Your immunesystem, pathogens and vaccines (more or less).

It's going rampant on the internet right now, people not knowing how our immune system works and often dismissing the workings of vaccines due to their lack of understanding.
It causes people to think that vaccines are toxins (which they technically speaking are to a certain extend) and/or that our natural immune system can fend it off just fine on its own (which is sorta true as well).
However, there is far more to it and there are reasons why we vaccinate and why they are so helpful in fending off diseases.
In this post, I'll be going over some basics on how the immune system works when it encounters a pathogen (bacteria, fungi and viruses primarily), how we build up resistances to them and what role(s) vaccines play into this.
Please do note that this post only goes over most of the basics and as such is a pretty gross oversimplification.
Our immune system is really complex and there are still things about it that we do not fully understand yet so this post is not written to be the "end-all-be-all" but to hopefully giving you the understanding on why I'm pro-vaccine and why you should be as well.
I also want to point out that while I have done my fair share of research onto the subject, I'm not an expert, nor am I claiming that I am.
I'm just an independent blogger that wants to make this world a better place with a keen interest in science.
If you are an actual expert on this and found an error in my explanation then please feel free to contact me so we can get it sorted out.

How pathogens reproduce


Pathogens are like every other animal (humans included) or plant, we want our species to survive and thrive and to do this, we need to reproduce.
Like animals and plants, pathogens have their own way of reproducing.
A lot of plants use pollen and stigmas to reproduce (with the help of insects), a lot of animals get their gigs on intimately, while a lot of shellfish (like oysters) just unceremonially yeet their goodies into the water hoping it'll end up somewhere nice.
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Just in case you need a mental image of an oyster orgy... you're welcome!

It is important to understand how certain pathogens reproduce asexually in general terms before we can continue.
Please note that this is quite incomplete as bacteria and fungi can also reproduce "sexually", however, this is of little to no relevance for this post.

Bacteria reproduce by literally splitting themselves in half in a process referred to as "binary fission".
While fungi reproduce by creating spores which then spread (eg. by getting carried by the wind) and settle elsewhere.

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A crude diagram of 'binary fission'


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Fungal asexual reproduction using spores

The reproduction of viruses, however, is a bit more complicated.
Unlike bacteria and fungi which only need a source of nutrients to reproduce, a virus needs a host that can do the heavy lifting for them.
This host can be a bacteria (these viruses are known as "bacteriophages") or a cell of a plant or animal.
The process between a bacteriophage and one that targets plants or animals is roughly the same.
1. Enter the host cell.
2. Release own genetic material into the cell.
3. Genetic material of virus "merges" with that of the host cell.
4. Host cell becomes "reprogrammed".
5. Host cell creates replicas of virus (instead of fulfilling its original duty).
6. Host cell releases new viruses (sometimes leaving the cell alive to continue creating new viruses, sometimes killing the host cell).

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Lifecycle of an Influenza virus

Now that we understand the basics of how pathogens reproduce, we can start learning about our own defences against pathogens.

The first line of defence


The first line of defence is your so-called "Innate Defence System", also referred to as your "Non-specific Defence System".
This line of defence is split up into two groups: "External defences" and "Internal defences".

Your external defences are what the name may suggest, external.
They consist of things like our skin acting as a physical wall between the outside world and our bodies internals and our mucous membranes meant to trap anything trying to get in and dispose of it accordingly (eg. by sending it to our stomachs instead of our lungs).
Think of them like a wall at the border and the checkpoints to cross this border.

Our external defences, however, are not perfect.
Our skin can get wounded (like a hole in the wall) and our mucous membranes can't catch everything (like smugglers bypassing the checkpoint).
This is where our internal defences come in, consisting of antimicrobial proteins and some types of white blood cells (macrophages" and"neutrophils").
They patrol our body constantly and when they see anything out of the ordinary, they attack it ruthlessly...

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Totally accurate representation of a Neutrophil attacking a pathogen



Most of the time, this suffices, however, sometimes neutrophils and macrophages can't handle it on their own so we need something better...

