Viral Dynamics Mathematical Modeling Training

The Viral Dynamics Primer is intended to introduce the concepts of viral dynamics to researchers who are conducting studies of this type, are analyzing data from studies of this type, or who would like to learn more about research in this area. No experience in mathematics or statistics is assumed.  If you have any questions about this service, please contact Sarah Holte at sholte at

Introduction To Concepts:
Description: Introduction to most basic models used in both HIV and hepatitis. Most other models in the literature are refinements and extension of these models.
•           Viral dynamics in human immunodeficiency virus type 1 infection.  Xiping Wei, Sajal K. Ghosh, Maria E. Taylor, Victoria A. Johnson, Emilio A. Emini, Paul Deutsch, Jeffrey D. Lifson, Sebastian Bonhoeffer, Martin A. Nowak, Beatrice H. Hahn, Michael S. Saag & George M. Shaw.   Nature Jan 12 1995, Vol 373 pp 117-122.
•           Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection.  David D. Ho, Avidan U. Neumann, Alan S. Perelson, Wen Chen, John M. Leonard & Martin Markowitz.  Nature Jan 12 1995, Vol 373 pp 117-122. Nature Jan 12 1995, Vol 373 pp 123-126. 
•           HIV-1 Dynamics in Vivo: Virion Clearance Rate, Infected Cell Life-Span, and Viral Generation Time Alan S. Perelson, Avidan U. Neumann, Martin Markowitz, John M. Leonard, and David D. Ho Science 15 March 1996 271: 1582-1586
•           Decay characteristics of HIV-1-infected compartments during combination therapy Alan S Perelson,  Paulina Essunger,  Yunzhen Cao,  Mika Vesanen,  et al. Nature. London: May 8, 1997.Vol.387, Iss. 6629;  pg. 188
•           Density-dependent decay in HIV-1 dynamics.  Sarah Holte, Ann Melvin, James Mullins, Nicole Tobin, Lisa Frenkel.  J Acquir Immune Defic Syndr.  2006 Mar;41(3):266-76.
Viremia Blips.
Description: Examination of blips as random variation around a low-level steady state.
•           Intermediate HIV-1 Viremia (Blips) and Drug Resistance in Patients Receiving HAART. Nettles RE, JAMA Feb 16 2005. Vol 293 No 7.pages 817-829.
HIV Relative Fitness. 
Description: Estimating relative fitness from time series data.
•           Estimating relative fitness in viral competition experiments. Maree AF. Keulen W. Boucher CA. De Boer RJ. Journal of Virology. 74(23):11067-72, 2000 Dec.
•           Procedures for reliable estimation of viral fitness from time-series data.  Bonhoeffer S. Barbour AD. De Boer RJ.  Proceedings. Biological Sciences/The Royal Society. 269(1503):1887-93, 2002 Sep 22.
•           Modeling and estimation of replication fitness of human immunodeficiency virus type 1 in vitro experiments by using a growth competition assay.  Wu H. Huang Y. Dykes C. Liu D. Ma J. Perelson AS. Demeter LM.  Journal of Virology. 80(5):2380-9, 2006 Mar.
Hepatitis B and C Viral Dynamics. 
Description:  Hepatitis viral dynamics models, including effects of treatment. 
•           Hepatitis C virus dynamics in vivo: effect of ribavirin and interferon alfa on viral turnover.  Zeuzem S, Schmidt JM, Lee, J-H, et al.  Hepatology 1998; 28:245-52.
•           Hepatitis C viral dynamics in vivo and the antiviral efficacy of interferon-alpha therapy. Neumann AU, Lam NP, Dahari H, Gretch DR, Wiley TE, Layden TJ, Perelson AS.  Science. 1998 Oct 2;282(5386):103-7.
•           Effect of ribavirin on hepatitis C viral kinetics in patients treated with pegylated interferon.  Herrmann E, Lee J-H, Marinos G, et al.   Hepatology 2003; 1351-58.
•           Modelling how ribavirin improves interferon response rates in hepatitis C virus infection. Dixit NM, Layden-Almer JE, Layden T, et al.  Nature 2004; 432(7019):922-4
•           Kinetics of hepatitis B viral load during 48 weeks of treatment with 600 mg vs 100 mg of lamivudine daily.  Wang CC, Holte S, Huang ML, Sacks SL, Engelberg R, Ferrenberg J, Shuhart M, Corey L. J Viral Hepat. 2004 Sep;11(5):443-7.