The H1N1 flu strain got a lot of attention in 2009. Most of the headlines made it sound dangerous. Early in the epidemic we thought that a very high percentage of infected people were getting sick, and it was quite scary.

But the real story isn’t how bad H1N1 was. The real story is that we are lucky it wasn’t worse because we were almost completely unprepared for it.

When an epidemic breaks out, there are four steps to try to contain it. The first is to gather data about the disease—where it is and how it is spreading. Second is to limit the movement of people from place to place—with quarantine a last option. Once a disease is widespread this is very hard to do. Third is to have drugs of some type that reduce how much someone infects others and that reduces the severity of the sickness. Fourth is to make a vaccine that is effective against the disease and give it to anyone who is at risk.

We did a reasonable job of gathering data, partly due to the capacity that had been set up to track avian flu. But for all the other steps, we didn’t manage to do anything that would have stopped a serious epidemic. In other words, the modest death toll from this flu epidemic is entirely because we were lucky.

Hopefully this outbreak will serve as a wakeup call to get us to invest in better capabilities, because more epidemics will come in the decades ahead and there is no guarantee we will be lucky next time. The 1918 flu killed more than 50 million people. Nothing other than bioterrorism could kill that many people again, and most of the things we need to do to reduce the impact of an epidemic will also reduce the impact of bioterrorism.

The ability to make a vaccine quickly and manufacture it in huge quantities is a critical part of a response to an epidemic. You need to get production going in less than a month instead of more than five months, which is what it took in this case. You also need to be able to make vaccine at a rate ten times faster than what was achieved.

Most flu vaccines today are made by injecting parts of the virus into chicken eggs, which is a laborious process. Given the approved approaches, the vaccine industry did a great job getting the vaccine out as quickly as it did. (Ironically, now that the disease is proving to be relatively mild, a lot of the vaccines they hurried to make will not be bought.) This is one place where innovation can make a big difference.

There are new manufacturing approaches that reduce the lead time and increase the production rate, but government rules don’t allow the vaccine companies to use them yet because of safety concerns. Although governments are right to be conservative about vaccine safety, they have to find a way to help the vaccine industry incorporate these new approaches and expand its capacity in the next few years before the next epidemic comes along.