_HIV_infected_cells_1 beta e_rt s2 s4 STATE_TRANSITION 2016-01-19T15:12:09Z default Constant_flux__irreversible s 
Mohri H, Perelson AS, Tung K, Ribeiro RM, Ramratnam B, Markowitz M, et al. Increased turnover of T lymphocytes in HIV-1 infection and its reduction by antiretroviral therapy. J Exp Med. 2001;194:1277-88.
 STATE_TRANSITION 2016-01-19T15:13:00Z default d s4 
Klatt NR, Shudo E, Ortiz AM, Engram JC, Paiardini M, Lawson B, et al. CD8+ lymphocytes control viral replication in SIVmac239-infected rhesus macaques without decreasing the lifespan of productively infected cells. PLoS Pathog. 2010; 6:1-11.
 STATE_TRANSITION 0.5989307501543264,-0.49011499331677466 2016-01-19T15:09:09Z default k1 s3 
Murall CL, Bauch CT, Day T. Could the human papillomavirus vaccines drive virulence evolution? Proc Biol Sci. 2015;282:20141069.
 STATE_TRANSITION 2016-01-19T13:10:53Z default epi s12 
Murall CL, Bauch CT, Day T. Could the human papillomavirus vaccines drive virulence evolution? Proc Biol Sci. 2015;282:20141069.
 STATE_TRANSITION 0.6986661182795828,-0.027215403204690958 0.6843999795029223,-0.39345167488350485 0.9842187947201655,-0.4051306295816144 2015-12-16T13:35:04Z default Rate_Law_for_Production_of_HPV_due_to_HPVinfected_1 k1 mu s12 
Murall CL, Bauch CT, Day T. Could the human papillomavirus vaccines drive virulence evolution? Proc Biol Sci. 2015;282:20141069.
 STATE_TRANSITION 2015-12-16T13:37:02Z default Death_of_HPV_self_proliferating_due_to_Effector_cells a s12 s16 
Murall CL, Bauch CT, Day T. Could the human papillomavirus vaccines drive virulence evolution? Proc Biol Sci. 2015;282:20141069.
 STATE_TRANSITION 2015-12-16T13:38:45Z default k1 s13 STATE_TRANSITION 2015-12-16T13:39:18Z default Logistic_term_for_Effector_cells_1 b omega s13 s16 s4 
Murall CL, Bauch CT, Day T. Could the human papillomavirus vaccines drive virulence evolution? Proc Biol Sci. 2015;282:20141069.
 STATE_TRANSITION 2015-12-16T13:39:50Z default Death_of_HPV_self_proliferating_cells_due_to_effector_cells a s13 s16 
Murall CL, Bauch CT, Day T. Could the human papillomavirus vaccines drive virulence evolution? Proc Biol Sci. 2015;282:20141069.
 STATE_TRANSITION 0.0777351247600766,0.26775431861804266 2015-12-16T13:40:53Z default mu s12 
Murall CL, Bauch CT, Day T. Could the human papillomavirus vaccines drive virulence evolution? Proc Biol Sci. 2015;282:20141069.
 STATE_TRANSITION 0.2887192139635619,0.45316710985223274 2015-12-16T13:41:28Z default k1 s14 
Murall CL, Bauch CT, Day T. Could the human papillomavirus vaccines drive virulence evolution? Proc Biol Sci. 2015;282:20141069.
 STATE_TRANSITION 0.6245118465704547,-0.4842486965017212 2015-12-16T13:42:01Z default Proliferation_of_HPV_self_proliferating epi r s13 
Murall CL, Bauch CT, Day T. Could the human papillomavirus vaccines drive virulence evolution? Proc Biol Sci. 2015;282:20141069.
 STATE_TRANSITION 2015-12-16T13:42:58Z default Productionof_HPV_infected_cells N2 p phi psi s12 s14 s2 
Murall CL, Bauch CT, Day T. Could the human papillomavirus vaccines drive virulence evolution? Proc Biol Sci. 2015;282:20141069.
 STATE_TRANSITION 2015-12-17T10:50:57Z default Rate_Law_for_Production_of_Effector_cell_1_1 omega s13 s16 
Murall CL, Bauch CT, Day T. Could the human papillomavirus vaccines drive virulence evolution? Proc Biol Sci. 2015;282:20141069.
 2016-04-26T13:07:00Z default Production_of_HPV_due_to_HPV_self_proliferating_1 k2 mu s13