Virology – Biology W3310/4310

Spring 2014

Click here for all materials from the 2013 virology course

viral video

This Columbia University virology course is offered each year in the spring semester.

Prerequisite: Two semesters of a rigorous, molecularly-oriented Introductory Biology course (such as C2005), or the Instructor’s permission (

Course Name: Virology
Sessions: M, W 4:10 – 5:25 PM
Start date: Wednesday, January 22, 2014
Points: 3
Location: Northwest Corner 501
Course #: Biology W3310.001 or W4310.001
Instructor: Prof. V. Racaniello


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.


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 should read Prof. Racaniello’s virology blog for information relevant to the course.

2. Students should 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.

3. Lecture slides (pdf) will be posted at this website before each class.

4. Videocasts of all lectures (slides plus audio) will be posted at this website.

Click here for material from the 2013 virology course

Lecture Schedule, Spring 2014
Note: Several videocast file types are available: Large works for desktops, laptops, and tablets; small works for smartphones. Right-click and save as to download. Videos are also available at YouTube.

Date Topic Reading Slides Videocast
1/22 Lecture 1: What is a virus? Flint Vol I Chp 1
The virus and the virion
Cell size and scale
pdf Large Small YouTube
1/27 Lecture 2: The infectious cycle Flint Vol I Chp 2
Influenza virus growth in eggs
Influenza hemagglutination inhibition assay
The amazing cells of Henrietta Lacks
The Wall of Polio
Small fragments of viral nucleic acid
pdf Large Small YouTube
1/29 Lecture 3: Genomes and genetics Flint Vol I Chp 3
The Baltimore scheme
pdf Large Small YouTube
2/3 Lecture 4: Structure Flint Vol I Chp 4
Structure of influenza virus
Virus images at ViperDB
pdf Large Small YouTube
2/5 Lecture 5: Attachment and entry Flint Vol I Chp 5
Influenza virus attachment to cells
Influenza virus attachment to cells: Role of different sialic acids
A single amino acid change switches avian influenza H5n1 and H7N9 viruses to human receptors
pdf Large Small YouTube
2/10 Lecture 6: RNA directed RNA synthesis Flint Vol I Chp 6
Influenza viral RNA synthesis
The error prone ways of RNA synthesis
pdf Large Small YouTube
2/12 Lecture 7: Viral DNA replication Flint Vol I Chp 9 pdf Large Small YouTube
2/17 Exam I
2/19 Lecture 8: Transcription and RNA processing Flint Vol I Chp 8 and 10 pdf Large Small YouTube
2/24 Lecture 9: Reverse transcription and integration Flint Vol I Chp 7
Museum pelts help date the Koala retrovirus
Unexpected endogenous retroviruses
pdf Large Small YouTube
2/26 Lecture 10: Translation Flint Vol I Chp 11 pdf Large Small YouTube
3/3 Lecture 11: Assembly Flint Vol I Chapters 12 and 13
Packaging of the segmented influenza virus genome
pdf Large Small YouTube
3/5 Lecture 12: Infection basics Flint Vol II Chapters 1 and 2
Transmission of influenza
Slow motion sneezing
Chikungunya an exotic virus on the move
Do the tropics have a flu season?
pdf Large Small YouTube
3/10 Lecture 13: Intrinsic and innate defenses Flint Vol II Chapters 3 and 4
The inflammatory response
Natural antibody protects against viral infection
pdf Large Small YouTube
3/12 Lecture 14: Adaptive immunity Flint Vol II Chapter 4 pdf Large Small YouTube
3/17 Spring Recess
3/19 Spring Recess
3/24 Lecture 15: Viral virulence Flint Vol II Chapter 2
Antimicrobial peptides induced by herpesvirus enhance HIV-1 infection
HIV gets the zinc finger
pdf Large Small YouTube
3/26 Lecture 16: Acute infections Flint Vol II Chapter 5
Acute viral infections
Chronology of an acute infection
pdf Large Small YouTube
3/31 Lecture 17: Persistent infections Flint Vol II Chapter 5 pdf Large Small YouTube
4/2 Exam II
4/7 Lecture 18: Transformation and oncogenesis Flint Vol II Chapter 7 pdf Large Small YouTube
4/9 Lecture 19: Vaccines Flint Vol II Chapter 8
Influenza virus-like particle vaccine
Poliovirus vaccine safety
pdf Large Small YouTube
4/14 Lecture 20: Antivirals Flint Vol II Chapter 9
Treating hepatitis C by blocking a cellular microRNA
TWiV 270: Homeland virology (developing a smallpox antiviral)
pdf Large Small YouTube
4/16 Lecture 21: Evolution Flint Vol II Chapter 10 pp 311-333
Virulence – a positive or negative trait for evolution?
Increased fidelity reduces viral fitness
•Why do viruses cause disease?
pdf Large Small YouTube
4/23 Lecture 22: Emerging viruses Flint Vol II Chapter 10 pp 333-end
Heartland virus disease
The zoonotic pool
pdf Large Small YouTube
4/28 Lecture 23: Unusual infectious agents Flint Vol II Appendix A
Virophages engineer the ecosystem
pdf Large Small YouTube
4/30 Lecture 24: HIV pathogenesis Flint Vol II Chapter 6
The HIV hideout (podcast)
pdf Large Small YouTube
5/5 Lecture 25: H5N1 Asymptomatic H5N1 infection
A bad day for science
pdf Large Small YouTube
5/12 Exam III
  • ashwini

    Hello Dr. Racaniello,

    Thank you for your wonderful lectures. I have A question about end point dilution assay. When you make a uniform suspension of virus and plate replicates/dilution in a a plate. How come the cytopathic effect is observed in whole-number (rather than fraction)of well. So could it have half cytopathic effect in all the 10 wells (1/2 per well) and still be TCID50?
    PS -I am new to virology

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  • Pix

    You still go to parties. You’re not weird. I’m the girl that talks to the wall about those things, lol!