The second line of defence


If a pathogen managed to get through our Innate Defence System, we would have normally been in trouble...
Luckily, we have our "Adaptive Defence System", also referred to as your "Specific Defense System".

Let's assume a hypothetical virus called "Covert-20" has breached our first line of defence is now going around to wreak havoc.
The Macrophages at this point have called in private investigators called "Dendritic Cells"!
They go around and collect samples of Covert-20 then travel all the way to the closest lymph nodes where the so-called "Virgin Helper T-Cells" are waiting.
The Helper T-cell will accept the sample carried by the dendritic cell and the Helper T-cell will rapidly multiply.
But something interesting happens as well, something very important, not all Helper T-cells will go to the battlefield, some stay around as "Memory T-Cells" and some go deeper into the lymph node where a spicy weapon is located: the "Virgin B-Cells".
Once a Helper T-Cell meets a Virgin B-Cell, they'll communicate.
The Helper T-Cell tells the Virgin B-Cell that it needs to start replicating and produce antibodies.

This process takes a hefty toll on the B-Cells and they will quickly die off from exhaustion, however, good ol' Helper T-Cell got our back.
They'll tell the B-Cell to keep going on.
You can do it B-Cell, I believe in you!
This causes the B-Cell to keep going on for just a bit longer until it finally really dies.

Back at the site of infection, a fierce battle is still going on.
Macrophages are dying but the Helper T-Cells that arrived here also tell the Macrophages to keep ongoing.
You can do it Macrophage, we need you, I believe in you!
At some point, the cavalry will arrive, countless of anti-bodies will flood the battlefield and start incapacitating the virus so that the Macrophages and Neutrophils can easily wipe them up, basically marking them for DEATH.

In the aftermath, the Macrophages and Neutrophils will die off as they are no longer needed.
Often, the "dead bodies" can be found as puss (like with a zit!).
The Memory T-Cells and Memory B-Cells will remain for when they encounter the invader again.

While this was all going on...


Our immune system isn't perfect at holding up intruders and sometimes, some slip by our detection.
But fear not, while the Macrophages and Neutrophils were having fun at the primary infection site, something else was going on elsewhere in the body.
"Natural Killer Cells" have been patrolling the body and checking up on cells that got infected by the virus (or is otherwise "sick").
Were they to find such a cell, they'd tell it to die, which most of the time happens just fine (if the cell isn't cancerous).

Additionally, the body is likely to raise the body temperature, causing a fever.
This causes vasodilation (the expansion of the blood vessels) and increase metabolism of the cells, which benefits in the recovery process as well as aid in the transport of more anti-bodies and white bloodcells to the battlefield.

Telling friend from foe


You may now have gotten the question "how does our immune system tell friend from foe?" and that's an absolutely brilliant question.
This is done by means of "antigens", small bits on the surface of each cell to identify it.
If a white blood cell encounters a cell, it'll check whether the antigens presented by the cell are known to be "friendly", if so, it'll leave the cell be.
If not, our immune response takes place.

This is also why we must match blood types when donating blood as donating the wrong type of blood (with the wrong antigens) can cause a serious immune response, often leading to death.

How do vaccines work?


So now you may wonder where vaccines come into the picture, and you'd be forgiven.
Vaccines work by injecting a mixture (see "What goes into vaccines?" below) into the body.
This vaccine contains weakened or dead pathogens as well as some adjuvants to increase the immune response a tiny bit.
They use a weakened or dead pathogen as opposed to "the real deal" to create a safe and controlled way for your body to fight the virus without being in a real against-the-clock race.
They are sort of like learning the basics of driving a car (giving gas, braking, shifting and turning) on a calm parking lot vs going on the open-road immediately.
A lot of people may say that going on the open-road immediately (or "fighting the virus head-on" in this case) is fine but I think it'd be agreeable to drive safely first and get the basics down before we do such things right?

Furthermore, the bodies response will be just like when we fight the pathogen head-on (as discussed in "The second line of defence").
- find the virus
- learn about it
- fight it off
- remember how we fought it off

Vaccines are designed to teach our body how to fight off the pathogen without exposing ourselves to the danger of the real thing (since it's too weak - or outright dead - to do anything).

