Monday, October 8, 2018


Ozone is a duplicitous character. We hear that it is bad for us (as a component of air pollution) and we hear it is good for us (as an atmospheric layer that protects us from harmful solar UV radiation). Which one is it? Where does it come from? How does it work? In this article I hope I can dispel some ozone mystery. The journey will take us through complex and interesting terrain: atmospheric chemistry, biochemistry and free radical chemistry.

The word ozone comes from a Greek word meaning "to smell," so named because this clear pale blue gas has a peculiar odour. You may have smelled ozone while operating a poorly working (sparky) appliance or you might have noticed it as that unique fresh scent right after a thunderstorm. I find it a bit sharp on the nose and weirdly pleasant.

Ozone is produced on Earth in three ways. First, when air is subjected to an electric spark such as lightning, ozone is created.  Second, ozone is produced as a byproduct of fuel combustion - from car engines, forest fires and industry. If ozone is present in high enough concentration over time, it is harmful to animals, plants and humans. This is called ground level, or tropospheric ozone, after the atmospheric layer in which it exists. A third method of production is natural and it occurs at very high altitude. Ozone is created when ultraviolet (UV) light from the Sun passes through oxygen in the stratosphere. This ozone forms a protective blanket that strongly absorbs UV light, a harmful form of radiation, preventing it from reaching Earth's surface. To see where the troposphere and stratosphere exist, the layers of Earth's atmosphere are shown below. The troposphere is the bottom layer in which we live. This relatively thin layer contains about 80% of the atmosphere's mass and almost all of its water vapour. It's where all of our storms occur. The stratosphere is the almost cloud-free layer just above it. Air here is much thinner. Atmospheric pressure here is about 1/1000 that at sea level. Jets rarely fly above the lowest part of the stratosphere.

Ozone Is Composed of Oxygen Atoms

Ozone is an allotrope of the element, oxygen. Oxygen allotropes are different ways in which oxygen atoms bond together. Oxygen can exist in a highly reactive atomic form, O1, or as the familiar stable colourless O2 gas we breathe in. Liquefied oxygen gas is pale blue. Oxygen can also exist as unstable and reactive ozone, O3, a pale blue gas or dark blue liquid under pressure. Oxygen can even exist as a dark red metallic solid, O8, under immense pressure.

Oxygen is a reactive element, in any allotropic form. O2 binds readily with most other elements and compounds to form oxides - chemical compounds that contain oxygen atoms. About half of Earth's crust consists of oxides and about one fifth of our atmosphere consists of O2. Having so much of this reactive gas in our atmosphere indicates that our planet bears life. No abiotic (non-life) processes are known to constantly replenish oxygen that is constantly sequestered into oxides by rock and minerals. The source is green plants. Green plants release oxygen gas into the atmosphere as a waste product of photosynthesis, a process that uses the Sun's energy to grow and make food. Oxygen-breathing animals like us evolved to use oxygen. We can trace our origins to ancient unicellular life forms that gained the ability to utilize this chemically reactive gas in order to power a series of reactions called cellular respiration. This process turns the food we eat and the air that we breathe into the power to move, grow and repair our bodies. Plants in turn utilize our waste gas, carbon dioxide, along with the Sun's energy, to grow and make food for us, in what is a wonderfully elegant symbiotic partnership.

Why Is O2 So Important to Life?

All of the oxygen allotropes mentioned earlier are present on Earth naturally. Each allotrope has different physical properties and chemical reactivity due to the unique structures and strengths of the chemical bonds between the atoms. O2 is the most chemically stable oxygen allotrope at atmospheric pressure and temperature. Essential for life for animals, fungi, protists and some bacteria, O2 has a unique electron configuration that keeps it stable in the air but reactive enough for life to exploit.

In O2, two oxygen atoms are bound together by a covalent double bond. This means that two pairs of electrons are shared between the two atoms. The diagram below gives you an idea of how this works. Electrons are the small green and purple circles below. The large central circles represent atomic nuclei. The oxygen atom belongs to group 6 on the periodic table, which means it has 6 outer electrons, available for bonding. These are called valence electrons.

Each oxygen atom has 8 electrons, 6 of which are valence electrons. The valence electrons have the same energy so they belong to the same (outermost) shell below. All atoms are most stable when the valence energy shell is full, with 8 electrons. Energy shells are shown as rings in the simple O2 electron shell diagram below. By sharing two pairs of electrons, two oxygen atoms are stabilized in a molecular structure that fills each valence shell. By bonding, each atom can attain 8 valence electrons.

The diagram left is a very simple way of looking at the bond in an oxygen molecule. This diagram is helpful but it doesn't show us one important fact. It doesn't show us how the electrons pair up with each other, as electrons tend to do. The oxygen molecule is quite unusual in fact because it has two unpaired valence electrons. These unpaired electrons explain why O2 is so useful to life. We can show this additional fact by drawing a modified Lewis diagram:

"A" to the left represents an ordinary Lewis diagram of O2. There is a double bond between the two oxygen atoms, drawn using two parallel lines. The un-bonded electrons of each atom are shown as two electron pairs. It makes sense - we learn early on in chemistry that electrons like to pair up. But it isn't quite accurate. If we refine our viewing lens once again, this time from a Lewis structure to a more complex and accurate atomic orbital representation, we discover that the double bond is actually composed of two orbital bonds: a sigma bond and a pi bond. An atomic orbital is a three-dimensional shape outlining where a particular electron might be orbiting a nucleus. This updated version takes into account that electrons are actually quantum wave functions. This model describes electron energy in much better detail and this helps us understand the bonding behaviours of the atom.

