Course 2012
Virology – Biology W3310
Spring 2012
This Columbia University virology course is offered each year in the spring semester. Below are the complete, archived course materials for the Spring 2012 version of this course. Materials for the 2013 virology course can be found at virology.ws/course.
Course Name: Virology
Sessions: M, W 4:10 – 5:25 PM
Start date: Wednesday, January 18, 2012
Points: 3
Location: Hamilton Hall 517
Course #: Biology W3310.001
Instructors: Prof. V. Racaniello, Prof. S. Silverstein
Description
The basic thesis of the course is that all viruses adopt a common strategy. The strategy is simple:
1. Viral genomes are contained in metastable particles.
2. Genomes encode gene products that promote an infectious cycle (mechanisms for genomes to enter cells, replicate, and exit in particles).
3. Infection patterns range from benign to lethal; infections can overcome or co-exist with host defenses.
Despite the apparent simplicity, the tactics evolved by particular virus families to survive and prosper are remarkable. This rich set of solutions to common problems in host/parasite interactions provides significant insight and powerful research tools. Virology has enabled a more detailed understanding of the structure and function of molecules, cells and organisms and has provided fundamental understanding of disease and virus evolution.
The course will emphasize the common reactions that must be completed by all viruses for successful reproduction within a host cell and survival and spread within a host population. The molecular basis of alternative reproductive cycles, the interactions of viruses with host organisms, and how these lead to disease are presented with examples drawn from a set of representative animal and human viruses, although selected bacterial viruses will be discussed.
Textbook
The recommended textbook is Principles of Virology. Vol I: Molecular Biology, Vol. II: Pathogenesis and Control (S.J. Flint et al., Third Edition, ASM Press 2009).
Other course resources
1. Students are expected to read Prof. Racaniello’s virology blog which will contain information relevant to the course.
2. Students are expected to listen to the weekly podcast “This Week in Virology”, produced by Prof. Racaniello, for additional material about viruses relevant to the course. You can subscribe to TWiV at iTunes or at the Zune Marketplace.
3. Lecture slides (pdf) will be posted at Courseworks and at this website before each class.
4. Videocasts of all lectures (slides plus audio) will be posted at Courseworks, at this website, and at iTunes University.
Lecture Schedule, Spring 2012
Note: Several videocast file types are available – right-click and save as to download.
| Date | Topic | Reading | Lecturer | Slides | Videocast (right click, save as) |
| 1/18 | Lecture 1 What is a virus? |
Flint vol 1 chapter 1
Are viruses alive? (take the poll on the last webpage) |
VRR | iPod iPhone iPad mac pc |
|
| 1/23 | Lecture 2 The infectious cycle |
Flint vol 1 chapter 2
Influenza virus growth in eggs |
VRR | iPod iPhone iPad mac pc |
|
| 1/25 | Lecture 3 Genomes and genetics |
Flint vol 1 chapter 3
Simplifying virus classification: The Baltimore system Clinical benefit of lentiviral gene therapy in two patients with a rare neurological disease |
VRR | iPod iPhone iPad mac pc |
|
| 1/30 | Lecture 4 Structure of viruses |
Flint vol 1 chapter 4 | VRR | iPod iPhone iPad mac pc |
|
| 2/01 | Lecture 5 Attachment & entry |
Flint vol 1 chapter 5
Influenza virus attachment to cells Influenza virus attachment to cells – Role of different sialic acids |
VRR | iPod iPhone iPad mac pc |
|
| 2/06 | Lecture 6 RNA-directed RNA synthesis |
Flint vol 1 chapter 6 | VRR | iPod iPhone iPad mac pc |
|
| 2/08 | Lecture 7 Replication of DNA virus genomes |
Flint vol 1 chapter 9 | SJS | iPod iPhone iPad mac pc |
|
| 2/13 | Exam I | Lectures 1-7 | Review questions (pdf) | ||
| 2/15 | Lecture 8 Transcription and RNA processing |
Flint vol 1 chapters 8, 10 | SJS | iPod iPhone iPad mac pc |
|
| 2/20 | Lecture 9 Reverse transcription and integration |
Flint vol 1 chapter 7 | VRR | iPod iPhone iPad mac pc |
|
| 2/22 | Lecture 10 Translation |
Flint vol 1 chapter 11 | VRR | iPod iPhone iPad mac pc |
|
| 2/27 | Lecture 11 Assembly |
Flint vol 1 chapters 12, 13 | VRR | iPod iPhone iPad mac pc |
|
| 2/29 | Lecture 12 Infection basics |
Flint vol 2 chapters 1,2 | VRR | iPod iPhone iPad mac pc |
|
| 3/05 | Lecture 13 Host defense |
Flint vol 2 chapter 4 | VRR | iPod iPhone iPad mac pc |
|
| 3/07 | Lecture 14 Viral evasion strategies |
Flint vol 2 chapters 3, 4 | SJS | iPod iPhone iPad mac pc |
|
| 3/12 – 3/14 | Spring Recess | ||||
| 3/19 | Lecture 15 Virus-host interactions |
Flint vol 2 chapters 2, 4 | VRR | iPod iPhone iPad mac pc |
|
| 3/21 | Exam II | Lectures 8-15 | Review questions (pdf) | ||
| 3/26 | Lecture 16 Persistent infections |
Flint vol 2 chapter 5 | SJS | iPod iPhone iPad mac pc |
|
| 3/28 | Lecture 17 Acute infections |
Flint vol 2 chapter 5 | VRR | iPod iPhone iPad mac pc |
|
| 4/02 | Lecture 18 HIV pathogenesis |
Flint vol 2 chapter 6 | VRR | iPod iPhone iPad mac pc |
|
| 4/04 | Lecture 19 Transformation and oncogenesis |
Flint vol 2 chapter 7 | VRR | iPod iPhone iPad mac pc |
|
| 4/09 | Lecture 20 Vaccines |
Flint vol 2 chapter 8 | VRR | iPod iPhone iPad mac pc |
|
| 4/11 | Lecture 21 Antivirals |
Flint vol 2 chapter 9
New hepatitis C virus antiviral drugs |
VRR | iPod iPhone iPad mac pc |
|
| 4/16 | Lecture 22 Evolution |
Flint vol 2 chapter 10 pp 311-333 | VRR | iPod iPhone iPad mac pc |
|
| 4/18 | Lecture 23 Emerging viruses |
Flint vol 2 chapter 10
Lujo virus, a new hemorrhagic fever virus from Southern Africa |
VRR | iPod iPhone iPad mac pc |
|
| 4/23 | Lecture 24 Unusual infectious agents |
Flint vol 2 Appendix A | VRR | iPod iPhone iPad mac pc |
|
| 4/25 | Lecture 25 XMRV |
Flint vol 1 chapter 7
Why John Coffin doesn’t sleep well |
VRR | iPod iPhone iPad mac pc |
|
| 4/30 | Lecture 26 H5N1 |
TWiV 177: Live in Dublin | VRR | iPod iPhone iPad mac pc |
|
| 5/07 | Final exam | Lectures 16-26 | Review questions (pdf) |
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