We may get a universal flu vaccine, thanks to mRNA technology

The mRNA vaccines for Covid-19 are an amazing story: a new vaccine developed in a matter of weeks for a brand-new virus, SARS-CoV-2, at the beginning of the pandemic in early 2020. Clinical trials moved forward at record speed, and by December of that year we had an approved vaccine that was safe and over 90% effective against Covid-19.

Why not use this mRNA technology for other vaccines, especially for the flu? When I asked this question last year, I didn’t realize that a group of scientists at the University of Pennsylvania were already hard at work making this idea a reality. They’ve just published their first results, and the news is very encouraging.

But first, some background. Messenger RNA (mRNA) vaccine technology was the big breakthrough behind the Covid-19 vaccines. Invented by Katalin Karikó and Drew Weissman at the University of Pennsylvania, the idea is, at its core, very simple: take the genetic code for a protein from the virus (any protein can be used, and for Covid-19 this protein is called Spike), and inject it into someone’s arm. (The genetic code I’m referring to here is the mRNA that encodes the protein.) From there, the cells of the human host manufacture the protein–not too much, though, because mRNA quickly degrades once it’s in your body.

What’s kind of amazing is that the human immune system will then recognize the Spike protein as an invader, and generate antibodies against it. From that point on, the person who received the vaccine will be prepared to fight off a real infection by Covid-19. In other words, they’ll be immunized.

The actual development of this technology was much more complicated than I’m describing here. First, you can’t just inject mRNA without causing a lot of inflammation, which can be dangerous. Weissman and Karikó solved that problem by using chemically modified mRNA. Second, you need to package the mRNA in something; the scientists discovered that they could use little packages of fat molecules called liposomes to make an effective container. Eventually, they got it to work, and the rest is (recent) history. Both the Moderna and Pfizer/BioNTech vaccines use mRNA technology.

Now about this new “universal” flu vaccine, and why it’s so much better than what we currently use. The annual flu shot contains pieces of one protein from 4 different influenza strains. Each year, as the flu itself evolves, the 4 strains used in the flu vaccine are fine-tuned in an effort to keep up. In some years, this effort fails and the vaccine just doesn’t work very well, for reasons I explained here.

One huge problem is that the current flu vaccine process grows the flu virus in chicken eggs, and sometimes the darned thing just won’t grow! So in those years, the vaccine manufacturers must switch to another flu strain, one not as well-matched to what’s circulating. The result is a vaccine that sort of sucks, although it’s usually better than nothing.

With mRNA, you don’t have to grow anything in chicken eggs, and you aren’t limited to just 4 strains. As the new research shows, you can put ALL 20 known influenza strains in the same vaccine, and it protects subjects against all of them. It even protects against other flu strains that weren’t in the vaccine. To create the vaccine, scientists simply synthesized the mRNA that encodes the surface protein of the flu, hemagglutinin, from 20 different flu strains. The synthesis process is already being done on an industrial scale for the Covid-19 vaccines, and the same process will work for any mRNA, from any virus.

In the new research, scientists at UPenn led by Scott Hensley and Drew Weissman (the co-inventor of the mRNA vaccine) inserted all 20 flu strains in a single vaccine. They found “that the vaccine dramatically reduced signs of illness and protected from death, even when the animals were exposed to flu strains different from those used in making the vaccine.”

Did I mention that the subjects in the new study were mice and ferrets, not people? Well, this experiment is just the beginning: we’ll need further trials to test the safety and efficacy of this vaccine in people. Those are much, much more costly, though, and it’s not clear when or even if those trials will happen.

If we had a universal flu vaccine, we might no longer need the annual flu shots that we beg everyone to get each year. So when can we expect to see this new 20-strain vaccine?

Well, there’s the rub. Even if this new flu vaccine works perfectly in human testing, we might never get it. At the moment, we are completely dependent on private companies to develop vaccines. At the beginning of the Covid-19 pandemic, the U.S. created incentives for vaccine manufacturers by promising to buy millions of doses, and–fortunately–that worked. We’ve never tried anything like that with the flu vaccine.