Every single chemical bond consists of one sigma bond. It is the strongest bond and it is simply the head-on overlapping of two atomic orbitals. A double bond has an additional pi bond. This bond is the sideways or lateral overlapping of atomic orbitals and it makes the bond stronger. A triple bond, stronger still, consists of a sigma bond and two pi bonds. To help you visualize these orbital-overlapping bonds, check out the simple diagrams on this site.

O2 bonding is rather unique. It is a double bond but in this case, the pi bond acts like two half-pi bonds plus two unpaired electrons. Take a look again at right hand drawing in the diagram above. The unpaired electrons are shown in red for emphasis in "B". This unusual configuration leaves two unpaired electrons with equal energy. Having two unpaired electrons allows O2 to reach the lowest potential energy state possible. This is something all atoms and molecules tend to do. If some heat were applied to the O2 molecule, those two electrons would pair up and the molecule would have slightly more potential energy. What we learned in school still holds up: these two unpaired electrons "want" pairing. This means that an oxygen molecule greedily accepts electrons from other atoms and molecules. It is chemically reactive in other words.

Most molecules tend to have paired electron spins. O2's unpaired electrons don't match up well with the valence electron pairs of other molecules. They are an awkward "third wheel" in the interaction. The consequence of this is that atmospheric O2 reacts slowly with most other substances, rather than rapidly. This is good because otherwise the oxygen in our atmosphere would trigger spontaneous combustion. An example in nature is the gradual process of rusting, the oxidation of iron exposed to air, into ferric oxides (rust). Oxygen is an oxidizing agent, which means it causes other substances to lose electrons. By doing so, oxygen itself gains electrons. This makes sense when you look at its two unpaired electrons. They "want" electrons so they can become pairs. The word "oxidation" was coined by Antoine Lavoisier, while observing reactions with oxygen. It is a bit of a misnomer because these types of reactions, more accurately called redox (reduction/oxidation) reactions, simply involve electron transfer. They don't have to involve oxygen.

How do our bodies utilize oxygen's unusual unpaired electrons? Mitochondria, the tiny "power plants" inside our cells, use oxygen as a final and powerful electron acceptor along a string of reactions called an electron transport chain. An electron transport chain is a series of redox reactions. Electrons are transferred from one molecule to the next. Differences in Gibbs free energy (chemical energy available to do work) between the reactants and the products drives this process forward. The beauty of this set-up is a) it's spontaneous and b) it transfers chemical bond energy to a molecule that can store and readily release it when required. Along the way, a molecule called ATP is produced. ATP (adenosine triphosphate) is the all-important energy storage molecule for all life - plant and animal. Like a tiny battery or fuel cell, ATP powers almost all cellular reactions. Driven backwards, the electron transport chain "burns up" ATP to provide energy for growth and for mechanical energy such as a sperm's flagellum or a contracting heart muscle.

Trivalent Oxygen, Ozone, O3

Now that we understand the chemical nature of O2, how does O3 compare? Ozone is a bent molecule. It has a triangular shape like water, H2O. The three oxygen atoms bond with a double and a single bond that resonates back and forth. Ozone is an example of a resonance hybrid.

The O-O bonds are a hybrid between a single sigma bond and a double sigma-pi bond. This means that the bond strength is in between that of a double and a single bond. Ozone's hybrid bonds are slightly weaker than O2's double bond.

Unlike its somewhat tamer cousin, ozone is a chemically unstable molecule. A resonant structure tends to stabilize a molecule but it is not enough to make ozone stable. The valence electrons in ozone are shared across three nuclei rather than two. Six valence electrons each are fighting for space while packed into a bent shape. Electrons with opposite spins like to pair up but electrons in general don't like to be too close to one another. This bent shape is the most stable lowest-energy arrangement possible but it still has high potential energy and that means it is unstable.

The hybrid bond structure means that the valence electrons in ozone are delocalized. These delocalized electrons spread out to form a loose molecular orbital cloud. Their enhanced motility allows them to react more readily than the localized electrons in O2 do, even though O2 has reactive unpaired electrons and ozone does not.

Ozone is one of the strongest oxidizers known, much stronger than O2. Because ozone is unstable, it readily decomposes into stable O2 gas and extremely reactive chemically unstable lone oxygen atoms. These lone atoms are the key to why ozone is such a strong oxidizer. Although these atoms have 6 valence electrons each, they don't all pair off. Two form pairs and two exist as lone electrons. Those two lone electrons mean that these atoms "want" electrons very intensely in order to stabilize themselves. They will immediately react and borrow electrons from almost any other substance they come across. Ozone is a much stronger oxidizer than O2 because O3 is less chemically stable. O3 offers up lone oxygen atoms that form as soon as ozone decomposes. Lone oxygen atoms are much stronger oxidizers than O2 oxygen molecules, because they so unstable (and therefore reactive).

