Der Feuervogel aufersteht.

Yesterday morning were reported 642 cases in 41 states and 2 deaths. The second death was in a woman with chronic underlying health conditions, which made her more vulnerable. Today we're up to 896 cases in 41 states. It's everywhere, pretty much. (200 cases in Illinois? Huh.)

CDC has nifty maps of the cases now.

Revere wonders what so far, so good means in this context. The idea this is "mild" flu virus is so far true, but mild is a relative term, as we have pointed out here. And "so far" is another important qualifier. This virus is spreading relatively quickly, but it isn't everywhere and not much time has passed. He reminds us that we should pay attention to the upcoming flu season in the southern hemisphere, because it might give us a clue for what to expect this fall. Or not.

Case count (US): 160; 1 death.

Pictures! (of the virions)

Will shutting down the borders and stopping air travel make it better/go away? Nope. The horse is out of the barn.

Are we (the public health community) overreacting? Probably not.

After all, “The thing I wish officials would say more often ... is the following two sentences,” he said.

“'This is the way a devastating pandemic could well look at this early stage.' That’s the first sentence. And the second sentence is: 'This is the way a false alarm could well look at this early stage.'”

“Reading the tea leaves now to see which of those is happening simply can’t be done,” Sandman said. (source)

True that.

I hope I'm not boring *everybody* to death with this; I think infectious disease epidemiology is pretty cool. That's why I took that certificate program through UNC School of Public Health in field epidemiology (and I like being able to use what I learned!)

Yesterday, WHO raised the pandemic alert level to 5, out of a maximum of 6. OMG WE'RE ALL GONNA DIE! NO. Stop panicking. Here's what level 5 means: Phase 5 is characterized by human-to-human spread of the virus into at least two countries in one WHO region. While most countries will not be affected at this stage, the declaration of Phase 5 is a strong signal that a pandemic is imminent and that the time to finalize the organization, communication, and implementation of the planned mitigation measures is short.

To translate this: We've got a novel virus (never seen infecting humans before. See PSA #1 for why that's a problem.) It's been confirmed in more than one country. That's all.

It doesn't mean it's any "worse" than an average flu season, though the flu season in the northern hemisphere is just ending. It does mean, however, that there's *potential* for it to get worse, depending on what the virus does.

Remember in PSA #1 when I said RNA viruses are lossy? That means they mutate pretty easily. Some mutations may confer higher transmissibility and infectivity (fancy words that mean it's more contagious); others may confer higher virulence (which means it makes you sicker if you get it.) One thing we've learned from HIV is that some mutations that confer resistance to drugs make the virus weaker: there's a trade-off. AZT won't stop its replication anymore, but it's also not as good at infecting the host.

If a pathogen is *too* virulent, it will die out before it can infect too many people. If it makes a person so sick that they can't leave their house, it'll be confined to their house. (simplifying.)

The pathogen wants to strike a good balance between transmissibility and virulence. With viruses, you've got an incubation period where you're infected but not symptomatic (or only mildly), which means you can still pass on the virus before you know you're sick.

We *still* don't know why the Mexican cases were more severe. The only deaths have been reported in Mexico and in one 2-year-old who had been in Mexico recently. Is it because we've got better health care in the US and Europe? Is it because of poorer health and sanitary conditions in and near Mexico City?* Is it something different in the virus?

*It has been suggested that one of the reasons the Plague of 1340ish was so bad was because of the famine from about 20 years prior, so the kids didn't develop healthy immune systems. (The Great Mortality)

A couple paragraphs up, I mentioned that balance between transmission and virulence. If the virus traded off high virulence for increased transmission, it would be able to see more places. But remember that RNA viruses can mutate easily. There's a possibility that it'll mutate into something more lethal as time progresses.

The genomes from the Mexican cases have still not been released, but two isolates from cases presumably picked up in Mexico (from a NY tourist and a German tourist) are not very different from each other or from other published genomes, so the hypothesis that the difference is because of differences in the virus itself is less likely. (source)

Also, the man-bird-pig hybrid has basically been disproved. The lineage shows human and avian genetics several steps up the family tree, but the original strain was all porcine. (source) We can stop calling it swine flu, because it's basically mutated into a human virus.

UPDATE: Tara looks at the WHO scale, among other things, here.

luckykitty asked me in comments why this swine flu's got the health types freaked out. (Concerned, really. We're not panicking. Yet.) Isn't it just another flu? While answering, I thought I might as well make it a real post, since others of you might be wondering the same thing. (Note: I'm simplifying a LOT.)

Swine flu is worrisome because it's new. This one, influenza A(H1N1), appears to be a mixture of avian, human, and pig flu viruses. How does that work? Well, influenzaviridae are RNA viruses, so they've just got a bunch of genetic material hanging out. RNA viruses are really lossy, to borrow a CS term. When they copy themselves, it's easy to make a mistake. Also, the flu viruses have a tendency to recombine with other flu viruses. The flu genome is in 8 pieces, floating loose. So if you've got two different flu viruses in a cell, they can mix and match, and you'll get different viruses.

What do those H and N things mean? Well, the flu has two different surface antigens: hemagglutinin and neuraminidase. There are 16 known types of HA and 9 of NA. Not all subtypes can infect all species, but some can infect multiple species. H1N1 is one of them. (I once saw a nice graphic of which subtypes could infect which species, but my google-fu is failing me.)

It's a big deal because the antigens are completely unlike any in human flu strains -- which means we don't have proper antibodies or antibodies similar to the strain. Which means it's harder for our immune systems to fight off. I'm not sure, but that may be part of the reason that young, healthy people are disproportionately affected by it and the cytokine storm hypothesis for 1918 Spanish flu. (Basically, the immune system's first response is cytokines, which are the natural killer cells. They're not very smart, so they come in and say "Us? OK. Not us? KILL IT WITH FIRE!" That gives the body time to mount the antibody response, and when the antibodies come on the scene, the cytokines chill out a bit. But if there's no antibodies, the cytokines keep killing with fire.)

The body remembers everything it's been exposed to that caused it to make antibodies. B cells are the ones that make antibodies, and memory B cells remember them.

So, the flu has antigenic shift and antigenic drift. Drift is a small change in the proteins that the body recognizes as NOT US. Depending on how far it drifted, the memory B cells might be able to help out while new antibodies are being made. Kind of like taking a key that kind of works to open the door while you get a locksmith to make a new one.

Antigenic shift, however, is a lot harder for the body to compensate for. It's something your body's never seen, so there aren't any similar keys to try, and it has to wait for the locksmith to do anything (except the NK cells killing everything with fire.)

What's worrisome is that in Mexico, the fatality rate is pretty high (though we obviously don't know the true number of cases, only the 100 or so potential deaths from swine flu and the 20 confirmed.) In the US, it's true that the cases have been non-fatal and largely mild. (I hesitate to call anything requiring hospitalization "mild.")

US case count today is up to 64. These are laboratory-confirmed cases only. What we don't know, as I mentioned above, is how many people got mild infections earlier and passed it off as a regular flu. Many of the cases have been identified since the news broke from Mexico, and many of them are from the NYC school (45!) where 100 kids were sick. Case-finding efforts are underway, which means that hospitals are searching their records of recent admissions for upper respiratory illnesses to see if any fit the clinical criteria list and testing for influenza if possible (and sending samples to the CDC if they find any suspicious ones.) There's a rapid test that can show if someone has influenza and whether it's influenza A or B; further subtyping requires molecular-level testing. (Influenza B does not have subtypes like A. It's also less common.)

Don't panic. Be concerned, be aware, and be prepared, but don't panic. Add Effect Measure to your daily reading list or RSS aggregator.