Teaching about swine flu

These are some notes I put up on the JREF forum last April. I have updated a bit of it, fixing some minor errors. I figured this would be a good place to start things off.

I moved a bit away from my planned lectures on environmental science for my two freshmen biology sections to focus on this current and very teachable event, and thought that other educators may find these lecture notes and resources useful.

First off, the google swine flu map provides an excellent resource for teaching how modern transportation can make preventing the spread of flu practically impossible. Unlike the original google map, this map has a very easily understood legend. For details on national and regional outbreaks, zoom in. For instance, Kentucky, my home state, currently has an orange circle with 167 in it. This means that there have been 167 confirmed cases, but no deaths. Florida on the other hand, has a tri colored circle with 2895. Click the circle, and you get these details.

Suspected Cases: 1
Confirmed Cases: 2865
Fatal Cases: 29

For more detail, zoom in further. Miami-Dade has these details, plus information on some cases.

Reported Location: Miami Dade County, FL
Confirmed Cases: 917
Fatal Cases: 10
This is an aggregated report based on 24 reports near the same location.

Next up is the structure of the virus. All viruses have genetic material that is either DNA or RNA, proteins that surround and protect the genetic material, and spike proteins that allow it to interact with the environment and bind to target receptors on the cells it can affect.

The flu virus has RNA for genetic material, and typically has 8 short stretches of RNA, which exist in a fashion similar to mini chromosomes. It also has two spike proteins which also are the antigens that our immune system recognizes, and give the name and classifications for these viruses. Hemagglutinin targets the virus to infect a specific cell type, and is the H of the H1N1 of the current flu type. Neuraminidase helps the virus bud off of the cell, and is the remaining N. For each different group of flu virus, HxNy describes a related group with lots of strains with minor mutations between them.

Since most of us have had H1N1 flus or flu shots recently, we have some minor immunity to members of this group, which is great news. However, mutant strains may be different enough to sneak past our immune system and make us sick. Because the flu virus mutates quickly, this is why you need to get a flu shot every year. The strain is a little different every time. In the case of the H1N1 swine flu virus, it isn’t a minor mutant, but a new combination of genes, so we really don’t know if previous shots will offer any help at all.

Also of interest is that the flu virus is an envelope virus. As it buds off of the host cell, it surrounds itself with some of the host’s cell membrane. This means that the host cell doesn’t die when viruses are released. It may die later if the virus causes the cell to use too much of its own resources to make viruses, or if the immune system detects the infected cell and targets it for killing.

I mentioned that the genome is set up as mini chromosomes, each with one or two genes, and this is very important to this particular strain. You may have heard that his flu virus has a mix of avian (bird), swine and human flu genes. Well, this is unusual, but not unheard of, and is certainly not evidence of genetic engineering and conspiracy as some CTrs (conspiracy theorists)  are claiming.

First, many different groups of animals have their own flu viruses, but only these three groups do a particularly good job of infecting humans. Lets say we have a hog farm, maybe with some ducks and pigeons in the area, and of course, humans.

The birds pass one virus to a hog, which is also infected with its own flu virus. This means that the animal (Animal I in my blackboard notes) has two different viruses in it’s cells. The mini chromosomes would sort separately, just like chromosomes in meiosis, and each new virus would have a random mix of bird and swine flu genes.

Lets say this gets passed along for a bit from one pig to another, or perhaps back to some birds. At some time, another animal (Animal II) becomes infected with the hybrid virus and a third virus, this time from a human flu group. Again, we have a mixture of genes being produced, and the most fit ones (not necessarily the ones that cause the worst disease) spread through the population.

If the genes are just right, the virus ends up moving into the human population and can be spread from one person to another.

Also of great value is the HHMI’s biointeractive website. Under the lecture tab, holiday lectures, infectious disease, you can find the 1999 lecture, which is a little out of date, but there is one part of the 4th lecture that specifically deals with the flu, and you get most of the above information.

The Holiday lectures are targeted towards advanced high school students, but I think that the lecturer probably used words and terms that were a bit more advanced than are needed. I don’t mind showing it to my college students, but even so, I know that some probably still didn’t follow parts of it. Alas, you can’t reach them all.

One question I received on the JREF: What are the chances for a mutation to make it particularly deadly? That’s my biggest concern?

Well, it is possible. Since the flu is an RNA virus, the rate of mutation (1/10,000) is about the same as the length as the entire viral genome, you could expect every virus to have a mutation. Most of these do nothing (no appreciable change to the 3D shape of a protein), and some will be negative and inhibit the mutant and its offspring. Occasionally, a strain will get really a really nasty mutant coming from it, but that is completely unpredictable.

If a disease kills quickly, though, it won’t get a chance to spread very far, and the outbreak would burn itself out. That isn’t very likely for the flu though, because even really bad cases take several days to progress to pneumonia or cytokine storm (extreme immune response, very nasty), including time where you are feeling OK enough to be around people. The 1918 pandemic was around 2.5 – 5% mortality, and so far, this one isn’t nearly there (even though we don’t have good numbers yet).

It is hard to estimate the case fatality ratio, because we tend to undercount the number of real cases, especially if people don’t need to go to the hospital for mild cases. The we have to figure out how many people actually died from flu and not something else, so that number is hard to get. Divide deaths by cases, and you at least have an idea of how bad it is.

Of course, we now have some anti-flu drugs and better medical care, so at least the developed world shouldn’t be affected as badly. The reason we are so concerned about bird flu is that some strains of it don’t appear to respond to these drugs, so we may have one less tool to use (at least from the few cases that have been seen).

Best, and teach on.