The flu vaccine is working well this year. It's not too late to get it.

Current flu trends for 2018-19. Brown shows H1N1 strains,
red shows H3N2, and yellow indicates the strain was not
genotyped.

The flu is widespread and increasing right now, according to the CDC.  At least 42 states were reporting high levels of flu activity as of the end of December 2018, and the rates are still climbing. In other words, we're in the midst of flu season.

Other than that, though, the news is relatively good. Here's why.

First, the dominant strain of flu this year is H1N1, which is the "swine flu" that first appeared as a pandemic in 2009. But pandemics don't have to come with high mortality rates, and as it turned out–luckily for humankind–the 2009 flu was milder than the previous dominant strain, H3N2, which first appeared way back in 1968.

This season, nearly 90% of the flu cases tested by the CDC are turning out to be H1N1, the milder variety. Although 10% of people are still getting the much-nastier H3N2 flu, it's good news compared to last year, when H3N2 dominated.

Back to the bad news (although this is old news): the 2009 swine flu (H1N1) didn't completely displace the older flu strain. Instead, we now have both types of influenza circulating, along with two strains of the even milder influenza B virus. Since 2009, the flu vaccine has to combat all 4 of these flu viruses, which is why you might see the term "quadrivalent" associated with the vaccine. That just means it targets all 4 different strains.

Back to the good news again: the vaccine this year contains just the right strains! This doesn't always happen; actually it happens much less frequently than anyone would like. But now that the flu season is under way, the CDC can test the circulating flu viruses and compare them to the strains that are targeted by this year's vaccine. This year, both the H1N1 and the H3N2 viruses match the vaccine strains really well, which means that if you got the shot, you are likely to be very well protected.

(Keep in mind that even in a good year, the vaccine isn't 100% effective, and you can still get the flu. But you are much less likely to get it than anyone who is unvaccinated.)

While I've got your attention, let me answer one of the top 10 health questions of the year: "how long is the flu contagious?" According to the CDC,

• the flu is most contagious in the first 3-4 days after becoming sick.

It continues to be contagious for up to a week, so if you have the flu, stay home! And make sure those around you avoid physical contact, as much as possible, and wash their hands frequently.

And while I'm at it, let's debunk a common myth:

• No, you can't get the flu from the vaccine.

So if you've put off getting the flu vaccine, it's not too late! The season is in full swing, but if you get the vaccine today, you'll likely have excellent protection for the rest of the season. Go get it.

Whatever happened to swine flu?

What happened to the flu pandemic?  In 2009, a new flu strain swept across the world. The new strain, called H1N1, emerged from pigs and jumped over to humans sometime in late 2008, and then swept through the human population starting in the spring of 2009.  Panic ensued.  Egypt responded by slaughtering all of its pigs, about 300,000.

Was the panic justified?  If so, where are all the victims?

I first wrote about this soon after the outbreak began, and we now know that hundreds of millions of people were infected, somewhere in the range 11% to 21% of the population.  That's an awful lot of sick people.  However, H1N1 turned out to be a very mild flu: many people experienced little more than a few days of sniffles, much like a common cold.  This surprising mildness of swine flu led to great confusion.  Conspiracy theorists claimed that the threat had been overblown, hyped by vaccine manufacturers and their government co-conspirators.  A wacky German lawmaker, Wolfgang Wodarg, even claimed that the swine flu vaccine caused cancer, a claim that was picked up and amplified by famed internet snake oil salesman, Joseph Mercola.

The swine flu now seems routine, just another human flu circulating among the population. As I wrote back in 2010, the seasonal flu vaccine now includes the H1N1 pandemic strain, so if you get your flu shot, you're protected.  But as this figure from the CDC shows, the current season has been dominated by H3N2. 

See the little tiny brown bits at the top of each bar?  Those are swine flu cases.  The swine flu has nearly vanished.

This is a big surprise, because in all three of the previous pandemics: 1918 ("Spanish" flu), 1957, and 1968, the new pandemic strain completely replaced the older strain.  That hasn't happened this time, and it looks like the old strain, H3N2, is winning.  That's rather unfortunate, because H3N2 is a much nastier flu than the swine flu.  And this year we had a big spike in deaths due to flu, all because of H3N2.

