Warp Speed Notes on Viruses and Vaccines

18 min readFeb 13, 2021

I spent a weekend learning about viruses and vaccines in preparation for taking the covid-19 vaccine. The result is the following set of notes.

My goal was to answer a series of question, eventually leading up to “will mRNA vaccines cause unknown or long-term side effects”. My starting point was “what is a virus?” My biology knowledge is limited to an introductory class in freshman year of university where I learned the basics of the central dogma of biology (DNA → RNA → protein).

As an outsider to the field, I learned at a high level of abstraction, rarely diving into specific mechanisms, pathways, or biochemical details. I’m sure there are plenty of oversimplifications or flat-out errors in my notes. Nevertheless I feel like these notes have mostly answered the question I set out to answer.

This blogpost by no means tries to provide medical advice (if you feel inclined to take medical advice from someone with freshman biology, please check yourself). Rather, I intend it as a diving board for those who want to learn more about the potential risks of the mRNA covid vaccines. Links/sources provided at the end of each section.

What is a virus?

Smaller than a cell (about ~1/100 the size)
Can’t actually see with optical microscopes, need electron microscope
replicates only inside the living cells
Infect single cellular organisms (to plants!) to humans, which makes you wonder why there are emergent consequences like fever, sneezing because clearly these don’t exist when a single cell organism is infected
Consist of 3 parts:

single/double stranded RNA/DNA (usually RNA and usually single stranded)
Capsid (a protein) which surrounds and protects RNA
Envelope (wrapping of different lipids and proteins)

Diagram of the coronavirus — Covid-19 Virus

Envelope doesn’t exist in some viruses
It might be unclear the difference between capsid and envelope since they’re both made up of proteins, envelope usually functions to attach the virus to a host cell (source)
It’s wrong to think capsids only serve as a protective shell for the RNA, as a protein it can perform complex mechanical functions like “injecting” the RNA into the cell (see Escherichia virus T4 below)
Viruses come in 4 (capsid) topologies/3D structures + 1 “complex” category for any virus that doesn’t fit the 4 categories

Helical: topology of capsid mimics that of a DNA helix.
Icosahedral: polyhedron with 20 (triangular) faces, it’s approximately a sphere. Most common topology for animal viruses.
Prolate: basically a polyhedron stretched in one direction, approximately an ellipsoid
Enveloped: where the virus wears a (modified) membrane of the cell

Sources:

https://www.wikiwand.com/en/Virus

How do viruses infect hosts and subsequently what limits the range of hosts it can infect?

There are 6 stages to the virus infection cycle (see accompanying diagram below).

Attachment: capsid or envelope attaches to receptors on the host cell. This specificity determines the host range and type of host cell of a virus.

Entry: there are a few ways the virus gets past the surface of the host

Membrane fusion (between virus and host membranes)
Endocytosis: host engulfs/eats the virus
Injection of RNA into host. This is more common with bacterial viruses since they need to penetrate a cell wall

Uncoating: peeling capsid off RNA.

Replication: replication involves a subset of the following smaller steps: translating the RNA/DNA into mRNA, producing virus protein, replicating virus RNA/DNA.

Assembly: new proteins and new RNA/DNA are assembled into new virus units.

Release: cell bursts and dies (lysis), releasing the new viruses.

So the attachment specificity determines if infection can occur.
For reference the number of virus particles required to cause infection in humans, norovirus: 10² particles, SARS: 10² particles, MERS: 10³ particles
So ballpark 10²-10³ particles for a typical virus to infect humans
Attachment specificity also seems to determine which parts of the body a virus can infect, e.g. covid binds to ACE2 receptors which are common in the nasal tract and lungs

Sources:

How do viruses cause symptoms?