We need to re-think our dependence on private, for-profit companies for this critically important public health technology. Perhaps it’s time for the government to step in and make sure we get this vaccine, whether through incentives like the ones used to create the Covid-19 vaccine, or through a direct effort by the government itself (as other countries have done) to create a universal flu vaccine. A universal flu vaccine will save tens of thousands of lives every year. Let’s hope we get there.

Scientists have re-created the deadly 1918 flu virus and used it to infect animals. WTF?

With all the controversy about gain-of-function research and all the concerns about how dangerous it is, you might think that scientists have stopped doing that kind of work.

Well, no.

In the latest news, a team of scientists in Canada and the U.S. report that they have re-created the 1918 influenza virus and used it to infect macaques. Let’s be clear here: the 1918 flu vanished from the Earth, long ago. It’s simply not a threat, or it least it wasn’t, until someone figured out a way to bring it back.

Why would anyone do this? I’ll get to that, but first a little background.

The 1918 flu pandemic was the worst plague since the Black Death, which occured in the mid-14th century. During World War I, a new flu virus swept the planet, killing upwards of 50 million people. It probably infected a third of the entire world population at the time.

Since Covid-19 appeared, the 1918 flu pandemic has been cited often (sometimes called the Spanish flu), usually to compare or constrast it with Covid-19. Sure, Covid is bad, but at least it’s not as bad as what the world experienced in 1918.

About 20 years ago, a small team of researchers led by Jeffery Taubenberger and Ann Reid figured out how to sequence the genome of the 1918 flu. In a series of papers spread over six years, they described how they recovered pieces of the flu virus from human samples that had been frozen for nearly 100 years, including corpses buried in the permafrost of Siberia and Alaska. In 2005, they reported the complete sequence in the journal Nature. Their main discovery was that the 1918 flu had originally been a bird flu, which jumped into humans sometime before 1918. Taubenberger and others, including Adolfo Garcia-Sastre at Mt. Sinai School of Medicine, also re-constructed the virus and tested it on mice, that same year. Not surprisingly, the mice died.

It didn’t take long before gain-of-function researchers said “hey, why don’t we reconstruct the flu virus and see what happens in primates?” The tools of modern genetics make it possible to reconstruct a virus from scratch, using just the sequence.

In 2007, only two years after the 1918 flu sequence was completely decoded, influenza researcher Yoshihiro Kawaoka at the University of Tokyo and the University of Wisconsin described, in a paper in Nature, how he and his colleagues used the sequence to create live, infectious 1918 flu viruses. To demonstrate that these really were flu viruses, they infected 7 macaques with them. Not surprisingly, the macaques got severely ill, and the scientists eventually euthanized all of them.

(Insiders may recognize Kawaoka’s name: he and Dutch scientist Ron Fouchier are widely known for their gain-of-function research that aimed to give deadly bird flu the ability to infect mammals. I’ve called them out on this in the past, and I’ve openly asked why NIH was funding this work.)

In the new paper, a team of researchers at the Public Health Agency of Canada, the University of Manitoba, and Oregon Health & Science University re-created the 1918 flu virus again, and infected 15 macaques. This time they used more realistic doses, and the macaques didn’t get so sick, suffering only “mild” or “moderate” disease. Maybe macaques “are not ideal for the development and testing of novel pandemic influenza-specific vaccines and therapies,” they concluded.

So let’s review: flu scientists have been using the sequence of a long-vanished, extremely deadly virus to reconstitute the virus and infect animals, and then observe how sick they get. (Kawaoka did it a second time, in a study published in 2019.)

Why do they do it? All of the papers give essentially the same reason: these experiments, they say, will help us develop animal models in which we can test vaccines. These same justifications have been used for decades, but flu vaccines haven’t improved one whit, as far as I can tell.

But hold on a minute! Even if you accept their argument that infecting macaques and other animals with influenza virus will help develop better vaccines, why use the 1918 influenza virus at all?

They don’t answer that question, because there really is no good answer. The fact is that the experiments will be more relevant if they use currently circulating flu strains–because those are the strains that we need vaccines against.

I imagine that the scientists doing this work truly believe the arguments they make, about how their work will help design better vaccines and therapies. But they’ve been making similar arguments for decades, and it just hasn’t played out that way.

