Influenza 101

Soon after the new influenza H1N1 strain emerged in April 2009, I began a series of blog posts on basic aspects of influenza virus replication and pathogenesis. The goal of this series is to provide information that will allow everyone to better understand the events surrounding emergence and spread of the new pandemic strain.

Unfortunately blog posts tend to become invisible after a certain period of time, which does not befit educational material. Therefore I have made a list of these articles, with links, to make it easier for everyone to take Influenza 101.

Class is still in session.


Structure of Influenza virus

Influenza virus RNA genome

The A, B, and C of influenza virus

The neuraminidase of influenza virus

Influenza virus RNA: Translation into protein

Entry into Cells

Influenza virus attachment to cells

Influenza virus attachment to cells: role of different sialic acids

Cutting through mucus with the influenza virus neuraminidase

Release of influenza viral RNA into cells

Influenza HA cleavage is required for infectivity

RNA Synthesis

Influenza viral RNA synthesis

The error-prone ways of RNA synthesis

The quasispecies concept

Viral quasispecies and bottlenecks


Assembly of influenza virus

Packaging of the segmented influenza RNA genome

Reassortment of the influenza virus genome

Influenza virus reassortment, then and now

The neuraminidase of influenza virus


David and Goliath: How one cytokine may take down influenza

Gut microbes influenza defense against influenza

The D225G change in 2009 H1N1 influenza virus

It’s not easy to make the 2009 H1N1 influenza virus a killer

Influenza virus transmission

Viruses and the respiratory tract
How many people die from influenza?
Seasonality of influenza
Innate immune defenses
The inflammatory response

Adaptive immune defenses

Adaptive immune defenses: Antibodies

Virus neutralization by antibodies

Prevention and Control

How good is the influenza vaccine?

Pandemic influenza vaccine was too late in 2009

Universal influenza vaccines

Secondary changes allow spread of oseltamivir resistant influenza virus

Headless HA: Universal influenza vaccine?

Protection against 2009 influenza H1N1 by immunization with 1918-like and classical swine viruses

Reinfection with 2009 influenza H1N1

Influenza neuraminidase inhibitors work

Tamiflu-resistant pandemic influenza H1N1 virus selected by prophylaxis

Propagation and Measurement

Influenza virus growth in eggs

Influenza hemagglutination inhibition assay

Influenza microneutralization assay

Detecting viruses: the plaque assay

How many viruses are needed to form a plaque?

Measurement of viruses by end-point dilution assay

79 thoughts on “Influenza 101”

  1. Vincent, this is fantasic. Could you also add a section on the human immune response? I think understanding the human side is just as important as understanding the viral side.

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  3. Hello,
    It would be good to hear your thoughts on A/Shanghai/71T/2009 that has just appeared with both the PB2 E627K and D701N mutations. It took 43 days to adapt! D701N is thought to allow E627 viruses to become infectious to humans and perhaps has led to the E627K arising. Both are quite scary individually and together I think they look very worrying – transmissibility should be increased due to more efficient replication in the cooler temperatures of the respiratory tract.

  4. This is a great resource — especially for a journalist like me who is based in India.

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  6. Looks like a red herring. The sequence has recently been corrected and updated in the database — see GenBank GQ253501.2 GI:241914528. Neither the E627K nor the D701N mutations are present.

  7. After years of tamiflu treatment, seasonal flu became mild resistent strain.
    But with h1n1 new virus, after only 2 month of experience, just has appeared in denmark and japan the new H274Y mutation on treated patients. It seems to be a swift ,smart (and chilling) virus. what's next?

  8. By definition it is antigenic drift, because the subtype – H1N1 – is the same as the previous seasonal H1N1 viruses. It's different from what we have seen before, because the HA differs by many more amino acids than one would expect to occur from one season to another. However, there are certainly drifted strains of the same subtype many years apart that differ by that much. So It's drift, albeit an unusual form.