So no, the panic back in 2009 wasn't justified, but the warnings beforehand, about the possibilities of a pandemic, were legitimate.  All we knew in early 2009 was that a new pandemic strain had jumped from pigs to humans, and we didn't know for several months how bad (or mild) it would be.  The human species got lucky this time.

Can anyone say when the next pandemic will arrive?  Well, no.  Look at the past century: 4 pandemics, separated by 39 years, 11 years, and 41 years.  From that record it seems we should be safe for a while.  But until 2009, the pandemics had always pushed out the previous flu.  We're still living with the 1968 flu strain, and no one knows when a new flu will truly replace it.

Meanwhile, get your flu shot, because the flu mutates so fast that we need a new vaccine every year to keep ahead of it.  Work continues to try to develop a permanent flu vaccine - one that we will only have to take once in a lifetime.  If you like that idea, then keep supporting NIH, which is the biggest source of funding for flu research.

Oh right: we just cut NIH across the board because Congress couldn't get its act together.  I guess we may have to wait a bit longer for a better flu vaccine.

Is the government hiding something about the next flu pandemic?

Remember the flu pandemic? The one that swept the world just two years ago? You might be forgiven if this has slipped your mind - after all, it doesn't seem like such a big deal now. That's because we got lucky: despite many dire warnings about the danger of another 1918 "Spanish flu", when the 2009 pandemic arrived, it was far milder than previous pandemics. Hundreds of millions of people got the flu in 2009, but for most of them, it wasn't so bad. In fact, the new flu is less severe the old flu - the strain that was circulating before the new pandemic hit.

Now we have two flus circulating: the "old" H3N2, and the 2009 pandemic flu, called H1N1. (And the vaccine protects against both of them, so get your flu shot! Your friends, neighbors, and co-workers will all benefit.)

We really dodged a bullet in 2009. Despite our best efforts, it took 7 months (April to November) before a new vaccine was ready. Before we realized how mild it was, people were desperately snapping up stores of Tamiflu, an anti-viral medicine that only barely helps to treat the flu. If it had been like 1918, Tamiflu wouldn't have helped much, and tens of millions would have died.

The 2009 pandemic originated in pig farms in Mexico. We don't know precisely where it made the first leap into humans, but it appears that two different strains joined together in a pig somewhere to create the new H1N1. The flu has a nasty habit of jumping the species barrier, hopping to humans from both pigs and chickens.

So now that we know all this, next time will be different, right? The world's influenza scientists are monitoring pigs and chickens closely now, keeping a close eye on any new flu strains. Right? RIGHT???

Er, no. Not exactly. For one thing, surveillance in pigs appears to be nonexistent. I checked to see how many flu sequences from pigs in Mexican have been desposited in the public archive at GenBank since 2009 (using this terrific database). The result? One, in 2009. Nothing from 2010 or 2011. Hello, is anyone awake at the CDC and the WHO?

This despite the fact that scientists have serious concerns that the deadly H5N1 avian flu (the "bird flu") could combine its genes with H1N1 and create a really nasty new flu strain. And scientists have long had concerns that pigs could be the mixing vessels for new flu outbreaks - exactly what happened in 2009.

But wait… maybe they are monitoring the flu, but they're just not telling us. That would feed into all the fringe government conspiracy groups that claimed the 2009 pandemic was an intentionally engineered government-funded enterprise (see this BMJ article for more). I don't believe any of those conspiracy theories - most of them are just nuts - but read on.

Sharing data about flu viruses has been a touchy subject with the WHO and the CDC for years. As reported by the University of Minnesota's CIDRAP,

"In late 2006, virus sharing became an international flash point when Indonesia broke a long tradition of free international sharing of flu virus specimens by withholding its H5N1 virus samples as a protest against the high cost of commercial vaccines derived from such samples. The controversy has drawn attention to the problem of equitably distributing vaccines in the event of a pandemic."

A few months ago, the WHO finally agreed on a new set of principles on data sharing, which states that

"The WHO GISRS laboratories [which includes the CDC] will submit genetic sequences data to GISAID and Genbank or similar databases in a timely manner."

