Support The World's Smartest Network

Help the New York Academy of Sciences bring late-breaking scientific information about the COVID-19 pandemic to global audiences. Please make a tax-deductible gift today.

This site uses cookies.
Learn more.


This website uses cookies. Some of the cookies we use are essential for parts of the website to operate while others offer you a better browsing experience. You give us your permission to use cookies, by continuing to use our website after you have received the cookie notification. To find out more about cookies on this website and how to change your cookie settings, see our Privacy policy and Terms of Use.

We encourage you to learn more about cookies on our site in our Privacy policy and Terms of Use.

Got Antibodies?

Got Antibodies?

Seasonal influenza is a strong foe; our bodies its battleground. Can vaccines—our front-line defense—keep us healthy?

It seems simple enough—pop into a doctor's office or, increasingly, any neighborhood pharmacy, to get a shot or nasal spray and, poof, you're protected from the nastiest dish on the cold-weather illness buffet—that ache- and fever-inducing slide into delusional daytime naps and tossing, turning nights that we know as seasonal flu. Receiving the flu vaccine takes just a few minutes. But what we don't often think about—the process behind the vaccine—is a much longer affair. And how much protection does the vaccine really afford?

'Always limping behind'

Earlier this year, in an NIH conference center in Rockville, MD, the Vaccines and Related Biological Products Advisory Committee (VRBPAC) convened its members. At this meeting, the VRBPAC, part of the FDA, announced the specific flu strains approved to be included in 2013/2014 U.S. flu vaccines, based on recommendations from the World Health Organization (WHO). While it may seem like a boon to get this information into the hands of researchers and vaccine manufacturers so far ahead of the next flu season (which typically begins in late Fall), many flu experts indicate that this early-decision process is simply an indication that vaccine production time is too long.

"We are always limping behind," says Peter Palese, the Horace W. Goldsmith Professor and Chair in the Department of Microbiology at Mount Sinai Medical Center in New York. "We base our vaccine choices on strains that circulated in Australia during their winter, so they are already 6 months outdated by that point." And, once vaccine strains are approved, the production process is still another 6–8 months away from being ready for an arm or nose near you.

This feeling of always chasing an adversary just out of your reach is a familiar one for most flu researchers. The problem: seasonal flu mutates faster than we can adapt current vaccines. Every time the flu virus undergoes a significant mutation, it produces a new influenza "strain" (denoted by Hs and Ns). Vaccines must be tailored to the strains currently in the environment in order to be effective.

"We created a measles vaccine in the 1950s and we are still using that exact same vaccine because the virus doesn't change. It's the same with Polio and hepatitis B," says Palese. "But you can't do that with flu."

An adaptable enemy

Perhaps the skill most prized by military strategists is the ability to adapt—and seasonal flu, a worthy enemy to our bodies' complex defense systems, has mutation down pat. Flu, formally known as influenza, is an RNA virus that uses its hemagglutinin (HA) protein to bind to, and infect, healthy cells. The HA molecule contains a head and a stalk, with the head being the most adaptation-skilled part of the virus, and not coincidentally, the part of the virus that attaches directly to healthy cells. Thus, the reason we require an annual flu vaccine: as flu adapts to our defenses, we require new weapons.

The feeling of always chasing an adversary just out of your reach is a familiar one for most flu researchers.

The body's primary weapons are antibodies (or immunoglobulin), our cells' first-line defense to invaders—the proverbial messenger pigeon sent to warn the troops. Antibodies are immune proteins that alert the rest of the immune system and, in some cases, attack unwelcome guests directly. Flu vaccines are designed to stimulate antibodies, allowing our bodies to build up reservoirs of antibodies for specific virus strains—akin to basic training at the cellular level.

Current vaccines work in one of two ways. The most common vaccine, which comes in an injectable trivalent shot-form, inserts inactivated flu virus into the body, allowing the body to respond with antibodies, but without the threat of actually contracting flu. The same method is employed by the intradermal shot, which features a smaller needle injected into the skin. A nasal spray, FluMist®, uses weakened flu virus to achieve the same goal: activate an army of antibodies before the body comes into contact with the real enemy, readying it to pounce when the time is right.