The 1918 flu disappeared long ago, and there’s no way it could possibly re-appear naturally. There’s only one way that the 1918 flu becomes a threat to human health again: through a lab leak. Re-creating the virus in a lab makes that possible.

We’re still trying to figure out if Covid-19 had a natural origin or whether it started as a lab leak. Even if it turns out to have a natural source, the intense discussions about the lab leak hypothesis have been useful, because they made it clear that lab leaks happen, and that they should be considered a genuine risk.

In recognition of this risk, scientists and non-scientists alike have called for a worldwide ban on gain-of-function research. That hasn’t happened yet, although NIH has issued a carefully worded statement about the kinds of work that it supports.

Most of the recent controversy over gain-of-function research has focused on research that makes viruses more deadly. I hope it’s clear that re-creating a deadly virus from scratch is another form of gain-of-function research, one that carries equally great risks with little or no potential benefit. We should put a halt to both types of work.

There’s an easy way to eliminate the risk that a lab leak might release the 1918 influenza virus into the human population: stop re-creating the virus. The 1918 flu disappeared from the natural world long ago–or to be more precise, it evolved into a much, much milder form of influenza. The deadly form that was recently re-created in several labs does not exist in nature today. Let’s keep it that way.

The mRNA vaccines are defeating COVID. Let's use them for the flu.

 

The last year has been a story of triumph in the vaccine world, with the rapid development of two highly successful vaccines for Covid-19, one developed by Moderna and the other by Pfizer and BioNTech. Now that flu season is approaching, why are we still using 50-year-old technology for the flu vaccine?

The reason the Covid-19 vaccines were developed so quickly is that they used a new, much faster and easier-to-create type of vaccine technology, based on messenger RNA, or mRNA. What’s even more exciting is that we now have an overwhelming amount of evidence, from real-world experience, that these vaccines are remarkably safe and effective.

Now, anti-vaxxers and the “vaccine hesitant” are claiming they don’t trust the vaccine because it was developed too fast. That’s ridiculous: the real reason they don’t trust the vaccine is because they’re consuming a steady diet of anti-vaccine nonsense, promoted by a combination of right-wing media and the Disinformation Dozen (who include left-wing as well as right-wing zealots). But let’s not go down that rabbit hole today.

So what is an mRNA vaccine? Here’s a brief explainer, and then we’ll look at the flu vaccine. (Note: feel free to skip ahead if you already understand the technology.)

Messenger RNA vaccines have been under development for decades, since long before Covid-19 appeared. The technology required a series of breakthroughs over the years, as described in a recent Nature news story, and many scientists contributed. It wasn’t used in vaccines in part because it wasn’t ready, but also because we rely on private companies to develop vaccines, and few of them were interested in investing in a new, not-yet-approved technology. But I digress.

Messenger RNA is the stuff that all of your cells use to translate your genes, which are encoded in DNA, into proteins. The basic process is that the DNA for a gene is copied into pieces of mRNA, where the DNA letters, ACGT, are replaced by slightly different (chemically) RNA letters, ACGU.

Every cell in your body is filled with mRNA, all the time. It’s the stuff of life, so of course it is totally safe. Each cell uses mRNA to make proteins, which do most of the actual work that keeps you alive.

Here’s the brilliant thing about mRNA vaccines: all they do is introduce some mRNA into your cells that encodes a single protein from the virus, which is called “Spike” in the case of the Covid-19 vaccines.

Your own cells then make the Spike protein, but they don’t make very much! They just make a few copies, because mRNA doesn’t last very long. And because there is no DNA copy of the Spike protein in your genome, once the mRNA in the vaccine breaks down, it’s gone forever.

The other brilliant thing is that your own immune system recognizes Spike as a foreign protein, and it generates cells that will recognize any future infections where the Spike protein is present. If you’re later infected by SARS-CoV-2 (the Covid-19 virus), your immune system is primed and ready, and in a large majority of cases it attacks and destroys the virus before you get sick.

