Down With The Sickness: Guidelines For Running During And After The Flu

A look at when and how to run during and after a bout with the flu.

By on February 11, 2014 | Comments

Stay the CourseUltramarathoners are, in general, a very healthy lot. Even the research says so. We have a built-in sense of invincibility against injury and illness by way of our virtuous pursuits. With respect to our running habit, numerous studies point out that moderate aerobic exercise boosts the immune system.

However, as revealed in the recent overtraining posts, there is such a thing as too much of a good thing. The very same exercise habits that protect us can wear down the immune system if done to excess. But, if one is mindful and conservative with all parts of his life–training, work, family, and nutrition–the feeling of invincibility is undeniable.

But despite treating one’s body like a temple, Infectious Acts of God can and do happen.

* * * * *

I am proof of that. Since adopting better nutritional habits–including mounds of raw vegetables and fruits each day, and more recently, the exclusion of refined sugars and inclusion of more good fats and proteins–I can count on a single hand the number of common colds I’ve had in the past five years. Moreover, I haven’t had any serious infection requiring a ‘stay-at-home day’ for close to a decade.

Until New Year’s Eve.

The conditions were ripe for disaster: a month of hard training in preparation for a focus race, Bandera 100k, Holiday season stressors, a few minor, common-cold infections, and copious travel preceded Infection Day. But for me, perhaps the most notable element was working as a health-care provider. Prior to infection, I had treated several patients who had become infected, including one individual who was recently ill on my final day of work before traveling east to visit family.

Within three days of arrival, it hit. And hit hard.

Influenza Infection Trends

Each year, influenza viral infections explode during the winter months. Contrary to myth, it is not the cold temperatures but the tendency to stay indoors–with windows closed–that contributes to seasonal infections, which commonly spread through the air. Each year, the strains of flu viruses vary. One of this year’s most common strains is the H1N1 which is known for causing the 2009 flu pandemic that sickened millions and killed tens of thousands in the U.S. over a two-year span. But it may be more famous for the epic influenza pandemic of 1918, which infected 500 million people worldwide, killing 50 to 100 million–the largest ‘natural disaster’ in modern history.

What is most notable about H1N1 is who it strikes. Often, we feel that the flu is dangerous only to the youngest, oldest, and ill-est. The hallmark of the H1N1 strain is that it causes a cytokine overload, where healthy immune systems to go into hyperdrive, and overload: the stronger the immune system, the more severe the reaction. As such, it tends to strike hardest in those with the strongest immune systems: young, healthy, and athletic people. In the 2013-14 flu season, the average age of those hospitalized by viral infections is a mere 40 years of age.

Indeed, across long distance running social media, cases of athletes hard-hit by the flu this season are numerous, with a micro-epidemic following this past December’s The North Face Endurance Challenge 50 Mile Championship in San Francisco, where several prominent runners were infected before, during, or after the race. Common to these stories was the negative impact on both racing and training. But more surprising was the duration of effect: runners being sidelined for weeks or suffering relapses after returning to running too soon.

Influenza Signs, Symptoms, and Effects

The flu virus differs from the common cold and other viruses based on several factors, including what parts of the body are affected, and how the symptoms, as a whole, impact the body and its function.

Most mild or moderate viral infections–such as the common cold or strep throat–stay local to the respiratory system: the nose, lungs, and throat. Viruses enter our system through the air, or through the eyes, nose, or mouth. They deposit in the surface cells of the respiratory system, and once there, viruses bind to cell surfaces, break into them, and dump their genetic material into the cell. The virus hijacks the lung-cell nucleus, and uses it to reproduce many new virus copies. The poor cell–now sick and bloated like an overhydrated, over-salted ultrarunner–eventually bursts, releasing the slew of new virus copies into the system. This process repeats itself, until the body develops antibodies–or virus-specific destroyer cells–to kill them. Symptoms of this process include cough, sore throat, and congestion.

