Are we *sure* Ebola isn’t airborne?

Since yesterday’s post, several people have asked me on various social media outlets about the airborne nature of Ebola. Didn’t I know about this paper (“Transmission of Ebola virus from pigs to non-human primates“), which clearly showed that Ebola could go airborne?

Indeed I do–I wrote about that paper two years ago, and it in no way changes my assertion that Ebola doesn’t spread between people in an airborne manner.

Let me back up. The paper in question was an experimental study done in the wake of the 2008 finding of the Reston Ebola virus in pigs and a previous study looking at the Zaire virus in pigs. In the air transmission study, they inoculated pigs with Ebola and examined transmission to macaques (who were not in direct contact with the infected pigs). They did find aerosolized Ebola in air samples, and some of the macaques did come down with symptoms of Ebola. So, it looked like pigs could spread Ebola through the air, which is something that had already been suggested by the epidemiology of the 2008 pig Ebola outbreak. It’s always nice when experimental data matches up with that observed during a real-life occurrence of the virus.

*However*, the kicker was not that Ebola is transmitted by air in human outbreaks, but rather that there may be something unique about pig physiology that allows them to generate more infectious aerosols as a general rule–so though aerosols aren’t a transmission route between primates (including humans, as well as non-human primates used experimentally), pigs may be a bigger threat as far as aerosols. Thus, this may be important for transmission of swine influenza and other viruses as well as Ebola.

So unless you’re sitting next to an Ebola-infected pig, seriously, airborne transmission of Ebola viruses isn’t a big concern. (Perhaps this corollary should be added to this handy diagram examining your risk of Ebola).


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The microbiology of zombies, part IV: hidden infections

(As previously, spoilers abound)

So on this week’s Walking Dead soap opera, we find that Daryl/Michonne’s group is still out and about searching for medical supplies. Back at the prison, the food situation is dire (apparently all the food stores were in the cell block where the infection broke out), so Rick and Carol head out to look for both medicines and food from the local ‘burbs. During their outing, discussion ensues of Carol’s attempt to stop the prison’s apparent influenza outbreak by killing two people who, at that point, were the only ones showing symptoms of disease. Rick decides he can’t trust her, and ends up banishing her from the group.

Carol said multiple times that she was trying to do the right thing, to protect the rest of the group from those who were sick and was only trying to end the outbreak. However, here’s where some knowledge of infectious disease would have helped her. Every disease has an incubation period: the time when the microbe is multiplying in your body, but you’re not showing any physical disease symptoms yet. This can be short–as little as perhaps a few hours for something like Salmonella food poisoning. It can be extremely extended, as I mentioned with rabies virus in my previous post, where the incubation period can be months to years. With influenza, the typical incubation period is 2 days, but it can be as short as 1 or as long as 4-5. The kicker is that a person who’s incubating flu can still spread it even before they show symptoms of the illness. So just because Karen and David were the only ones actively coughing and looking miserable, Carol was mistaken in her assumption that they were the only ones infected, and that she could stop the outbreak by snuffing them.

This is the difference between two similar concepts, quarantine and isolation. People who have been *exposed* to an infectious agent, but are not yet showing any signs of illness, can be quarantined to keep them away from others due to their *potential* to spread a disease. Those who are already showing signs and symptoms are placed into *isolation* to keep them from spreading it–they’re a known quantity. The prison group has used primarily isolation to keep the infection from spreading: they’re putting the ill in the Death Row cell blocks as an isolation area, and those who are well can roam around as they choose. (Maggie, for instance, hasn’t been sent to quarantine even though she clearly was exposed to the illness by being in such close contact with Glenn).

However, one thing that the group hasn’t yet determined (probably because no one has recovered as of yet) is how long they’re going to keep anyone who gets better in the isolation area. Though adults usually stop releasing influenza virus even before their symptoms are completely gone, kids can shed the virus for a long time: up to two weeks after their symptoms started according to one study (and others have found similar results). So while right now they have the healthy young children segregated from everyone else for their own protection, in theory, if Lizzie (the flu-infected child currently in held in isolation) gets well and is released back to the healthy kid’s room, she could simply re-start the outbreak there, among the most susceptible. 