Excellent! If they do it.

As every biomedical scientist knows, GenBank is a free, public database of genetic sequence data that contains millions of sequences, from humans, bacteria, viruses, you name it. But GISAID is another database, in Switzerland - one that I initially supported - just for flu data. The original mission of GISAID was that data deposited there would go to GenBank as well, with little or no delay. But in a classic bait-and-switch move, the GISAID board changed that policy after the database was up and running, and now they can sit on data as long as they want.

OK, you say, but it's a private database, so they can do what they want. True enough. But here's the surprising bit: the CDC deposits most of its flu sequences ONLY in GISAID, where they can milk them for scientific results for years without sharing them with others. As one of GISAID's original supporters, I have an account there, and here's what I found.

So far, the CDC has deposited sequences from 6,801 flu isolates in GISAID, of which only a tiny handful are in GenBank. 3201 of these originated in the U.S., so there can't be any foreign government insisting that they be kept secret. These provide critical data that could help scientists predict what is coming in the next flu season. But you can't get these sequences without a GISAID account. And even if you have a GISAID account, as I do, you have to agree not to release the data as a condition of getting a look.

So why does the CDC deposit sequences in GISAID? I think it's precisely because of the restrictions. CDC's scientists don't want others to look at "their" data, because they're afraid someone else might discover something important and publish it before them.

The CDC, of course, is part of the U.S. government, and all its work is funded by the public. But it seems that the CDC flu scientists have forgotten their public health mission - or at least, they appear to be more concerned about their own careers (and the papers they might publish) than about making sure the world is ready for the next pandemic.

And by the way, even these sequences don't seem to include anything from pigs in Mexico. Hello, CDC? You are looking at swine flu now, aren't you?

Perhaps I'm being a bit harsh. I love the CDC: they do a terrific job most of the time, providing vital services to protect the public from infectious diseases. But their internal scientists sometimes seem to operate within a cocoon, and I'm afraid that's happening here. This culture of secrecy has got to stop, and I suspect that will only happen under pressure from the outside. The CDC Director, Thomas Frieden, needs to tell his flu people to start sharing what they know with the rest of the world. And they can start by putting their data in GenBank.

At the movies: popcorn and anti-vaccine fearmongering

The anti-vaccinationists have launched a new campaign this holiday season to spread cheer – oops, I mean fear – to moviegoers everywhere. Yes, the folks at SafeMinds and Age of Autism have produced an advertisement that they are trying to place in AMC theaters across the country. In fact, they almost succeeded, but quick action by skeptical science bloggers at SkepChick, Respectful Insolence, and their readerships convinced AMC to cancel the ad – for now.

The ad that SafeMinds is trying to run is intended to scare people away from getting their flu vaccine, just as flu season is beginning. The vaccine this year will protect you against both the new “swine” flu, called H1N1, and the previous flu strain, H3N2. Early data from the CDC makes it clear that both strains are still around, with H3N2 showing up somewhat more frequently so far this fall. The vaccine not only protects you, but also your family, your colleagues, and the many other people you might come into contact with each day while at work, shopping, or elsewhere.

Why try to scare people? Well, the people behind SafeMinds and Age of Autism believe that the preservative thimerosal, which is used in some but not all flu vaccines, causes autism. This theory has been thoroughly investigated over the past 10 years, and just as thoroughly discredited. In fact, it never had any positive evidence to support it in the first place, but it has been promoted aggressively by a journalist, David Kirby, who made his fortune off a book based on the thimerosal-autism hypothesis. (I’m not providing a link – Kirby has already made far too much money off this bogus claim, and I don’t want to give him the web traffic.)

Thimerosal was introduced into vaccines in the 1930s, and it is a very effective means to prevent the growth of bacteria without affecting the potency of the vaccine itself. In over 60 years and hundreds of millions of doses, it has proven to be quite benign. Nonetheless, it contains a form of mercury called ethylmercury, which anti-vaccinationists claim causes autism and other neurological disorders.

