Virology 101

A new class is starting at virology blog: Virology 101.

I began this blog in 2004, to give back what I’ve learned from studying viruses for 30+ years. I’ve written many posts on basic virology, but they tend to disappear with time. To remedy this problem, I’ve collected all these posts with links back to the original article, arranged by topic. They are typically short and easy to read; if you start from the top, soon you will have a good basic understanding of virology.

I’ve also included relevant episodes of the podcast TWiV, where we discuss basic virology about once a month.

For the more adventurous, see the video podcasts from my Columbia University virology course, W3310. This course is taught in the spring semester each year. I’ve also included some of my other lectures to medical and undergraduate students.

If you are specifically interested in influenza virus, there is always Influenza 101.

Class will always be in session: there is much more to come.

With this virology course you also get access to a virology professor. If you have any questions, send them to vincent@virology.ws.

Basic Background Information

What is a virus? (W3301)

Introduction to virology I and II (Medical school lecture)

What is a virus?

Are viruses living?

Discovery of viruses

What color is a virus?

How viruses are classified

Virus classification (TWiV 43)

Simplifying virus classification: The Baltimore system

Viral genomes (TWiV 49)

Genomes and genetics (W3310)

The infectious cycle lecture (W3310)

Measurement (also see the virology toolbox)

Detecting viruses: The plaque assay

How many viruses are needed to form a plaque?

Measurement of viruses by end-point dilution assay

Multiplicity of Infection

The western blot

Detection of antigens or antibodies by ELISA

Detecting viral proteins in infected cells or tissues by immunostaining

Virus Structure

Virus structure (TWiV 39)

Virus structure (W3310)

Attachment and Entry into Cells

Virus entry into cells (TWiV 46)

Attachment and entry (W3310)

Nucleic Acid Synthesis

RNA synthesis (W3310)

Making viral RNA (TWiV 60)

Making viral DNA (TWiV 96)

Making viral DNA II (TWiV 106)

Genome replication of DNA viruses (W3310)

Transcription (TWiV 162)

Reverse transcription (W3310)

Reverse transcription (TWiV 66)

Transcription and RNA processing (W3310)

Processing viral RNA (TWiV 216)

Protein synthesis

Translation (W3310)

Virion Assembly

Assembly (W3310)

Pathogenesis and Immunity

Infection Basics (W3310)

Host Defense (W3310)

Virus-Host Interactions (W3310)

Viral Pathogenesis (Medical school lecture)

Acute Infections (W3310)

Antigenic variation explains recurring acute infections

HIV Pathogenesis (W3310)
Transformation and Oncogenesis (W3310)

Innate sensors of DNA

Immunopathology: Too much of a good thing

Innate immune defenses

The inflammatory response

Adaptive immune defenses

Adaptive immune defenses: Antibodies

Virus neutralization by antibodies

The complement system

C1q and the collectins

Natural antibody protects against viral infection

Prevention and Control

Vaccines (W3310)

Antiviral Drugs (W3310)

Tamiflu-resistant pandemic influenza H1N1 virus selected by prophylaxis

Vaccines lecture (Immunology course, different from W3310 version)

Discussion of new HCV antiviral on Futures in Biotech 60
(download the HCV part of the discussion here)

Evolution and Emergence

Viral Evolution (W3310)

Emerging Viruses (W3310)

Viruses and the tree of life

The abundant and diverse viruses of the seas

Chikungunya: An exotic virus on the move

Lujo virus, a new hemorrhagic fever virus from Southern Africa

The error-prone ways of RNA synthesis

The quasispecies concept

Viral quasispecies and bottlenecks

The number of possible viral variants

Pushing viruses over the error threshold

Increased fidelity reduces viral fitness

Why don’t DNA based organisms discard error repair?

The trajectory of evolution

Virulence: A positive or negative trait for evolution?

