An open letter to all science lovers who want to defend science ... please don't.

Last week I had an animated discussion on Facebook over an older post in which I describe some literature I dug out on possible (underline “possible”!) correlations with autism. True, my post is highly incomplete, but it was meant as a discussion starter to point at things that scientists have been looking at in an attempt to unravel what feels like a rise in autism. Is autism the new childhood plague of our modern society or has it always been around and we just became more aware of it? And if the rise is real, what caused it?

To me the most intriguing bit is that if you type 'autism gut microbiota' into the PubMed search field (for those not familiar with PubMed, it's a repository for medical literature), you find an incredible number of studies and reviews: apparently there is an association between autism and disruptions of the gut microbiota, but whether the two are truly correlated or the correlation is spurious is still unclear.

Before I go on analyzing the literature I found on this topic, let me open a parenthesis on the Facebook discussion because it's something I deeply care about. You might think that the animated discussion I got into was with anti-vaxxers who believe that vaccines cause autism. Instead, my post was criticized by pro-vaccine people who, with the same unflinching certainty typical of the anti-vaxxers, believe that the rise in autism is fiction invented by anti-vaxxers, that autism has always been around, and that any difference between gut microbiota of autistic children and non-autistic children has been disproved. "By whom?" I asked. By this one report:

"Children with autism have no unique pattern of abnormal results on endoscopy or other tests for gastrointestinal (GI) disorders, compared to non-autistic children with GI symptoms, reports a study in the Journal of Pediatric Gastroenterology and Nutrition."

Notice that this opening line is a bit misleading because here is the actual paper [1] whose conclusion, quoting from the abstract, are a bit more cautiously stated:

"This study supports the observation that children with autism who have symptoms of gastrointestinal disorders have objective findings similar to children without autism. Neither non-invasive testing nor endoscopic findings identify gastrointestinal pathology specific to autism, but may be of benefit in identifying children with autism who have atypical symptoms."

Notice also the difference from the abstract and the title of the report. You can tell which one was written by a scientist, right? Because when you do a search on PubMed using keywords autism and gut microbiota you find a long list of references and decades of research. So to me what this says is that the question is still open and we need to understand the issues better. It takes way more than one paper to disprove hypothesis-raising questions spurred from decades of research.

Now here's the mother of all problems: the Internet has made everyone (EVERYONE!) an expert. Today you no longer need a medical degree to speak authoritatively about vaccines, disease, and health. This has generated movements like the anti-vaxxers, but, even more unfortunate is the rise of groups that reply to the anti-vaxxers without a scientific mind-set: these people are doing even more damage to the community than the anti-vaxxers themselves. I found myself in a conversation that had the same one-ended arguments used by anti-vaxxers except these were people who are actually in favor of vaccines: for every paper on autism and gut microbiota I brought up they would dismiss it with another one that said the opposite, demonstrating no understanding of the difference between raising hypotheses and making a claim.

As a scientist, I can tell you that this behavior is the very opposite of scientific thinking. All the people who are in favor of science but DO NOT adopt a scientific attitude when counter-arguing non-scientific claims are hurting the scientific community. It's happening for vaccines, for evolution, and for global warming. For example, people who support intelligent design are mistaken about evolution because they don't understand the meaning of the word "theory" and they don't understand how scientific thinking works. We need to educate people on scientific thinking, not give bad examples of undebatable and absolute notions.

So, PLEASE, all science fans, I beg of you: support us by giving us a cheer, by always citing original papers, and by keeping an open mind because that's what a real scientist would do. We are raising hypotheses, not discussing the meaning of Bible verses. And if you know you can't do any of the above, then the best support you can give us is to shut up. Let real science speak for itself.

I'm fully aware that I'm preaching to the choir so I'll stop now and resume my discussion on autism and gut microbiota. As an additional side note, let me emphasize how difficult it is to discuss a topic like autism because of its extreme complexity: it's a relatively new diagnosis (first described in the early twentieth century), and even though no exact etiology has been found of date, the genetic studies conducted so far have implicated as many as 400 genes such that a malfunction in any of these genes could possibly result in autism [2].

Let's start from the facts: our body hosts more microbial cells than human cells, with the vast majority residing in the gut. These organisms, which we collectively call the "human microbiota" (and “gut microbiota” when referring to the ones residing in the gut) interact with our cells in symbiosis and in fact, some experiments have shown that they can affect our health and even gene expression (see this old post for a striking example of how genes expressed by gut bacteria can affect whether we are fat or lean). All this has been known for a long time, but it's only recently that, thanks to the advent of new DNA sequencing techniques that scientists have been able to look deeper into the composition and classification of the human microbiota. Metagenomic studies have found over 3 million distinct microbial genes (collectively called the "microbiome") in human stools, which is astonishing if you think that the human genome, in comparison, contains about 20-30 thousand genes. The gut microbiome is rich in enzymes without which our body would be unable to digest important nutrients. In fact, it's estimated that roughly 10% of our dietary energy intake comes from byproducts of fermentation from the gut bacteria.

That's all fine and dandy, but what does this have to do with behavior and brain health? A lot, actually, to the point that scientists coined the phrase "gut-brain axis" to denote the deep interaction between the nervous system and the gut microbiota. A 2011 PNAS study [3] used a mouse model to demonstrate how the gut microbiota affects mammalian brain development and behavior. This can happen in a number of ways, but one interesting hypothesis is that a healthy gut microbiome can help modulate the concentration of chemicals that are important for brain development as well as important nutrients that are precursors of neurotransmitters like serotonin.

Several studies done on different populations of children affected by autism spectrum disorders (ASD) have reported some form of gastro-intestinal (GI) dysfunction (such as food intolerances, abdominal pain, diarrhea and flatulence), with proportions ranging from 20-60% of the study population [4]. It's true that ASD children are often very picky eaters with drastic dietary habits, which would of course cause the GI issues. However, given the previously mentioned evidence that the gut microbiota shapes brain development since early infancy, the question of which is the cause and which is the effect at this point is legitimate. In other words, what came first, the chicken or the egg?

Studies have pointed at alterations of the gut microbiota in ASD children who experience gastro-intestinal issues, and some have reported that ASD children receiving antibiotics seemed to experience behavioral improvements. Drastic changes in diet (for example adopting a gluten-free and/or casein free diet) have shown behavioral improvements in some ASD studies, but not in all (meaning that some studies still didn't observe any improvement). Some papers report a higher risk of ASD in children who have not been breast-fed or who have been weaned after the first month of life. All of these instances would cause the gut microbiota to change, including breast feeding, which plays a fundamental role in establishing a healthy bacterial flora in infants. But why aren't any of these studies conclusive? And why are some conclusions the opposite of others? Such differences in results can be explained by differences in sample sizes (too few patients, for example, would cause a false negative), and also by the fact that many of these children have impaired communication skills, and therefore the symptoms, rather than being self-reported, are gathered from the observations of the parents, which can potentially introduce a bias.