The influenza virus’ effect is systemic: it continues to infect lung cells, embedding deeper into the tissue and closer to the bloodstream, until those new viral copies enter the bloodstream, where the classic flu symptoms including fever and body aches are then experienced.

From there, the influenza virus can infect cells throughout the body.

Including muscle cells.

Effect of Influenza Infection on Muscle Cells and Running Performance

When I awoke ill on the morning on New Year’s Eve, I wasn’t worried. I so rarely got ill that I believed, no doubt, that I would recover in a day or two, and be completely rested and recovered for Bandera, which was 12 days away.

But the fever experienced that day only worsened, and soon was accompanied by muscle aches, or myalgia. Running was out of the question. If fact, simply sitting up and reading a book was painful. Hopes for a speedy recovery slowly evaporated as the fever persisted: a day turned into two, three, and four. Finally, a week later, the fever broke and I truly began to improve.

Running During Acute Infection

The fever experienced during the flu is the result of both the influenza virus’ effect on the cells, and the inflammatory immune system response. In what seems to be a paradox, the immune systems creates an inflammatory response (not unlike that which happens during a running injury), causing a temperature spike, which actually facilitates faster cell destruction and viral spread! But this is part of the immune-system strategy: by increasing the temperature, cells are broken open sooner, with less viral reproduction. In short, the body attempts to cut its losses by self-destructing some cells, thus thwarting the spread of the infection, all the while developing and releasing antibodies to seek and destroy the virus.

So what happens if a stubborn runner decides to run during a fever-rich viral infection? The exercise has two prominent effects:

  • It takes vital energy resources necessary for recovery away from the immune system, and redirects it toward exercise. Thus immune-system activity is decreased.
  • It increases core body temperature even further, thus facilitating greater viral spread. This is most dangerous in the early stages of infection, when the body has yet to develop virus-killing antibodies.

Thus, acutely, running during early infection is ‘ill advised,’ indeed!

* * * * *

After I was infected, I shut everything down. I was close enough to taper time, so there was no question. However, after more than a week of next to no running, my initial return was difficult: the respiratory tract was still inflamed and irritable, especially to the bitter cold and/or dry, indoor-track air of Wisconsin, where I was pre-race. Even short runs were labored, as if running at altitude. Volume was kept conspicuously low.

Post-Infection: Recovery and Running Performance

Systemic-influenza infection causes myriad negative effects, but perhaps none is more relevant to runners than the effect on muscle cells. Research indicates that various strains–namely the H1N1–can severely impact muscle cells. During the 2009 flu pandemic, numerous cases of ‘influenza-associated myopathies’ and outright rhabdomyolysis were found in many affected people. In short, the flu virus directly infects and then destroys the muscle cells. This viral effect is markedly similar to what is seen and universally feared during long ultramarathon races: muscle-cell destruction, and kidney failure secondary to the clogging effect those destroyed cells have on the kidney. Indeed the ‘body aches’ classic to the flu are due to this muscle cell infection and, possibly, destruction.

The muscle cells can be indirectly affected, as well. The heat stress from prolonged fever can indirectly damage muscle cells, also similar to the heat stress experienced during heat exhaustion and heat stroke.

Whether by direct or indirect means, the influenza virus affects both skeletal-muscle and heart-muscle cells by decreasing function. Studies of athletes exercising post-infection–even several weeks after–show diminished performance. Several studies indicate that muscle strength, endurance, and even cardiac output is significantly lower in those recently infected by various viral strains.

Just how long these effects linger is variable. What is known is that these cardiac and skeletal-muscle effects last well beyond the cessation of fever.

* * * * *

By mid-week prior to Bandera, my energy finally felt close to 100%. Clearly, I was ‘rested;’ I had run only a few times in the past two weeks, and, being off work, stress was minimal and rest and nutrition ample. On the few easy jogs in the days pre-race, my energy and strength was good, but my legs felt heavy. I attributed that to the prolonged inactivity not uncommon to the average taper. I prepared for race day as usual.