Viruses cause host cell to die
Why high-level symptoms like fevers, coughs occur is not completely understood
As a first approximation, there seems to be 3 high-level reasons

Directly from cell death disrupting tissue or organ function
Body’s immune response
Complications (higher-order effects) from cell death or immune response such as the buildup of dead cells

It’s useful to note that symptoms is a suit-case word, it may refer to different categories of phenomena
Some symptoms are strictly bad for the body (build up of dead tissue) but others like fevers can help recovery

Fever case-study (type 2)

immune response thought to help recovery. True mechanism is not known. Leading hypotheses include, heat slows down viral reproduction, heat increases metabolic rate (and hence availability of virus fighting cells?), and more general “stimulates the immune response”.

Inflammation case-study (type 2 or is it 3?)

contains 4 subsymptoms of redness, heat, swelling, and pain. Immune system tries to bring in immune cells to kill infected cells. This causes increased blood flow, constriction of capillaries that carry blood away from the infected area, and hence redness and heat. Permeability of capillaries increases, allowing cells and fluid to enter surrounding tissue. These fluids have a higher protein content than the fluids normally found in tissues, causing swelling.

Covid-19 case-study

Alveoli, where oxygen and CO2 are exchanged between lung and blood

The main mode of death for covid is respiratory illness caused by disruption of alveoli function
Alveoli are sacs in the lung where gas is exchanged with the blood stream
Pneumonia: generally refers to illness caused by a buildup of pus in the lung/alveoli. Immune system fights covid and leaves a stew of fluid and dead cells (pus) behind. Symptoms include coughing (type 2); fever (type 2); and difficult breathing (type 3).
Acute respiratory distress syndrome (ARDS): i.e. difficulty breathing is the main cause of death for covid. Autopsies show alveoli full of fluid, white blood cells, mucus, and debris from dead lung cells. X-rays and tomography scans show air can’t get into alveoli. Could be type 1 symptom because breakdown of lung tissues prevents breathing. Or type 3 symptom because the buildup of fluids/junk is preventing breathing.
Organ failure: higher-order type 3 symptoms such as kidney/liver failure. E.g. kidney failure caused by decreased blood pressure.
Generally, people who harbor high levels of viruses have more severe symptoms and are more likely to pass on the pathogens to others. This makes sense since more viruses = more cell death.
Interestingly, for the coronavirus, some people have no symptoms but similar viral load to people with symptoms

Sources

What is a vaccine?

A vaccine is a biological preparation that provides active acquired immunity to a particular infectious disease. A vaccine typically contains an agent that resembles a disease-causing microorganism and is often made from weakened or killed forms of the microbe, its toxins, or one of its surface proteins. The agent stimulates the body’s immune system to recognize the agent as a threat, destroy it, and to further recognize and destroy any of the microorganisms associated with that agent that it may encounter in the future. Vaccines can be prophylactic (to prevent or ameliorate the effects of a future infection by a natural or “wild” pathogen), or therapeutic (to fight a disease that has already occurred, such as cancer).

Reading Wikipedia’s definition, clearly vaccine is a catch-all term
The unifying principle is intake of a substance that provides immunity to a virus or antigen (aka the part that causes an adaptive immune response, typically a surface protein on the virus), and we might even claim it involves inducement of the adaptive immune defense system to produce antigen-specific antibodies

Vaccines can differ along these dimensions:

Prevent future disease vs cure current disease
The immunity-inducing “stuff”, and hence mechanism of action
Physical realization of immunity-inducing “stuff” (the term “biology preparation” is very general and may not refer to an injection)

How do vaccines defend the body against viruses?

First, how does the body naturally defend against viruses?

Innate (aka memoryless) Immune Defense

This is a catch-all category for subprocesses of the body that are constantly scanning for foreign genetics material or protein and destroying them
The unifying qualities of these processes are:

Memoryless: meaning the immune response is exactly the same the second time the same virus appears
Short (immediate?) response time
Operates by release of Cytokine proteins which “raise the alarm” and activates other immune responses to destroy virus
Detectors of foreign materials are usually a protein inside cell cytoplasm or on cellular membranes

RIG-I case-study: the RIG-I protein exists in cell cytoplasm and detects RNA with a 5′-triphosphate pattern. These patterns usually only exist in infected cells. When RIG-I binds viral RNA, a response mechanism is triggered, producing cytokines. Cytokines bind to nearby cells, alarming them to produce other proteins which have antiviral function.