Studies that have compared the microbial composition of stools in children affected by ASD with healthy children have had mixed results: the majority report some differences in the composition of the microbial populations, while a few found no significant differences. And despite many studies have looked into it, no ASD-specific gut disturbance has been found, meaning that whatever gut issues ASD children may experience, they are no different than the ones healthy children may experience as well. At the same time, there is some evidence that probiotics help relieve some of the gastro-intestinal issues ASD children experience and at the same time, improve some of their behavioral issues.

What conclusion can we draw from this? Well, first of all that there's no black and white but a lot of gray and anyone who will tell you it's either black or white does not understand how science works. Look at Lamarck's theory of the evolution of traits, first dismissed by Darwin and now (sort of) coming back in the form of epigenetics. Science is not a means to get a definitive and absolute truth, rather, it is our drive to keep asking questions in the search for working answers. [On a side note, this is exactly why I do not like certain showmen out there who proclaim themselves scientists just because they promote science "truths"; real science educators should be promoting scientific thinking, instead.] More than once in the history of science we've corrected and generalized theories. That doesn't mean that we were wrong, rather, it means that we've expanded our knowledge and acquired better investigative tools.

Unfortunately we don't have historic data on autism, since the term was first used in the early 1900s and the definition of the disorder has changed over time. This questions whether or not case prevalence has been truly rising over time, or, instead, the rise we're seeing is simply the effect of a more comprehensive diagnosis. Regardless of whether this is true or not, the fact that most cases are reported in industrialized countries raises an important speculation: these are countries that have seen the most drastic dietary changes over the past 100 years and also lifestyle changes in terms of hygiene and use of antibacterial products, both in household items, as well as in livestock farming (and the use of antibiotics in livestock farming has indeed been increasing over the past few decades). There is no denying that dietary changes and increased use in antimicrobial products will affect the bacteria coexisting in our environment. Are these changes significant? Can they be play a role in the rise in autism prevalence? Can they play a role in the etiology of other disease whose prevalence appears to be on the rise, such as asthma, food allergies, and autoimmune disorders?

I do believe that these are legitimate questions that call for a deeper understanding of how our body interacts with the environment, both outside and inside. Throughout time, evolution has provided us with ways to adapt, but such adaptations are slow. Instead, over the past 100 years we've introduced drastic changes both in the environment as well as in our lifestyle in ways that are too fast for our genetic make-up to adapt. Anything concerning humans is complex, layered by multiple interactions between genetics, environment, and behavior. That’s why we need to keep looking and, most importantly, that’s why we need to always keep an open mind on things. Anyone who claims to know the absolute truth has misunderstood what science is about. Fighting bogus facts like the ones brought forth by the anti-vaxxers with analogous “absolute truths” will only reinforce the globally spread misunderstanding of what science is and what function it covers in our path toward understanding the world. The day we stop asking questions because we’ve found all the answers is the day we’ve stopped growing.

[1] Kushak RI, Buie TM, Murray KF, Newburg DS, Chen C, Nestoridi E, & Winter HS (2016). Evaluation of Intestinal Function in Children with Autism and Gastrointestinal Symptoms. Journal of pediatric gastroenterology and nutrition PMID: 26913756

[2] Li, Q., & Zhou, J. (2016). The microbiota–gut–brain axis and its potential therapeutic role in autism spectrum disorder Neuroscience DOI: 10.1016/j.neuroscience.2016.03.013

[3] Heijtz, R., Wang, S., Anuar, F., Qian, Y., Bjorkholm, B., Samuelsson, A., Hibberd, M., Forssberg, H., & Pettersson, S. (2011). Normal gut microbiota modulates brain development and behavior Proceedings of the National Academy of Sciences, 108 (7), 3047-3052 DOI: 10.1073/pnas.1010529108

[4] Mulle, J., Sharp, W., & Cubells, J. (2013). The Gut Microbiome: A New Frontier in Autism Research Current Psychiatry Reports, 15 (2) DOI: 10.1007/s11920-012-0337-0

How one vaccine can protect you from more than one disease

The paper I'm discussing today came out last May in Science but, as you probably noticed, I've been busy posting about other things and neglected the science aspect of the CHIMERAS blog. Apologies to my science readers.

Viruses are pesky little things that have the innate ability of inserting genetic material into our cells. As such, they are capable of permanently changing our immune system: for one thing, our immune system learns to recognize the pathogen and that "memory" will be used to prevent future infections. Viruses can also alter the expression of certain genes within the infected cells, shutting off the production of proteins that would otherwise prevent the virus from replicating.

Viruses that infect preferentially cells from the immune system are particularly nasty. HIV, for example, gradually depletes the host's reservoir of T-cells (the "sentinels" of the immune system) until patients die of a common infection simply because their body can no longer fight pathogens.

HIV is not the only virus that attacks the immune system. Measles is another one. The virus enters cells through a receptor that's expressed on the surface of many immune cells such as dendritic cells, macrophages, and lymphocytes. All of these cells have a very important function: they retain "immune memory." What does it mean? Every time the immune system encounters a new pathogen (a virus, a bacterium, etc.), bits of proteins from the pathogens are presented to the immune cells. The immune cells create an "impression" of these proteins so that they can bind to them and destroy them. using a metaphor, they create a "mold", a special receptor that binds to the pathogen. Lots of cells with the special "mold" are created, so they can bind to the pathogen, capture it, and destroy it. A whole army of cells needs to be created in order to get rid of the million viral particles in the body, but once the infection is over and the full army is no longer needed, only a few of these cells with the special "mold" are saved. These few are the ones that preserve the memory of the specific pathogen, so that next time it enters the body it is recognized immediately and destroyed before it can start the infection.

Back to the measles virus. This nasty pathogen has a special receptor that allows it to enter the cell membrane of "mature" immune cells [1], i.e. cells that carry that special "mold" for a particular pathogen. By infecting and killing those cells, the measles virus effectively erases immune memory, making the host prone to be reinfected by pathogens it has already encountered. So, on the one hand, the virus stimulates immune responses that will protect from future measles infections. On the other hand, however, it erases some of the existing defenses against other pathogens. It's called the "measles paradox." Immune memory of previous pathogens is eared and replaced by measles-specific immune responses. [2]

A study published in Science last May [3] corroborated this finding by looking at child mortality data from England, Wales, the United States, and Denmark during the decades immediately preceding and following the introduction of the measles vaccine. The researchers showed that immune memory loss caused by measles infection lasted from 6 months to several years, and that vaccination against measles significantly reduced child mortality caused by non measles infections.