O3 is formed when O2 reacts with highly reactive atomic oxygen, O1 (or just O). Fee atomic oxygen reacts and disappears almost instantly from Earth's lower atmosphere, but in the stratosphere it is continuously replenished. Stratospheric O2 is bombarded by UV (ultraviolet) radiation from the Sun, cleaving its bond into two free O1 atoms. In the stratosphere, O3, O2 and O1 all exist and are all part of a cycle. In low-Earth orbit, far above the stratosphere, the very sparse atmosphere is almost entirely composed of atomic oxygen, O1. This diffuse but highly reactive gas corrodes all the outer materials on spacecraft that pass through low Earth orbit. It is a significant challenge that all space agencies must take into account.

In the stratosphere, the O2 + O → O3 synthesis reaction is triggered whenever O is available. O is created when solar UV radiation breaks apart the O2 molecular bond into two free oxygen atoms. Whenever atmospheric O2 comes into contact with free atomic oxygen it quickly combines into O3, ozone. Because ozone is a much more powerful oxidant (electron acceptor) than O2 is, it is much too reactive to be useful in any cellular electron transport chain. In fact, its oxidizing action makes ozone pollution a serious health hazard. It can damage respiratory systems in animals and cause tissue damage in plants.

Although O2 is less reactive than ozone, it too is an oxidation hazard inside living cells, and this is something life has learned to live with. Various intracellular sequestering processes reduce this hazard. It is an evolutionary trade-off between cell damage and oxygen's electron-acceptor powers.

Free Radicals

You may have heard of how bad free radicals are for our health. These mysterious-sounding chemicals are simply atoms or molecules (or even ions) that have an unpaired valence electron. Radicals are an important part of biochemistry and atmospheric science. We already explored a radical when we looked at the molecular bonding of O2. The O2 molecule is a di-radical. It has two unpaired valence electrons. We also came across free monatomic oxygen, which is another di-radical, and a much more powerful oxidizing agent.

Like O2, all radicals are reactive, some more than others depending on their stability. Radicals are always oxidants because they accept electrons. Inside cells, free radicals can cause oxidative stress. Oxidative stress is basically a disturbance in the normal intracellular redox balance. The mitochondrial (and in plants, chloroplast) electron transport chain is an ingenious natural invention, but it's not perfect. A few electrons always "leak" out of the chain and react directly with O2 at the end. This reaction creates negatively charged O2, which is a free radical called superoxide. This is the Lewis diagram for it:

This highly reactive charged molecule causes oxidative stress inside cells. It reacts with biologically important molecules such as DNA and proteins. Like a bull in a china shop, it breaks DNA strands haphazardly so they cannot replicate and transcribe accurately and it denatures proteins, so they can no longer function as enzymes, hormones, antibodies and so on. This microscopic damage gradually builds up at the cellular level and in the body as a whole, an overall effect we observe as aging.

Stratospheric Ozone

Stratospheric ozone is the "good" ozone. It makes all surface life on Earth possible. In the stratosphere, ozone forms and breaks apart continuously. When atomic oxygen (O) reacts with molecular oxygen (O2), ozone (O3) forms:

O + O2 + M → O3+ M

A significant amount of energy is released during this reaction. It requires an additional body (M), such as a non-reacting molecule nearby that can carry that energy away. There are two reasons why energy must be released. First, the chemical bond energy of O2 (498 kJ/mol) is slightly higher than that of O3 (445 kJ/mol) so some energy must be released. Second, the free oxygen atom in the reaction is in an excited (high-energy) state, and that energy must be released as well.

Excitation can be explained using atomic orbital notation. An orbital, once again, is a three-dimensional cloud where an electron can be found. When atoms and molecules react with one another, their outermost electrons interact to form or break chemical bonds. In its ground (lowest energy) state, the electrons in an oxygen atom occupy the three lowest energy orbitals available: 1s22s22p4. The lowest energy 1s orbital can hold two electrons; it's full. The next higher energy 2s orbital can hold 2 electrons; it's full too, so these two orbital clouds hold 4 electrons in total. Next, the p orbital starts to fill up. In an oxygen atom, it holds 4 of 6 possible electrons. Oxygen's outermost orbitals are those with n=2 orbital energy. These are the 2s and the 2p orbitals. These n=2 orbitals equip oxygen atom with a total of 6 electrons available to react chemically. These are the valence electrons. In theory, electrons could occupy any of a very large number of possible orbitals in any atom but in a ground state (lowest energy) atom, electrons always minimize energy by occupying the innermost orbitals possible. In an excited state, one or more electrons move outward into higher energy orbitals. An excited oxygen atom is most simply denoted as 1s22s22p33s1 where one outermost (valence) electron has jumped up to a higher-energy 3s (n=3 energy) orbital. This electron configuration contains one unpaired valence electron, which makes it a radical too. Oxygen radicals are denoted as O(1D). I won't go into the reason for the "D" here, but if you want to know, this NASA page explains it well. Not all radicals are in an excited state. Recall that a lone ground-state oxygen atom is a radical too; in fact it's a di-radical. The whole story of oxygen radicals can get pretty confusing. The important thing to remember is that all radicals are highly reactive because the unpaired electron always "wants" to pair up with a valence electron in another atom or molecule. When it does so, the system releases potential energy and stabilizes.