The antibodies produced are specific to the strains in the vaccine. If researchers, such as those who attended the recent VRBPC meeting, don't select the right strains for the upcoming flu season, the population is at greater risk of contracting flu—a risk not taken lightly by those who are familiar with its high costs, whether measured in healthcare dollars, lost work hours, or, unfortunately, mortality. Choosing strains for upcoming vaccines is a gamble, but, for now, an essential one.

How effective are vaccines?

Despite the challenges, researchers have a good track record when it comes to predicting which strains will be circulating half a year to a year into the future, says Doris Bucher, PhD, Associate Professor of Microbiology and Immunology at New York Medical College. "But that's what's been so disappointing this flu season. We did have a match with regard to strains, but efficacy was still not great, especially for people over 65; seniors did not produce a good immune response to this year's vaccine."

There is reason to believe, however, that this year's vaccine may not have been less effective than previous years; efficacy may simply have been measured more accurately this time around. According to a 2012 report from the University of Minnesota's Center for Infectious Disease Research and Policy (CIDRAP) Comprehensive Influenza Vaccine Initiative (CCIVI), reports of vaccine efficacy were generally cited at about 70% to 90% from studies as early as the 1940s through 2012.1 The report also indicates that these estimates may have been significantly overstated.

It should be noted that vaccine effectiveness, or VE, is not measured in absolute terms. Tests for influenza, while available (the CDC's real-time reverse transcription-polymerase chain reaction, or rRT-PCR, protocol is an example), are prohibitive to administer to large portions of the population. Instead, VE relates to the percentage that people who were vaccinated are less likely to need to see a healthcare provider for influenza-like illness symptoms.

By reviewing vaccine efficacy and effectiveness studies from 1967 to 2012, CCIVI researchers found that trivalent injectable vaccines protected healthy adults (aged 18 to 64) at a rate of about 59%; there was inconsistent evidence of protection in children and seniors.1 Interestingly, these data match VE reports from the 2012/2013 season rather closely—estimated at 47% against influenza A (H3N2) and 67% against B virus infections, with lack of statistical efficacy for those over 65.2

Is a VE of 60% for just part of the population good enough? Michael T. Osterholm, PhD, MPH, one of the lead authors of the CCIVI report, titled The Compelling Need for Game Changing Influenza Vaccines, doesn't think so. "We need new influenza vaccines that work for everyone, most of the time." Furthermore, he feels that overstating current vaccine efficacy could hamper efforts to produce novel vaccines. But what would those new vaccines look like?

New avenues of inquiry

In 2012 the FDA approved Flublok®, which is based on cell-based technology, namely a modified baculovirus from insect DNA in which the genetic sequence of hemagglutinin, the key antigen of the influenza virus, is inserted. This new method could offer several benefits over current vaccines, says Bucher, including the ability to produce HA for the vaccine in cell incubators instead of eggs, which can be both expensive and time consuming. And, because the vaccine uses a genetic sequence rather than inactivated virus grown in eggs or cells, there's no adaptation process required; a more antigenically similar hemagglutinin could mean better efficacy.3 "It's truer to what's out there in people," says Bucher, who calls the FDA approval of Flublok, "quite an achievement."

"Theoretically, you could ramp up production and create unlimited quantities, although the strains included in the vaccine will still have to be based on the decision of the VRBPAC, and the manufacturer can't start making the vaccine without that recommendation," says Bucher. And, this is where Palese gets hung up—"Flublok is a new production modality, but ultimately it's an incremental improvement."

What Palese, and scores of other researchers and companies, have been working on is the so-called universal vaccine—one that creates antibodies to the conserved portions of the HA stalk (those genetic sequences that remain constant across flu strains), not the ever-mutating head. If such a vaccine could be achieved, it could be effective across flu strains, and perhaps boosted only a few times throughout the life cycle.

Vaccinating with inactivated novel, pandemic influenza strains could be one possible way to elicit stalk antibodies.

