Course

 

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 (vrr1@columbia.edu).

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

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 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
Pandoravirus
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
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  • Svitka

    Thank you ever so much for making these materials available to the interested public.  It is a terrific service.

  • Aake Bjoerk

    Thanks for putting this up !
    Great to be at home and take this in at your own pace.
    I am a little disabled so all Internet services are a tremendous benefit !

    Downloading slides 1-14 worked ok.

    Downloading videocasts worked ok, except for lecture 9 and 13.

    Would be great if  I could get hold of these as well.

    Best regards Aake from Sweden

  • http://www.virology.ws profvrr

    I believe I have fixed the errant files, please try again. If not let me know.

  • Aake Bjoerk

     Lecture 9 and 13 are now fixed !

  • Saintson

    Dear Prof. V. Racaniello

    Thank you very much for providing so many materials. But I can not download the pdf  for Exam I.

    Best wishes

  • http://www.virology.ws profvrr

    Sorry, that file is fixed and should now be available.

  • smsavage

    I was wondering if there was anyway that the answer sheet may be posted for the two sets of review questions? I have done them, I am just wanting to check my answers to see if I am correct. Thanks

  • http://www.virology.ws profvrr

    I can do that, but it will take a bit more time, perhaps a week or two.

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  • Guest

    Dr. Racaniello,My boxing instructor was quizzing me on the questions in the study guide for the final exam today, and if I hadn’t before, I had really come to appreciate everything that I’ve learned in your course then. Most notably, I was so surprised to hear him say that he and his friends thought that HIV arose from humans having sex with monkeys, and that homeopathic medicine could cure HIV.  In discussing and explaining the different topics to him, I really think that you are fulfilling a great need by educating the public about viruses.  I am so thankful for everything that I’ve learned, and I appreciate the opportunity that your course has given me to bring the science and reality of viruses to others.  Thanks!

  • Manuel

    Hello Proffesor
    Is it possible to have the student questions on subtitles or something? i learn also from questios of the other students and if i dont have them i can get lost in the middle of the clas.

  • Adrian Tween

    I am a biology student. I finished my undergraduate studies and I thank you for giving me something to do while I figure out where to study next as I can’t apply for anything sooner than Spring 2013 this year. Thanks a lot.

  • Andy A.

    Hello professor,

    Thank you for these lectures! These are great video lectures that really captivate me and help supplement my learning at UTSA. I was wondering if you had answer sheets you could post up for the review questions you have on here? That would be fantastic.

    Thanks again!

  • P Yk Chong

    Dr. Racaniello, I have a little suggestion, maybe you can keep us update with some of the good journal papers time by time? It will be a good kickstart for those who love to immerse themselve in fascinating virology. =)

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  • Farheen

    Hi, I’m new to this and absolutely thrilled to have found this course! Wondering if I’m too late to start or is this self-paced? Do we get a certificate at the end, like the Coursera or Udacity courses? Thank you.

  • Phil

    Hi Prof Racaniello,

    Would it be possible to upload the videocasts for the second half of the course again please? I’m studying Virology MSc in London, UK and find the videocasts extremely helpful learning material.

    Many Thanks,

    Phil

  • http://www.virology.ws profvrr

    Phil, all the lectures from 2012 are still online – there is a link at the very top of this page. The lectures on the current page are from this year’s course which is still in progress.

  • Phil

    Found it! Thank you.

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  • Linsey Marr

    Thank you very much for making your lectures available to all. It’s a fantastic resource for my research group that is studying aerosol transmission and as an example as I think about moving my own courses at least partially online.

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  • Daniel Weiand

    Dear Prof Racaniello. Thank you for the very useful files! Unforunately, it looks like pdf’s9 and 12 are not available for download, though. Best wishes!

  • wang

    Thank you very much!

    I can’t download the pdf of lecture 9.

  • http://www.virology.ws profvrr

    I’ve fixed the pdf of lecture 9, should be available now.

  • http://www.virology.ws profvrr

    Fixed!

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  • Syed Ahmed

    sir may i get the English subs for these lectures?

  • Paul

    RE particle/pfu ratio: How can a particle be considered a non-infectious virus if all viruses are considered to be infectious, obligate intracellular parasites? If i a particle isn’t infectious, it doesn’t have the 5 characteristics of a virus, so how can there be a non-infectious virus?

  • http://www.virology.ws profvrr

    All viruses are not infectious – they are always a mixture of infectious ones (called virions) and non-infectious particles.

  • Paul Delle

    eIF4E (E is first letter of End, the cap is the end)
    eIF4A (A for “ase” it’s the helicase)
    eIF4G (the Great big protein in the middle that binds many others)

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  • Moulay

    Hi,
    Thank you so much for this wonderful course. I was wondering: do you teach a Virology Lab course? If yes, where and when?
    Thanks.

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  • MelissaMM

    I’m currently a business major at UF (3rd year!) and discovered my passion for viruses about a year ago. I’ve been studying as much independently as I can; reading books, textbooks, taking notes, and generally falling in love with viruses and the science that comes with that love. I’ve never been big on science, but I find myself trying harder and going the extra mile to understand concepts previously insurmountable to me. I’m officially the weird girl who talks about Machupo and Lassa facts at parties because I don’t get how EVERYONE isn’t fascinated with the subject. Thank you so much for posting these videocasts! Since realizing how studying viruses makes my brain light up in a way no other subject has before, studying Business brings me little joy. I want to finish this degree since I’ve put so much time into it, and your lectures are a lovely reprieve between Macroeconomics classes.