Atomic oxygen radicals (O(1D)) are very reactive because they are radicals and they are very energetic because they are excited. The unpaired electron in the valence shell of this atom combines rapidly with any O2 molecule it slams into to form ozone. In order to exist at any concentration in the stratosphere, energetic free oxygen atoms must be continuously made. They come from the photodissociation of molecular oxygen, O2. Photodissociation means the splitting of molecules by electromagnetic radiation, or light ("photo"). High-energy, and therefore short wavelength, UV radiation pierces the stratosphere and cleaves O2. UV photons with wavelengths shorter than 242 nm (nanometres) have enough energy to break the bond between two oxygen atoms in an O2 molecule. This energy corresponds to 498 kJ/mol. That's the bond energy of O2. The two oxygen atoms released in the reaction absorb some UV energy, leaving them in an excited state.

In the stratosphere, ozone cycles continuously, forming and decomposing O3. Both processes absorb harmful solar UV radiation, particularly of wavelengths shorter than 242 nm. This is why the ozone layer is a protective blanket against UV radiation. As we just learned, ozone absorbs short (<242 nm) wavelength UV radiation when it is produced. Ozone isn't chemically stable, so it doesn't stay around for long in the stratosphere. When it itself is bombarded with stratospheric UV radiation, it readily photodissociates back into O2 and O. The molecular bond energy of ozone is 445 KJ/mol, which is less than that of O2 (498 kJ/mol). This means that less energetic UV wavelengths will break ozone apart, those between 240 and 320 nm. The ozone photodissociation reaction formula looks like this:

O3 + UV (240nm -320 nm) → O2 + O(1D)

Excited free oxygen atoms from this reaction continue the cycle, creating ozone once again.

Stratospheric Ozone Absorbs Deadly UV Radiation

All of these reactions are fast; a whole cycle takes place in just over a minute. It is a very effective life-protecting "UV absorption machine" that converts UV radiation into thermal energy. That energy is carried by the excited fast-moving free oxygen atoms. The stratospheric layer, above the thermosphere, ranges from about 20 km in altitude in the tropics to just 7 km in altitude at the poles. It is a generally stable layer of air that ranges from about -51°C at the top of the troposphere to just -3°C at the top of the stratosphere. You expect the temperature to go down as you move upward through the atmosphere, but the thermal energy created by the ozone cycle is most active at the top of the stratosphere where incoming solar UV radiation bombards oxygen.

The Sun bombards Earth with all wavelengths of UV radiation (and other EM radiation as well). UV radiation ranges from 10 nm to 400 nm. Wavelengths shorter than 121 nm ionize air so strongly that they are absorbed long before they can harm life on the surface. An atom or molecule is ionized when it gains or loses electrons to form charged ions. Another short mini-lesson here: What makes an atom an ion is when the number of electrons doesn't match the number of protons, so the atom therefore has an unbalanced charge. High-energy UV photons have enough energy to cleave various atmospheric molecules apart into ions while the photons are absorbed in the process. A radical is an atom that has at least one unpaired electron. In this case the electron number may still match the proton number and in that case it isn't electrically charged, but it is very reactive. The charged superoxide radical we encountered earlier is both an ion and a radical.

UV radiation between 100 and 280 nm is deadly to almost all life on Earth. This is the wavelength range, especially 230 to 270 nm, utilized in special mercury, LED and xenon germicidal lamps. It kills almost all known microorganisms. Most microorganisms have not evolved protection against concentrated mid-range UV bombardment. It is the right energy to break apart chemical bonds in DNA, proving deadly. Rare exceptions are extremophiles and ancient bacteria that lived before Earth had a protective ozone blanket. These organisms oxidized iron and built protective "rust blankets" around themselves to shield them from UV radiation. There is evidence that photosynthesis evolved in these bacteria.

Fortunately for us, the most DNA-damaging UV range (130 nm and 260 nm) is completely absorbed by stratospheric ozone. However, a small amount of slightly longer wavelength UV radiation, between about 260 and 300 nm, does make it to the surface. This is the UV radiation (especially between 265 and 275 nm) that causes sunburns and can lead to deadly melanoma. It also causes eye cataracts and other eye damage.

As you might have noticed, it is within the range that is germicidal. How does it kill germs but not us? We and other multicellular life survive because, first of all, the natural solar bombardment of this UV radiation is far less intense than a concentrated beam from a lamp. Our cells therefore have a chance to repair the damage as it happens. Secondly, we have evolved some protection through our skin. A pigment called melanin absorbs UV radiation, directing it away from vulnerable cellular proteins and DNA. Our skin even makes use of some UV exposure (280 to 315 nm) to make Vitamin D.

Tropospheric Ozone

Tropospheric or surface ozone is the "bad" ozone. It is a respiratory irritant and it can cause plant tissue damage as well.

Ozone As Ground Level Pollution

Ground level ozone is a pollutant and it is a key ingredient in smog. A pollutant is a substance that is introduced into an environment that has undesirable effects on it or on the life that depends on it. We tend to think of pollutants as man-made but not all of them are. Some are created naturally such as volcanic dust and volcanic gases. Ozone is technically called a secondary pollutant because it is created in the atmosphere when - react in sunlight. These primary pollutants come from combustion engines in vehicles, from industry and from forest fires.