The claim that thimerosal causes autism was the central question of a large, multi-year Autism Omnibus trial, which ruled definitively last year that thimerosal does not cause autism. I wrote about that ruling at some length back in March, and I won’t repeat it here, except to quote again from the Special Master’s decision:

“The numerous medical studies concerning the issue of whether thimerosal causes autism, performed by medical scientists worldwide, have come down strongly against the petitioners’ contentions. Considering all of the evidence, I find that the petitioners have failed to demonstrate that thimerosal-containing vaccines can contribute to the causation of autism.”

The anti-vax crowd will not give up, unfortunately. Rather than spending their time and effort trying to find the true causes of autism, they continue to repeat claims that have already been shown false. For example, the SafeMinds website lists 5 “key points” that are just flat-out wrong. Here are the first two:

1. “The autism epidemic that began in the late 1980’s is likely due primarily to toxins adversely affecting fetus and infants during development.” Wrong, in at least two ways. First, there is no autism “epidemic.” The best evidence today indicates that the rising rates of autism are due to a combination of factors, primarily (a) rising rates of diagnosis due to increased awareness among physicians and patients and (b) a dramatically broader medical definition of autism that was introduced in the early 1990s.
2. “Mercury is likely a major contributor to this toxin-induced autism, whether the source of the mercury is from vaccines or environmental mercury exposure.” Wrong again. This is the claim that was so thoroughly refuted in the lengthy Autism Omnibus trial, with hundreds of pages of testimony from dozens of experts, and epidemiological data from literally hundreds of thousands of people.

But data doesn’t seem to have any effect on the anti-vax zealots at Age of Autism and SafeMinds.

Because AMC refused to run their ad, Age of Autism is telling its readers to stay away from AMC theaters this holiday season. I hope they do! Why? Because these unvaccinated individuals are a genuine threat to public health. Movie theaters, and the malls in which they are located, are an ideal place for infectious diseases to spread. Without vaccines, countless thousands of people would fall ill every holiday season after mingling with other shoppers, and some would likely die. My message to the unvaccinated crowd at SafeMinds is: stay away from the rest of us.

And I encourage everyone else to get your flu shot, get your kids vaccinated, and then go see a movie at an AMC theater. Meanwhile, you can also tell them at this link that you appreciate their taking a stand against misinformation and for the benefit of public health.

Meet the new flu, same as the old flu*

Next year we’ll be back to one flu vaccine, thank goodness. The flu vaccine protects you against three different strains of the influenza virus, but for the past year, we had a separate vaccine for the new pandemic (“swine”) flu. It’s always hard to get people to take their shots (or “jabs,” as they say in England – why can’t we come up with a less painful-sounding word?), and asking everyone to go out and get two shots was never ideal.

For the next flu season, the vaccine will include these 3 strains:

1. The 2009 “swine flu” strain, H1N1
2. The previous seasonal flu, H3N2
3. Influenza B, a milder flu that has been around for decades.

What happened? Well, the WHO, the CDC, and the FDA have decided to replace one of the three strains in the flu vaccine with the new H1N1. The strain they replaced was also called H1N1, which is rather confusing. Let’s look at the history of these strains, which is an interesting picture of virus evolution.

In 1918, the Spanish flu (which originated in the U.S., despite its name) spread throughout the world and killed an estimated 30-40 million people, in the worst flu epidemic in recorded history. This was the original H1N1 flu. It soon evolved into a milder flu, which was around until...

In 1957, a new pandemic strain appeared, H2N2 or "Asian flu." This completely replaced H1N1 in the human population, although H1N1 continued to fluorish in pigs (more on that below). H2N2 dominated until...

In 1968, the Hong Kong flu pandemic, H3N2, swept the world and replaced H2N2.

Then, very suspicously, in 1977 the H1N1 strain reappeared in Russia. It is widely believed that this was an accidental escape from the Soviet Union’s biowarfare program. This H1N1 strain didn’t replace H3N2, but both strains have co-circulated ever since, with H3N2 generally causing more serious illness.

All along, the milder influenza B strain has been around as well. That’s why the vaccine contains 3 strains: H3N2 (from 1968), H1N1 (from 1918 via Russia in 1977), and flu B.