To further corroborate their analysis, the researchers applied the same techniques to pertussis, which is also known to cause immunosuppression. This time they found no correlation with the incidence of pertussis and non-pertussis infectious disease mortality, corroborating the hypothesis that it was the measles vaccine to cause the drop in mortality.

"MV infection and vaccination produce strong and durable herd immunity against subsequent epidemics. Our results thus suggest an extra dynamical twist: MV infections could also reduce population immunity against other infections in which MV immunomodulation could be envisioned as a measles-induced immune amnesia; hence, measles vaccination might also be preserving herd protection against nonmeasles infections [3]."
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[1] Tahara, M., Takeda, M., Shirogane, Y., Hashiguchi, T., Ohno, S., & Yanagi, Y. (2008). Measles Virus Infects both Polarized Epithelial and Immune Cells by Using Distinctive Receptor-Binding Sites on Its Hemagglutinin Journal of Virology, 82 (9), 4630-4637 DOI: 10.1128/JVI.02691-07

[2] de Vries, R., & de Swart, R. (2014). Measles Immune Suppression: Functional Impairment or Numbers Game? PLoS Pathogens, 10 (12) DOI: 10.1371/journal.ppat.1004482

[3] Mina MJ, Metcalf CJ, de Swart RL, Osterhaus AD, & Grenfell BT (2015). Long-term measles-induced immunomodulation increases overall childhood infectious disease mortality. Science (New York, N.Y.), 348 (6235), 694-9 PMID: 25954009

So you're afraid of vaccines. Why don't we take a look at how they actually work?

March Moonrise, ©EEG

A few days ago a 4-year-old child died in a hospital in Rome, Italy. She had contracted Dawson encephalitis, a rare and chronic form of brain inflammation which is a complication from the measles virus. No, the child had not been vaccinated. Last February, an 18-month-old toddler also died of measles, this time in Germany.

Back when the smallpox was killing and blinding people, parents didn't have to choose whether or not to vaccinate their children. The choice back then was to whether or not expose the children to pus from an infected person's pustules or let them get the disease from natural exposure. People still contracted the disease through this primitive form of inoculation, yet the risk of dying was far less. So that's what parents did back then. Can you imagine purposely exposing your child to a deadly and impairing disease just because the chance of dying from it was so high anyways? Don't you feel privileged that you don't have to make that kind of decision for your own children?

People say vaccines are not natural. Yet when your own child gets sick and his/her fever spikes, you don't think twice about giving them ibuprofen or whatever medication it takes to lower the fever. That's because the consequences could be devastating. Yet ibuprofen is not natural. You don't normally find it in the body, and prolonged consumption has serious consequences on the liver.

Viruses, on the other hand, are natural. They are so natural that bits of viruses are embedded in our own DNA. Back when a smallpox vaccine didn't exist, parents who smeared pus from smallpox pustules on their healthy children were causing the body to make immune memory. That's because once the immune system "recognizes" the virus it can build a response strong enough to destroy the pathogen before it can start the infection. But the immune system has to "see" the virus for the first time in order to recognize it. That's why people who survived the infection never got it again. The principle is simple and completely natural. The risk was very high, though: pustules from infected people contained live virus, and many died in the attempt to avoid the disease.

Today we have a beautiful, safe way to create immune memory without having to go through the actual infection. We take little bits of chopped virus and put it inside the body. The chopped up virus can't cause the infection because it's missing some of its part. At the same time the immune system learns to recognize those extraneous proteins and builds immune memory.

So, you see, you can watch your child get sick and load him/her with drugs and medicine on top of risking serious complications. Or you can take him/her to the doctor and have them take a shot. One shot at the time, you don't have to load up in one sitting if that's what concerns you. At the end of the day, both the child who got sick and the vaccinated child will have built immune memory. But one has gone through days of fever, pain, and medications. The other one just got a shot.

So what's more natural to you?

And no, I have no financial gain from telling you this. I get my salary whether or not you get a shot. In fact, if you think about it, it's the unvaccinated child that's causing more of an economic burden right now. And whenever there's an economic burden, it means somebody is making a financial gain out of it. So, if nothing else, I'd say it's the parents who opt out of vaccinations who are financially manipulated.

But that's just me. What do I know? All I know is that a 4-year-old died. And in the twenty-first century no child should die of a complication from the measles virus.

Yes, autism is on the rise. Read this before blaming vaccines.

Waiting for the rain, © EEG

Because I work on HIV vaccine design, lately I've often been involved in debates concerning the safety of vaccines. I have the greatest respect for parents who struggle with disabilities of any kind, especially in children. I'm a parent too and can't even imagine what life is like when your child has a permanent disability. But I'm also a scientist, and I believe in the good cause of my work. My boss has been working day and night for thirty years on a vaccine against HIV because her best friend died of AIDS. We have pictures of AIDS orphans on our desks. We are not monsters, we are not part of a conspiracy, we are not paid by companies to fool people.

In fact, because we do basic research, our salary will be paid whether or not we do succeed in finding a vaccine. It's just our job, and we have no financial gain in this. If you want to point fingers, do it at companies who do make a profit out of health care, or out of selling plastic (and hence bypassing necessary health testing), or out of selling food. As a parent, I am the first to be concerned about the health of our children. I don't accept anything blindly without doing research, be it a vaccine or a drug or a type of food.

I've discussed aluminum in vaccines and why it's a good idea to spread out the shots during the first year of life; I've also discussed why I decided to wait before letting my daughter have the HPV shot. At the same time, parents concerned about autism are right to be alarmed: if you look at the latest numbers published by the CDC, the prevalence of autism in children has doubled. However, this trend has supposedly started in the last two decades whereas vaccines have been around much longer than that [1]. It's true that the US have an aggressive vaccine schedule for infants and I suspect it's tailored to reduce the number of office visits as copays are expensive and insurance companies need to make their profits. So yes, just like other parents, I am bitter at the system. I am bitter at companies profiting out of the health of my own children, not at researchers working hard at finding a cure for deadly diseases. My plea today is to separate the two: the cure, which, just like any other cure, should be used wisely and with good measure and balance, and the people making profits out of the cure.    

For example, nobody argues that antibiotics save lives. Unfortunately, today you find antibacterial stuff in soaps, detergent, even toothpaste. Doctors overprescribe antibiotics all the time. And then of course, poultry, beef and pork come loaded with antibiotics. This has led to extremely aggressive, antibiotic resistant superbugs like CRE. Yet nobody dreams of refusing antibiotics when they are really needed. That's because we all know that if you don't take them you might in fact lose your life.