This is why disease eradication is so difficult, and why it’s been accomplished for so few pathogens to date: many pathogens can spread on the sly, even when people don’t know they’re sick. For influenza, even if it’s knocked down in this group (and of course, it soon will be one way or another–at some point, the susceptible hosts in the prison will be exhausted, either by infection & recovery or by death), there is always another reservoir of disease out there. It may be other humans. Darryl/Michonne’s group finally made it to the veterinary school mentioned two episodes ago, and the zombies they ended up fighting there had clinical signs that looked an awful lot like the survivors had seen at the prison: blood that had come from the eyes and nose. Had flu been circulating there as well? It’s a vet school, pigs could certainly be housed (there were a number of animal cages, and could easily be an outdoor space for livestock somewhere). So pigs could be serving as a reservoir. Flu can also come from a number of other animals–most notably, birds, who don’t even have to appear sick to transmit the infection to people.

Infections can be sneaky and unseen, as this group should well know.

See also:

Part I: the microbiology of zombies

Part II: ineffective treatments and how not to survive the apocalypse

Part III: “We’re all infected”

The microbiology of zombies, part II: ineffective treatments and how not to survive the apocalypse

(Spoilers. And things.)

After the start of season 4 of the Walking Dead and the introduction of a new nemesis: a fast-spreading, deadly infectious disease that seems to be a strain of influenza, I was looking forward to the plot arc of this season.

And then episode 3, “Isolation”, happened. From an infectious disease standpoint, I say, bah.

At the end of the previous episode, “Infected”, the group had decided to lock up anyone who was showing signs of the infectious disease within the death row cellblock, so that they would not further spread the disease, and to put the children and elderly (as the most vulnerable population) in another area to keep them safe from the infection. Quickly it was seen that this wasn’t working well, as people were becoming sick all over and more and more were moving into the isolation cellblock.

So, a council meeting was called of the leaders of the group. One of the decisions which was made, on the advice of Hershel the veterinarian, was to try to scavenge supplies from a college of veterinary medicine approximately 50 miles away from their location at the prison. What supplies?


For the micro people reading, you’ll see why my rage started boiling a bit at this point. Hershel was the one who’d suggested this was an influenza outbreak (and therefore, caused by a virus) in the prior episode. He is familiar with the disease (and there is another physician, Dr. Subramanian, who has been treating the ill and has seen the rapid course of the disease–of course, he is now sick himself). It is true that influenza can be complicated by a secondary bacterial infection: that those sick with the flu could develop pneumonia due to Staphylococcus aureus or other bacteria, and that these bacterial infections would respond to antibiotic treatment. But, when the course of disease is as rapid as it appears to be during this outbreak, it’s more likely that people are dying from primary influenza infections, which are most certainly NOT treatable with antibiotics. There are antiviral drugs that can treat influenza infections if given early in the disease course (such as oseltamivir or zanamivir ), but I think the odds of those being stocked at a veterinary school would be pretty slim.

So, rather than at least try for some kind of medically plausible scenario (is that really too much to ask?), Daryl, Michonne, Tyreese and Bob the medic take off in search of completely ineffective antibiotics,and run into an enormous zombie horde on the way. Hershel, in the interim, leaves the relative safety of the prison (he was ensconced with the children as a “high risk” individual) and wanders out into the woods to pick berries and leaves to brew elderberry tea. A folk remedy, there are a few peer-reviewed publications which suggest that elderberries or elder flower might have some properties that do work to treat influenza, so at least here Hershel is, well, sucking somewhat less here when it comes to proposing medical interventions to help those suffering than he did with his terrible antibiotics idea.