The reactions that create ozone occur best on hot sunny summer days, when there is plenty of solar (UV) radiation. High temperatures promote ozone accumulation by increasing the rates of reactions that form ozone and by reducing the ability of plants nearby to absorb ozone out of the atmosphere. Plants absorb a variety of air pollutants including as much as 20% of atmospheric ozone production. However, during heat waves, stressed plants close their stomata ( (epidermal pores) in order to conserve water and this means that they cannot absorb ozone and other pollutants.

Both NOx and VOCs come from natural sources as well as man-made sources. A significant amount of VOCs is released from coniferous forests, volcanoes and wildfires. NOx compounds are released during lightning storms and wildfires. There are many man-made sources of these pollutants, ranging from motor vehicle exhaust, oil refining, paints, insecticides and industrial solvents to chemical manufacturing, but most man-made NOx and VOCs come from motor vehicle exhaust. Motor vehicles are responsible for at least half of the concentration of these pollutants, especially in large cities even though catalytic converters have been mandatory since 1975 (at least in North America).

In Canada, ground level ozone advisories are issued when average levels per hour exceed 82 parts per billion. Toronto, for example, typically experiences about 10 ozone advisory days each summer. To see live readings for various Ontario cities, check this government website. In Edmonton, close to where I live, ozone pollution risk is usually low. Our cities are a bit smaller than Toronto but just as importantly we don't tend to experience summer days as hot as Toronto does.

This past summer saw Edmonton and the surrounding area blanketed in thick haze blown in from several large forest fires to the west in British Columbia. We experienced many consecutive days in August where air quality health indexes (AQHI) sat over 10+ (very high risk). The air quality health index measures the combined health risk of all fine airborne particulate matter as well as ozone and nitrogen dioxide. If at any time fellow Albertans want more specific information than an AQHI reading, check out this Alberta website that shows current Edmonton/central Alberta levels of ozone, NO2, fine particulate matter, sulphur dioxide and carbon monoxide. To get an idea of how major cities in Canada stack up internationally, this Canada government website compares the average annual ozone levels (in ppb) of various Canadian cities with selected international cities. Across the globe, tropospheric ozone levels range between less than 10 ppb over remote tropical oceans and over 100 ppb downwind of large metropolitan cities in hot weather.

Some ozone can enter the troposphere from the stratosphere through disturbances such as hurricanes that can draw some lower level stratospheric air downward. However, the vast majority of ground level ozone is created when it forms from reactions of precursor compounds such as VOC's and nitrogen oxides. Ozone is highly reactive so it leaves the troposphere quickly, but plants, animals and people downwind from large cities on hot days or downwind from large forest fires can face a significant ozone hazard.

In the stratosphere, we now know that ozone forms from the photodissociation of O2 into oxygen atoms, which recombine with O2 to form ozone. However, this reaction doesn't happen where plants, animals and humans live because short wavelength UV light (<242 nm) doesn't penetrate down into the lower troposphere. As in the stratosphere, the production of ozone requires atomic oxygen. Here, surface nitrogen dioxide (NO2) does the job of supplying it. Its photodissociation requires much less UV photon energy than molecular oxygen does - anything under about 420 nm (slightly more energetic than visible violet light) will work:

NO2 + UV (<420 nm) → O(1D) + NO

The oxygen radical produced in this case is not in an excited state. It will react with oxygen gas to create ozone:

O(1D) + O2 + M → O3 + M

However, in unpolluted air, there is no net production of O3 because O3 quickly reacts with the product NO to create O2 and NO2 once again, in a cyclic reaction (which isn't shown).

When other ozone precursors such as man-made pollutants like carbon monoxide (CO) and hydrocarbons such as methane (CH4) are also present in the air, net ozone build-up can occur. This is when ozone can spike to unhealthy levels. Some of these reaction mechanisms are extremely complex, but two fairly simple surface ozone production pathways, using carbon monoxide and methane as precursors, are fairly easy to show. Their formulae are written below.

Both reactions require hydroxyl radicals (*OH).

A hydroxyl radical, denoted *OH, is the electrically neutral form of the hydroxide ion (OH1). It has one unpaired electron as shown in the Lewis diagram below left.

Hydroxyl radicals are created when surface ozone is exposed to the longer UV radiation that reaches Earth's surface:

O3 + UV (240nm -320 nm) → O2 + O(1D)

The free radical oxygen atom produced then reacts with water vapour to create hydroxyl radicals and oxygen gas:

O(1D) + H20 → 2*OH + O2

Hydroxyl radicals are highly reactive and they are an important part of atmospheric chemistry. Denoted *OH, hydroxyl is sometimes called an atmospheric detergent because it reacts with many pollutants, decomposing them into smaller less harmful compounds. In this case, however, *OH is a step in producing a pollutant: ground level ozone. Compounds commonly present in combustion vehicle exhaust, such as nitrogen monoxide (NO), nitrogen dioxide (NO2) and hydroperoxyl radicals (HO2), serve as reactants and as catalysts. Catalysts in this case increase the reaction rate of surface ozone formation reactions. Faster production means that ozone can build up temporarily even though it is unstable.