That brings us to late 2008. Several strains of Spanish flu (H1N1) had been circulating in pigs for decades. Two of those strains combined to create the new pandemic flu, which jumped from pigs to humans. Oddly enough, we don’t have any reports of a pandemic among pigs, which is why “swine flu” is a misnomer. Here are the latest statistics for human infections in the U.S., for the last week of March 2010:

• 3.7% of people tested turned out to have influenza. (In other words, the season is over, as I predicted in mid-January.)
• 98% of positive influenza specimens were pandemic H1N1.
• 2% of positive specimens were influenza B.

So it seems that the swine flu has replaced the Russian flu. At least it has in the vaccine. It might even be safe to get rid of H3N2 in the vaccine, but there’s little harm in keeping it in the vaccine for one more season, just in case H3N2 stays with us a bit longer. So next fall we’ll be back to one shot, and “pandemic flu” will be just plain old “seasonal flu” once again.

The CDC's advisory panel also (rather quietly) expanded their recommendation on who should get vaccinated “to include all people aged 6 months and older.” That’s right, everyone, even the elderly. Wait until the anti-vaccination movement gets hold of this – they’ll have a field day. Actually I’m surprised they haven’t already. Maybe they don’t know about the nanobots we’ll be putting in vaccines in the very near future.

*with apologies to The Who.

The flu pandemic may be over, but it wasn’t a hoax

It’s over. Or it’s nearly over. The great influenza pandemic of 2009 – often called the swine flu – has peaked and declined, and it might be over until next year. Not only is it over, but in a remarkable demonstration of evolution at work, it may already have pushed the “old” seasonal flu out of the human population.

Don’t get me wrong: it could still come back in a second wave, as epidemiologists at the CDC and the WHO have been warning. They’re right, too: we just don’t know enough about this pandemic to be sure it’s over. Dr. Keiji Fukuda from the WHO said on Thursday:

“We see that activity is declining or has declined but we also continue to see in these areas a transmission of the virus, so it has not disappeared, and it is has not gone back to baseline. Based on the situation, our current assessment is that it remains too early to say that the pandemic is over. And it is unclear whether we will see in the northern hemisphere over the next few months during the winter and spring period another significant wave of activity.”

Further down in this post I’ll show why I think it’s over. I think this is great news, but not surprisingly the conspiracy theorists have to make some wild claims to grab attention while there’s still time. Let me address them first.

As reported in the Irish Times, the UK Daily Mail, and elsewhere, the WHO is being accused of inventing the pandemic in order to boost the profits of drug makers. Where did this conspiracy theory come from? Why, my old friend Wolfgang Wodarg, head of health at the Council of Europe:

“Council of Europe parliamentarian Wolfgang Wodarg called for an inquiry into what he called a `false pandemic' and the way it was handled at national and European levels, claiming pressure from pharmaceutical firms.” (Source: Irish Times)

Wodarg’s resolution calling for an investigation was just passed by the Council of Europe.

The last time I wrote about Wodarg, he was claiming that the flu vaccine causes cancer. As I wrote then, Wodard doesn’t know beans about the flu. Anyone who makes such unfounded, irresponsible claims deserved to be ignored, but because he’s a high-profile politician, the WHO had to respond. Dr. Fukuda, speaking for the WHO, said:

“The allegation by some, that the H1N1 pandemic is a fake is both scientifically wrong and historically inaccurate.”

As for the conspiracy claim, he said

“WHO has reached out to all parties who could help to reduce harm from the pandemic but we did take very great care to make sure that the advice received was not unduly influenced by commercial or non-public health interests.”

As for whether it was real, this map shows the deaths caused by pandemic flu this year:
You don’t have to be an epidemiologist to see that this has been a worldwide pandemic, with plenty of deaths. And keep in mind that these are just confirmed deaths due to flu; in many countries where surveillance is minimal or non-existent, we have no idea how many people were infected. It’s true that the number of deaths has been much lower than we feared, but back in the spring of 2009, no one knew how virulent this strain would be.

What I’d say to Wodarg (and what Dr. Fukuda might have wanted to say) is: Wodarg, you don’t know what you’re talking about. Your irresponsible claims are doing more harm than good. If you truly care about public health, then educate yourself before you speak out on the flu next time.