So that’s it: an mRNA vaccine is simply a little package made of fat molecules (called liposomes) that contains a few copies of mRNA encoding a viral protein. There’s nothing to prevent us now from creating similar vaccines for the flu, or for other viruses where we need new vaccines. (In the case of flu, we can use mRNA for a gene called hemagglutinin, but again I digress.)

We make new flu vaccines every year, because the flu is constantly mutating. Most years, the flu vaccine isn’t a great match for the circulating strains of the virus, and therefore the vaccine isn’t very effective. In a good year it might be 60-70% effective, but in bad years it might be much worse. A big part of the problem comes from how we create the vaccine.

In the U.S., we make most of our flu vaccines by growing influenza viruses in chicken eggs. No, I’m not making this up. Around February of each year, a panel of experts selects 4 strains of the virus that they think will most likely match the viruses for the following flu season, which usually ramps up in November or December. (Here are this year’s choices.)

Once the experts have selected the vaccine strains, the manufacturing process begins, first by checking to see if all 4 strains will grow robustly in chicken eggs. If they don’t, the panel may have to switch to different strains that are less likely to work. No, I’m not kidding: the success of the flu vaccine depends on how well it grows in eggs. That’s one reason why, in some years, the flu vaccine is a flop. This would simply never happen if we used mRNA technology.

With mRNA vaccines, we don’t have to grow any viruses at all. The mRNA from a single gene–hemagglutinin for influenza–can simply be synthesized in large quantities, just as we’re now doing for the Spike protein in SARS-CoV-2. Or for an even more effective vaccine, we might add the gene for neuraminidase, the other protein in influenza that our immune system can “see.”

An mRNA vaccine for flu would be far cheaper to manufacture, not requiring huge chicken farms. (This year, 82% of flu doses in the U.S. were made this way.) Even more important, though, is that an mRNA vaccine for flu would likely be far more effective at controlling the severity of the infection itself.

Why aren’t we doing this already? Simply put, it’s because we rely on private companies to take the initiative, and it’s not worth it to them to test and validate an entirely new vaccine, which requires a substantial investment. There’s also a simple solution, the same one we used for Covid-19: the government should take the lead.

We’re now at the beginning of flu season, which almost disappeared last year thanks to our social distancing and masking behavior. I’ve had my flu shot, and millions more are being administered around the world. Just last week, an early report out of Europe indicated that the flu season this year might be “severe,” which is the last thing we need with Covid-19 still raging.

We don’t yet know if this year’s flu shot will be effective or not, but odds are, based on past performance, that it won’t be great. (It’s still much better than nothing, I should add.) If we want a better flu vaccine, now is the time to start developing a new one using mRNA. If private industry doesn’t step up, any one of dozens of countries have the expertise to do so instead.

We've totally crushed the flu virus this year

 As awful as the Covid-19 pandemic is, it’s given us at least one benefit: we’ve utterly crushed the flu virus.

That’s right–the flu has almost completely disappeared this year. A combination of social distancing, closed schools and businesses, dramatically reduced travel, and high flu vaccination rates has achieved something that most flu experts never thought possible.

Flu levels are so low, in fact, that one has to wonder if the flu will even come back next year. The levels now are far lower than we’ve ever seen in modern history. Let’s take a look at the numbers:

nfluenza cases reported to the CDC by US public health laboratories, 2020-2021 season. Data from the CDC, graph created by the author.

As you can see here, the very worst week had just 24 confirmed cases in the entire U.S. That is truly astonishing. And in 2021 so far, we’ve had 5 or fewer cases in the entire country each week. Basically, the flu is gone. To see how dramatic this is, let’s look at data from last year (the winter of 2019-2020), which was a typical flu season:

Influenza cases reported to the CDC by US public health laboratories, 2019-2020, season. Data from the CDC, graph created by the author.

As you can see above, the U.S. had about 3,000 cases per week in January and February of 2020, with a peak at nearly 4,000 cases.

The rate of influenza this year is over 100 times lower than it’s ever been. Why did this happen? It’s obvious: all of the precautions we’re taking to reduce the spread of Covid-19 have worked wonders to prevent the flu as well. In fact, they’ve worked far better for influenza than for the Covid-19 virus.