Palese feels that such a vaccine is not only possible but imminent, pending FDA approval of human trials. "We can identify the conserved domains and we can protect mice, but there are many hurdles to [get to] human trials." While he understands the concerns of moving to human testing and new vaccine production (very rare side effects may only present in a larger population, not in a small clinical trial, notes Bucher), he is eager to get away from imperfect animal models and start human trials. "In the meantime, tens of thousands of people a year are getting sick, and some are dying," says Palese.

One of the great fears of vaccine researchers, a large-scale novel influenza pandemic in which large portions of the population get very ill, came to fruition in 1957, 1968, and, most recently in 2009. While nightmarish for patients and the healthcare field, the 2009 pandemic "spurred the accumulation of data on epidemiology and risks of influenza," according to the WHO.3

One of the novel findings researchers uncovered was that the pandemic strain of the virus elicited the creation of much sought-after stalk antibodies, and typical seasonal H1N1 influenza virus strains were all but eliminated that year.4 This gives rise to the theory that vaccinating with inactivated novel, pandemic influenza strains could be one possible way to elicit stalk antibodies. Other methods to obtain multi-strain immunity that are currently being explored include creating headless HA molecules, combining several conserved regions of influenza viruses into one molecule, and activating T cells in combination with antibody-producing influenza proteins.5

'Still our best bet'

While current vaccine methods and their efficacy across populations are perhaps not ideal, the CCIVI report, as well as Drs. Palese and Bucher, are quick to note that vaccines are by far the best option we have for preventing influenza, and that every person who is eligible should get an annual flu shot. Vaccines have a very good safety record note the researchers, who are both quick to criticize anti-vaccine talk and lobbying efforts.

Just as polio has been eradicated in all areas of the world except for those areas in which vaccination efforts are actively thwarted, flu could be better controlled if more people got vaccinated every year, says Palese. According to the WHO, "Universal vaccination in pediatric groups can reduce disease burden in high risk children."3 In other words, flu vaccines don't just protect the person getting vaccinated—they can have a group protective effect if enough people get them.

"Vaccines are the best we have," states Palese. But that doesn't mean that he won't be hard at work in the lab trying to find a better way forward.


  1. University of Minnesota's Center for Infectious Disease Research and Policy Comprehensive (CIDRAP) Comprehensive Influenza Vaccine Initiative (CCIVI) report, The compelling need for game changing influenza vaccines.
  2. Centers for Disease Control and Prevention, Morbidity and Mortality Weekly Report, February 22, 2013.
  3. World Health Organization meeting presentation, The first WHO integrated meeting on development and clinical trials of influenza vaccines that induce broadly protective and longlasting immune responses, January 24–26, 2013, Hong Kong Baptist University, Hong Kong SAR, China.
  4. Pica N, Hai R, Krammer F, Wang T, Maamary J, Eggink D, et al. (2102). Hemagglutinin stalk antibodies elicited by the 2009 pandemic influenza virus as a mechanism for the extinction of seasonal H1N1 viruses. PNAS.
  5. Richards, S. (2013, Jan. 14). Universal flu vaccines charge ahead. The Scientist.


Diana Friedman is executive editor of The New York Academy of Sciences Magazine.

Photo credit: Tatyana Sokolova /


Computational Epidemiologists Tackle Influenza With Data

It's fairly evident when flu hits a given area—employees start taking sick days, lines become longer at the doctor's office, and emergency rooms fill up. But what if people, particularly healthcare workers and those not yet vaccinated, could get just a little more warning that flu was coming, or that the current flu season had not yet peaked? These were questions Rajan Patel, PhD, senior scientist at Google Inc. and two of his coworkers, Jeremy Ginsburg and Matthew Mohebbi, asked themselves in 2007.

While the CDC has its own method for estimating flu outbreaks—mainly by relying on select doctors around the country to report counts of influenza-like illness back to the CDC. But those reports must be collected, aggregated, and disseminated—which creates about a 2-week lag time between data collection and public reporting. Patel and coworkers embarked on a project to create a real-time measurement of flu—measurable down to the city level, even in remote areas where it is hard to collect data from on-the-ground physicians—using the data source they knew best: search engine data.