Now, why am I saying the pandemic is over? Well, in the U.S., the weekly surveillance reports from the CDC paint a very clear picture: the flu peaked in October and then declined rapidly, much like the seaonal flu does every year. Normally the peak occurs in January or February. Take a look at the latest data:
In the past three pandemics, in 1918, 1957, and 1968, our surveillance wasn’t nearly as good, so maybe there will be two flu seasons this winter. It could happen – we could get a second wave – but I’m putting down my $0.25 that it’s over.

Notice something else about this figure? The normal seasonal flu hasn’t been seen at all! The graph shows that virtually all cases are pandemic H1N1 flu. In contrast, here are the past 4 years of flu seasons: See what I mean? Just one peak each year, and the color-coding shows that the normal seasonal flu is a mixture of H3N1, an older H1N1 (not the new strain), and influenza B.

How about Europe? It’s fading there too: the European CDC report for January 15 says

“Sentinel physicians collected 735 respiratory specimens, of which 139 (19%) were positive for influenza virus. This proportion has now decreased for the seventh consecutive week. … Of the 15 486 influenza viruses detected by sentinel networks and subtyped since week 40/2009, 15 393 (99%) were the pandemic virus."

So in Europe too the pandemic is on the wane, and the normal seasonal flu strains are virtually absent. For those who follow the evolution of the flu, this is quite remarkable. It means that exposure to pandemic H1N1 provides protection against all three of the seasonal flu strains, and it suggests that a large proportion of the population has been exposed to pandemic flu – otherwise, more people would be getting sick with seasonal flu. Pandemic H1N1 has out-competed the old strains in less than a year – the blink of an eye in evolutionary time.

So I think it’s over. But get your H1N1 flu shot! I just got mine. Why? Well, there is a small chance of a second wave, and there’s no downside to the vaccine: after 60 million flu vaccinations in the U.S., there hasn’t been a single reported case of injury due to the vaccine. In addition, the flu might come early again next fall, just as it did this year, and a vaccination now will likely protect you through next season. And finally, don’t forget that vaccinating yourself is also protecting your family, friends, and community.

Flu vaccine shortage

This is just a brief post to point out a news article on the wires today (from Agence France-Presse) quoting me at some length about the shortage of H1N1 (swine) flu vaccine in the U.S. The article discusses why the egg-based vaccine production method, which is woefully obsolete, needs to be replaced if we're to avoid such shortages. I also made a point about how risky it is for us (as a society) to be relying on chicken eggs for a virus that could wipe out chicken flocks. See the article at Yahoo news, here, or at the Daily Telegraph in the UK, here.

It’s the 2009 Mexican flu - or is it S-OIV H1N1(A)?

Millions of people have already been infected by the new pandemic influenza virus, and the number may well climb over a billion. The CDC recently estimated that up to 40% of U.S. citizens may be infected over the next year, a startlingly high number. Close to home (for me), several children in my neighborhood came down with influenza just last week. They all recovered, fairly quickly. They almost certainly had the new H1N1 pandemic strain, which seems to be spreading rapidly despite the fact that flu season is normally in the winter. A postdoc in my lab was the first person I know who caught the new pandemic flu – he came down with it in early May, and was very sick for a week. (He stayed home, and no one else was infected, as far as I know.)

But the media are still calling this “swine flu”, in headlines all over the world. Government authorities decided early on to call it 2009 H1N1(A), a catchy name if there ever was one. In one of the earliest scientific publications, CDC scientists called it S-OIV, for “swine-origin influenza virus”.

Nice try, but the media aren't buying it. The problem with the name "swine flu" is that it’s not a swine flu any more. Once an influenza virus has become established in humans, it’s a human flu. If you catch the “swine flu”, you’ll get it from another human – not from a pig. So what to call it?

The choice of a name is actually pretty clear: each of the three 20th-century flu pandemics was named after the geographic location where people believed it originated: the 1918 Spanish flu, the 1957 Asian flu, and the 1968 Hong Kong flu. As best we can tell, the new H1N1(A) virus originated in Mexico, and therefore we should call it the 2009 Mexican flu. This will be accurate and consistent with historical precedent.