What our society needs is stop pointing fingers, quit all the conspiracy crap, and instead sit at the table and discuss better health practices that don't put profits first but health and good care instead.

How should we address the rise in autism cases? I don't have an answer to this, but I did find a bunch of papers that got me thinking. I list them below.

DISCLAIMER: I'm not discussing these papers to point at a cause of autism. In fact, I believe that we will never find a cause, just like we will never find a cause of cancer. Like I stated in my post last week, we need to think of our lives as a complex orchestra where DNA, RNA, proteins and the environment all play together to create the beautiful symphony of our life. There never is one such thing as a direct cause. Often it's just genetics. Even more often is a genetic predisposition combined with multiple sets of environmental exposures, lifestyle, and diet. If your child has autism, please focus your energy in taking care of that child rather than trying to find a cause.

1) This study [1] looked into the raising numbers of autism cases:

"Diagnosed autism prevalence has risen dramatically in the U.S over the last several decades and continued to trend upward as of birth year 2005. The increase is mainly real and has occurred mostly since the late 1980s. In contrast, children's exposure to most of the top ten toxic compounds has remained flat or decreased over this same time frame. Environmental factors with increasing temporal trends can help suggest hypotheses for drivers of autism that merit further investigation [1]." 

So the threat is real. Yet vaccines have been around much longer than the 1980s.

2) Studies have found a higher incidence of autism in California, in higher educated families. This may be biased by the fact that people with a higher education will be more inclined to have their children tested for autism. But one study in particular [2] found another possible association:

"Our study adds to previous work in California showing a relation between traffic-related air pollution and autism, and adds similar findings in an eastern US state, with results consistent with increased susceptibility in the third-trimester [2]." 

The researchers monitored the air particulate at the birth address of the child starting from preconception through the child's first birthday.

 3) Breast feeding may play a protective role against autism spectrum disorders [3].

4) Inflammation may play a role. Le Belle et al. [4] used a mouse model to test the following hypothesis:

"A period of mild brain overgrowth with an unknown etiology has been identified as one of the most common phenotypes in autism. Here, we test the hypothesis that maternal inflammation during critical periods of embryonic development can cause brain overgrowth and autism-associated behaviors as a result of altered neural stem cell function [4]."

What they found supports the idea that, paired with genetic susceptibility, an infection in the pregnant mother could indeed higher the risk of developing autism in the child.

5) But one of the most fascinating associations I found is between gut microbiome and autism. Newborns are born without any bacteria in their guts and colonization begins right after birth. Vaginal birth vs. cesarean, breast fed vs. formula seem to be factors associated to the gut microbiota found in infants.

"Over the first years of life the gut microbiome is changing and remodeling, ultimately resembling an adult gut microbiome by year 3. This suggests there is a “core microbiome” that is the hallmark of a healthy individual [5]." 

This is particularly important because the microbiota community carries millions of genes whose expression affects our own physiology. The type and number of bacteria in our guts can influence the health and good functioning of our immune system.

Now, here's the worrisome bit:

"Broad-spectrum antibiotics are often prescribed to infants in the Western world in an attempt to protect the developing child from disease. In addition to conferring antibiotic resistance in infancy, antibiotic over usage can significantly disrupt the overall ecology of the gut microbiota, alter the abundances of resident gut bacteria, and potentially bias the child toward certain diseases [6]."

I'm not making a case that antibiotics are bad, just like I will never say that vaccines are bad. I'm just raising a flag that, like in all things, a good measure should be practiced. Antibiotics are a great means to fight infections. But is it safe to use them routinely to prevent infection?

The following study [7] is from 2000, so maybe a bit outdated, and the sample number is awfully low. Still, this is what it had to say:

"In most cases symptoms of autism begin in early infancy. However, a subset of children appears to develop normally until a clear deterioration is observed. Many parents of children with "regressive"-onset autism have noted antecedent antibiotic exposure followed by chronic diarrhea. We speculated that, in a subgroup of children, disruption of indigenous gut flora might promote colonization by one or more neurotoxin-producing bacteria, contributing, at least in part, to their autistic symptomatology [7]."

The study has a huge limit: they tested their hypothesis on 11 children that matched the above criteria (the onset of autism symptoms were observed after administration of antibiotics and subsequent diarrhea), which is an extremely small number. The children were given oral antibiotics and a slight improvement in behavior was noted, not the effects had completely waned by follow-up. Nothing conclusive, but definitely this study makes a case for further investigation.

In a more recent review, Critchfield et al. suggest that:

"Autism spectrum disorders are a diverse group of disorders caused by a complex interplay between genetic and environmental components. There is a range of indications that alterations in the intestinal microbiota in the gut might contribute to the disorder in a substantial number of individuals. Probiotics can be useful to restore the microbial balance in the intestine, to relieve gastrointestinal problems and to attenuate immunological abnormalities. Whether the use of probiotics by children with autism can lead to improvements in behaviors needs to be established in well-controlled trials with sufficient group sizes [8]." 

Please don't take any of this as prescriptions or recommendations. I am NOT a medical doctor. I'm a scientist and I like to pose questions and investigate possible answers. If you have particular concerns about your children, talk to your doctor. The references mentioned above are meant as guidelines. Print them out, read them carefully, and then discuss them with your physician.

[1] Nevison CD (2014). A comparison of temporal trends in United States autism prevalence to trends in suspected environmental factors. Environmental health : a global access science source, 13 PMID: 25189402

[2] Kalkbrenner AE, Windham GC, Serre ML, Akita Y, Wang X, Hoffman K, Thayer BP, & Daniels JL (2015). Particulate matter exposure, prenatal and postnatal windows of susceptibility, and autism spectrum disorders. Epidemiology (Cambridge, Mass.), 26 (1), 30-42 PMID: 25286049

[3] Al-Farsi YM, Al-Sharbati MM, Waly MI, Al-Farsi OA, Al-Shafaee MA, Al-Khaduri MM, Trivedi MS, & Deth RC (2012). Effect of suboptimal breast-feeding on occurrence of autism: a case-control study. Nutrition (Burbank, Los Angeles County, Calif.), 28 (7-8) PMID: 22541054

[4] Le Belle JE, Sperry J, Ngo A, Ghochani Y, Laks DR, López-Aranda M, Silva AJ, & Kornblum HI (2014). Maternal inflammation contributes to brain overgrowth and autism-associated behaviors through altered redox signaling in stem and progenitor cells. Stem cell reports, 3 (5), 725-34 PMID: 25418720

[5] Mulle, J., Sharp, W., & Cubells, J. (2013). The Gut Microbiome: A New Frontier in Autism Research Current Psychiatry Reports, 15 (2) DOI: 10.1007/s11920-012-0337-0

[6] Arrieta, M., Stiemsma, L., Amenyogbe, N., Brown, E., & Finlay, B. (2014). The Intestinal Microbiome in Early Life: Health and Disease Frontiers in Immunology, 5 DOI: 10.3389/fimmu.2014.00427

[7] Sandler RH, Finegold SM, Bolte ER, Buchanan CP, Maxwell AP, Väisänen ML, Nelson MN, & Wexler HM (2000). Short-term benefit from oral vancomycin treatment of regressive-onset autism. Journal of child neurology, 15 (7), 429-35 PMID: 10921511

[8] Critchfield, J., van Hemert, S., Ash, M., Mulder, L., & Ashwood, P. (2011). The Potential Role of Probiotics in the Management of Childhood Autism Spectrum Disorders Gastroenterology Research and Practice, 2011, 1-8 DOI: 10.1155/2011/161358

Ten years into the making, the HIV-1 mosaic vaccine finally goes into human trial

© Bette Korber et al.