No one knows what the flu season will look like next year, but for now, at least we’ve won a clear victory against the influenza virus. That’s a bit of good news.

Some odd truths about viruses, and about the COVID-19 viruse

The virus that has devastated the world this year, SARS-CoV-2, is not a living organism. Viruses are not alive. Think of them instead as biological machines, incredibly small ones.

What, exactly, is a virus? Many people outside the world of science and medicine don’t really know, so today I’m going to describe just a few of their essential features.

Viruses have, in general, just two functions: they invade your cells, and then they borrow your own cells’ machinery to copy themselves. (Note: for simplicity I’m describing viruses that infect humans, but in reality they infect pretty much every living thing, from bacteria to plants to animals.) After making many copies, they break out, usually destroying the cell they’ve invaded, and do it again.

Here’s a weird thing about viruses. All living things on this planet are made from instructions encoded in DNA. Some viruses are also made of DNA, but many are made of RNA instead. RNA is a lot like DNA, but it doesn’t have that famous double-stranded helix structure; instead, it’s just a single strand.

Now consider how small they are. The Covid-19 virus, SARS-CoV-2, has just 29 genes that are encoded in just under 30,000 letters of RNA. Other viruses can be even smaller: the influenza virus has just 10 genes, encoded in 13,588 letters of RNA. In contrast, the human genome has about 3 billion letters of DNA, and over 20,000 genes. In other words, our genome has 100,000 times more information encoded in it than the Covid-19 virus.

And yet these simple machines with a handful of genes can destroy us. Think of it like throwing a wrench into a running engine: the wrench is simple, but that doesn’t mean it can’t gum up the works of a far more complicated device. So too with viruses and their hosts.

It’s not just that they have a small genetic code: viruses are also physically small. So small, in fact that they cannot be seen under a normal microscope. Bacteria are huge compared to viruses; in fact, bacteria suffer viral infections just like humans do.

(Aside: the exciting new technology known as CRISPR is actually a mechanism created by bacteria to fight off viral infections!)

One consequence of virus’s tiny size is that when the 1918 flu pandemic swept the world, no one knew it was caused by a virus. Scientists didn’t have the technology to see a virus at that time. The influenza virus–the true cause of flu–wasn’t discovered until 15 years later, in 1933.

(Another aside: a bacterium called Haemophilus influenzae was given its name because scientists thought it caused the flu. It doesn’t. It does cause ear infections and sometimes-deadly meningitis, though, and for that reason the Hib vaccine, which prevents infection from this bacterium, is a critical part of the childhood vaccine schedule.)

Another odd fact about viruses: they’re not cells. They don’t have a proper cell wall, as such, just a shell made out of a few proteins. The shells encapsulate the tiny genetic code of the virus. We call them “particles” for lack of a better word.

Viruses are everywhere, and they are far more numerous than bacteria. Bacteria, in turn, are far more numerous than plants and animals. Viruses are also devastatingly effective at what they do (infecting living cells and hijacking those cells to make more viruses), which is why we will never rid ourselves of them.

While we can’t get rid of them, we can fight the viruses that cause human diseases like Covid-19. The best way to do that is to prevent viruses from invading our cells. How? There’s only one good way that we know of so far, and that’s to use the human immune system to fight them off at the molecular level. (While viruses are simple, the immune system is really complicated. I can’t possibly explain it here, but check out Ed Yong’s recent story at The Atlantic for an excellent attempt to de-mystify the immune system.)

This is where vaccination comes in. When a virus invades us, our immune system creates custom-designed cells (see that Ed Yong article) that recognize and destroy the virus. Then it becomes a race: if the immune system wins, it destroys all of the viral particles. If the virus overwhelms the host, the result can be fatal.

For Covid-19, most people mount an immune response quickly enough to avoid getting seriously ill. However, for those that don’t, the results are extremely serious. A vaccine works by “showing” the immune system part of the virus, but doing this in a way that isn’t actually an infection. One strategy used by several of the Covid-19 vaccines under development is to just package up one of the SARS-CoV-2 proteins, without the rest of the virus. The vaccine itself will prime the immune system to recognize the Covid-19 virus without actually causing an infection. Then, if that person is actually infected, the immune system swings into action quickly, and fights off Covid-19 before it ever gets established.

