Viruses, the immune system, and coronavirus

Viruses are small packets of proteins and genetic material.  They have no metabolism on their own, but have proteins on their surface that can bind to one or more proteins on the surface of the host’s cells.  This binding of viral protein to host protein can act like an ‘all access pass’, triggering the host cell to pull the virus into itself.  Once inside, the viral packet comes apart, releasing a small set of viral proteins into the host cell that begin to co-opt host cell machinery to copy the viral genome in order to make viral proteins and more copies of the virus’s genetic material. 

In essence, the virus is simply a set of instructions that force host cells to make more viruses (or more sets of instructions).  Because viruses have almost no machinery of their own, and rely almost entirely on the machinery of their host, they are very hard to target with drug treatments.  When your cells are infected with a virus, the virus is using your own cells, and their machinery, to make more of itself. Any drug that blocks the production of new virus will likely also block your own cells’ ability to make their own proteins, and copy their own genetic material. 

Viruses do have a few weak spots, features of their infection process that are virus-specific.  For example, viruses use their own virus-specific proteins to attach to target cells.  If the virus can’t make those attachment proteins, or if they are blocked by something (a drug, for example), the virus can’t attach to a cell, blocking infection before it starts.  In fact, your own immune system protects against viral infections by making ‘neutralizing’ antibodies that block virus surface proteins, preventing them from attaching and initiating an infection.  Once in a cell, viruses must go through a complex set of challenges in order to ‘recruit’ cell machinery to make new viruses.  To overcome these challenges, viruses bring in a small set of their own proteins to infiltrate the host cell system.  Because these proteins are viral in origin, it is possible to develop drugs that interfere specifically with them, leaving host cell machinery (hopefully) untouched. 

Antivirals are a very different set of drugs than antibiotics.  Antibiotics target the cellular machinery of bacteria.  Because bacteria are living organisms, they have their own cellular machinery which is fairly different from the machinery in our own cells.  That machinery provides many possible targets for the development of drugs that interfere with bacterial growth and survival while leaving our own cells (hopefully) untouched.  Unsurprisingly, we have many more antibiotic drugs than antivirals.  In addition, those antibiotics are often effective against wide ranges of bacteria, while antivirals tend to be useful only for specific, or closely related, viruses.  I must add that antibiotics have no affect at all on viruses, due to the fact that they target bacterial cell machinery, which human viruses do not ever make use of (… since viruses use host cell machinery, and humans are not bacteria…)

Ultimately the best way to fight a virus is not with a prescription, but rather to rely on what our own bodies have been doing for thousands of years… mounting an immune response to the infection.  Humans and most other vertebrates have a two-part immune system.  Our ‘front line’ defense can recognize and guard against general types of problems (Bacteria! Fungus! Virus!).  This ‘innate’ immune response is something that we are born with, and generally speaking, all humans have roughly the same ability to recognize and remove pathogens with this response.  However, pathogens have strategies for evading this front line response, ways of being ‘less visible’ to our innate immune cells.

If a pathogen isn’t cleared by our innate immune response, our second line of defense is to develop a specific response directly to that pathogen.  This targeted, or ‘acquired’, immune response produces both cells (T-cells) and proteins (antibodies) that bind that sneaky pathogen in ways that it can’t avoid.  We are not born with the ability to recognize these new pathogens, rather we have to develop and ‘teach’ our immune cells to recognize them once they’ve made themselves known.  Unlike the innate immune response, we are all quite different in how our acquired immune responses tackle a particular pathogen. Each person’s acquired immune response is unique, a ‘one of a kind’ way of finding and removing a problem.  While some people may mount a very vigorous response to one virus (COVID-19, for example), others may find it more challenging to tackle.