I hope you will all forgive me if this week I'm gushing over my amazing mentor Bette Korber, as last week she shared some awesome news on Facebook:

"A landmark in my life happened yesterday, a major step in a long story. A decade ago I had an idea for making an HIV vaccine that had the potential to work globally. After a struggle (in my first 2 failed proposals, reviewers declared what I proposed was impossible), I got an internal grant from Los Alamos to develop the idea (third time's a charm). With that funding I could bring together a group of computational people to work together on expressing the idea -- a talented guy named Simon Perkins wrote amazing code to make it so, with computational design suggestions from the group, particularly my husband James Theiler. Then James, Will Fischer, Tanmoy Bhattacharya, and I put it through its paces, optimizing running conditions and devising ways to compare mosaics with natural proteins, with additional help from our friends Karina Yusim, Carla Kuiken and Bob Funkhouser. We called it a mosaic vaccine.

After so many years of hard work, and with the collaboration of experimentalists at Harvard and at Duke (Drs. Haynes, Letvin, and Barouch), two weeks ago a phase I safety trial finally opened, and an HIV mosaic vaccine went into the arm of a human volunteer for the very first time. "Safety trial" means that this is just the first phase in testing the safety of the vaccine (I explained the three phases of human trials in this post). We will gather immune responses and we are hoping to see the same good results we saw in monkeys [2-5]. If all goes well, HIV mosaics are in the pipeline for 4 more human vaccine studies. I'm so excited about this study and so proud of my mentor.

When I explain to people the challenge we are facing when designing an HIV-1 vaccine, I usually make a very simplistic comparison with the flu virus. Influenza evolves from one season to the next, which is why every year we need a new flu shot. So, basically, the flu evolves into a new virus every year. Well, HIV evolves so rapidly that every person has a different virus. In our database alone we have half a million distinct HIV viral sequences: how can you vaccinate people against half a million different viruses?

In the past, successful vaccines against diseases like polio or the measles have been made by taking a real virus, inactivating it (for example, you just take one or two of its proteins, but not the whole virus, to ensure it loses its ability to infect cells), and then injecting it into the body. The immune system "sees" the viral proteins and initiates a response. The response is then "saved" into memory cells, which, next time they encounter the pathogen, will remember how to produce the right response that will promptly clear the virus before it can start an active infection.

So, as you can see, the problem with HIV is that the viral population is so diverse that no one virus found in nature will protect people from contracting the infection. How to bypass the obstacle, then? Bette's idea is to basically use a computer that mimics HIV's evolutionary mechanisms to create an in-silico virus [1], something I've discussed in this post. The algorithm takes as input a population of, say, 100 different HIV sequences, and then recombines them creating a new population of artificially constructed viral sequences. HIV viruses can naturally recombine when infecting the same cells, and what the algorithm does is mimic this mechanism making sure that after every recombination step the new sequence is still a viable and functional virus. The computer mimics this process, iterates it multiple times and then the best representative is selected as a potential vaccine.

The first caveat is: is this new, artificially constructed sequence a real virus? After all, it was never found in nature. It was created by a computer algorithm. It turns out that when reconstructed in a wet lab, the mosaic proteins are functional and viable.

The second hurdle was to prove that these artificially constructed sequences are safe to be used in a vaccine and that they do elicit protective responses against not just a few HIV viruses, but many, many HIV viruses -- enough to prevent infection. So, you get an idea of why the mosaic vaccine took 10 years from concept to the first human trial.

Animal studies [2-5] demonstrated that mosaic vaccines elicit good immune responses. In one study in particular [3], compared to controls, vaccinated monkeys required many more challenges to get infected (for a risk reduction of 80%), and once infected, they were able to control the viral load and survive the infection.

So, as Bette said, we are hopeful. Hopeful and excited!

[1] Fischer W, Perkins S, Theiler J, Bhattacharya T, Yusim K, Funkhouser R, Kuiken C, Haynes B, Letvin NL, Walker BD, Hahn BH, & Korber BT (2007). Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants. Nature medicine, 13 (1), 100-6 PMID: 17187074

[2] Nkolola JP, Bricault CA, Cheung A, Shields J, Perry J, Kovacs JM, Giorgi E, van Winsen M, Apetri A, Brinkman-van der Linden EC, Chen B, Korber B, Seaman MS, & Barouch DH (2014). Characterization and immunogenicity of a novel mosaic M HIV-1 gp140 trimer. Journal of virology, 88 (17), 9538-52 PMID: 24965452

[3] Barouch DH, Stephenson KE, Borducchi EN, Smith K, Stanley K, McNally AG, Liu J, Abbink P, Maxfield LF, Seaman MS, Dugast AS, Alter G, Ferguson M, Li W, Earl PL, Moss B, Giorgi EE, Szinger JJ, Eller LA, Billings EA, Rao M, Tovanabutra S, Sanders-Buell E, Weijtens M, Pau MG, Schuitemaker H, Robb ML, Kim JH, Korber BT, & Michael NL (2013). Protective efficacy of a global HIV-1 mosaic vaccine against heterologous SHIV challenges in rhesus monkeys. Cell, 155 (3), 531-9 PMID: 24243013

[4] Santra S, Muldoon M, Watson S, Buzby A, Balachandran H, Carlson KR, Mach L, Kong WP, McKee K, Yang ZY, Rao SS, Mascola JR, Nabel GJ, Korber BT, & Letvin NL (2012). Breadth of cellular and humoral immune responses elicited in rhesus monkeys by multi-valent mosaic and consensus immunogens. Virology, 428 (2), 121-7 PMID: 22521913

[5] Barouch DH, O'Brien KL, Simmons NL, King SL, Abbink P, Maxfield LF, Sun YH, La Porte A, Riggs AM, Lynch DM, Clark SL, Backus K, Perry JR, Seaman MS, Carville A, Mansfield KG, Szinger JJ, Fischer W, Muldoon M, & Korber B (2010). Mosaic HIV-1 vaccines expand the breadth and depth of cellular immune responses in rhesus monkeys. Nature medicine, 16 (3), 319-23 PMID: 20173752

A mosaic vaccine that could potentially protect from different ebola strains

Disclaimer: The mosaic vaccine paper discussed in this article is from my own group and overlaps with some of the research I do. 

