Seminars
Viral Dynamics Journal Club
Description
The Viral Dynamics Journal Club 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. Meetings will be a mixture of lectures by Dr. Sarah Holte on recent research articles and group questions and discussions about these articles.
The journal club is open to all investigators, and does NOT assume experience in mathematics or statistics. The goal of the journal club is to discuss the concepts of viral dynamics in a way that is relevant to clinical and laboratory scientists and to foster new ideas for ongoing and future studies of this type.
The CFAR Viral Dynamics Journal Club will meet once a month at both Harborview Medical Center and the Fred Hutchinson Center at Seattle Lake Union. For at least the first few meetings, similar material will be discussed at both locations; the two meeting locations are designed to allow as many people as possible to participate. Once the introductory material has been covered, the Harborview meetings will focus on examples from the hepatitis literature, and the Hutch meetings on examples from the HIV literature. Depending on interest level, other types of math modeling/viral dynamics literature will be discussed.
Please review the references (listed below) before the meeting time. If you cannot obtain the references (via PubMed, etc.), please contact Sarah Holte.
Contact info:
Sarah Holte, PhD
Phone: (206) 731-3647
E-mail: sholte@fhcrc.org
Meeting Times and Locations
Dates: 1st Monday of each month at 10am.
Location: Harborview Medical Center. Center for AIDS
Research Conference Room (3EC24, 3rd Floor East Clinic Room 24) or see scheduled
meetings below for room changes.
Maps: http://depts.washington.edu/cfas/contact/.
OR
Dates: 3rd Thursday of each month at 2 pm.
Location: Fred Hutchinson Cancer Research Center at South Lake
Union. Public Health Sciences (PHS) Arnold Building (Building M in map). Rooms
listed below for each scheduled meeting.
Maps: http://www.fhcrc.org/about/maps/
Meeting Schedule
Monday, May 1, 2006: Introduction to Viral Dynamics I.
Time and location: (NOTE: Room change from usual meeting
location.) 10am-Noon in STD Clinic Conference Room (Ground EC 25/26, Ground
Floor East Clinic Room 25/26).
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.
References:
- 1. 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
- 2. 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
Handouts: HMC-May1-2006.pdf
OR
Thursday, May 18, 2006: Introduction to Viral Dynamics I.
Time and location: 2-4pm at Fred Hutch at South Lake Union,
PHS Arnold Building, Room M3-C204 (Building M, 3rd floor, Room C204). If
you don’t have a Hutch entry card, meet at the receptionist desk on the
first floor main entrance to the PHS Arnold Building.
Description: See description of the Monday May 1, 2006 meeting
for details and references.
Handouts: FHCRC-May18-2006.pdf
Monday, June 5, 2006: Introduction to Viral Dynamics II.
Time and location: 10am-Noon in CFAR Conference Room (3EC24, 3rd Floor East Clinic Room 24).
Description: Introduction to most basic models used in both HIV and hepatitis (continued).
References:
- 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.
Handouts: HMC-FHCRC-June-2006.pdf
OR
Thursday June 15, 2006: Introduction to Viral Dynamics II.
Time and location: 2-4pm at Fred Hutch at South Lake Union, PHS Arnold Building. Room M1-A303 (Building M, 1st floor,
Room A303).
Description: See description of the Monday June 5, 2006 meeting for details and references.
Handouts: HMC-FHCRC-June-2006.pdf
Monday, July 3, 2006: Introduction to Viral Dynamics III and viremia blips.
Time and location: 10am-Noon in CFAR Conference Room (3EC24, 3rd Floor East Clinic Room 24).
Description: Introduction to most basic models used in both HIV and hepatitis (continued) and discussion of viremia blips.
References:
- Intermediate HIV-1 Viremia (Blips) and Drug Resistance in Patients Receiving HAART. Nettles RE, et.al. JAMA Feb 16 2005. Vol 293 No 7.pages 817-829.
OR
Thursday, July 20, 2006: Introduction to Viral Dynamics III and viremia blips.
Time and location: 2-4pm at Fred Hutch at South Lake Union, PHS Arnold Building. Room M1-A303 (Building M, 1st floor, Room A303).
Description: See description of the Monday July 3, 2006 meeting for details and references.
Monday, August 7, 2006: Hepatitis B and C viral dynamics.
Time and location: 10am-Noon in CFAR Conference Room (3EC24, 3rd Floor East Clinic Room 24).
Description: Discussion of hepatitis viral dynamics models, including effects of treatment. This meeting will be conducted more like a standard journal club meeting. Sarah Holte will lead the discussion of the paper, but there will not be a formal presentation.
References:
- 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.
- 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.
OR
Thursday, August 17, 2006: Title TBA.
Time and location: 2-4pm at Fred Hutch at South Lake Union, PHS Arnold Building. Room M2-A823 (Building M, 2nd floor, Room A823). If you don’t have a Hutch entry card, meet at the receptionist desk on the first floor main entrance to the PHS Arnold Building.
Description: See description of the Monday August 7, 2006 meeting for details and references.
Monday, September 11, 2006: Hepatitis B and C viral dynamics (continued).
Time and location: 10am-Noon in CFAR Conference Room (3EC24, 3rd Floor East Clinic Room 24).
Description: Review of basic models, with slightly more detailed discussion of what the diagrams and equations mean and how to interpret them. This review will include several papers that have not been previously discussed, and also the first Perelson paper covered in the first meeting. The second hour will focus on hepatitis C viral dynamics. We will begin to review a number of papers in the literature, and work through the papers listed below during upcoming meetings, as pace of discussion dictates.
References:
- Introductory review papers for first 30-60 minutes:
- 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.
-
From the first journal club meeting:
- HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Perelson AS. Neumann AU. Markowitz M. Leonard JM. Ho DD. Science. 271(5255):1582-6, 1996 Mar 15.
- Hepatitis C papers for remainder of September meeting and subsequent meetings:
- 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.
- 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
OR
Thursday, September 21, 2006: HIV relative fitness I.
Time and location: 2-4pm at Fred Hutch at South Lake Union,
PHS Arnold Building. Room M1-A303 (Building M, 1st floor, Room A303).
Description: Estimating relative fitness from times series data.
References:
If there is sufficient interest, we'll start with a brief review (~30 minutes)
of the basic ideas of mathematical models, based on the article:
- 1. 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. NOTE: This article has not yet been discussed at any journal club meetings, but precedes the articles discussed at the very first meeting.
We'll also begin a review of three articles on estimating relative fitness from times series data. We won't cover all three articles in one meeting, but will work through these articles over the next few meetings. We'll be starting with the Maree article on Thursday Sept 21.
- 2. 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.
- 3. 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.
- 4. 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.
October: No meetings will be held this month.
Monday, November 6, 2006: Hepatitis B and C viral dynamics.
Time and location: No hepatitis meeting held this month.
OR
Thursday, November 16, 2006: HIV relative fitness II.
Time and location: 2-4pm at Fred Hutch at South Lake Union, PHS Arnold Building. Room M1-A307 (Building M, 1st floor, Room A307).
Description: Estimating relative fitness from times series data (continued).
References: See September 21st meeting for references.
December: No meetings will be held this month.