Hershel does end up with his tea, taking it into the isolation cell block and distributing it to the infected. This includes Dr. Subramanian, who repays the favor by coughing bloody sputum all over Hershel’s face. (Seriously, he doesn’t even know how to cough into his elbow? Even the little girl talking to Carol did that correctly).

From the previews of next week’s episode, “Indifference”, it appears there will be more searches for drugs, while presumably the horde advances toward the prison. I anticipate a miracle cure of some kind for Glenn at the least, but remain annoyed that the writers are touting antibiotics for a viral infection when flu season is upon us.

See also:

Part I: the microbiology of zombies

Part III: “We’re all infected”

Part IV: hidden infections

The microbiology of zombies, part I

(Spoilers below!)

For Walking Dead fans and readers of this blog, you probably know why I was all excited about some of the plot elements that have been included thus far this season: possible zoonotic disease, and in particular, a potential influenza outbreak that may have originated in pigs. I muse about this and other infections in an article for, and will have additional thoughts about zombies and infectious disease more generally in the coming days.

See also:

Part II: ineffective treatments and how not to survive the apocalypse

Part III: “We’re all infected”

Part IV: hidden infections

Student guest post: New Study Finds that the Flu has Multiple Ways of Spreading

Student guest post by Sean McCaul

Sean pic 1

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The next time somebody in your office or household has the flu, you might want to consider keeping your distance.  A new study published this month in Nature Communications suggests that about half of the transmission of influenza A results from inhalation of microscopic infectious droplets created by the coughing and sneezing of people infected with the flu.  The flu virus hitches a ride in these droplets, and may infect nearby susceptible people who breathe them in.1

The influenza A virus generally causes fever, coughing, body aches, runny nose, sore throat, headache, and fatigue.  Vomiting and diarrhea may occur, but are more common in children.3 Fever and most other clinical signs usually resolve within 5 to 7 days, but coughing may last two weeks or more.2 Children under 2 years old and the elderly are at greatest risk for complications such as pneumonia, and over 90% of influenza deaths are in people over age 65.2

Seasonal outbreaks of influenza are common in the United States, and typically occur during winter months.  During and average outbreak, 5% to 20% of the people in a community may become ill with the flu, and up to half of the people in environments like schools and nursing homes may get sick.2

In adults with healthy immune systems, the flu virus is shed in highest numbers during the first 3 to 5 days of illness, making spread of the flu most likely during this time.  Children may shed the virus for up to 10 days, and people with weakened immune systems may shed the virus even longer.2 In a typical outbreak, a person sick with the flu passes the illness on to an average of 1 to 2 other people.1,2

Previously, influenza A viruses were thought to be transmitted primarily by direct contact and by larger (but still very tiny) droplets generated by coughing, sneezing, and talking.1,2,3  These droplets are capable of travelling 1 to 2 meters, where they may come to rest in the eyes, nose, or mouth of a susceptible person and cause them to become sick with the flu.  These droplets may also fall upon nearby surfaces and objects, where the flu virus can survive for hours.  A person touching these surfaces or objects may get the flu virus on their hands, and then transfer the virus to their eyes, nose or mouth and become ill.1,2

The recent study, published on June 4, 2013, used a mathematical model of influenza virus transmission to evaluate the data from two previously published studies of the effectiveness of hand hygiene and facemasks for the reduction of transmission of influenza A viruses.   It suggests that the flu virus may survive in very tiny droplets created by coughing and sneezing that can remain suspended in the air as an aerosol long enough to be inhaled by nearby susceptible people.   The study shows that aerosols are an important route of transmission of the virus, and may account for as much as 50% of the spread of the flu.1

Sean pic 2

Image Source:

How you get the flu may determine, in part, how ill you get.  Influenza researchers have long suspected that inhalation of aerosols containing the flu virus can lead to more severe illness than exposure to the flu virus by direct contact or by the settling of larger droplets in the eyes, mouth or nose of susceptible people.  This is thought to be because larger droplets are trapped by the defense mechanisms of the upper respiratory tract, such as the large surface area of the nasal turbinates and the mucus lining the nose, pharynx, and trachea.  Smaller droplets, meanwhile, are capable of being inhaled deep into the lungs, resulting in infection in the lower respiratory tract which can cause more severe disease.  The current study found that there was an increased risk for fever plus cough in people suspected to have contracted the flu by inhalation of infective aerosols, which is consistent with current ideas regarding the importance of the route of infection.1

Understanding the routes of transmission of influenza is also important for designing control measures to reduce the spread of this disease.    Interventions such as increased hand hygiene and facemasks help to limit transmission of influenza by larger droplets produced by coughing and sneezing, but may offer little protection from inhaled aerosols.1 Additional methods for controlling the spread of influenza through aerosols, such as improved ventilation of enclosed spaces, ultraviolet lights (which are capable of killing the flu virus), and minimizing exposure to those infected with the flu could reduce the risk of becoming sick.1

So, what can you do avoid getting the flu?  The most effective way is to get vaccinated before flu season.  In the United States, flu season can start as early as October, though the peak months for flu are January and February, and sometimes even later.3 Because the flu strains circulating through the population change from year to year, you should be vaccinated each year.  The vaccine is developed to prevent illness caused by the flu strains likely to cause outbreaks during the flu season, but may not prevent illness from novel or unanticipated strains causing outbreaks.  Some people, such as babies less than 6 months old and those with allergies to eggs should not receive the flu vaccine.3  So the CDC recommends that you take additional preventive measures, such as good hand hygiene, avoid close contact with people who are sick with the flu, avoid touching your eyes, nose, and mouth, and practice good health habits such as remaining well hydrated, eating a healthy diet, exercising, and getting plenty of rest.5

If you do get the flu, what can you do to avoid infecting your family, friends, and colleagues?  First, avoid close contact with others.  Stay home from school or work if at all possible, and don’t run errands while you are sick.  In this way, you can avoid exposing others to your illness.  Second, cover your nose and mouth when you cough or sneeze.  Experts recommend that you cough and sneeze into a cloth or into your elbow, so that you don’t contaminate your hands, which are commonly implicated in the spread of the flu.  This simple practice can reduce the amount of infectious material you spread into your environment.  Practice good hand hygiene, particularly before touching doorknobs and other items that may leave the virus where others are likely to become exposed.5


  1. Cowling, B.J., Dennis, K.M., Fang, V.J., Suntarattiwong, P., Olsen, S.J., Levy, J., Uyeki, T.M., Leung, G.M., Malik Peiris, J.S., Chotpitayasunondh, T., Nishiura, H., & Simmerman, J.M. (2013).  Aerosol Transmission is an Important Mode of Influenza A Virus Spread.  Nature Communications, DOI: 10.1038/ncomms2922  LINK
  2. Bridges, C.B., Fry, A., Fukuda, Shindo, N., & Stohr, K. (2010).  Influenza (Seasonal).  In Heymann, D.L. (Ed.).  Control of Communicable Diseases Manual.  American Public Health Association, Unbound™ Mobile Platform
  3. Centers for Disease Control (February 13, 2013), Key Facts About Influenza (Flu) and Flu Vaccine, accessed at , June 8, 2013
  4. Centers for Disease Control (May 6, 2013), What You Should Know for the 2013-2014 Flu Season, accessed at, June 8, 2013
  5. Centers for Disease Control (January 11, 2013) Preventing the Flu: Good Health Habits Can Help Stop Germs, accessed at, June 8, 2013
  6. Flu Virus Image:  Tom Yulsman (May 26, 2009), U.S. and Other Countries Fail to Adequately Monitor Pigs for Flu, accessed at, June 8, 2013
  7. Sneeze Image:  Ben Mauk, photo credit Andrew Davidhazy/RIT (November 28, 2012), Why Do Bright Lights Make Me Sneeze?, accessed at, June 8, 2013

Student guest post: Chirp, Chirp, Sneeze!