Topics that don’t fit anywhere else

Unusual Infectious Agents (W3310)

Picornaviruses

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  • jaleeskhan

    good attempt

  • http://www.marshvorspan.com/ Austin Green Building

    test

  • p mckenzie

    Thankyou for taking time to create these online classes for the masses.
    I share them with my family and staff at the hool where I teach.

    We are all nervous about H1N1 after our experience wit SARS.

    regards. PM.

  • http://fluoridation-twoer.blogspot.com/ Richard

    Re: H1N1 Letter Addressed to Health Care Professionals

    http://video.google.com/videoplay?docid=-867440

  • DaJuan

    Awesome, in the way you have set up this forum to inform, teach, and breakdown virology in a way that is digestible, for lack of a better word, thanks I will continue to tune in.

  • duncan

    In an interview for the AIDS-documentary “House of Numbers”, Dr. Luc Montagnier – Recipient of the 2008 Nobel Prize in Medicine for the discovery of the Human Immunodeficiency Virus (HIV) – spoke out for nutrition and micronutrients in the fight against HIV/AIDS:

    In the interview (see video below), Dr. Montagnier stated that:

    http://www.youtube.com/watch?v=WQoNW7lOnT4

    There are many ways to decrease the transmission of HIV just by utilising simple measures such as nutrition, giving antioxidants, hygiene measures and fighting the other infections that are present in patients.
    If you have a good immune system your body can get rid of HIV naturally.
    We should push for combinations of measures, such as antioxidants; nutrition advice; nutrition; fighting the other infections that are present in patients ­ such as malaria, tuberculosis, parasitosis and worms; education and promoting genital hygiene.
    People always think of drugs and vaccines because there is no profit in nutrition.
    If you take a poor African patient who has been infected with HIV and you build up their immune system it should also be possible for them to get rid of HIV naturally.
    All of the above constitutes important knowledge which has been completely neglected.

  • SDS

    It is true that good hygiene and diet are very important for controlling the secondary, and eventually fatal, infections that are the result of HIV infection. With good habits and anti-retroviral drugs, an HIV+ individual may be able to live a long, relatively normal life. However, I can not see how clean habits alone can “get rid of HIV naturally.” The virus effectively evades and diminishes cell-mediated immunity.

  • SDS

    It is true that good hygiene and diet are very important for controlling the secondary, and eventually fatal, infections that are the result of HIV infection. With good habits and anti-retroviral drugs, an HIV+ individual may be able to live a long, relatively normal life. However, I can not see how clean habits alone can “get rid of HIV naturally.” The virus effectively evades and diminishes cell-mediated immunity.

  • Kurniawan_oki1

    I really interest with your subject Mr. Vincent

  • Unknown

    Could you write something about what are viral replicons and why they are useful in studying biology of viruses?

  • http://www.facebook.com/profile.php?id=774811254 Jessica Parilla

    For the lecture on viral evolution, i had a question. If you were to sequence two random members of the quasispecies, what would be the sequence identity between the two? Just how dissimilar (on average) are the individuals that comprise a quasispecies?

  • Aikaterini Savvaki

    Hey can someone please explain the actual difference between a virus and a virion? and the structure of the latter! thanks! :)

  • http://www.virology.ws profvrr

    Virus is a generic name for all of the obligate, intracellular
    parasites; for example, influenza virus, poliovirus. The virion
    specifically refers to the infectious virus particle.

  • http://profiles.google.com/aletheiazc Aletheia Zoe Chiang

    Canadian undergrad 4th yr student studying for my Virology final. Formerly dying but I’ve discovered your site. Pretty sure I’ve learned more from your podcasts and blog in the past two days than I have over the course of the term. You are so, so amazing. I love how you’ve made virology open access and tremendously enjoy your lectures. THANK YOU Dr. Racaniello! :-)

  • Veronica Araujo

    Hi Vincent! I’m working on Europe’s only Pathogen Safety event – was wondering whether you would like to take part as our blogger? this is my email veronica.araujo@iqpc.co.uk – get in touch if interested – Thank you!