I slept well the night before, and awoke well-rested and in good spirits. The warm-up felt great.

When the race commenced, the pace was quite reasonable and comfortable. The early uphills were uncomfortable, but they always are: I typically take a while to warm into the neuromuscular gear to tackle big climbs.

However, the first indication of trouble was on the flats: I felt I was unable to make my legs move, even with perfect footing and smooth, gentle grades. I watched eventual champion Jorge Maravilla slowly pull away on one such flat. Committed to listening to my body and racing my plan, I let him go and focused on my splits, taken from my 2012 race, written on my hand.

The news there was no better: aid stations at Bandera are spaced every four to six miles. Over the first 15 miles, I was two minutes slow of each split. Energy was good, but the legs were unresponsive. I pushed along, hoping for that warm-up to come.

Instead, three interesting things happened:

  • My breathing became significantly more labored, despite running on mellow, flat singletrack, despite slowing even more.
  • My legs became heavier and heavier, and began to shut down. The sensation was marked by mile 20 and, by mile 25, resembled the end stages of a 100-mile race.
  • I felt very cold. Weather in Texas can vary greatly in January, but race day 2014 was gorgeous, if not a bit warm: by the end of the first lap (11:30 a.m.), it was over 70 degrees Fahrenheit. Yet I felt cold.

By mile 25 I knew I was done, and when I finally make it to the finish of the first lap, there was no doubt.

Treatment and Prevention Options

In retrospect, a handful of things could have been done to prevent what transpired. Such are lessons that may be helpful for other runners when looking to avoid illness and its effects on winter races:

Prescription flu treatments. While there are thousands of cold and flu medicines available over-the-counter, most simply mask symptoms and make life manageable while the immune system takes its course. There are several remedies out there that many people swear by–megadoses of vitamin C, or multi-vitamin and mineral mixtures (such as Airborne)–but none of these products has been widely substantiated by research.

There are a handful of prescription medications that have been shown to slow the replication of influenza, namely a class of medications known as neuraminidase inhibitors. These are drugs that act to block the enzymes responsible for breaking down healthy lung cells, the main entry for the virus into the cells. Commercial examples include Tamiflu, Relenza, and Inavir. These medications are available only by prescription, presumably to prevent overuse, as several influenza strains are already resistant to these medications.

If antiviral medications are unavailable, consider controlling the fever using anti-inflammatory medications such as ibuprofen and acetaminophen. Given what the research has noted about the effect of fever, especially on muscle cells, minimizing the fever and resolving it as soon as possible should be a top priority.

* * * * *

I did not seek medical attention for my flu. While I felt bad, it never felt ‘bad enough’ to seek treatment. Moreover, I was traveling and most assuredly ‘out of network,’ raising the cost. But in retrospect, had an antiviral med reduced my fever from six to seven days down to one to two? I can only imagine the muscle-cell stress would have been significantly reduced.

Influenza Vaccination. Each year several governmental organizations work together to formulate a vaccine. The World Health Organization studies previous influenza outbreaks from the previous year and shares this data with individual countries. In the U.S., the Food and Drug Administration determines the unique viral combinations to use and works with drug companies to produce it.

Efffectiveness of the vaccine depends on how closely these organizations get to what actually spreads. In a sense, scientists at these public health organizations are putting bets on various numbers on the roulette wheel. Thankfully for us, they are remarkable good at this prediction. This year’s vaccine has shown to be nearly 75% effective at preventing H1N1 infection, the most dominant strain in North America this season.

As for side effects, there are relatively few. Contrary to popular belief, it is not possible get infected by the vaccine, since vaccines use inactivated viral components. Minor side effects seem to be reserved to the substrate of the vaccine and are short-lasting. Vaccines are fairly affordable–$30 or less–and, in most years, are widely available.

* * * * *

Despite working in a health-care field for five-plus years, I have never had a flu shot; my employers never mandated a vaccination (as many hospitals do). I admit there was a certain degree of arrogance in that decision. In classic ultrarunner mindset, I welcomed the challenge of suffering.