Student guest post by Julia Wiederholt

I don’t think there is a single person that can claim to have never had the joyous experience (sarcasm intended) of suffering from the influenza.  We all recognize the common symptoms that accompany this infectious little virus taking up residence in our bodies: the chills accompanying a fever, the total body ache, the nausea, and overall feeling of malaise.  Typically this virus comes and goes within a week without serious side effects.  When novel strains of the influenza pop up however, there can be more serious complications as your body lacks a sufficient immune recognition of the virus.  An example of a new strain of influenza that presents a great risk for the human population is the H7N9 influenza, also known as Avian Influenza A.

H7N9 was first recognized earlier this year in China and thankfully has yet to be reported in the US. The majority of the people infected have had direct contact with poultry or an environment that has contained infected poultry.  Some of the people diagnosed however, report having had no direct contact with poultry opening up the possibility of human to human transfer of the disease.  The infected poultry have shown no obvious symptoms of being infected, but when humans become infected it can cause severe respiratory problems and fever.  As of May this year, LiveScience reported that there have been a total of 131 reported human cases of H7N9 with 32 reported deaths.

While all of that may not sound too impressive, here’s what makes H7N9 such a concern as an emerging infectious disease.  The first major concern regarding this specific influenza is the fact that it is the first time the H7N9 virus has been reported in humans.  The H in the name H7N9 stands for hemaglutinin, which is the attachment protein found on influenza viruses.  This protein not only enables the virus to attach to the cells it is trying to infect, it also is provides the host’s immune system a way of recognizing the virus as a foreign threat.  The fact that this is the first time this specific virus has been found to infect humans means that we lack any prior immunity to it and are therefore, more susceptible.

Another factor that raises the alarm for this influenza is the fact that the infected poultry that have been found so far have shown no outward signs of being sick.  This is a huge concern because it makes controlling the spread of the disease much more difficult.  When poultry and livestock exhibit obvious signs of being infected, it allows the infected to be separated out from the healthy and either isolated or culled to prevent further spread of the disease.  In some cases, the disease may have already spread amongst all of the animals in the vicinity requiring the entire herd or flock to be culled.  When it is difficult to distinguish between healthy and infected animals however, any evidence that the disease has been found within the animals will more than likely lead to the entire herd or flock being culled.  This not only results in greater economic losses for the poultry farmers but also a higher number of people being exposed to infected animals before realizing the danger that is present.

Possibly the greatest concern with H7N9 is the fact that it could be jumping from person to person.  The original thought was that the only way it had been spreading was from direct contact with sick poultry, which would limit the at risk human population to people coming into contact with the infected birds.  Some of the people who have been diagnosed with H7N9 however, are claiming to have had no contact with poultry suggesting that the disease may be capable of human to human transmission.  This would greatly increase the reproductive rate of the disease because people would no longer need to come into contact with poultry to be exposed to it.  The reproductive rate, commonly referred to in scientific communities as the Ro, is a way of measuring the predicted number of new infections that one infectious case is likely to create.  Another factor that suggests the possibility of human to human transfer is the fact that there have been three reported family clusters of H7N9.  While this does not necessarily mean that the virus is capable of sustained human to human transfer, it is highly suggestive that human to human transmission has occurred in these particular instances and that with the right (or depending on how you look at it, wrong) mutation, it could transfer between humans with ease.

While all of these things explain why H7N9 is being watched so closely and why it is important to have a healthy respect for just how dangerous it could be, there’s no reason for people to start panicking quite yet.  As mentioned earlier, this strain of influenza has only been reported in people that either live in or have recently traveled to China.  Unless you are planning to travel out of the country in the near future, there is no reason to become overly concerned about H7N9 at the moment.  Also, the majority of the cases have either had direct contact with infected poultry or close contact with someone who has had contact with poultry.  This means that unless the virus becomes proficient at human to human transmission, the majority of the population is at a low risk.