And by the way, this idea has already been proposed, but the Mexican government objected, so government health authorities, including the WHO, immediately backed down and looked for a more politically acceptable name. Several countries have already started using the term Mexican flu, including Belgium and Israel, as the AP reported yesterday – although the English-speaking world is still using “swine flu.”

As a side note, we now know that the Spanish flu should have been called “American flu” or possibly “Kansas flu” (where it really started), but during World War I, the U.S. didn’t want to admit that it had a serious health crisis, nor did any of the European countries involved in WWI. The Spanish got stuck with the name – incorrectly – because they didn’t try to hide the fact that they had a pandemic on their hands.

So a note to headline writers in the media: I don’t blame you for calling it swine flu and ignoring alternative names such as S-OIV and H1N1(A). But it’s misleading to use the term “swine flu”, which is already used to refer to influenza viruses circulating among pigs. Calling it “swine flu” also led to the foolish decision by some countries to slaughter large numbers of pigs, which was completely ineffective at controlling the spread of the new virus.

It’s a human flu, and it started in Mexico, so let’s call it Mexican flu.

A tale of two pigs

I don't usually mix my own research into this blog, but I make exceptions for influenza. As everyone knows (if you're awake and sentient), there's been a huge outbreak of swine flu recently, starting a few weeks ago in Mexico, which has now spread all over the U.S., Europe, New Zealand, and elsewhere. You can read all about it in the major news media, so I'll just focus on a couple of things you might not find elsewhere.

First, the swine flu has been reported to be a mixture of human, avian, and swine influenza viruses. Although the source of these reports is the CDC, that's not an accurate picture. I read today in The Washington Post that this epidemic started when a single pig was infected simultaneously by bird, pig, and human viruses. That's a reasonable inference from the reports in the media, but it's not true.

In fact, as a number of researchers have now discovered, the new swine flu is a mixture of two different swine flu viruses. It's definitely a novel strain, but it's pretty clearly a mixture of two already-circulating pig strains. That sounds less exotic than the "human-bird-pig" theory, and it is. The reason for the "triple reassortant" story is a bit complex, but (to simplify a bit): the history of one of the two parental swine flu strains indicates that part of that strain originated in birds - well over a decade ago. That strain is sometimes called "avian-like" as a result, but it's not an avian flu strain now. Second, the history of the other strain includes a small piece (one gene) that appears to have originated in humans - over 15 years ago. Again, it's a swine flu virus now, but there's a piece of it that might have come from humans. The event that created today's swine flu - the one we're worried about - is a combination (called a reassortment) between two pig strains, pure and simple.

The other point I wanted to make is about data sharing. The sequences from the U.S. isolates have been deposited in GenBank - the public DNA database - immediately, and this allows people like me to start our analysis without delay. Many of us have been arguing for years how important it is to get the data out to the community fast, in order to accelerate the pace of scientific discovery. However, the isolates from Mexico have NOT been put into GenBank, even though these sequences first went through the CDC. Instead, they went into a database called GISAID, which was originally set up to facilitate sharing of avian influenza. Unfortunately, GISAID changed their data release policy about six months ago, and there's no guarantee that sequences deposited there will ever become public.

The CDC has been depositing influenza sequences in GISAID as if this were equivalent to making them public. It's not, and they shouldn't pretend otherwise. The CDC has not always been supportive of publicly releasing flu data - in fact, for years they deposited some of their sequences in a private database. They've recently made public statements about their commitment to public data release of influenza sequences, but it doesn't seem that they are following through with this commitment for all of the sequences from the swine flu outbreak. (Don't get me wrong: the CDC is doing a fantastic job in trying to track and understand this outbreak, and their work is incredibly important to public health, especial concerning the flu. I'd just like them to be a big more open with their data.)

One last note, a technical one. I've looked at the Mexican sequences (I have a GISAID account) and the California sequences, and they are virtually identical. So it would appear that any differences in virulence are due to differences in the people being infected, not to the virus itself. At least that's what it looks like so far - the situation is changing rapidly.