This is also why we need to constantly develop new vaccines.
Pathogens naturally mutate (some do it really quick, some really slow) and with each mutation, the required antigen needed for a pathogen may change.

What goes into vaccines?


A vaccine commonly consists of 3 core components (the exact composition may vary):
- weakened or dead pathogens
- adjuvants
- carrier fluid

People (especially anti-vaxxers) say vaccines contain toxins and this is actually true (as seen in the list below) but before you think "SEE, THEY JUST WANT US DEAD!", I want you to hear me out.
These toxins are there for a very specific reason: they stimulate the immune response.
Remember, when your immune system encounters something foreign, it'll become more alert and start investigating, this is exactly why we add these toxins.
In some cases, they are used to decrease the risk of infections from the injection themselves or to preserve the vaccine longer.
They, however, are in such low amounts that they won't cause any harm outside maybe making vaccines too reactogenic which can lead to minor symptoms like a fever or some soreness but unless you have an allergic reaction, no life-threatening of lasting effects will be caused by these adjuvants.

Common adjuvants include but are not limited to:
- Aluminium Hydroxide
- Aluminium Phosphate
- Paraffin oil
- Thimerosal/Ethylmercury (not to be confused with the dangerous Methylmercury)
- Formaldehyde
- Gelatin
- Monosodium Glutamate
- Antibiotics (to lower the risk of a bacterial infection)

Now you may start yelling about the Ethylmercury ("C2H5Hg+") and Formaldehyde that they put into the vaccines, again, I want you to hear me out.
Ethylmercury is not to be confused with the much more dangerous Methylmercury ("C3Hg+")  and metal mercury ("Hg").
Ethylmercury and Formaldehyde are used for the same reason: they are used as a preservative to prevent contamination by bacteria or fungi.
The highest amount of Formaldehyde present in a vaccine is .02mg per dose, an infant aged 2 months would have around 1.1mg already floating in its body naturally with higher amounts for older children.
Ethylmercury, on the other hand, has been nearly phased-out since 1999, only very few vaccines (none of which are given to infants and children) contain this substance at the time of writing this post.
Additionally, Ethylmercury-free alternatives are often available for the vaccines that do still contain it.

So fortunately for us, there is no real issue with vaccines.
They are rigorously tested to make sure they are safe and you are often screened to make sure that the chances of you getting an adverse reaction are slim to none.

Herd Immunity


You may have heard of the term "herd immunity" before but may not have understood this properly.
In the context of diseases and vaccines, it refers to the principle in were a bigger group (the "herd") helps fending off a disease for those unable to.
A vaccination not only helps you fending of a pathogen on your own, it also protects those around you.

Let's assume 3 people:
- Alice (A colleague of yours)
- Bob (A good friend of yours)
- You

Alice is currently infected with our hypothetical virus Covert-20, however, she is asymptomatic, meaning that while she carries the virus and is able to spread it, she doesn't show any symptoms and as such, is unlikely to be aware that she is infected.
Bob suffers an autoimmune disease and unfortunately is unable to get vaccinated and unlikely to survive an infection with Covert-20.

Now Let's assume two hypothetical scenarios:
- One in which you are not vaccinated and never encountered the virus.
- One in which you are vaccinated or have encountered the virus.

Let's start with the scenario in which you are not vaccinated and never encountered the virus.
You and Alice are colleagues at work and often interact with one and another, getting drinks for one and another, vaping outside during breaks and passing along documents to one and another.
Unknowingly, you accidentally get infected with the virus as well.
As we've already learned, it can take days until the virus is fought off because you have not encountered it yet.
During this time, you are able to spread the virus along after it got the chance to reproduce.
The next day, you visit your friend Bob.
You do whatever friends do, play some cards, watch Snooker on TV and just have a fun time.
Sadly, you were infected and there is a good chance that you unknowingly passed on the virus to Bob.
Bob can't fend off the virus on his own, gets very sick and ends up on the intensive care of of the hospital.
Bob's life is now in danger.