When cytokines enters the bloodstream, they cause symptoms typical of many viral infections, including fever, sleepiness, lethargy, muscle pain, loss of appetite, and nausea.
Innate immune defenses are usually sufficient to eliminate small doses of pathogens at onset of infection, if virus replication continues then adaptive immune defense activated (I’m guessing it’s one of the reasons you need 10²-10³ virus particles to actually infect someone)

Adaptive (aka memory) Immune Defense

The adaptive immune defense system has 2 main mechanisms: antibodies and T cells
Antibodies work by attaching to the virus, disrupting either its attachment to host cell or function

An antibody. The Y segment is the hypervariable region.

The fork of the Y shape is called the hypervariable region, which can topologically change to have high specificity for an antigen (virus/bacteria)
The first time an antigen appears, the body needs to perform an optimization of the hypervariable region so that it binds to the antigen. This takes on the order of days and is why people are usually sick with flu symptoms for a couple of weeks
Once the hypervariable region is optimized, some short-term antibodies are released to neutralize the antigen while other antibodies/subset of B and T cells called memory cells store the information for later use. These cells survive years in the body
The second time someone is infected, memory cells allows immediate production of antibodies and viruses are destroyed before symptoms appear

X-axis: time. Y-axis: adaptive immune reseponse. The red curves show that a second infection leads to much quicker, and intense response. Blue curve doesn’t show anything interest.

Antibodies neutralize viruses in a number of ways (see accompanying diagram below)

Stop attachment to host receptors
Stop entry into hosts
Prevent uncoating of RNA in the cell
Aggregation or clumping of virus particles (which interferes with attachment?)
Signal other cells or proteins to destroy the virus, e.g. “serum complement” proteins will lyse (rupture) enveloped viruses

Left: typical viral infection cycle. Right: antibodies (grey) binding to the viral molecule and disrupting the infection cycle at various stages.

Binding is necessary but insufficient for neutralizing a virus, sometimes antibodies can bind but the virus still replicates
Bodies vary in how successfully they are able to optimize the hypervariable region against a specific virus or antigen
Some people find antibodies with high binding specificity for the virus and eliminate the virus quickly
Other people find antibodies with medium specificity and obtain partial protection. Virus replication is slowed but the virus still causes a degree of infection and symptoms
Some people find little or low specificity antibodies leading to prolonged infection with more severe symptoms. These people are likely to be re-infected in the future.
Question I have: but then how do these people get rid of the virus eventually?

The unifying principle of how vaccines work is a modified antigen or protein responsible for viral attachment to host cells is inserted into the body. The body identifies the antigen or protein, and produces antibodies to neutralize it. Then in the future, when the body is exposed to the “real” virus, it is also neutralized due to similarities in structure with antigen from the vaccine. Details of how each type of vaccine achieves this is discussed below.

Sources:

What are the different types of vaccines today?

There are experimental vaccines but the below 8 are the only ones being used today (aka FDA approved?).

Inactivated vaccines (aka non-replicating vaccines)

“Inactivated” is a really poor word choice, what we’re really trying to say is “non-replicating”
Very generally non-replicating vaccines work by partially destroying the virus with heat, chemicals, or higher-frequency radiation. We want the resultant virus to satisfy 2 criteria:

Replication is no longer possible
Capsid or proteins that allow antibodies to attach to the virus are intact (or at least close enough to the original virus for antibodies to work)

Because viruses can no longer replicate, they cannot cause cell death or symptoms
Because viruses can no longer replicate, the body will only produce antibodies for the specific version of the virus in the vaccine, it may not be immune to mutants

Attenuated vaccines (aka replicating vaccines)

“Attenuated” is a really poor word choice, what we’re (usually) talking about is “replicating” (but weakened)
The problem is replication=cell death=symptoms but replicating vaccines can work for 2 reasons

The modified virus does not replicate quickly
The modified virus does not cause symptoms/illness, i.e. not virulent (to what extent is this the same as the first point? Some ways it could differ is cell death doesn’t happen or the virus infects a different region of the body?)