But after this experience, and how the influenza virus ruined an important race, my mindset has changed. There is useful suffering and useless suffering. Just as working on your feet all day might prepare a person for a 100-mile race; clearly it is not the best way to prepare. Likewise, frying skeletal and cardiac muscle from the inside-out might ‘stress’ the system, but not in any sort of way that would benefit future performance.

Moreover, given that flu season typically peaks in January or February and can continue as late as May, it behooves each of us with winter and spring racing aspirations to be vaccinated to prevent serious repercussions on training and racing.

Recommendations for Training and Racing After the Flu

There are no precise guidelines for exercise–and namely intense training and racing–post-influenza infection. Varying medical sources indicate that gradual resumption of exercise may occur after fever has abated, and that intensity should remain low.

Anecdotal evidence from other runners indicates that after-effects from severe flu infections can impact ultramarathon performance for weeks after symptoms have abated. Recent reports of runners relapsing with symptoms after trying to run too far or too intensely are numerous.

Given the uncanny similarity of flu effects to hard racing–including severe myalgia and muscle-cell breakdown, global-tissue strain, and fatigue–perhaps a suitable guideline is to treat a severe flu infection like a hard 100-mile race: most would agree that resumption of hard running and racing should occur no sooner than two to four weeks and, for most of us, four to eight weeks.

However, given the variability of infection and the impact of fever on recovery, another guideline may be: for each day of fever, rest (or avoid hard running or racing) for four to seven days.

This means, for me, hard training and racing is not recommended for four to seven weeks. Given how my recovery has gone, this number feels accurate for me.

* * * * *

This personal experience was once again full of lessons that apply to us all. That day in Texas, after miserably shuffling into the start/finish in defeat, an important lesson was learned:

Don’t Mess With the Flu.

Call for Comments (from Meghan)

  • Have you been knocked down by a flu virus this winter? If so, what has been your experience with recovery and resumption of normal training?
  • Have you had a big race ruined by the flu? If so, what happened to you?


  • “Canadian Study Finds Flu Vaccine Working Well against H1N1.” CIDRAP. Center of Infectious Disease Research and Policy, 6 Feb. 2014. Web. 07 Feb. 2014.
  • Desdouits, Marion, et al. “Productive Infection of Human Skeletal Muscle Cells by Pandemic and Seasonal Influenza A (H1N1) Viruses.” PloS one 8.11 (2013): e79628.
  • Friman, G., et al. “Does fever or myalgia indicate reduced physical performance capacity in viral infections?.” Acta Medica Scandinavica 217.4 (1985): 353-361.
  • Friman, G. and Lars Wesslén. “Infections and exercise in high-performance athletes.” Immunology and Cell Biology 78.5 (2000): 510-522.
  • Roberts, J. A. “Viral illnesses and sports performance.” Sports Medicine 3.4 (1986): 296-303.
  • “Seasonal Influenza (Flu).” Centers for Disease Control and Prevention. Centers for Disease Control and Prevention, 31 Jan. 2014. Web. 06 Feb. 2014.
  • Smith, A. P., et al. “Effects and after-effects of the common cold and influenza on human performance.” Neuropsychobiology 21.2 (1989): 90-93.
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Joe Uhan

Joe Uhan is a physical therapist, coach, and ultrarunner in Auburn, California. He is a Minnesota native and has been a competitive runner for over 20 years. He has a Master’s Degree in Kinesiology, a Doctorate in Physical Therapy, and is a USATF Level II Certified Coach. Joe ran his first ultra at Autumn Leaves 50 Mile in October 2010, was 4th place at the 2015 USATF 100k Trail Championships (and 3rd in 2012), second at the 2014 Waldo 100k, and finished M9 at the 2012 Western States 100. Joe owns and operates Uhan Performance Physiotherapy in Eugene, Oregon, and offers online coaching and running analysis at