The last time we reported on Swine flu, or 2009 H1N1 virus, the Centers for Disease Control and Prevention was considering whether or not to invest in a vaccine for the new influenza strain.

Now, after several delays, the first batches of vaccines — first, a nasal spray version, then an injectible vaccine — is due to hit hospitals and clinics across the country (and around the world) in the first weeks of October. It's up to each state to decide which groups to prioritize, but pregnant women, young children, and those with certain preexisting conditions such as asthma may be considered priorities. Over the following weeks, the flow of vaccines, produced at five different labs across the country, will steadily increase until, officials hope, any American who chooses to be vaccinated has access to a dose.

To learn more about where to get the vaccine, call: (800) CDC-INFO (800 232-4636) or visit www.cdc.gov/flu.

Here's another good resource for basic H1N1 vaccine info.

In this piece, we profile work taking place at the University of California, San Francisco's Viral Diagnostics and Discovery Center. This lab is home to the ViroChip – a powerful viral diagnostic tool that won its inventor, Joseph DeRisi, a MacArthur "Genius" Grant back in 2004. TheViroChip and other tools are critical to the fight against 2009 H1N1 . Among other things, they may be the first to alert us should the virus mutate into a form that's resistant to the leading antiviral drug, Tamiflu. (Several cases of Tamiflu-resistant 2009 H1N1 have already been reported, but so far they appear to be isolated incidents.)

They'll be looking out for another important mutation too: That's if 2009 H1N1 changes enough so that the current vaccine for it — the one coming out in October — no longer works. (This kind of subtle virus mutation is the reason we need new flu vaccines every year.) So far, this does not seem to be the case.

Listen to the Predicting Swine Flu radio report online.

The swine flu virus. Credit: C. S. Goldsmith and A. Balish, CDC.

As this story is being produced, the reports on swine flu are changing hourly. Cases are popping up closer and closer to home, and the CDC is updating several times a day on the spread of the virus, and plans to fight it.

The $64,000 question is how worried we should be.

Swine flu is largely untreatable: The two effective antiviral drugs, Tamiflu and Relenza, must be taken within 48 hours of infection to stop the spread of the virus.

That leaves a vaccine. Vaccines are relatively straightforward to create, but they take time. If swine flu becomes a deadly pandemic (meaning it's not only widespread — a pandemic – but more lethal than it appears to be so far) the demand for vaccines would likely far outpace supply. According to Art Reingold, at UC Berkeley's School of Public Health, it could take years for doses to reach everyone in the world who's vulnerable to the disease. Here in the US, we have very few vaccine producing facilities, which means we'd be competing with other countries' priorities to treat their own citizens.

Our story focuses on what could, one day, be the answer to pandemics like this one: a universal vaccine. Scientists like Harvard Medical School's Wayne Marasco believe that, in just a few years, we might be able to inoculate ourselves against nearly all influenza viruses – like a tetanus shot, against the flu. Universal vaccines will come too late for our current swine flu pandemic. But they may well be our response to pandemics of the future.

Listen to the Swine Flu and You radio report online.

You're as likely to be struck by lightning
as to have a severe reaction to a vaccine.

I was reading an article in Time last week about parents not vaccinating their children. The story was about how this phenomenon is becoming more widespread.

These kinds of stories are weird to me because vaccines are pretty safe. The risk of an adverse side effect is incredibly small. For example, the risk for anaphylaxis from the Hepatitis B Virus vaccination is around 1 in 600,000. This is about the same risk as being struck by lightning (1 in 700,000).

Of course, the article wasn't talking about known risks. Instead, it was referring to a hypothesized link between vaccines and autism.

People proposed this link when they noticed that cases of autism and the number of vaccinations were rising at the same time. Of course, just because two things happen to occur at the same time, this does not mean they are causally linked. For example, the increase in global temperature is not related to the decrease in the world's populations of pirates (despite what the Pastafarians say).

So how could an increased number of vaccinations cause an increase in the number of cases of autism? I have seen two ideas put forth. The first is that thimerosal is to blame. The second is that there are so many vaccinations now that we are stressing out the body's immune system. Most likely neither idea is valid.

Thimerosal is a mercury-based preservative that used to be used in vaccines. Even though there haven't been any good studies on the effects of thimerosal on brain development, everyone knows mercury is bad for the brain. So the idea behind thimerosal makes some sense.

Back in 2001, vaccine manufacturers decided to eliminate thimerosal from their vaccines. We would predict, then, that cases of autism should go down significantly if thimerosal was linked to autism. They haven't. In fact, in one California study, cases have continued to climb. So thimerosal is most likely not to blame.

Another point that has been made is that there are so many vaccines now that we are stressing out our bodies' immune systems. Again, this concern is unfounded.

Vaccines are injections of viral proteins. Our bodies see the proteins and raise antibodies to them. Then when a virus invades, we have antibodies that recognize the virus and target it for destruction.

It is the number of viral proteins that matter in terms of taxing the body's immune system and not the number of vaccinations. All of the current vaccines put together do not have as many viral proteins as the old smallpox vaccine (150 vs. 200). So the number of vaccines is unlikely to be the issue.

What all of this means is that vaccines are probably not responsible for the significant increase in the number of cases of autism. What is responsible? No one knows for sure.

It may be that the rise just comes from all of us recognizing the symptoms more. Or it could be due to some cause we don't know about or understand.

What we do know is that vaccines save many lives. I assume no one wants to go back to the early 20th century when polio epidemics swept the country. For example, 2,500 cases of polio ended up at one Los Angeles hospital between May and November of 1934. And in 1952, the U.S. had 21,000 cases of paralytic polio.

We can prevent this sort of thing from happening by making sure everyone is vaccinated. And yet there are people who choose to hide behind the people who take the miniscule risk of getting vaccinated.

Is this a matter of free choice? Should parents be allowed to opt out of vaccinating their children even if it risks society at large?

One idea, I suppose, is to have people who choose not to be vaccinated to sign a waiver saying they accept full responsibility for their actions. In practice this would mean that health insurance and the government would not be responsible for their children's health care bills if they become ill with one of the diseases they refused to be vaccinated against.

And if your infant, grandma, or immuno-suppressed cousin came down with a disease these folks refused to be vaccinated against, then you could sue the un-vaccinated for damages. The common good isn't enough to encourage these folks. Perhaps threats to their pocketbook will be.