If the virus satisfies one of these criteria, it is called “attenuated” which basically means it’s not as dangerous/virulent
The idea is roughly to mutate the original (virulent) virus into an attenuated virus satisfying these 2 criteria:

Modified virus is attenuated
Modified virus is similar enough to original virus such that antibodies produced for modified virus will work on original virus

There are 2 broad techniques for producing attenuated vaccines

Natural mutations or just allow the virus to replicate and mutate until an attenuated mutant arises. Success seems to be largely determined by luck: you need to mutations that are non-virulent but are also similar enough for antibodies to neutralize the original virus.
Designed mutations or construct a viral RNA/DNA that will code for an attenuated mutant

Natural mutation example: original virus population is put into a foreign host. Through natural genetic variability or induced mutation, a small percent of the viral particles should infect the new host. These strains replicate and mutate and gradually lose their replication speed or virulence in human hosts since there’s no selection pressure to replicate quickly in humans.

Influenza case-study: influenza is a virus where the RNA is stored as 8 segments. 2 of the segments control the antigen (or surface proteins for antibody attachment) while the other 6 control other things (presumably replicating rate or virulence). Flu vaccines are built by combining the 2 segments from a wildtype (original virus) and the 6 segments from an attenuated virus.

Because the virus is replicating, the virus lasts longer in the body and causes more antibodies to be created, hence longer immunity
Because the virus is replicating, it can mutate. This is both an advantage and disadvantage.
Disadvantage because it can mutate into a virulent mutant. Case-study
Advantage because mutants will also trigger antibody response and hence immunity against viral variations is achieved (preemptively protect against mutations in the “real” virus). Case-study
Because virus replication is a push-and-pull process between replication affinity of the virus and replication suppression by the immune system, the virus will replicate at different rates in different people. If the vaccine counts on the replication rate to be slow in a healthy person, replication can be too fast in immunocompromised people. Hence replicating vaccines are not recommended for those immunocompromised.

Toxoid vaccines

This is the odd one out. Instead of targeting the pathogen, toxoid vaccines target the toxins released by the pathogen. It’s only relevant when (1) the pathogen releases a toxin and (2) the toxin is the cause of illness
Radiation or chemicals are used to change the toxin into a toxoid satisfying the 2 criteria:

Triggers immune response that will also trigger on the toxin
No longer damaging to the body/cause illness

Conjugate vaccine

Seems niche and only used when antibodies cannot bind to the antigen
The idea is to bind a different antigen the body does respond to, to the original antigen and somehow the body will now respond to the original antigen

Heterologous vaccine

Works by exposing the patient to another virus (different Species) within the same Genus as the original virus
Due to antigen similarities, antibodies produced from exposure to the other virus will neutralize the original virus
If we think about it, this is basically the same principle as an attenuated virus except the mutation is great enough to deem the other virus a different species
This is especially true when you consider how arbitrarily biologists assign Species and Genus classifications to viruses (this paper is proposing a new definition of Species in 2018!): viruses are typically named and assigned to species according to their genome structure and the original host that they infect (original host that they infect? That doesn’t describe the genetics or structure at all!)
It might be useful to think of heterologous vaccines as those where we do not need to mutate the original virus into the vaccine virus, but a suitable vaccine candidate naturally exists. Hence “heterologous” is a description of how we arrive at the vaccine rather than the nature of the vaccine
E.g. cowpox is used to prevent smallpox. Cowpox is also attenuated first to prevent its undesired symptoms

Recombinant vaccine

Producing a new virus by inserting the RNA/DNA encoding the antigen (e.g. spike protein of covid) of the original virus into another (non-virulent) virus
The end result: a new virus with the 2 properties of (1) contains antigen which will trigger immune response when the “real” virus attacks and (2) is non-virulent
Recombinant vaccines are different from attenuated vaccines from natural mutations because natural mutations create viruses that are “close to the original virus in virus space” while recombinant viruses are likely “far from the original virus in virus space” since it’s a frankenstein way of constructing a new virus from 2 sources. This has implications for what mutated variants can show up in the body after taking the vaccine (assuming the vaccine is replicating).