Utilizing search engine data

"We built a simple linear model that used the cumulative frequency of search terms, normalized for total search volume, to estimate the influenza-like illness rates provided by the CDC," says Patel. They had to start by filtering billions of potentially flu-related search engine queries through a correlation analysis, determining which queries best related to CDC information on symptoms of influenza-like illness. "If we just guessed at the most likely search terms, we could have had misses," says Patel.

Google has found that certain search terms are good indicators of flu activity. Google Flu Trends uses aggregated Google search data to estimate current flu activity around the world in near real-time. The above chart shows activity in the US currently (dark blue) vs. past years (light blue). Image courtesy


The process of building, tuning, and validating the model took about a year. The results, published in a 2009 Nature paper, showed that data from the new model, called Google Flu Trends, was consistent with CDC data, although Flu Trends could often predict influenza upticks in a given area at least a few days earlier.1 Because the project was undertaken through, the search engine giant's not-for-profit organization, Flu Trends results are completely open access, available at

Patel has since moved on to other projects, including strengthening a core search algorithm that seeks to provide better search responses to users' search engine queries (such as "What do I do if I have the flu?"). And other researchers have since created similar epidemic-tracking models for locations around the world.

Social networks & epidemic forecasting

"I hope that other companies with social network data can think of ways to use it for good," says Patel. Answering his wish, Lucky Gunasekara, founder of data firm Vulcan, is looking at using social network data for epidemic modeling. Gunasekara explains that in contrast to Google Flu Trends, which relies on large volumes of search engine data to capture incidence, models based on social networks could "look at the actual drivers and pathways of an epidemic."

"If you know the topology of a network, essentially its structure, then you would just have to survey certain people—your canaries in the coal mine." These people would allow you to predict who the flu might hit, based on their social interactions. The key, says Gunasekara, is identifying the right people and the right data—"it's a very bad idea to collect all data from everyone and assume that because we have so much, we'll be able to do something useful with it."

"Say there is a potential bioterrorism alert in New York City. Would you need every person to check into emergency rooms to find out who is actually sick, inciting mass panic along the way? Or would it be better to figure out models of the epidemic within our social networks and to directly message or call a sample of potentially infected people to say, 'Are you feeling sick?'," says Gunasekara.

A tall order

There are still large challenges to overcome before social network data can be successfully used for wide-scale epidemic forecasting, says Gunasekara, not the least of which is ensuring that forecasting doesn't spill over into profiling territory. "Technology should enable personal agency, not take it away." It's also necessary to distinguish between data that indicates online interaction (like commenting on a friend's status) and data that could reasonably indicate real-life, person-to-person interaction (such as photo-tagging). "It's also really hard to incentivize people to provide you with their personal data for something with such a high social stigma as being sick," says Gunasekara.

But Gunasekara and other data scientists are not discouraged, rather energized, by the many challenges facing them. "Nicholas Christakis at Harvard has already started to put together a successful epidemic surveillance model using key individuals within social networks to identify the emergence of a new epidemic," he says. The finding emerged out of a campus-wide flu study conducted amongst Harvard undergraduates and published in PLOS One in 2010.2 The findings could be applicable, as Dr. Christakis articulated to the TED community, for not just the early detection of seasonal flu but also "viral" memes and fads in both the real and online world.3

"People like Nicholas and myself are trying to build thoughtfully designed and scientifically rigorous social experiments and models that, yes, could lay the basis for massively beneficial public services and platforms. Scale though doesn't equal scientific quality," says Gunasekara.

"The key challenge in front of us is better understanding the science behind the dynamics of these epidemics and then translating those findings into the design of new services and products that we can all collectively benefit from through one common shared experience."

Diana Friedman


  1. Ginsberg J, Mohebbi MH, Patel RS, Brammer L, Smolinski MS, Brilliant L. Detecting influenza epidemics using search engine query data. (2009, Feb 19). Nature, 457(7232):1012-4.
  2. Christakis NA, Fowler JH. Social network sensors for early detection of contagious outbreaks. (2010, Sept. 15). PLOS ONE, 5(9): e12948.
  3. TED Talk, Nicholas Christakis: How social networks predict epidemics.