Virology – Biology 3310/4310

Spring 2017

The complete 2016 virology course materials are available at

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 20, 2016
Points: 3
Location: Schermerhorn 501
Course #: Biology UN3310.001 or GR4310.001
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 2015).

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.

Lecture Schedule, Spring 2017

Date Topic Reading Slides Study Questions Video
1/18 Lecture 1: What is a virus? Flint Vol I Chp 1
The virus and the virion
Cell size and scale
pdf pdf YouTube
1/23 Lecture 2: The infectious cycle Flint Vol I Chp 2
Influenza virus growth in eggs
The amazing cells of Henrietta Lacks
The Wall of Polio
Small fragments of viral nucleic acid
pdf pdf YouTube
1/25 Lecture 3: Genomes and genetics Flint Vol I Chp 3
The Baltimore scheme
pdf pdf YouTube
1/30 Lecture 4: Structure Flint Vol I Chp 4
Structure of influenza virus
Virus images at ViperDB
pdf pdf YouTube
2/1 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
Molecular movies of viruses
pdf pdf YouTube
2/6 Lecture 6: RNA directed RNA synthesis Flint Vol I Chp 6
Influenza viral RNA synthesis
pdf pdf YouTube
2/8 Exam I
2/13 Lecture 7: Transcription and RNA processing Flint Vol I Chp 8 through p277 Chp 10 through p364 pdf pdf YouTube
2/15 Lecture 8: Viral DNA replication Flint Vol I Chp 9 pdf pdf YouTube
2/20 Lecture 9: Reverse transcription and integration Flint Vol I Chp 7
Museum pelts help date the Koala retrovirus
Unexpected endogenous retroviruses
A retrovirus makes chicken eggshells blue
Reverse transcription animation
pdf pdf YouTube
2/22 Lecture 10: Translation Flint Vol I Chp 11 pdf pdf YouTube
2/27 Lecture 11: Assembly Flint Vol I Chapters 12 and 13
Packaging of the segmented influenza virus genome
What if influenza virus did not reassort?
pdf pdf YouTube
3/1 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 pdf YouTube
3/6 Exam II
3/8 Lecture 13: Intrinsic and innate defenses Flint Vol II Chapter 3
The inflammatory response
Natural antibody protects against viral infection
pdf pdf YouTube
3/13 Spring Recess
3/15 Spring Recess
3/20 Lecture 14: Adaptive immunity Flint Vol II Chapter 4 pdf pdf YouTube
3/22 Lecture 15: Mechanisms of pathogenesis Flint Vol II Chapter 5 pdf pdf YouTube
3/27 Lecture 16: Acute infections Flint Vol II Chapter 5
Acute viral infections
Chronology of an acute infection
pdf pdf YouTube
3/29 Lecture 17: Persistent infections Flint Vol II Chapter 5 pdf pdf YouTube
4/3 Lecture 18: Transformation and oncogenesis Flint Vol II Chapter 6 pdf pdf YouTube
4/5 Exam III
4/10 Lecture 19: Vaccines Flint Vol II Chapter 8
Influenza virus-like particle vaccine
Poliovirus vaccine safety
pdf pdf YouTube
4/12 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 pdf YouTube
4/17 Lecture 21: Evolution Flint Vol II Chapter 10
Virulence – a positive or negative trait for evolution?
Increased fidelity reduces viral fitness
pdf pdf YouTube
4/19 Lecture 22: Emerging viruses Flint Vol II Chapter 11
Heartland virus disease
pdf pdf YouTube
4/24 Lecture 23: Unusual infectious agents Flint Vol II Chapter 12
Detecting prions by quaking and shaking
Prions in plants
Prions in the emergency room
Prion disease from contaminated beef
pdf pdf YouTube
4/26 Lecture 24: HIV and AIDS Flint Vol II Chapter 6
Blocking HIV infection with two soluble receptors
pdf pdf YouTube
5/1 Lecture 25: Viral gene therapy Clinical benefit of gene therapy pdf pdf YouTube
5/8 Exam IV