Posted by: sayamika, the killer bunny | 2009 April 26

Influenza virology for fun and profit

When I was a microbiology student many years ago, I had a virology professor who studied measles and influenza. He was convinced that these two viruses were going to become more and more important over the coming years.

He used to talk about the potential for an influenza pandemic. His students saw him as the bearded guy with the pamplets and sandwich board saying “The End Is Near!” and giggled behind our hands.



The current outbreak of influenza in Mexico has the experts up in arms for a number of reasons.

We are overdue for a flu pandemic. Flu epidemics are cyclical, with new strains becoming prevalent every year due to genetic drift, or slow mutation of currently circulating viruses. Because these are closely related to viruses we have encountered in the past, we have partial immunity, either from infection or from vaccination in previous years.

Once every 60 or so years over the past few centuries, there is evidence of a genetic shift associated with a lack of immunity in the population.

The 1918 pandemic which killed an estimated 60 million people worldwide is an example of what happens with a shift.


The influenza virus is an unusual virus in that is has eight distinct “chromosomes.” These are segments of RNA which each encode a different functional protein. They are in separate pieces.

The segments of interest to us are the hemagglutinin (H) and neuraminidase (N) segments. These segments encode the proteins on the outside of the virus, the proteins that our immune systems can therefore recognise.

These are the proteins used to design vaccines. There are sixteen known distinct versions of H and nine of N. Usually only one or two of each are circulating in any given year, and there are only a few at any one time known to infect humans.

H and N proteins change a little from year-to-year, and so the flu shot one gets one year may not give full protection the next year.


Influenza infects two other types of animals: birds and pigs. The flu virus that infects other animals usually is only slightly able to infect people, because the six other proteins are different between human and animal flu. They are specific to the host they infect: avian flu best spreads in birds, swine flu best spreads in pigs.

A person who is highly exposed to one of these animal viruses could get infected, but usually cannot pass it on to another person, because these six other proteins just don’t work as well in humans.

The tricky bit is this: sometimes a person who already is infected with human influenza may get infected with animal influenza. This is a very unlucky soul indeed.

If the two viruses mix around, sometimes a new virus is produced which has an animal version of H and N, and a human version of the other six pieces.

This is trouble.

This virus is what is called a shift. It is not anything like the other flu viruses in the human population, because its entire outside has only been in either birds or pigs in the past. Our immune systems cannot recognise it. Our vaccines are not ready for it.

But it has all the machinery to spread in humans.

This has been the fear with avian flu, but so far human outbreaks have been limited: there has been no virus which has picked up both avian hemagglutinin and neuraminidase, and all six human functional proteins. We may not be as lucky, I fear, with the Mexican outbreak. Human-to-human transmission is happening.

Looks like my prof was right.


H1N1 cases confirmed in Nova Scotia, in kids just back from a school trip to Mexico. The kids are doing fine, with relatively mild cases.



  1. […] no, not in general. This year is a little different. * Did you know that many MDs that recommend the flu shot DON’T get […]

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