For the germaphobes out there that are still freaking out over the possibility of catching H7N9, there are several ways to reduce the risk of catching it, or any other influenza for that matter.  Good hygiene practices such as frequently washing your hands and avoiding touching your face will help minimize the risk of introducing the influenza virus into your body.  Eating a well-balanced diet and getting plenty of rest will help keep your immune system in tip top shape in the event of a virus managing to get past your innate defense mechanisms.  In regards to reducing the risk of catching a zoonotic strain of influenza, practices such as thoroughly washing your hands after handling any animals and avoiding contact with sick poultry or livestock will reduce the risk of transmission.  So rest at ease, the world isn’t coming to an end due to H7N9…at least not yet.


Cong Dai, Min Jiang, “Understanding H7N9 Avian Flu,” BMJ, Available online 3 May 2013.  <>.

“Frequently Asked Questions on Human Infection Caused by the Avian Influenza A (H7N9) Virus.”

World Health Organization. WHO, 30 Apr. 2013. Web. 12 June 2013. <


Guang-Wu Chen, Michael M.C. Lai, Suh-Chin Wu, Shih-Cheng Chang, Li-Min Huang, Shin-Ru Shih, “Is avian influenza A (H7N9) virus staggering its way to humans?”, Journal of the Formosan Medical Association, Available online 3 June 2013, ISSN 0929-6646, 10.1016/j.jfma.2013.04.015. <>.

“H7N9: Frequently Asked Questions.” Centers for Disease Control and Prevention. Centers for Disease

Control and Prevention, 22 Apr. 2013. Web. 12 June 2013. <


Kannan Tharakaraman, Akila Jayaraman, Rahul Raman, Karthik Viswanathan, Nathan W. Stebbins, David Johnson, Zachary Shriver, V. Sasisekharan, Ram Sasisekharan, “Glycan Receptor Binding of the Influenza A Virus H7N9 Hemagglutinin,” Cell, Available online 6 June 2013, ISSN 0092-8674, 10.1016/j.cell.2013.05.034. <>.

Rettner, Rachael. “H7N9 Bird Flu Cases Declining, Health Officials Say.” LiveScience. N.p., 10 May

2013. Web. 12 June 2013. <



Student guest post: Seasonal Flu Vaccine: Why we need it

It’s time for this year’s second installment of student guest posts for my class on infectious causes of chronic disease. Fifth one this year is by Nai-Chung Chang. 

Of the many health problems that everyone is bound to have at some point, influenza, or just “the flu,” is one of the most prominent. In fact, we call the time during which it is most prevalent the “flu season”. It has now become a regular occurrence in the U.S. to just get a shot before the flu season hits, and be free of it for the rest of the year. In some cases, like me, people just decide not to get the vaccine at all. I say to myself all the time: “It is just the flu. If I do get it, I’ll just take a nap, and I’ll be fine.” However, there are serious complications with influenza if the individual is afflicted with certain diseases, making the vaccine a necessity. Even in the general population, influenza infections could lead to serious health problems, at a lower rate, that could complicate the daily lives of individuals.

Influenza is a generic description of a variety of strains of influenza viruses, including influenza A (H1N1, H3N2), and influenza B. It is a widespread virus, and can infect both human and animals, albeit with different strains. (1) The influenza virus is difficult to completely control since it constantly undergoes different changes through antigenic drifts and shifts, small and abrupt changes in the virus constructs, respectively. (2) It causes fever, coughs, sore throat, runny nose, and a host of other symptoms that target different parts of the body. In extreme, severe cases, it may cause the death of the infected individuals. It can spread from person to person up to 6 feet away through coughing and sneezing, spraying droplets containing infectious particles into the air. The droplets either lands in the other individual’s mouth, or is inhaled into the lung. Influenza is very contagious, due to the fact that it can infect others prior to the development of symptoms, as well as a period after. In addition, there exist asymptomatic carriers that can infect others without knowing. There are vaccines provided every year prior to the start of the “flu season:” a period of time in which the population is most likely to acquire the disease. Once the symptoms develop, it can be treated with antiviral medicine, such as Tamiflu (oseltamivir) and Relenza (zanamivir).