I'm sure you've been following the latest news about the Ebola virus outbreak in Africa.

"The Ebola outbreak in West Africa is the world's deadliest to date and the World Health Organization has declared an international health emergency as more than 1,000 people have died of the virus in Guinea, Liberia, Sierra Leone and Nigeria this year." [Source: BBC News]

The ebola virus was first described in 1976, with outbreaks reported starting from 1967 [3]. It's part of the Filovirus family and its natural reservoir is believed to be fruit bats, though there is evidence that it could be wider than we think. In fact, ebola can infect other animals like monkeys and pigs. Because the virus is transmitted through bodily fluids and it can survive for a few days after the host's death, it can be easily spread through the butchering and consumption of bushmeat.

You've probably heard from the news that two infected Americans were treated with "serum". Some headlines even dubbed it a "secret serum." The serum is actually no secret and has been used not just for ebola but also for other viruses like RSV [1]. The treatment, called passive transfer of antibodies (or antibody serum), is based on the transfer of antibody serum from one organism to another. The idea behind it is that the immune system of a person previously exposed to the virus has developed antibodies that can help other immunologically naive patients fight the infection. For the ebola virus, the therapy is still in the experimental phase and, up to these two patients, had only been tested in animals.

There are several vaccines currently being tested, each one at various experimental phases. Friedrich et al. [1] list a nice summary of all the current testing in their review. The one they do not mention in their review is a mosaic vaccine being developed by my group, which is based on ideas originally designed for an HIV vaccine.

What is a mosaic vaccine?

A vaccine is an attenuated form of a virus. Even though unable to start a full infection, when injected into the body, the attenuated virus is detected by the immune system, which can then mount the appropriate response and "create" neutralizing antibodies. Typically, the attenuated virus is created from the natural virus found in organisms.

And then came HIV and baffled everyone.

The problem with HIV is that every single HIV-infected person has a different virus. In order to protect from every possible infection, one would need to put into a vaccine the over half a million genetically distinct circulating strains. Clearly, that's not possible. How do you protect people from a viral population that's so diverse? Natural strains are no longer sufficient. You have to come up with clever ways to 'summarize' the whole population of viruses with just 2-3 viral strains.

That's when computers come in handy: the mosaic vaccine is a vaccine created in silico. Suppose you want to create one genetic sequence that "summarizes" all the genetic variants found in a population of 100 strains. The algorithm that creates the mosaic starts from the 100 strains and it literally reshuffles them bit by bit. The "bits" are not cut out randomly but in a way that, when reassembled in a full genome, the proteins are still functional and working. In other words, you want to make sure that after the reshuffling you still have functioning viruses. You repeat the reshuffling for a few times and at the end of the iterations you pick the one strain that best represents the original pool of 100 genomes.

HIV-1 mosaic vaccines have given great results in guinea pigs and monkeys. But what would be the advantage of using them for ebola?

If you are familiar with phylogenetics, you will certainly object that the two viruses (HIV and ebola) are quite different: while HIV spreads out in a star-like fashion (which translates into the fact that no two individuals have the same virus), ebola evolves more like the flu, with new emerging viruses causing new outbreaks. So, why would the mosaic vaccine help with ebola?

"While the techniques used here are very similar to those used for HIV-1 mosaic vaccine design, a pattern of repeated introductions of the filoviruses into humans (and primates generally) gives a crucial difference from HIV-1. HIV-1 shows great diversity within the pandemic, but that diversity has developed continuously, leaving intermediate isolates in its wake. In contrast, known filovirus diversity has episodically increased as new outbreaks are found to result from novel viruses, lacking intermediates." [3]

The fact that the ebola virus "lacks intermediates" seems to indicate that there are reservoirs that we don't know of where the virus accumulates diversity. This is worrisome: we not only need to protect from the current outbreaks, but also be prepared for new viruses that might emerge in the future. In [3], Fenimore et al show how the mosaic algorithm can be readapted from HIV to ebola, accounting for the evolutionary differences between the two viruses.

A mosaic vaccine would protect from all ebola subspecies and also against new strains that could potentially develop from the current outbreaks. The problem with ebola is that its reservoir could be wider than we think. The viral diversity found in bats has not matched the diversity of the ebola strains found in humans. So, where are the new viruses coming from? There are likely pockets of diversity that come from reservoirs we don't know of.

"The implication is that a vaccine against the filoviruses should strive for good coverage of common epitopes from the maximum number of types and strains currently available, in the hope that future outbreaks will retain these elements, so the vaccine will still be effective when challenged by a novel strain in a new outbreak." [3]

The authors tested the ebola mosaic vaccine on a mouse model and compared it with a vaccine created with a single natural strain from Zaire. All vaccinated mice in either group (mosaic or natural) survived the challenge. The natural strain vaccine provided 82.8% coverage of other Zaire strains, but only 14.0% coverage of non-Zaire strains. On the other hand, the single mosaic vaccine provided 54.7% coverage of other Zaire strains (still sufficient to protect the mice from infection) and 23.2% coverage of non-Zaire ebola virus strains, proving that a mosaic can indeed improve protection against different subtypes. Furthermore, comparing a cocktail of a two-mosaic vaccine with a two-protein natural cocktail and a vaccine that was previously tested in macaques (Hensley et al., 2010), the mosaic cocktail achieved the highest coverage.


[1] Friedrich BM, Trefry JC, Biggins JE, Hensley LE, Honko AN, Smith DR, & Olinger GG (2012). Potential vaccines and post-exposure treatments for filovirus infections. Viruses, 4 (9), 1619-50 PMID: 23170176

[2] Fischer W, Perkins S, Theiler J, Bhattacharya T, Yusim K, Funkhouser R, Kuiken C, Haynes B, Letvin NL, Walker BD, Hahn BH, & Korber BT (2007). Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants. Nature medicine, 13 (1), 100-6 PMID: 17187074

[3] Fenimore PW, Muhammad MA, Fischer WM, Foley BT, Bakken RR, Thurmond JR, Yusim K, Yoon H, Parker M, Hart MK, Dye JM, Korber B, & Kuiken C (2012). Designing and testing broadly-protective filoviral vaccines optimized for cytotoxic T-lymphocyte epitope coverage. PloS one, 7 (10) PMID: 23056184

Aluminum adjuvants in vaccines: are they safe?

