Course

Virology – Biology W3310

Spring 2013

Click here for material from the 2012 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 23, 2013
Points: 3
Location: Northwest Corner 501
Course #: Biology W3310.001 or W4310.001
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.

Click here for material from the 2012 virology course

Lecture Schedule, Spring 2013
Note: Several videocast file types are available – right-click and save as to download. Videos are also available at YouTube.

Date	Topic	Reading	Lecturer	Slides	Videocast (right click, save as)
1/23	Lecture 1 What is a virus?	Flint vol 1 chapter 1 Are viruses living? What is a virus? Are viruses alive? (take the poll)	VRR	pdf	iPod iPhone iPad/mac pc
1/28	Lecture 2 The infectious cycle	Flint vol 1 chapter 2 Influenza virus growth in eggs Influenza hemagglutination inhibition assay The amazing HeLa cells of Henrietta Lacks	VRR	pdf	iPod iPhone iPad/mac pc
1/30	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	pdf	iPod iPhone iPad/mac pc
2/04	Lecture 4 Structure of viruses	Flint vol 1 chapter 4 Structure of influenza virus Virus images at ViperDB	VRR	pdf	mac iPod iPhone iPad pc
2/06	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	pdf	mac iPod iPhone iPad pc
2/11	Lecture 6 RNA-directed RNA synthesis	Flint vol 1 chapter 6 Influenza viral RNA synthesis The error prone ways of RNA synthesis	VRR	pdf	mac iPod iPhone iPad pc
2/13	Lecture 7 Replication of DNA virus genomes	Flint vol 1 chapter 9 Making viral DNA I (TWiV) Making viral DNA II (TWiV)	SJS	pdf	mac iPod iPhone iPad pc
2/18	Exam I	Lectures 1-7		Study questions (pdf)
2/20	Lecture 8 Transcription and RNA processing	Flint vol 1 chapters 8, 10 Processing VIRALGUUAACACCAGRNA(TWiV) Study questions (pdf)	SJS	pdf	mac iPod iPhone iPad pc
2/25	Lecture 9 Reverse transcription and integration	Flint vol 1 chapter 7 Museum pelts help date the koala retrovirus Unexpected endogenous viruses Study questions (pdf)	VRR	pdf	mac iPod iPhone iPad pc
2/27	Lecture 10 Translation	Flint vol 1 chapter 11 Study questions (pdf)	VRR	pdf	mac iPod iPhone iPad pc
3/04	Lecture 11 Assembly	Flint vol 1 chapters 12, 13 Packaging of the segmented influenza RNA genome Study questions (pdf)	VRR	pdf	mac iPod iPhone iPad pc
3/06	Lecture 12 Infection basics	Flint vol 2 chapters 1,2 Transmission of influenza Slow motion sneezing Chikungunya, an exotic virus on the move Do the tropics have a flu season? Study questions (pdf)	VRR	pdf	mac iPod iPhone iPad pc
3/11	Lecture 13 Host defense	Flint vol 2 chapter 4 The inflammatory response Natural antibody protects against viral infection Study questions (pdf)	VRR	pdf	mac iPod iPhone iPad pc
3/13	Lecture 14 Virus-host interactions	Flint vol 2 chapters 3, 4 Immunopathology – Too much of a good thing Severe cases of pandemic influenza Antimicrobial peptides induced by herpesvirus enhance HIV-1 infection Study questions (pdf)	VRR	pdf	mac iPod iPhone iPad pc
3/18 – 3/22	Spring Recess
3/25	Lecture 15 Viral evasion strategies	Flint vol 2 chapters 3, 4 Study questions (pdf)	SJS	pdf	mac iPod iPhone iPad pc
3/27	Lecture 16 Persistent infections	Flint vol 2 chapter 5 Persistent viral infections Study questions (pdf)	SJS	pdf	mac iPod iPhone iPad pc
4/01	Exam II	Lectures 8-16
4/03	Lecture 17 Acute infections	Flint vol 2 chapter 5 Acute viral infections Chronology of an acute infection Study questions (pdf)	VRR	pdf	mac iPod iPhone iPad pc
4/08	Lecture 18 HIV pathogenesis	Flint vol 2 chapter 6 TWiV 133: The HIV hideout A tale of two viruses Study questions (pdf)	VRR	pdf	mac iPod iPhone iPad pc
4/10	Lecture 19 Transformation and oncogenesis	Flint vol 2 chapter 7 TWiV 163: What Rous wrought Study questions (pdf)	VRR	pdf	mac iPod iPhone iPad pc
4/15	Lecture 20 Vaccines	Flint vol 2 chapter 8 Influenza virus-like particle vaccine Poliovirus vaccine safety Study questions (pdf)	VRR	pdf	mac iPod iPhone iPad pc
4/17	Lecture 21 Antivirals	Flint vol 2 chapter 9 New hepatitis C virus antiviral drugs An antiviral for enveloped viruses TWiV 146: Draco’s potion Study questions (pdf)	VRR	pdf	mac iPod iPhone iPad pc
4/22	Lecture 22 Evolution	Flint vol 2 chapter 10 pp 311-333 Virulence: A positive or negative trait for evolution? Increased fidelity reduces viral fitness Study questions (pdf)	VRR	pdf	mac iPod iPhone iPad pc
4/24	Lecture 23 Emerging viruses	Flint vol 2 chapter 10 Lujo virus, a new hemorrhagic fever virus from Southern Africa The zoonotic pool Study questions (pdf)	VRR	pdf	mac iPod iPhone iPad pc
4/29	Lecture 24 Unusual infectious agents	Flint vol 2 Appendix A Virophages engineer the ecosystem Study questions (pdf)	VRR	pdf	mac iPod iPhone iPad pc
5/01	Lecture 25 XMRV	Flint vol 1 chapter 7 Why John Coffin doesn’t sleep well HIV in XMRV out XMRV is a recombinant virus from mice Study questions (pdf)	VRR	pdf	mac iPod iPhone iPad pc
5/06	Lecture 26 H5N1	TWiV 177: Live in Dublin A bad day for science Study questions (pdf)	VRR	pdf	mac iPod iPhone iPad pc
5/13	Exam III	Lectures 17-26

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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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