  • darkspace08

    Like you has said in your lecture Darwinian machines, Is nature a big evolutionary or molecular biology or biotechnology lab? [NOT TALKING ABOUT CREATION] I think viruses is one of the natural tools for living objects to be changed, I can not say development as we do not know if that is good or to be better or to be worse!, but that changes occur chronologically due to reaction by chance and how is the rate of these reactions happen.
     Viruses are these reactions mediators. Because recent researches put hypotheses as Mitochondria had been an independent bacteria and under certain circumstances it had been embedded inside human cells. WHY DO NOT WE THINK THAT THE FIRST EVER DNA POLYMERASE IS FROM VIRUSES?! and under certain circumstances[ more complex than most complex DNA transcription] it formed the first ever ancient human or animal cell with the help of Mitochondria to produce energy.

    Thank a lot Dr.Racaniello 

  • http://www.prlog.org/11289974-phone-number-lookup-verizon-phone-number-reverse-lookup-to-get-information-you-need-quickly.html phone number lookup

    You seem to know your stuff very well

  • Philip penner

    Regarding HIV virus:
    a)Do the two single strands of RNA plus in a given virion vary in terms of their base sequencing?
    b)What is the significance of MHC on the surface of HIV?  Phil Penner 

  • Anonymous

    You are making making virology so much easier to understand than my intro. virology class. Thank you so much. I appreciate all your hard work and gosh, just thanks.

  • Mike

    Stumbled upon your class on iTunes U a few weeks ago. All I can say is wow. I wish I went to Columbia so that I could actually take your class. I am now considering a PhD in virology now instead of immunology. Love Twiv too. Thanks for putting all this information up and making it so easy to access. 

  • Questionlegacy

     Thank you. I am taking Microbiology at my local college. I am finding your explanations very clear and helpful for parts which my lecturer does not have the time to cover in detail

  • Recruiter

    Team Leader – Virology  -
    based, Speke, Liverpool, UK

    Please extend this role to your network!!! – Direct
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    Lead Technical Transfer / Assay Qualification
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  • Andy Robertson

    Is it possible to force a virus to ‘lose’ its zoonotic effect by changing its genes ?

  • biotec

    where i can find the limitation of kosh’s postulates? help please

  • Laura

    Hi,

    I’m an international student, and i’m looking for very good phD of virology. Can you tell me where i can find (a list could be great) ? I already saw the program of harvard, is it the best?

    I want to work on virus, and more particulary on very dangerous virus like ebola… I don’t realy want to make vaccin, but it’s a possibility. I would prefere to make more fundamental research.

    Thank you

    Best regards

  • Zoe

    Canadian undergrad 4th yr student studying for my Virology final. Formerly dying but I’ve discovered your site. Pretty sure I’ve learned more from your podcasts and blogs in the past two days than I have over the course of the term. You are so, so amazing. I love how you’ve made virology open access and tremendously enjoy your lectures. THANK YOU Dr. Racaniello! :-)

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  • Anonymous

    I’ve seen these stories about smart people out there who crack codes that the NSA can’t crack, solve problems that the scientific community can’t solve, etc. Is there some type of forum where people who have ideas on viruses communicate. I’m thinking maybe there are people who think more strategically than some people who learn all the biology, chemistry etc. to become a virologist but maybe are led in the specific directions without thinking about it. I don’t have examples of what I mean specifically, but what could it hurt?

  • Anonymous

    I suppose it could get tedious sifting through posts made by people ranging from the “not so smart” to the crazy, but maybe the legitimate people would stand out. Maybe a patent clerk could produce the biggest breakthrough we’ve seen in a while. Of course these forums could exist, but if they don’t it sounds like someone should try to set up a forum that specifically attracts the geniuses with good ideas who just never got into the field.

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  • sarath k s

    nice

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