Dear CDC,The news this week has been filled with reports of a new flu outbreak around the country. My own university has reported over 400 cases, the worst flu season in many years. Those of you who’ve followed this blog may remember that I predicted this would happen in a November blog post. Part of me wanted to be wrong – I didn’t want a bad flu season – but it turns out I was right.
Oh, if only you wouldn’t spurn me. Don’t you know we both want the same thing? Like you, I want the flu vaccine to work. I want everyone to get their flu shots. I know I’m an outsider, but maybe you could at least listen to my ideas? Is it my fondness for sequencing over serotyping? Or maybe my insistence that you should share all your sequencing data? Why not invite everyone to the party? It’d be much more fun. And think of all the flu viruses we could keep out.
The CDC had a press conference on Friday (15 February) acknowledging that the vaccine was a bust, but they didn’t explain why they’d chosen an old strain of H3N2 (from 2005!) for inclusion in the vaccine. As I explained in November, they already knew it was a bad choice – or they should have – last year.
So what is happening out there? Well, from the CDC website we can see results from the week of Feb 3-9 (the most recent data they have) summarized in this figure:
The red cases are H3N2, which are clearly dominant. The blue cases are H1N1 (the vaccine works against that strain!), and the yellow are influenza A but not typed as H3 or H1 – most of these are probably H3N2 as well.
The raw numbers for the season tell an even more compelling story of vaccine failure. Out of 65 H3N2 viruses that the CDC has genotyped, only 9 (14%) matched the vaccine strain. The remaining 91% are a new strain, for which the vaccine either limited or zero efficacy. (The CDC doesn't say when those 9 cases appeared, but I'm betting they were early in the season.) A newer, 2007 strain, which they have decided to put into the vaccine for the Southern hemisphere for the 2008 season, should provide far better protection. (The flu season down under occurs in their winter – our summer – so it peaks 6 months after ours, and they can use a newer vaccine.) We’ll get the newer strain in our vaccine next year too, assuming the FDA agrees when they meet next week to decide. Unfortunately it’s too late for this year.
Here’s a proposal to the CDC: release all the sequence data you have from this year’s strains right away, and put it in GenBank. And release any other data you use to pick the strains that go in the vaccine – and do this every year. Then everyone can look at it and double-check your decision about which strain should go in next year’s vaccine. Sure, it might be annoying to have other scientists checking your work. But wouldn’t it be great if researchers – including students – all over the world could look at the flu data and make their own predictions about what strain would dominate next season? The science would only get better.