Example 1: Carbon monoxide in an NO-rich environment:

CO + *OH → H + CO2
H + O2 → HO2
HO2 + NO → *OH + NO2
NO2 + UV (<420 nm) → O(1D)  + NO

Notice that the fourth reaction just above us is exactly the same reaction as in the natural O3 production reaction (the one that cycles and doesn't build up ozone). Here, however, the reaction takes place in polluted air where various pollutants catalyze ozone production. Ozone is therefore produced faster than it can be removed (which is by reacting with NO to create oxygen and nitrogen dioxide). The reaction scheme continues as the oxygen radical reacts with oxygen gas to create ozone:

O(1D) + O2 → O3

Example 2: Methane (CH4) in an NO-rich environment:

CH4 + *OH → CH3 + H2O
CH3 + O2 → CH3O2
CH3O2 + NO → CH3O + NO2
CH3O + O2 → CH2O + HO2
HO2 + NO → *OH + NO2
NO2 + UV (<420 nm) → O(1D) + NO
O(1D) + O2 → O3

In this case, both ozone and formaldehyde (CH2O) rapidly build up in the lower atmosphere. Ozone is gradually removed as it reacts with hydroperoxyl radicals. As ozone blows into non-polluted air where NO levels are low, it will react with HO2 generated in the reaction "line 4" above to create *OH radicals and oxygen gas. Further ozone depletion occurs when the *OH created then reacts with additional ozone to create new HO2 and more oxygen gas. Ozone is also deposited onto surfaces, where it can react with the surface it lands on. This is how plants are damaged by ozone. Ground-level ozone causes more plant damage than all other air pollutants combined.

Ozone pollution levels peak in the late afternoon, when solar UV radiation and therefore photochemical reactions peak. Ozone is much more likely to be a hazard near large cities and factories on long sunny days in calm air, rather than during short winter days, even though general air pollution levels might be similar or even higher as during a temperature inversion.

Ozone Is An Oxidation Threat To Our Bodies

Ozone is a toxic gas. That being said, we breathe in a tiny amount of it every day. In fresh unpolluted air at sea level, natural ozone makes up about 10-15 parts per billion (ppb) which means that every 15 billion air molecules will include an ozone molecule, on average. Our lungs breathe it in, handling it without noticeable damage. Highly polluted stagnant air, however, can contain more than 125 ppb ozone. Exposure to this much ozone over several hours or days can significantly harm humans and other animals. Long-term exposure essentially causes premature aging in our lungs. It can inflame lung tissues, cause throat irritation and shortness of breath, increase one's susceptibility to respiratory infections and it can aggravate asthma and COPD (chronic obstructive pulmonary disease). Ozone reacts with both the epithelial cells of the respiratory tract and with the molecules in the fluid that coats the tract, creating a variety of free radicals and other oxidant molecules that damage epithelial cells by causing oxidative stress. An enzyme released from the cytoplasm (cellular fluid) leaked from damaged epithelial cells attracts inflammatory cells, leading to reddening and swelling of the respiratory tract. This can in turn lead to difficulty breathing. Ozone also stimulates special nerve cells that exist in between the epithelial cells lining the respiratory tract. This stimulation causes the respiratory pathways to constrict. It also induces coughing and a reflex that reduces one's ability to inhale fully. All of these respiratory effects of ozone are reasons why it is a good idea to avoid strenuous activity outdoors during an air quality alert, even when you are healthy and especially when you already suffer from a respiratory problem. You can expect high ozone levels whenever pollution levels from combustion engines or industry are high or when you live downwind in the smoky hazy air blowing in from forest fires. Although individuals vary widely in their sensitivity to ozone, most of us recover completely from short-term exposure that lasts a few hours or less. Our respiratory tissues repair themselves quickly and they usually recover completely in about 48 hours.

While environmental ozone is a potent health threat, some cells in our bodies have actually evolved ways to use it and other similar oxidizing molecules to their benefit. For example, during an infection, activated white blood cells, called neutrophils, produce ozone and ozone-like oxidizing molecules. These potent oxidizers kill the bacteria invading our system by using a process that is sometimes called an oxidative burst. How it all works is still quite mysterious because, for one thing, it is difficult to examine what happens chemically during a process that occurs very rapidly inside living cells. Ozone and ozone-like radicals appear to be used in the creation of deadly nitric acid that is stored up inside tiny intercellular sacks called phagocytes. Phagocytes are like the trash compactor units of the cell. A phagocyte will engulf a bacterium into a nitric acid bath that denatures its DNA, killing it. It is also possible that the radicals themselves directly destroy the engulfed bacterial DNA.

Tropospheric Ozone Damages Plants

Plants species vary in their sensitivity to ozone but when ground level ozone exceeds 80 ppb for over four hours, plant damage can generally occur. This is the same ozone concentration that prompts human health advisories in Canada, so when we are at risk so are many of our plants. You will see broadleaf damage first show up as clusters of tiny reddish or purple dots in between the veins of leaves that are most directly exposed to sunlight.

Stippling on a red alder leaf caused by ozone pollution. Pat Temple, U.S. Forestry Service; Wikipedia
Often, leaves subjected to accumulating long-term exposure eventually turn autumn-like colours or brown prematurely and drop off. They basically succumb to oxidative stress. Plants look like they do at the end of their season, which makes it difficult to distinguish ozone damage that occurs in late summer. Plants already under stress, such as from drought for example, show more pronounced damage.