Multnomah Falls, © EEG

Disclaimer: I work on HIV vaccine design and I'm quite proud of it. I know that for three million HIV-positive kids in Africa, a vaccine is the only hope they have to grow into adulthood. So, when people tell me that vaccines are bad I cringe. Infant mortality rates have dropped since vaccinations have been introduced. We live longer, healthier lives thanks to vaccines. Diseases like polio can paralyze and kill, yet they are no longer a concern for children in the western world.

At the same time, I'm fully aware that medicine is not a science. When it comes to the human body, there are no certainties. We use statistics to measure effects, but statistics do not give you a yes/no answer: they give you averages, trends, probabilities. And as parents, we need to make decisions for our kids, not for the average child.

So, when my friend Autumn Kalquist asked me about aluminum and vaccines, I started digging up the literature right away.

In layman terms, this is how a vaccine works: the goal is to teach the immune system to recognize a certain pathogen, whether it is a virus, a bacteria, or a cancer cell. To do so, we take bits of proteins from the pathogen and we make sure that the immune system sees them. Since it's not the whole pathogen that's injected inside the organism, but only some of its proteins, the pathogen cannot mount an infection. On the other hand, the immune system will recognize the proteins as "extraneous" and will start making antibodies able to bind to them. The beauty of this mechanism is that once the immune system finds an antibody that perfectly matches the extraneous protein, the information will be stored in its "memory." Next time the immune system will come across the same protein -- this time from the whole pathogen -- it will be able to retrieve the "memory" of the right antibodies to use against the proteins. the antibodies will bind to them and initiate the process that leads to the destruction of the pathogen.

While the principle seems "straightforward", there are many obstacles to overcome when designing a vaccine. The first one of course is to select the right proteins that will elicit a strong enough immune response. This has proven particularly challenging in HIV because of the virus's extreme variability. Since no two viruses are identical, proteins from one particular virus are never enough to mount a response that's protective against all kinds of HIV strains.

But even when the virus is not as variable as HIV there are other challenges: the fact that you inject something inside the body doesn't automatically guarantee that the immune system will see it. In some cases the pathogen proteins alone are not enough to recruit a strong enough immune response. In these cases, additional molecules are added to the vaccine: these molecules, called adjuvants, are able to initiate signals that in turn alert the immune system to recruit lymphocytes.

And this is where we get to the controversy: many effective adjuvants contain aluminum, which for some has been a cause for concern. Though aluminum is quite efficient at stimulating the immune system, in high doses it can cause serious neurodevelopment damage. This is particularly true for small children since their growing brains are more permeable to toxic substances.

Are vaccines containing aluminum safe, then?

First of all, let me say that I'm appalled that the question is raised with regards to vaccines, but nobody seems to take notice that tattoo ink contains aluminum, too. I guess tattoos never had the pretense to save lives. So while it's not worth taking chances with aluminum to save a life, it's totally worth doing it in the name of skin branding? 

Back to vaccines: as it often happens when you try to address such questions, you start digging for information and you find both "yes" and "no" answers.

People who think they are safe tend to reason that (1) they've been used for over seventy years and by now we would've noticed if they weren't; (2) we are constantly exposed to aluminum since it is found in many foods, food additives and in foods prepared with aluminum utensils.

But you'll also find people who quite adamantly state that aluminum containing adjuvants are not safe since the vaccine doses are higher than the recommended IV solution doses. My friend Autumn brought to my attention Dr. Sears' position and questioned the comparison he makes:

The first document (see Resource 1) I came across discusses labeling of aluminum content in injected dextrose solutions (a sugar solution added to IVs in the hospital). [. . .] The second document (see Resource 2) discusses aluminum content in IV feeding solutions (called TPN). The FDA requires these solutions to have no more than 25 micrograms of aluminum in each liter of solution.

Currently used vaccines contain between 125 and 850 micrograms.

So, who's right?

The first thing one should do when setting off on a quest like this is make sure that we are comparing apples to apples and oranges to oranges. The arguments above are both wrong because the aluminum contained in vaccines is administered through intra-muscular injection, which is quite different than ingesting it with foods or receiving it through an intra-venous solution. In other words, both arguments above are comparing apples with oranges.

Aluminum in food might be safe to consume because our guts tend to be a quite efficient barrier that will ensure that not all of it will be absorbed into the bloodstream. On the other hand, as Autumn rightfully noticed, it's incorrect to compare intra-venous dilutions to intra-muscular injections: intra-venous solutions better have the lowest possible doses of aluminum since whatever you gets injected immediately enters the blood flow.

Animal studies have shown that aluminum administered through intra-muscular injections can take up to a month to be released into the blood stream [1]. This slow release and clearance ensures that at any given time during that month the circulating levels are much lower than the total level of aluminum contained in the original dose. In fact, in [1], author HogenEsch cites studies that have found aluminum based vaccines to induce fewer local reactions than vaccines without the adjuvant, a phenomenon that could be due to the fact that aluminum stimulates the immune response (which is why it's used in vaccines in the first place).

To play devil's advocate I also found a paper that, contrary to HogenEsch's review, raises a red flag against aluminum adjuvants. The authors, Tomljenovic and Shaw [2], compared ASD (autism spectrum disorder) prevalence from the US, UK, Australia, Canada, Sweden, Finland and Iceland, and contrasted it with the cumulative aluminum doses received through childhood vaccinations in each country. The authors found a strong correlation between cumulative exposure to aluminum through vaccines and higher ASD prevalence, and claimed that, based on Hill's criteria, this correlation is a strong statement in favor of causation.

Let's pause for a moment and make one thing clear: correlations DO NOT PROVE causation. A classical example is the correlation between crime rates and ice cream sales: they seem to rise at the same time during the year, and that time of the year happens to be summer. But it's pretty obvious that ice cream sales do not cause a rise in crime rates. However, the researchers in [2] argue that:

"The positive correlation between Al exposure from vaccines and prevalence of ASD does not necessarily imply causation. However, if the correlation is strong (criterion 1), consistent (criterion 2) and if
there is a biologically plausible mechanism by which it can be explained (criterion6),as well as an appropriate temporal relationship between the proposed cause and the outcome (criterion 4), then the satisfaction of these criteria supports the notion that the two events may indeed be causally related. Our results satisfy not only all four of these criteria applicable for establishing causation in neuropsychiatry,but also four others. These additional criteria are: (5) biological gradient, (7) coherence with the current knowledge, (8) experimental or semi-experimental evidence and (9) the analogy with similar evidence [2]."