In addition to the problems that a regular influenza infection can cause, in individuals with certain diseases, complications could develop from the interaction between the influenza virus and the disease currently affecting the patient. In asthma patients, the attacks are often triggered by respiratory virus infection, whether by the virus particle itself or the inflammation resulting from the influenza symptoms. Also, the influenza viruses could augment natural responses to allergenic particles resulting in a more severe than normal attack; influenza patients with asthma are often hospitalized as the result. (3) In patients with cardiovascular disease, influenza infections represent a high level risk. The infection could destabilize existing plaques (blocks in the artery) in atherosclerotic patients. In addition to the acute responses from the destabilization, influenza infections could also induce chronic inflammation in the body, as well as reduced clotting ability. (4) For patients with diabetes, infection with influenza represents a high risk of hospitalization and death. In diabetics, the immune system is weakened, making it difficult to fight of the disease. In addition, the infection can cause fluctuation in the level of blood sugar in the patients, through natural immune responses, or lack of desire to eat due to the effects of the influenza symptoms. There is also an increased risk of acquiring pneumonia as a complication of the infection. (5) As in the case with diabetics, patients with cancer and HIV/AIDS are also likely to have complications due to weakened immune systems from both treatment and disease.

From the variety of complications that could result from influenza infections, one can now see that it is extremely important for an individual to receive the vaccines when available. In some places, vaccines are often offered free of charge, especially in workplaces that have high exposure risks, such as hospitals and research facilities. In addition to reducing the likelihood of being affected by influenza, flu vaccines have shown to have reduced the development and progression of other diseases such as chronic obstructive pulmonary disease (COPD). (6) For individuals with HIV/AIDS, vaccines are especially important since they are more vulnerable to infections. In addition, they must be aware of the type of vaccines they are using, since certain vaccines do not work sufficiently in people with immune-deficient issues. However, there exist other treatments for the prevention of the disease, such as chemoprophylaxis, that would allow these individuals to be properly protected against possibilities of infection. (7) With the prevalence of the influenza virus in both the U.S. and globally, it is important that an individual keep up with the most current vaccines, as they are designed to combat the most common forms that would appear that flu season, since the strains changes every year.


  1. CDC. Seasonal Influenza (Flu).
  2. CDC. How the Flu Virus Can Change.
  3. Glezen, W. Paul. Asthma, influenza, and vaccination. Journal of Allergy and Clinical Immunology 188(6): 1199-1206.
  4. Madjid M, Nagahvi M, Litovsky S, Casscells SW, Influenza and Cardiovascular Disease. Circulation 108:2730-2736.
  5. CDC. Flu and People with Diabetes.
  6. Poole PJ, Chacko E, Wood-Baker RWB, Cates CJ. Influenza vaccine for patients with chronic obstructive pulmonary disease. Cochrane Database of Systematic Reviews.
  7. CDC. HIV/AIDS and the Flu.

What’s up with H7N9, the new avian influenza?

I have a new article up today at Slate, examining the emergent H7N9 avian influenzas, and a bit of a review of “bird flu” in general:

While we were carefully watching H5N1 in Asia and Europe, another influenza virus—2009 H1N1—appeared seemingly out of nowhere. Ultimately traced back to swine, this virus was easily spread between people, but unlike H5N1, it wasn’t any more deadly than our normal yearly influenza viruses (which, it should be noted, still kill on the order of 36,000 Americans each year). And now, while we’re still working on understanding how H5N1 and H1N1 have jumped between species, yet another influenza type has surfaced: H7N9.

Holy influenza, batman!