Here in Alberta, damage is first noticed on sensitive plants such as blackberries, ash trees and big-leaf lindens rather than more tolerant trees like spruce, pine and birch trees. Generally, the leaves on sensitive plants have more and/or larger stomata, pores that open to allow the plant to transpire (exchange gases) so they allow more ozone in. Ozone enters leaves like other gases do, through the numerous stomata. Once inside the leaf, ozone dissolves in the water inside the plant and reacts with other chemicals. It is a powerful oxidant that damages the photosynthetic apparatus inside the leaf. Once this damage happens, carbon dioxide levels begin to rise inside the leaf because it is not being consumed in photosynthesis. This stimulates the leaf to close its stomata, which further reduces photosynthesis. The plant, as a result, can longer make sugars effectively to maintain its health. There is evidence that leaves higher in antioxidants such as vitamin C have some resistance to ozone damage. By reacting with ascorbate (Vitamin C) in the watery cytoplasm inside the plant leaf cell, ozone is transformed into a variety of nontoxic products that the cell can handle.

Ozone damage to our global food supply is significant. A 2011 article suggests that global yield from three ozone-sensitive crops - wheat, soybean and maize - could be reduced by between 17% and 26% by 2030 based on projected upper and lower estimates of carbon-based emissions by the IPCC (Intergovernmental Panel on Climate Change). An effective way to reduce ozone crop loss is to move toward non-combustion green technologies in vehicles and in industry.

Ozone Threat is Close To Home

We might think of large international cities when we think of the threat of ozone pollution but the problem of ozone (and all air pollution) sits close to home. Alberta, famous for its clear blue skies, is also known for its oil, natural gas and coal production, and for its vast agricultural lands, all of which contribute to significant air pollution and, therefore, ozone pollution. In Alberta, we can expect higher ozone pollution downwind of our two major cities, Edmonton and Calgary, based on contributions of primary pollutants from vehicle exhaust and industries within city limits. However, ozone pollution can also be expected downwind of the oil sands in northern Alberta. The oil sands pump out between 45 and 84 tonnes of organic aerosols per day, a level comparable to that produced by the entire Toronto metropolitan area (about 67 tonnes per day). Organic aerosols are a poorly understood highly complex series of air pollutants, many of which interact with sunlight to create additional secondary pollutants, and which make up most of the fine particulate matter in air pollution.

Perhaps surprising is the fact that the smaller Alberta city of Red Deer has the worst air quality in Canada, according to numerous reports that came out in 2015. Current studies are still being done to figure out what the pollution consists of and where it comes from but the results so far seem to focus on two culprits - nitrogen dioxide and volatile organic compounds, compounds associated with industry and key ingredients of ozone production. Contributing to the problem is the fact that Red Deer sits in a bowl between river valleys, where air can sit and stagnate, and on hot summer days, one could expect high ozone levels as well.  Finally, if British Columbia continues to suffer from devastating wild fires every summer (the last two summers were record-breaking), Alberta will be blanketed by the smoke and haze as most wind flow is from west to east here. Fires tend to coincide with hot dry sunny weather, so Alberta will also suffer from seasonal ozone pollution.

Ozone is a fascinating Jekyll and Hyde type of molecule. Understanding how ozone works means understanding how chemical reactions work as well as how energy affects molecular interactions. The complex machinery inside our cells can make use of the redox chemistry that utilizes various oxygen allotropes but at the same time all living cells must protect themselves from the powerful oxidative activity of these same molecules. Ozone, originating from oxygen photosynthesized by plants, protects all life from deadly solar UV radiation. Yet, when it makes direct contact with the cells of life, it is a poison. An appreciation of the dual nature of ozone paves the way to an introduction of three challenging branches of chemistry: atmospheric and radical chemistry and biochemistry. It highlights how intimately these different branches are linked.

Saturday, February 17, 2018

The Flu

This winter (2017/2018) has been a particularly bad flu season around the world, and as of mid-February, it continues to get worse in the United States. One in ten deaths last week in the US were caused by either the flu or from pneumonia, a complication from the flu. As of February 1st, it was widespread across Canada and the United States and there are serious widespread outbreaks in Japan, the Koreas and in Europe. More than one strain of influenza appears to be responsible for these outbreaks. Here in Canada and in the US, the main culprits appear to be a strain of H3N2 as well as type B influenza, both of which are spreading at the same time. The current season's flu vaccine is estimated to be about 55% effective against type B influenza but only about 15% effective against the H3N2 type A virus.

What Is the Flu (Influenza)?

Both the common cold and the flu are caused and spread by viruses. Sometimes it is hard to tell the difference between flu and cold symptoms, especially if the flu is mild. According to, with either the flu or a cold, you typically feel congested. You have a sore throat and tend to sneeze. These symptoms as well as headache, coughing and chest discomfort are common to both the flu and the cold. If you also have a high fever and experience extreme fatigue and muscular weakness, you more likely have the flu. Young children might also suffer from vomiting as well, according to the CDC webpage on influenza. Another aspect that sets the flu apart is its symptoms tend to come on very rapidly. You feel hit by a bus. Neither virus is any fun but the flu is the one that tends to put us out of commission for 1-2 weeks, in bed, almost unable to get up. It can also be deadly, especially for those of us in high-risk groups, which I will detail.