  9. I don't think pandemic swine H1N1 can be called a drift variant, unless you are calling it a drift variant of swine H1N1 that has gained efficient transmissibility in humans. Although human H1N1 and swine H1N1 share the same serotype, the sequences are quite distinct and have been distinct since the first viruses were isolated in the 1930's. The first influenza isolate was H1N1 from a pig in Iowa in 1930, and the first human isolate was from a researcher in England in 1933. The two lineages were easily distinguished, and these seperate lineages have been maintained ever since (and probably also maintained well before the 1930's).

    Antigenic shift is reserved for reassortment where one of more gene segments jumps from one lineage to another and frequently involves different serotypes.

    The current swine is called a triple reassortant because it has one gene segment (PB1) from human flu, and two (PB2 and PA) from avian flu, but the H1 and N1 are swine and are not caused by any recent drifting, severe or mild. Swine H1N1 and human H1N1 are completly different lineages.

  10. Pingback: Swine Flu: The Next Wave | Pig Flu Vaccine

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  12. Vincent – I've been thinking about this shift/drift factoid all summer. In the end, I guess the distinction is purely academic but I think 2009/H1N1 is in fact an example of antigenic shift.

    Before April, most epidemiologist/virologist/public health types would mostly agree that shift is indicated by a newly circulating HA or at the very least NA. So by this example, shift would not fit; however, everyone would agree the 2009/H1N1 is a result of a reassortment and I have not found one single reference that places words 'reassortment' and 'drift' in the same sentence – reassortment is always associated with shift!

    Therefore I'm going with shift..there I feel better now (please don't flame me to bad on this one). BTW, love the new virology 101 section!!!

  13. Some notes on vaccines/vaccination and pros/cons of different modes of application and “adjuvants” would also be very appreciated.

  14. I forgot: I noticed that you do not discuss the vitamin D influenza hypothesis in your seasonality and innate imunity topics. What is your take on the hypothesis?

    Epidemiol Infect. 2006 Dec;134(6):1129-40.
    Epidemic influenza and vitamin D.
    Cannell JJ, Vieth R, Umhau JC, Holick MF, Grant WB, Madronich S, Garland CF, Giovannucci E.

  15. The 2009 H1N1 strain in some ways defies our definitions of drift and
    shift. Here are the textbook definitions. Antigenic drift: the
    appearance of virions with slightly altered surface proteins following
    passage in the natural host. Antigenic shift: a major change in the
    surface protein(s) of a virion as genes encoding completely new
    surface proteins are acquired. This dramatic change in virion
    composition results when a host is coinfected with two viral
    serotypes. The 2009 swine-derived H1N1 does not fit either definition.
    Antigenic shift, as you note, has typically involved a change in
    subtype: 1889 H2N2; 1900 H3N8; 1918 H1N1; 1957 H2N2; 1968 H3N2; 1977
    H1N1; 2009 H1N1. But perhaps a change in subtype should not be part of
    the definition of shift. As you point out, the 2009 H1N1 is very
    different from the human H1N1 and that is probably sufficient to make
    it shift. What confounds the problem is that as different as the swine
    and human H1 are, they are still H1 subtypes.

  16. Regarding egg-based vaccine production: could you explain how virus replicates in chicken eggs? Does replication occur in the embryo and if so, how does it end up so concentrated in the egg white? Thanks!

  17. Regarding egg-based vaccine production: could you explain how virus replicates in chicken eggs? Does replication occur in the embryo and if so, how does it end up so concentrated in the egg white? Thanks!

  18. The virus is inoculated into the allantoic cavity of embryonated
    chicken eggs (10-12 day old embryos). The virus multiplies in the
    cells of the allantoic membrane which surround the allantoic fluid. As
    these cells produce virus it is shed into the allantoic fluid. I'll
    put up a post on this with an illustration to make it clear.

