Thursday, January 2, 2020

Disease Post: Influenza

I had a few days off around the holidays and I was going to finish this and post it. But I didn't plan on not having access to internet for about six days. Insert facepalm here. So I apologize since I swore I would have this posted in December and ended up not being able to finish and post it until January. It is still relevant though, so I hope you can forgive me.

It's the right time of the year for this post--flu season!

There are a ton of misconceptions about the flu and the flu shot (influenza vaccination). So I will try to clear a bit of that up.


Influenza (or the "flu") is caused by a virus from the Orthomyxoviridae family. It is an RNA virus but the RNA is segmented into smaller pieces. This is an important feature that we will discuss in a bit.

There are four types of flu virus: A, B, C, and D. C and D cause little to no disease in humans. While humans can get C and D, they are more common in different animals and are usually very mild if a human catches it. A and B are more important for people so we will focus on those.

Influenza B has no subtypes. According to the WHO, there are different lineages and they are traced that way.

Influenza A is the type you will hear the most about. The WHO states, "Only influenza type A viruses are known to have caused pandemics." There are subtypes of this virus determined by proteins on the virus capsid. There are two main glycoproteins: hemagglutinin (or HA) and neuraminidase (NA). Each of these proteins has different forms and each is coded for on a different segment of RNA. There are 18 known HA subtypes and 11 known NA subtypes. And they can be combined in just about any way. This is how they are labeled, and you’ve probably seen or heard the short hand, like H1N1. Those are the HA and NA subtypes. As you can imagine, this allows for all sorts of recombinations and helps explain why the flu changes so much.

Basically, if two flu viruses infect the same host, they can recombine their genomes to create a new flu strain. This is aided by the fact that the genome is in smaller segments. Or if major mutations occur, the HA or NA can change completely. This reassortment or mutation of genes is called “antigenic shift.”

The following image is one taken from a book I have, sorry for the poorer quality. But this shows how recombination can occur with influenza A viruses.
Image from Medical Microbiology 6th Edition by Patrick R. Murray, Ken S. Rosenthal, and Michael A. Pfaller

To make things worse, the influenza A viruses are not very genetically stable and their genomes can go through smaller mutations very easily. This is called “antigenic drift.” Even small changes can alter the HA or NA enough for someone's immune system to not recognize it.

These things mean that even if you are only talking about H3N1, H3 is the variation of HA antigen and there are even different variations of H3. The flu viruses are always changing and that makes it very difficult to keep up with them. It is also why the vaccines have to be updated constantly.

An influenza type A virion. Image from the CDC.

How is it spread?

Influenza is a respiratory disease, though the "flu" has often been incorrectly used by people for other respiratory and stomach diseases, like the "stomach flu." Since it is a respiratory disease, it makes sense that it is spread in the air and infects the nose, throat, and/or lungs. When someone is sick with the flu, they cough or sneeze or speak and droplets that contain the virus are released into the air and another person inhaling the infected droplets can then get the flu.

It is also recommending that anyone who is sick should wash their hands frequently. If they sneeze or cough into their hands, flu can spread that way, too.

The CDC says that people are most contagious in the first three or four days of the illness, but estimate that they can be contagious from one day before symptoms appear and can remain contagious from five to seven days after becoming sick. The CDC also states that, "Some people, especially young children and people with weakened immune systems, might be able to infect others for an even longer time."


In general, the flu does not have a very long incubation time, meaning that people will start to feel sick pretty quickly after getting it. According to the CDC, the incubation period is about one to four days, with two days being the average.

Symptoms include a fever (but not everyone presents with a fever), chills, cough, sore throat, body aches, congestion, fatigue, and headaches. Rarely, flu can cause vomiting and/or diarrhea, but mostly in children, according to the CDC.

Story time: I got the flu, the actual flu, when I was a senior in high school. I felt a little off for a couple of days, then one day I had a mild fever, and then it hit me like a truck. My fever increased. I couldn't lift my arms to take my hair down. I couldn't stand long enough to shower for a week and when I was getting better, my mom had to put a chair in the shower so I could sit down. I lost my voice and my throat hurt so badly that I couldn't eat and could barely drink. I was completely miserable. It took a good week to start feeling better and another week to get back to my normal energy levels. This is pretty typical of the flu. And I was a young, healthy person. Just think how much worse it would be to be too young or old to have a good immune system. Or to be immunocompromised. That is why these people are usually the most at-risk. A huge part of flu shots is to help protect those at-risk people.

The flu may not sound very serious, but people die from the flu every year. Mostly the people who die are in the at-risk groups. But some flu strains kill people with healthy immune systems, like in the flu pandemic of 1918. Then it was usually the healthy people dying. The flu is no joke.

Prevention and Treatment:

Every year a new flu shot is developed and it is recommended that everyone six months or older should get it, unless you have a medical condition that does not allow you to get the vaccine (ie: if you are immunocompromised or you have an egg allergy).

It is new every year because of how much the flu viruses mutate. We don't often see the exact same flu viruses, espcially with influenza A. The WHO and others spend all year monitoring the flu all over the world. They track which strains are present, where, and for how long. They predict where and how far the strains will spread and they develop the vaccines based on that data. Which means that, yes, sometimes the viruses included in the vaccine are not the ones that people will encounter. But most of the time, that is not the case. The flu vaccine in the US usually covers four different flu strains. It used to be three until recently and there have been the odd year where the number will be different.

The flu shot is the best way to prevent the flu.

There is not a cure for the flu. Generally, care focuses on trying to relieve the symptoms and on hydration until your body can fight it off.

According to the WHO, there are neuraminidase inhibitos (like oseltamivir) available that help, but that many strains resistant to some other antiviral treatments.

And I want to talk briefly about the myths of the flu vaccine.
  • You CANNOT get the flu from the flu shot. The flu shot contains inactivated virus, they cannot cause an infection. Some people may feel a little feverish for a day after a flu shot. This is not the flu. This is your immune system reacting to the vaccine. It is actually a good thing, it means that your body is creating a strong immune reaction and studies generally show that a robust immune response gives you better protective immunity in the future. (Side note, this is why many vaccines use adjuvants. An adjuvant is something added to a vaccine like a protein that causes your body to give a better response. When you body responds to the adjuvant, it will respond to the vaccine better, too. It's like a way of making your immune system pay more attention to what is in the vaccine.)
  • You can still catch the flu if it is not one of the strains in the vaccine.
  • A bad cold is not the same as the flu.
  • Vaccines do not cause autism.
I hope that about covers it. Please reach out if you have questions! Thanks!

Medical Microbiology 6th Edition by Patrick R. Murray, Ken S. Rosenthal, and Michael A. Pfaller
World Health Organization (WHO): Influenza
Centers for Disease Control (CDC): Influenza 
The Great Influenza by John M. Barry

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