Unfortunately, for all of us, it takes time to learn… The very first time our immune system responds to a new pathogen (a ‘primary response’), it is slow to get going.  It takes a full week to ten days for us to generate our ‘seek and destroy’ T-cells and antibodies, and in that time the virus has almost free-rein over our bodies, infecting cells, copying itself, infecting more cells, copying itself, etc.  The amount of virus in our blood and tissues increases to high levels in that first week, leaving our immune cells to play catch up once they are fully functional.  So the next time a doctor says “if you aren’t feeling better in a week to ten days, call me”, they are telling you to wait and let your immune system handle the problem, because when it comes to viruses, your immune system is your best bet for clearing the infection.

Once our bodies have learned to recognize a pathogen, however, we have got it covered.  Our acquired immune response can remember a pathogen it has seen before, and if that pathogen gets past the innate immune response a second (or third) time, our ‘seek and destroy’ T-cells and antibodies are right there to take care of it.  These subsequent immune responses to a pathogen, or ‘secondary’ responses, are generally so fast that we don’t ever fully get sick… we may feel a bit ‘off’ for a day or two, but then we wake up feeling perfectly fine.  This is what vaccinations are all about – we inject a small amount of some part of a virus into our tissues to allow our acquired immune system to ‘see’ and ‘learn’ the virus from its pieces.  If we are then infected with that virus we can skip directly to a secondary immune response. Hooray for acquired immunity and immune memory! 

But there is a downside to our immune response to viruses.  In order to clear our bodies of a viral infection, our immune system must find, and destroy, infected cells.  Yes, our immune response to viruses damages our own cells and tissues.  This collateral damage, as it were, is usually low enough that it does not affect the overall functioning of our bodies, and the destroyed cells are quickly replaced.  If a primary immune response isn’t working as well or as fast as it perhaps should, it is possible that, in the free-for-all first seven or so days it took for our acquired immunity to gear up, the virus has managed to copy itself to very high levels.  This puts our immune system at a greater disadvantage, having to clear even more viral particles than if it had gotten started a bit sooner (rather like waiting a day or two longer to impose social distancing and quarantines, rather than enforcing strict policies earlier).  Added to this, a slower, less efficient immune system will likely also struggle to clear any virus that is present.  This slower, more sluggish response will extend the overall time needed for the immune system to clear the virus… all the while causing damage to our own cells and tissues. 

An immune response is a deadly balance – too little immune response and the virus overruns the system, too much immune response and the body becomes too damaged to recover. Younger people tend to have faster, more decisive, immune responses (if you are interested, I can write another blog post about why that is).  Running a strong immune system is expensive.  Even in younger people, underlying health problems can impact immune function, as can general ill health due to poor diet or chronic stress.  And on top of all that, remember that each of us mounts our own unique response to a virus… some of which are great, some of which are not so good.   In our current coronavirus outbreak, none of us have an immune memory of this pathogen; we are all seeing it for the first time.  Our immune systems will mount a primary response, and that will take seven to ten days to clear the virus.  Some of us will struggle to clear the virus and will start to build up damage in the tissues the virus infects, namely the lungs.  If our immune systems can’t tackle this virus fairly efficiently, this damage will lead to fluid build up (pneumonia) and reduced blood oxygen levels.  Sustained decreases in blood oxygen levels causes damage to organs that require high lives of oxygen (kidneys, liver).   Age and overall health play a role in whether we are at risk for this particular scenario, but even some younger people will run into trouble because their immune systems weren’t great at managing this particular virus.

What can we do to make sure our outcomes are as good as possible?  Get your immune system in fighting order!  Make sure you get your eight hours of sleep each night.  Keep a regular schedule.  Get outside and get some sun and exercise.  Eat well, take your vitamins, and find ways to enjoy your time and reduce your stress level.  Try to reduce your chances of being exposed to the virus.  If you catch a virus from just a few viral particles rather than many, it has a slower growth curve, giving your body more time to recognize it and remove it.   And remember, we have immune systems that were built for this.  You may feel bad for a while, but most likely you will bounce back just fine.  If not, we have hospital systems that were built for this!  If you are having shortness of breath or excessive weakness, make sure you reach out and get help.  This is going to be a long few months, but it will pass once we all have our acquired immunity to this particular virus, through exposure or through vaccination.

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