Subunit vaccine

This broadly means the original pathogen is not introduced to the body. Only an antigen is. The antigen is sufficient to cause the body to produce antibodies.
Injecting just the antigen (usually protein) typically doesn’t work since proteins in isolation will denature/be broken down by the body
Most subunit vaccines are recombinant vaccines where the genes coding the antigen are inserted into the genomics of another virus

mRNA vaccine (aka RNA vaccine)

Here’s the story with the other vaccine types (except toxoid):

Vaccine injection→
The vaccine-virus makes it into cells of the body →
The vaccine-virus RNA causes vaccine-virus proteins to be create, includng the antigen (i.e. surface protein) →
Body’s adaptive immune system responds to vaccine-virus proteins and the body achieves immunity against future real-virus attacks

mRNA vaccine consists of mRNA segments enclosed in a lipid nanoparticle. The nanoparticle consists of different parts that support and stabilize structure, helps release of mRNA into host cell cytoplasm, and increase the half-life of the particle.

Here’s how mRNA vaccines differ in each step.

(1) First of all it’s not a virus we’re injecting into the body, but rather a mRNA enclosed by a lipid nanoparticle (protective shell). What’s the difference? mRNA is not a stable medium for storing genetic material unlike RNA and DNA. Furthermore, the mRNA does not encode enough information for the system to replicate, a defining characteristic of viruses.
(2) mRNA vaccines target specific cells called dendritic cells (DCs) that are responsible for surveying the body for antigens and presenting them to the adaptive immune system.
(3) Usually RNA creates mRNA creates protein — mRNA vaccines deliver the mRNA directly, skipping the transcription step from RNA to mRNA.
(4) The antigen (spike protein) is presented to the adapative immune system at the surface of the DCs

In some ways, mRNA vaccines are “more synthetic” than the other types of vaccines which at the end of the day inject a virus which can plausible occur in nature into your body. Each component of the mRNA vaccine is engineered purely to achieve its end of goal providing the host immunity — there are no extra parts.

Furthermore, it’s not surprising why mRNA vaccines are developed so much quicker than other vaccines, such as attenuated vaccines. It’s non-trivial to attenuate a virus to satsify these 2 criteria: (1) Triggers immune response that will also trigger on the toxin and (2) No longer damaging to the body/cause illness. You’d have to wait around for a desired mutation to happen or find just the right treatment to attenuate the viruses. Swapping the mRNA segment in the mRNA vaccine is comparatively trivial.

Advantages

Since mRNA vaccines are non-replicating, you can’t get infected (hence not a danger to immunocompromised people for this particular reason, but maybe for other reasons)
For a subunit recombinant vaccine for example, the body may become resistant to the carrier-cell rather than the subunit protein itself. Then you can’t use the same carrier-cell to deliver another vaccine. For mRNA vaccines, it will always work. Just swap the mRNA.

To conclude, some of these 8 “classes” should actually be thought of as characteristics. For example, the AstraZeneca covid vaccine is a non-replicating, subunit, recombinant vaccine.