Now the scenario in which you are vaccinated or have encountered the virus.
Again, you and Alice do your work stuff, Alice passes on the virus to you.
Unlike the previous scenario, your body already knows to recognize the virus and is able to ramp up production of antibodies quickly before the virus has any real chance to reproduce.
The next day, you visit your friend Bob.
Again, you do what friends do, play some cards, watch Snooker on TV and have a fun time.
Luckily, your body was able to fend of the virus and you didn't pass it on to Bob.
Bob doesn't need to fend off the virus on his own because your body already did it for him.

This is the power of vaccines and is the reason why I always say: "Don't vaccinate for yourself. Vaccinate for those around you".
Herd immunity isn't 100%, however, it drastically lowers the chance that you accidentally pass on the virus to those less fortunate.
We healthy people can fend it off for those less capable of doing so.

HIV: A Vaccination edge-case


Now that you know quite a bit about your immune system and vaccines, you may be wondering "Why don't we have a vaccine for HIV yet?" and this is a valid question and while I'd love to see a working HIV-vaccine in my lifetime (I'm only 22 at this moment, so hey, who knows?), the answer at this moment is: "because it's extremely difficult to do so effectively".

We've already learned that in order to fight off a pathogen (in this case, a virus), we need to have the right antibodies that match with the antigens on a specific pathogen.
The problem with HIV (and HIV-1 is particularly good at this) mutates VERY rapidly.
This means that by the time your body has learned to fight an HIV-virus with the antigens AAA, it may have already had the chance to mutate to carry the antigens AAB instead, making our previous "effort" useless.
And, of course, by the time we can fight off the AAB-variant, it may have already mutated in ABA.
Due to this, it's extremely difficult to make a vaccine that can safely teach our body how to fight the virus because the chances are extremely high that if we contract it, it is not the same antigen we have vaccinated for.

Additionally, unlike most viruses that infects our "regular" bodycells (like those found in our muscles and liver for example), HIV instead infects our immune cells.
This means that we exponentially lose immune cells that could have fought off the virus (once it has reached a certain threshold, it is called "AIDS").
Most people that die from AIDS, don't die from the disease directly, they, instead, often die from secondary infections and their symptoms, eventually killing the person.
This is why most of the HIV medication tries to focus on different aspects to stop a person from developing AIDS:
- Entry Inhibitors: Prevent the virus from entering our immunecells.
- (Non)-Nucleotide Reverse-Transcriptase Inhibitors ("(N)NRTI"): Prevent the RNA of the virus from being "transformed" into DNA.
- Integrase Inhibitors: Prevent the viral DNA ("transformed" out of the virus' RNA) from integrating in our infected cell's DNA.
- Protease Inhibitors: Prevent a specific type of protease (a type of enzyme) from being produced, making cells unable to produce new viruses.

Some people have a natural "defense" against HIV that prevents them from developing AIDS (or severely slows down the development of).
This is often due to the immune cells of the person lacking the required receptors for the HIV virus to attach to it and infect it, however, more research has to be done on this subject.
However, people taking either the medication or having a natural defense against HIV are still capable of spreading it as HIV would normally spread (eg. sexual intercourse or blood) and will be very unlikely to ever get rid of the virus; They may just never develop AIDS.

Please be mindful of whom you get your gig on tonight and take neccessary precautions (like wearing a condom).

Final words


With all this information, I hope you now understand (or broadened your understanding of) how your immune system works in the global scheme of things.
I probably skipped over some information but a lot of it would go way, way too deep for this blog post.
If you still have any questions left, feel free to contact me about it and I will see if I need to update this post to address these questions.
But for now, this is it :)

I hope you enjoyed it, stay safe, vaccinate and see you in the next pandemic!

Updates


Below you can find a list of updates that I have done to add information or to correct misinformation.
- 14 November 2020 @ 2318: Added section "HIV: A Vaccination edge-case". (Previous revision)
- 12 November 2020 @ 2058: Added section "Herd Immunity" (thanks to a discussion on Facebook). (Previous revision)

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