Typically when we think of flying things and influenza viruses, the first images that come to mind are wild waterfowl. Waterbirds are reservoirs for an enormous diversity of influenza viruses, and are the ultimate origin of all known flu viruses. In birds, the virus replicates in the intestinal tract, and can be spread to other animals (including humans) via fecal material.

However, a new paper expands a chapter on another family of flying animals within the influenza story: bats.

I’ve written previously about the enormous diversity of microbes that bats possess. This shouldn’t be surprising–after all, bats are incredibly diverse themselves, encompassing about a fifth of all known mammalian species. Though rabies is probably the most famous bat-associated virus, other viruses that have been isolated from bats include Nipah and Hendra viruses, SARS coronavirus, Chikungunya virus, Japanese and St. Louis encephalitis viruses, Hantaan virus (a relative of the Sin Nombre hantavirus), and filoviruses, among many others. And of course, a bat->pig->human cross-species infection ended up being a plot line in the recent movie, Contagion (modeled after Nipah virus). However, bats still remain chronically under-studied, despite the fact that they can carry so many potential human pathogens.

This new research expands our knowledge of bat viruses a bit. The authors examined 316 bats from eight locations in Guatemala in 2009-10. Rectal swabs were obtained and screened for influenza virus using molecular methods (looking for influenza virus RNA). Three of the samples tested positive, and all were from little yellow-shouldered bats (Sturnira lilium). This could indicate some clustering and transmission of the virus within bat colonies–and indeed, two of the bats were from the same area in the same year (2009). However, the third bat was captured in 2010 at a location 50 km away from the other two, suggesting that the virus may be more widespread than in just one colony.

When we discuss the epidemiology of influenza viruses, we talk about two genes: the HA gene, which encodes the hemagglutinin protein and allows the virus to bind to host cells; and the NA gene, which encodes the neuraminidase protein and allows the virus to leave an infected cell and spread to others. This is where the “H1N1” or “H5N1” nomenclature come from. The novel bat virus was a completely new H type–type 17 (provisional, they note, pending further analyses). The NA gene was also highly divergent, but they are awaiting further analyses to more definitively classify this gene. (Currently there are 9 recognized types of NA genes).

Though they weren’t able to culture out the flu viruses, the authors did do some molecular work suggesting that these novel bat viruses could combine with human viruses and form a functional recombinant virus. What implications could this have for human health? Well, hard to say. We still know very little about all the implications of any distinct type of avian influenza virus, or swine influenza virus, much less something completely foreign like bat flu. It’s interesting that, like birds, influenza virus in bats was found in the intestine (though lung samples were also positive). Can it cause an intestinal infection as well as an upper respiratory infection (the latter being more common in other mammal species)? Does it cause any signs of disease in infected bats at all? If they can get this bat virus to grow, all sorts of interesting lines of research are just waiting.

The article also mentions that seroepidemiological studies are currently being carried out to better understand the epidemiology of bat flu. Looking at PubMed, there is one reference to some similar studies carried out in the early 1980s, but I can’t access anything beyond the title. There also is a report of H3N2 influenza in bats in Kazakhstan, but that article is in Russian and also not readily available. Either way, everything old is new again, and it looks like interest in bat influenza has resurfaced after a 30-year lull. Who knows what else we’ll find lurking out there as interest continues to increase in the wildlife microbiome.


Suxiang Tong, Yan Li, Pierre Rivailler, Christina Conrardy, Danilo A. Alvarez Castillo, Li-Mei Chen, Sergio Recuenco, James A. Ellison, Charles T. Davis, Ian A. York, Amy S. Turmelle, David Moran, Shannon Rogers, Mang Shi, Ying Tao, Michael R. Weil, Kevin Tang, Lori A. Rowe, Scott Sammons, Xiyan Xu, Michael Frace, Kim A. Lindblade, Nancy J. Cox, Larry J. Anderson, Charles E. Rupprecht, & Ruben O. Donis (2012). A distinct lineage of influenza A virus from bats PNAS Link.