  19. In my area (Italy) the incidence of A(H1N1)v influenza is rapidly decreasing. Cases have reached their peak during week 45, according to the sentinel surveillance of ILIs:
    At present, pediatricians point out that respiratory infections due to “minor” viruses (like common cold and others) seem to be absent. Waiting rooms are empty: respiratory infections that usually affect children during the winter apparently have disappeared . How can we explain this finding? Thank you

  20. Clearly it cannot be explained by the presence of influenza because,
    as the graph in that document shows, the number of infections are low
    (although not zero). I would be careful in trying to interpret what
    pediatricians point out, as this information could be erroneous.

  21. Marvellous, fabulus, splendid………………………explanation. very simple and scientific blog.

  22. Respected Professor VRR,
    I am chandra sekhar with computer science background,Recently i started my research in bioinformatics, I am very much interested to work with influenza related data,
    Could you please suggest me any research problem to work with influenza data .

    Thanks in advance

  23. We have very little 2009 H1N1 flu at this time, but what puzzles me is that there is NO seasonal influenza !!! What do you think has happened- cross immunity- high herd immunity? ….????

  24. Regarding H1N1 and its apparent massive inflamatory response in the airways. This would increase the alveolar capillary membrane thickness. Add this to the epithelial cell ulceration occuring . Its seems that this is the cause of the severe hypoxemia seen clinically. My question is are we treating the underlying cause of hypoxemia? I feel that these patients should be hit with high dose antihistamines and an inhaled steroids such as pulmicort as frequently as possible before it's top late. This may get the patient thru the massive inflammatory response which seems to be the culprit to so many deaths in H1N1. Maybe it will buy the patients enough time to tackle the virus which is supposed to be self-limited in nature anyways if the hypoxemia did not get in the way so much. What do you think?

  25. hellow sir i want to know clearly about hemagglutunin. I'm a student of biotechnology i'm taking seminar about H1N1 influenza i said to my frnds dat HA have trimester structure so dat wen it enters into host cell it binds to sialic acid as it have a trimester structure. But my sir said its wrong,it only binds to cabohydrate residue so dat it gets bound to sialis acid , can u plz suggest me about dis structure clearly

  26. hellow sir i want to know clearly about hemagglutunin. I'm a student of biotechnology i'm taking seminar about H1N1 influenza i said to my frnds dat HA have trimester structure so dat wen it enters into host cell it binds to sialic acid as it have a trimester structure. But my sir said its wrong,it only binds to cabohydrate residue so dat it gets bound to sialis acid , can u plz suggest me about dis structure clearly

  27. Why are most of the clinical articles recommending use of oseltamivir when it has greater capacity to cause resistance than zanamivir? Is it because zanamivir is inhaled vs. oseltamivir pill?

  28. Yes, inhalation is not as widely accepted as an ingested pill. It's
    probably driven by physician preferences. If the docs said 'do you
    want an inhaled formulation that is less likely to lead to
    resistance', I think many people would say yes, but the choice is
    rarely offered – tamiflu seems to be the default.


    This is a pretty cool article that came out the other day about making universal influenza vaccines by taking the head off of HA and using the stalk as an immunogen (in mice). Considering how rapidly influenza can evolve, could strains with different stalks emerge which escape the vaccine–or would that make the HA non-functional? Why does the immune system normally produce antibodies to the HA globular head rather than the stalk?

  30. thanks so much prof! I am studying about virus in master’s course. I really like these information. Have a nice day!

  31. Have a question concerning Hi path H5N1 vs Lo path H5N1–was told the difference between them is number of amino acids detected. Where are these located in the RNA and how are they detected.
    Thanks in advance

  32. Brilliant website!
    Just a question…
    How is sero-protection threshold define? (by vaccine industry I guess…). Usually for adults it’s 1/40. Is it also true for children?

  33. Please address issues with adjuvants M59,squalene,tween80 etc and their toxic or potentiating effects of Flu vaccine

  34. This is indeed a very useful website, Professor!  Can you write more about other viruses, e.g. HIV?

  35. Hi …..Just a question…For Flu vaccien.. which is better to early inactivation  and lately inactivation?

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