The above discussion is sensible, but it still does not take away the fact that the correlation they've found DOES NOT prove causation. The only way you could prove a causal relationship here would be to have an animal model and an experimental setting with several groups receiving increasing doses of aluminum. You then measure the prevalence of ASD in each group. Until we have such an experiment we cannot rule out the multiple factors that could possibly bias this correlation. For example, ASD diagnoses have been rising in the past decades because of better diagnostics tests.

At the same time, while Tomljenovic and Shaw DO NOT PROVE that aluminum adjuvants cause autism, they do raise some interesting points. The adjuvants are needed because without them the vaccines are not effective. However, part of the problem is that immune responses in infants under 6 months of age are weaker. Those are also the most delicate months from the neurodevelopment perspective, making the organism more fragile to aluminum exposure. So maybe one needed intervention could be to revisit the vaccination schedule in infants. I'm not a medical doctor, so I can't make any recommendations, but, as a parent, I do wonder: is it strictly necessary to vaccinate infants starting from their first day in the world as it's done in the US? Could we maybe wait a few months? Would this be too dangerous for babies in nurseries?

While none of this discussion brings a definitive answer, I hope it does provide food for thought. Clearly, if these adjuvants have been used for over 70 years, the vast majority of the population can tolerate them pretty well. The problem, of course, is that as parents, our children are not "the vast majority." They are individuals and we want the very best for them. I think that there is a lesson to learn here. First, we need more dialogue between the researchers, the medical providers, the FDA, and the parents. The debate lately has been too "black and white", whereas any time I try to dig into the literature I see too many grays. This is not a matter one can address with a definitive yes or a definitive no. My best advice is: (1) don't limit yourself to one opinion only, not even when it comes from a reputable source; (2) read a lot, read from all sources, and then use your best judgement based on your family history and your children's health history; (3) allow yourself some leeway. For example, if a stronger vaccine is necessary under 6 months of age, if there is a family history of ASD, it may be worth considering the pros and cons of delaying the vaccine schedule. Or maybe start off with the non-aluminum vaccines, like polio, for example.

And remember: your decision will affect not just your kids but also, to some level, the rest of the population. If you have a family history of ASD and/or immunological problems, by all means, take precautions. Your kids will still be protected by the phenomenon called "herd immunity" so long as the majority of the population keeps getting vaccinated. For the rest of us, the fact that vaccines have benefitted us all as a population should be undeniable.

If you like the content of this blog, please consider supporting me by purchasing my new book release, the detective thriller CHIMERAS. Thank you.

[1] Hogenesch H (2012). Mechanism of immunopotentiation and safety of aluminum adjuvants. Frontiers in immunology, 3 PMID: 23335921

[2] Tomljenovic L, & Shaw CA (2011). Do aluminum vaccine adjuvants contribute to the rising prevalence of autism? Journal of inorganic biochemistry, 105 (11), 1489-99 PMID: 22099159

This season's flu helps inform next season's vaccine

Last year I described the arm's race happening between virus and immune system during an HIV infection: as the immune system starts mounting its defense against the virus, the virus mutates trying to evade the attack. This is what pushes the virus to constantly evolve new strains, not just in HIV, but also in the flu virus, which evolves a new strain roughly every year. The HIV virus evolves within the same host to evade the host's immune response. On the other hand, the flu virus evolves more slowly: contrary to HIV, healthy individuals can clear the flu virus, and in doing so they acquire immunity against future infections from the same virus. This exerts pressure on the flu virus to evolve new strains capable of evading the population acquired immunity.

The process by which viruses constantly evolve new strains in order to evade immune responses is called antigenic drift.

The yearly evolution of the flu virus is closely monitored: surveillance data is collected throughout the flu season and, based on the data, a prediction is made on which strains will be most likely to reappear during the next season -- this step is important for flu vaccine design. The vaccine needs to be available prior to the start of the new flu season. Therefore, researchers have to make an educated guess on what the evolved flu virus will be like in order to make the appropriate vaccine.

"Due to the fast evolution of the influenza virus, the components of the influenza vaccine are changed for many flu seasons. Even though the vaccine is usually redesigned to match closely the newly evolved influenza virus strains, there occasionally has been a suboptimal match between vaccine and virus [1]."

The surveillance data comes from the World Health Organization Global Influenza Surveillance Network (GISN), a network of 136 national influenza centers scattered in 106 different countries. The data focuses on one influenza gene in particular, the hemagglutinin (HA) because the protein it codes seems to drive the antibody response.

The HA protein coats the outer surface of the influenza virus. It enables the virus to recognize and bind target cells. Once bound to the surface of the cell, the virus is engulfed in a sac called endosome. This is a mechanism by which cells engulf extraneous objects and then try to destroy (digest them through enzymes) while inside the endosome. However, the influenza virus uses the endosome to get inside the cell and once there the HA protein undergoes a conformational change (triggered by a drop of pH) and becomes a "hook" that breaks the endosome and frees the virus into the cytoplasm. Without the HA protein the flu virus is unable to bind to the target cell or break the endosome. Therefore, antibodies that bind to the HA protein successfully clear the virus, which is why it is vital for the virus to evolve mutations that enable it to escape those antibodies.

In order to anticipate the next flu strains, researchers need to understand how well the population is responding to the current strains. The flu vaccine usually carries three different strains, selected from the most predominant and geographically spread ones so that the resulting immunity is reactive to a wide range of flu strains. How "different" any two strains are is measured by a quantity called "antigenic distance," which, in layman terms, measures how well current immune responses ("animal antisera raised against the same or related strains, [3]") are able to block those strains. Viruses with a high antigenic distance will be poorly blocked by the current immunological responses and therefore are more likely to diverge from the current flu strains and spread into the following season.

In [3], Smith et al. reconstruct the antigenic map of the influenza A virus starting from 1968. The map retraces the genetic evolution of the virus, showing that strains tend to form clusters that last 2-3 years and then evolve into a new cluster (a new strain that requires a new vaccine). New surveillance techniques are being developed based on this concept of antigenic distance and antigenic maps in order to help inform future vaccine selection.

[1] Pan K, Subieta KC, & Deem MW (2011). A novel sequence-based antigenic distance measure for H1N1, with application to vaccine effectiveness and the selection of vaccine strains. Protein engineering, design & selection : PEDS, 24 (3), 291-9 PMID: 21123189

[2] Cai Z, Zhang T, & Wan XF (2012). Antigenic distance measurements for seasonal influenza vaccine selection. Vaccine, 30 (2), 448-53 PMID: 22063385

[3] Smith DJ, Lapedes AS, de Jong JC, Bestebroer TM, Rimmelzwaan GF, Osterhaus AD, & Fouchier RA (2004). Mapping the antigenic and genetic evolution of influenza virus. Science (New York, N.Y.), 305 (5682), 371-6 PMID: 15218094