So that’s it. Covid-19 is caused by a tiny, sub-microscopic biological machine, a virus with just 29 genes. The virus can be ruthlessly effective, but our immune system can wipe it out if we give it the right clues. Let’s hope we’ll have a vaccine soon.

Disclaimer: the content on this site is my personal opinion and is independent of my affiliation with Johns Hopkins University.

Scientists restart bioweapons research, with NIH's blessing

For more than a decade now, two scientists–one in the U.S. and one in the Netherlands–have been trying to create a deadly human pathogen from avian influenza. That's right: they are trying to turn "bird flu," which does not normally infect people, into a human flu.

Not surprisingly, many scientists are vehemently opposed to this. In mid-2014, a group of them formed the Cambridge Working Group and issued a statement warning of the dangers of this research. The statement was signed by hundreds of scientists at virtually every major U.S. and European university. (Full disclosure: I am one of the signatories.)

In response to these and other concerns, in October 2014 the U.S. government called for a "pause" in this dangerous research. NIH Director Francis Collins said that his agency would study the risks and benefits before proceeding further.

Well, four years later, the risks and benefits haven't changed, but the NIH has (quietly) just allowed the research to start again, as we learned last week in an exclusive report from Science's Jocelyn Kaiser.

I can't allow this to go unchallenged. This research is so potentially harmful, and offers such little benefit to society, that I fear that NIH is endangering the trust that Congress places in it. And don't misinterpret me: I'm a huge supporter of NIH, and I've argued before that it's one of the best investments the American public can make. But they got this one really, really wrong.

For those who might not know, the 1918 influenza pandemic, which killed between 50 and 100 million people worldwide (3% of the entire world population at the time), was caused by a strain of avian influenza that made the jump into humans. The 1918 flu was so deadly that it "killed more American soldiers and sailors during World War I than did enemy weapons."

Not surprisingly, then, when other scientists (including me) learned about the efforts to turn bird flu into a human flu, we asked: why the heck would anyone do that? The answers were and still are unsatisfactory: claims such as "we'll learn more about the pandemic potential of the flu" and "we'll be better prepared for an avian flu pandemic if one occurs." These are hand-waving arguments that may sound reasonable, but they promise only vague benefits while ignoring the dangers of this research. If the research succeeds, and one of the newly-designed, highly virulent flu strains escapes, the damage could be horrific.

One of the deadliest strains of avian flu circulating today is H5N1. This strain has occasionally jumped from birds to humans, with a mortality rate approaching 50%, far more deadly than any human flu. Fortunately, the virus has never gained the ability to be transmitted directly between humans.

That is, it didn't have this ability until two scientists, Ron Fouchier in the Netherlands and Yoshihiro Kawaoka at the University of Wisconsin, engineered it to gain this ability. (Actually, their work showed that the virus could be transmitted between ferrets, not humans, for the obvious reason that you can't ethically test this on humans.)

Well, Fouchier and Kawaoka are back at it again. NIH actually lifted the "pause" in December 2017, and invited scientists to submit proposal for this type of research. Fouchier confidently stated at the time that all he had to do was "find and replace" a few terms in his previous proposal and it would likely sail through peer review. It appears he was correct, although according to the Science article, his study has been approved but not yet actually funded. Kawaoka's project is already under way, as anyone can learn by checking the NIH grants database.

And by the way: why the heck is a U.S. funding agency supporting research in the Netherlands anyway? If Fouchier's work is so great (and it isn't), let the Netherlands fund it.

I've said it before, more than once: engineering the flu to be more virulent is a terrible idea. It appears the review process at NIH simply failed, as multiple scientists stated to Vox last week. This research has the potential to cause millions of deaths.

Fouchier, Kawaoka, and their defenders (usually other flu scientists who also benefit from the same funding) like to claim that their project to engineer a deadlier bird flu will somehow help prevent a future pandemic. This argument is, frankly, nonsense: influenza mutates while circulating among millions of birds, and no one has any idea how to predict or control that process. (I should mention that I know a little bit about the flu, having published multiple papers on it, including this paper in Nature and this paper on H5N1 avian flu.)