Sources

Potential side-effects of mRNA vaccines?

clinical trials have observed 10³- 10⁴ participants over months
no sigificant side-effects have been observed
unknown side-effects can be hidden due to the small participant size or short time-scale of the trials
side-effects hidden because of small participant size are necessarily rare side-effects (logically speaking)

Guillain-Barré Syndrome case-study: GBS is an autoimmune disorder. Vaccines are suspected to cause GBS with probability 1/10⁵ (1 out of 100,000 people who take certain vaccines).

when people think of long-term side-effects, they usually think of DNA modification which the research community seems to readily dismiss
here’s a blogpost discussing this

Further evidence: this Nature review paper makes the claim “First, safety: as mRNA is a non-infectious, non-integrating platform, there is non-infectious, non-integrating platform, there is no potential risk of infection or insertional mutagenesis”.

It doesn’t even bother to cite this statement!
If this is indicative of the research community’s general sentiment about mRNA vaccine side-effects then it indicates they are really not worried.
non-integrating means the mRNA won’t be integrated into host cell’s DNA
insertional mutagenesis means to cause base pairs to be inserted into host cell’s DNA

Some general reasons to believe mRNA vaccines don’t have long-term side effects:

mRNA is destroyed naturally by the body and we can engineer the halflife of it
mRNA is also created in other types of vaccines, e.g. subunit recombinant vaccines because RNA needs to transcribe into mRNA before protein is produced

But wait, mRNA vaccines are “more synthetic” than the other types of vaccines? In some way yes, scientists have had to optimize the mRNA and lipid nanoparticle to get the vaccine to work. Specifically, they had to overcome these 3 challenges:

Reduce body’s natural immune response to mRNA (human body destroys mRNA too quickly, or worse a strong immune response to the mRNA can threaten the human)
Make mRNA last longer in the body or signifciant immune response will not occur
Make mRNA translate into more protein, too little antigen and significant immune response will not occur

To achieve these ends, researchers had to:

Replacing rare codons in the mRNA with synonymous codons that increase protein production from mRNA.

There are 20 types of amino acids (building blocks) that make up proteins. 3 DNA bases (codon) code for an amino acid. There are 4³=64 possible DNA triplets. Hence 44 codons are redundant. I.e. there’s a many-to-one relationship between DNA triplets and amino acids. “Synonymous”, meaning coding for the same amino acid, codons could differ in effectiveness at producing protein. Scientists scanned through the mRNA sequence and figure out where they could replace synonymous codons to maximize protein production.

2. Swap out the U base in the mRNA for “naturally occurring chemically modified nucleosides”.

A, U, G, C are the 4 bases typically found in mRNA. It turns out if you replace the U bases with the Ψ base (formally known as pseudouridine and 1-methylpseudouridine), you can prevent activation of innate immune sensors that would destroy the mRNA before it can cause an immune response. Ψ also functions the same as U during protein translation.

3. Enrichment of G:C content in the mRNA.

I.e. increase the percentage of G and C base pairs versus A and Ψ, literally this

but with Ψ instead of T because we’re talking about a modified mRNA, not DNA. This enrichment has been shown to increase steady-state mRNA levels and protein production.

4. Don’t forget the lipid nanoparticle is also highly engineered to optimally deliver the mRNA to the GCs

These modification led to the above Nature review paper to point out these potential side effects:

Persistence of expressed immunogen
Stimulation of auto-reactive antibodies
Toxic effects of any non-native nucleotides and delivery system components. I.e. we don’t know how the body will get rid of the Ψ bases and junk from the lipid nanoparticles.
Presence of extracellular RNA during mRNA vaccination may contribute to oedema (swelling) and thrombus (a type of blood clotting). I.e. with other vaccines mRNA doesn’t usually end up outside of cells. With the mRNA vaccine, it might. Perhaps in the blood where immune reactions cause thrombus and oedema.

The nature paper was published in 2018 and we may now understand the risks of these side effects much better.

Sources

Warp Speed Notes on Viruses and Vaccines

What is a virus?

How do viruses infect hosts and subsequently what limits the range of hosts it can infect?

How do viruses cause symptoms?

What is a vaccine?

How do vaccines defend the body against viruses?

What are the different types of vaccines today?

Potential side-effects of mRNA vaccines?

Written by Kevin Shen