feuervogel: photo of the statue of Victory and her chariot on the Brandenburg Gate (Default)
Except twice as many cases today as yesterday. 1639 cases in 43 states.

Revere discusses the articles from NEJM this week.

The viral replication series at Virology Blog continues: Release of influenza RNA into cells and Viral RNA synthesis.
feuervogel: photo of the statue of Victory and her chariot on the Brandenburg Gate (Default)
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.
feuervogel: photo of the statue of Victory and her chariot on the Brandenburg Gate (i'm a doctor)
Sorry to miss yesterday and Sunday; there weren't many updates Sunday, and yesterday I was learning more about HIV and aging, as well as skin issues with HIV. (Including nasty photos! Oh, the things you get used to, working in medicine.)

Today's US case-count is 403 in 38 states, with 1 death (same as before, in a toddler who had been to/was from? Mexico and died in Texas.) Worldwide it's 1124 as of 6:30 GMT today. (For some reason, I can't load the WHO site to get updated numbers.)

Revere looks at where we are, and where it could be going. The key point is that flu season in the southern hemisphere is about to take off, so there's a possibility that H1N1 is going to be competing with the H3N2 virus circulating there. It's time for watchful waiting, to see which virus reigns supreme. (Sorry.)

Virology blog teaches about viral reproduction. Step 1: attachment. Viruses completely lack reproductive capabilities, so they have to hijack the host's apparatus. Kind of like sneaking in to use your office's copy machine because you haven't got one. First, they have to get inside the cell to do it. All viruses have different specific proteins to do it with (I think), but the mechanism is *basically* the same.

The Institute for Southern Studies takes a look at the relationship between NC-based Smithfield Farms' giant hog factories and H1N1. The currently-circulating virus bears a genetic relationship to a 1998 outbreak at a Smithfield hog factory. (Obligatory note: macro-scale animal farming is BAD, mmm-kay?)
feuervogel: photo of the statue of Victory and her chariot on the Brandenburg Gate (Default)
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.

True that.
feuervogel: photo of the statue of Victory and her chariot on the Brandenburg Gate (i'm a doctor)
US case count is 109 (soon to be updated, no doubt; CDC updates around 10:30 every morning*) 141 as of 11 am EDT. Still only one fatality. Worldwide confirmed cases are 331. Confirmed means that the PCR primer for this particular H1N1 strain matched to the RNA in the sample. (Don't ask me what that means; that's molecular biology stuff. Basically, the gene sequences match.)

Educational stuff

Virology blog has some awesome educational posts: Structure of the influenza virus and Influenza virus RNA genome. He also looks at some of the trade-offs I discussed yesterday: Tamiflu resistance may decrease aerosolization.

CIDRAP has facts on H1N1 and historical swine flus. It's fairly high-level terminology in some sections, but it's in convenient outline form.

Current updates

Virology blog thinks level 6 is inevitable. What does that mean? Yesterday I said that level 5 means that a novel virus has had sustained person-to-person spread in more than one country in a single WHO region. Level 6 means that there are community-level outbreaks in more than one WHO region (so North America and Europe.) It does not mean that we're all going to die, same as yesterday. It still means that we need to do common-sense things like wash your paws and cover when you sneeze.

MMWR takes a look at the outbreak in the NYC school. Lots of epidemiological details on how they found the outbreak and what steps have been taken to contain it. There's a lot of medico-babble, but most of you should be able to get through it.

Political stuff

Revere comments on the consequences of sick leave policies and people going to work sick. (ed note: I support mandatory sick leave for all employees or other measures that allow people to stay home when they've got contagious diseases.)

Ezra Klein looks at the case for overreacting (by the government, not by people, kthx.) It's better to prepare for something awful and it not happen than pull a GWB and ignore it and hope it goes away.
feuervogel: photo of the statue of Victory and her chariot on the Brandenburg Gate (i'm a doctor)
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.
feuervogel: photo of the statue of Victory and her chariot on the Brandenburg Gate (i'm a doctor)
First, some links:

The CDC updates its official page every day, adding to confirmed US cases every morning (around 11 am EDT). For international cases, visit WHO.

Virology blog has a daily update, featuring all the news up through yesterday.

Revere explains how Tamiflu works (also how influenza virus infects cells and its lifecycle).

Revere also takes a look at influenza pandemics and explains the adage "if you've seen one flu pandemic, you've seen ... one flu pandemic."

In a similar vein, Virology blog looks at seasonality of the flu and discusses 1918 a bit.

Sandra Porter looks at whether the California swine flu came from Ohio (which had an outbreak after a county fair in 2007) via their genetic sequences.

Tara rounds up a bunch of links.

Media got you paranoid? Global Health Report has a bunch of facts, and links to websites you can trust for calm, informed information. (Including several of the sites I've linked to.)

The virus is spreading beyond travelers, says the CDC (via CIDRAP). The latest onset of symptoms in confirmed cases was April 24, but that does not rule out transmission after that date. And, of course, if you're sick, stay home (unless you're going to the doctor, of course.)

Voluntary isolation is the current recommendation, and it's a damn good way to prevent spread. You can't transmit virus to coworkers, people at the store, etc, if you're not out in public.

You CANNOT get swine flu by eating pork.

And, as always, DON'T PANIC. You can be concerned -- I think it would be foolish not to be; there are a lot of unknowns involved -- and you ought to remain informed and be prepared. But it's not to the point of bar your doors and stock up on ammo.
feuervogel: photo of the statue of Victory and her chariot on the Brandenburg Gate (i'm a doctor)
[livejournal.com profile] 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.


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