Fouchier and Kawaoka have also argued that we can use their work to create stockpiles of vaccines in advance. Yeah, right. We don't even stockpile vaccines for the normal seasonal flu, because it mutates too fast, so we have to produce new vaccines each year. And the notion that anyone can predict a future pandemic strain so precisely that we could design a vaccine based on their prediction is laughable.

I can't quite fathom why NIH seems to be so enraptured with the work of these two labs that, rather than simply deny them funding, it has ignored the warnings of hundreds of scientists and now risks creating a new influenza pandemic. Much as I hate to say this, maybe it's time for Congress to intervene.

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.

The flu is getting worse, just as the government shuts down.

Uh oh, this is not good.

The flu season is looking particularly bad this year. We already had signs of trouble back in November and December, when it emerged that the flu vaccine was not very effective against the dominant strain that is circulating this year, which is called H3N2.

Until this past Friday, it seemed that the peak of the flu season might have occurred just around the new year, as shown in this chart from the CDC:

The chart shows a peak in the very last week of 2017, and then the number of reported cases seemed to decline. But then on Friday the CDC reported this alarming trend:

That red line spiking upward in the middle of the chart shows the number of flu-like cases reported by the CDC's national network this year. Rather than going down, the trend shows a sharp rise over the past two weeks. We don't know exactly what it is (these are not laboratory-confirmed flu cases), but more people are getting sick.

Even more alarming are the reports of young, healthy people dying of the flu. This past week the Washington Post reported on a healthy 10-year-old boy who caught the flu and died within just a few days. Just before Christmas, a healthy 21-year old young man in Pennsylvania came down with the flu, and went rapidly downhill until he was rushed to the emergency room on Dec. 27. The hospital was unable to save him, and he died the next day. These cases are truly alarming, and even though the CDC hasn't seen a statistically significant increase in deaths among young people (not yet, at least), everyone needs to take the flu very seriously this year.

With the government shut down, a difficult situation becomes worse. Most of the CDC staff will be forced to sit on their hands when they could be working–and many of them want to work, but they won't be allowed to. What's especially frustrating (and wasteful) is that the U.S. will almost certainly pay all federal employees for this forced time off, as it did in previous shutdowns.

We also need a better way to make the flu vaccine. The U.S. still relies on vaccines that are produced by growing the virus in chicken eggs, a decades-old method. This sometimes requires us to use a strain that doesn't match the circulating virus, because some strains just won't grow in eggs. So instead we manufacture a mediocre vaccine, rather than investing in new, modern technology that wouldn't need eggs and could produce more effective vaccines at lower cost. (Why are we stuck with old technology? It's a long story, but essentially it boils down to the fact that we rely completely on private companies to make the flu vaccine. The government doesn't make vaccines and has no plans to do so.)

With the right technology, we should be able to produce a universal flu vaccine, one that we can take once and never need again, like most other vaccines. Scientists are getting closer to that, with much help from the (currently shut down) NIH.

Meanwhile, we are looking at a particularly dangerous flu season, with few weapons to guard against it other than the not-very-good vaccine. (Aside: ineffective doesn't mean useless. Even if the vaccine is only 30% effective, as some estimates have it for this year, it's still a good idea. Everyone in my family got it.)

Oh, and one more thing: the flu shot cannot give you the flu. I only mention this because anti-vaxxers continue to promote this particular myth. 80% of people who have come down with the flu this year did not get vaccinated.

How to treat the flu: a shopping guide

Flu season is upon us, and your local pharmacy may feature special displays with products claiming to cure or treat the flu (which is caused by the influenza virus). The array of products, and the claims featured on their packaging, can be bewildering. Which of them should you buy? Here is a quick guide. (Spoiler: if you want to know what really works, skip to the end.)

This photo from a local RiteAid shows their display of "alternative" treatments. Let's consider a few of them.

Alternative pills that claim to treat the flu. 

1. Across the top we have vitamin C drops, helpfully labelled "Defense" in large letters. You might think these would defend you against the flu virus, but you'd be wrong. Vitamin C has no effect whatsoever on the flu, and it doesn't prevent colds either. People have been taking it for decades, but popularity is no substitute for evidence.

2. The shelves include 11 different formulations of Airborne, with the phrase "helps support your immune system" prominently displayed. Does this product help your immune system fight off the flu? Not even a tiny bit. Airborne is nothing more than an overpriced vitamin supplement (including vitamin C), and it's on the shelf because of clever and misleading marketing. Back in 2008, Airborne settled a $23.3 million lawsuit over false advertising, which was filed because they called their product a "miracle cold buster." After the lawsuit, they simply re-labeled it as an "immune booster," which is vague enough that they've been getting away with this claim ever since. Save your money.
3. Several of the products here, notably Zicam, are basically sugar pills supplemented with zinc. Some time ago, there was preliminary evidence that zinc might reduce the duration of a cold, but there was never any evidence that it could work for the flu. (Aside: colds are caused by completely different viruses.) Once scientists looked at it a little harder, they discovered that zinc doesn't work for colds either, as I explained in a 2012 column. Zicam is marketed as homeopathic, a clever ploy that allows it to escape government regulation. Their marketing constantly dances around what is permitted, usually by claiming it provides "immune support." Sound familiar?

Very expensive sugar pills.

4. On the bottom shelf you might notice Oscillococcinum, a homeopathic remedy that is just a sugar pill. Oscillo's claims to treat anything are almost laughably ridiculous: its "active" ingredient is supposed to be an extract from the heart and liver of a duck, which is then diluted until even that ingredient is no longer present.  As you can see in the close-up picture here, it's not cheap: $31 for 30 pills.
The box also claims that it "reduces duration and severity of flu symptoms," a completely false claim. The FDA has issued warning letters about this before, pointing out that "These products have not been approved or otherwise authorized by FDA for use in the diagnosis, mitigation, prevention, treatment (including treatment of symptoms), or cure of the H1N1 Flu Virus." Apparently the manufacturers of Oscillo (and the numerous places that sell it) are just ignoring the FDA.

These are just the "alternative" treatments. Most pharmacies have an even larger selection of flu treatments with real medicine in them. Here's a photo from the same RiteAid, right next to the alt-med selections.  

Medicines that try to treat the flu.

The selection here includes pills and liquids in many shapes and sizes, and all of them have active ingredients that do indeed have some effects. But they don't actually treat the flu itself: instead, they treat some of the symptoms, such as pain and congestion. None of them work very well, although those that contain ibuprofen or acetaminophen do help reduce pain.

So what does work? The latest medical science offers only two options:
1. Vaccination. Get your flu shot! The flu vaccine isn't perfect, and it varies in efficacy from year to year, but it usually provides some protection. In the best years it can reduce your chance of getting the flu by 75% or more. It's far better to avoid getting the flu in the first place.

2. Oseltamavir (Tamiflu), available only by prescription, is the only anti-viral medication that has been shown to have some effectiveness against the flu. It's not great, but it can reduce the severity of symptoms and maybe shorten the duration of the illness by about 1 day. You have to see a doctor to get it, which means taking your (sick) child or self to a doctor's office and exposing other people to the flu. 

The bottom line: none of the treatments that you can buy without a prescription will cure the flu. The "alternative" treatments are completely useless, and the real medicines might help a little bit with symptom control. 

Your best choice, by far, is the flu vaccine. Unfortunately, the internet is filled with misinformation such as claims that the vaccine doesn't work, or that it can give you the flu, or (worst of all) the utterly discredited notion that preservatives in the vaccine cause autism. Some of the anti-vaccine nonsense has even been promoted by presidential candidates, namely Donald Trump, Ben Carson, and Jill Stein. By spreading these false stories, Trump and Stein are doing real harm to the public health.

Flu advice from a future doctor.

Finally, I want to give props to RiteAid for trying to get people vaccinated. In front of the same store at which I took these pictures were two large signs saying "Get your flu shot today." Inside the store, they had a special table with science-based information about the flu vaccine, which featured artwork from local children (one of them shown here) encouraging other kids to get vaccinated. Well done.