While an ordinary bout of the flu is generally just awful, the flu can also become dangerous when complications develop as a result of the original viral infection of the upper respiratory tract. Anybody can become severely ill with the flu but most often complications from the flu strike the very young, the elderly, people suffering from chronic medical conditions and pregnant women. These complications can range from sinus or ear infections to pneumonia or inflammation of the heart or brain or muscle tissues. The latter complications can be life-threatening, and they obviously require hospitalized care. Severe inflammation of body tissues can be very dangerous, possibly leading to multi-organ dysfunction syndrome. In rare cases, the body's immune reaction to the virus rather than the virus itself can trigger an inflammatory response so severe that it leads to sepsis, which can rapidly (within hours) lead to death. It is difficult to square the fact that influenza, an annoying illness that always seems to wreck havoc with Christmas plans, is also the same virus that killed about 50 million people in 1918, some of them in matter of a day or two after contact with the virus.

This 4-minute National Geographic video offers a rather-sobering primer on how the influenza virus attacks:

I hope that this article will offer you the power of knowledge against this common and nasty virus. I found this to be true for myself, after doing the background research. There is hope that influenza will be eradicated once and for all, like small pox was and polio will soon be.

Flu Treatment

Antibiotics do not treat influenza or the cold, which are both viral infections. However, antibiotics can be used to treat flu complications such as bacterial pneumonia, an ear infection (if it is caused by bacteria; about half are viral and sinusitis (if it is bacterial, most sinus infections are viral).

All of the over-the-counter medications you find in pharmacies treat the symptoms of cold and flu viral infections rather then the virus itself. There is no treatment for the cold virus, but there are a few antiviral medications that can treat influenza, such as oral oseltamivir (Tamiflu), inhaled zanamivir (Relenza), or the intravenous drug peramivir (Rapivab). There are three main reasons why doctors don't tend to use these antivirals for a common bout of the flu without complications. First, even when they are started at the first appearance of symptoms, they tend to shorten the duration if the flu by only a day or two. Second, these drugs tend to cause nausea, vomiting and/or diarrhea (which may not be worth the trade-off), and they can interfere with other medications. Third, a concern more of the cost to the health system, is the fact that these drugs are expensive. A single adult course of Tamiflu (75 mg twice a day for 5 days) costs about $100 in Canada. These antiviral drugs are, however, useful to treat those of us who are at risk of serious flu complications and those of us who have weakened immune systems. They are obtained through a doctor's prescription (in Canda).

What To Do When You Get The Flu

Your body is busy fighting a battle that requires energy so it's best to give yourself a rest. Stay home. This will do not only yourself a favour but those around you as well by preventing its spread to others. Don't visit anyone in the hospital for this reason. Stay in bed or on the couch in a comfy blanket to ease those pesky chills. A fever (and the accompanying sweats) dries you out so drink plenty of fluids. Try to avoid the caffeine that might prevent you from napping and opt for herbal teas instead. Ginger teas help reduce nausea. If you can eat, do so but try to fuel your body with healthy choices. Homemade soups (no preservatives and usually much lower in salt) do triple duty by providing nutrition/fuel, hydration and comfort. Of course you don't want to cook when you're sick so it's not a bad idea to have a few containers made up in your freezer during flu season.

Do not work out, especially if you have a fever, any dizziness, a hacking cough or body aches. While regular day-to-day moderate exercise strengthens your immune system and offers increased protection against colds and flus, once you do get the flu, it is best to stop your routine especially if you have a moderate to severe case of flu. Intense exercise causes the body to release hormones, such as cortisol and adrenaline, both of which temporarily suppress the immune system. You don't want to fight against your body's natural defenses. A shift to gentle yoga (at home, not at the studio where you can spread it) and/or walking during a very mild flu not only can boost your mood but it eases some of the muscle stiffness associated with the flu, it helps stimulate the appetite, and it helps work up phlegm, easing breathing. If you have trouble getting out of bed, stay in bed and don't feel guilty (easier said than done especially for moms).

Over-The-Counter Flu Medications: Take With Caution

Taking an over-the-counter remedy can also ease symptoms. Be careful to read the labels, especially for dosage and side affects. It is all too easy to unknowingly double or triple the dose of a powerful drug by combining different medications such as a pill with a flu drink, for example. Many flu remedies contain acetaminophen, which treats pain and fever. An overdose of this drug can lead to liver damage or even acute liver failure.

It might be tempting to make up a hot toddy or some other boozy drink to deal with flu symptoms. There is some old mythology out there that alcohol sterilizes the virus somehow. When alcohol enters the body, it quickly enters the bloodstream (within minutes). It is then detoxified in the liver and excreted through the lungs, kidneys and in sweat, over a period of hours. So, yes, you will temporarily have alcohol in your blood but recall that even at the legal limit (here in Alberta) only 0.08% of your blood consists of alcohol, hardly a sterilizing strength. Alcohol dehydrates the body and it has been shown to weaken the immune response if several drinks are consumed.

Be warned, alcohol exacerbates the liver-damaging effects of acetaminophen. The evidence is preliminary but disturbing: combining even a small or moderate drink with a regular dose of acetaminophen can damage your liver. However, some alcoholic drinks such as wine appear to offer the body some immunoprotective antioxidants, a benefit, mind you, that is undone by consuming more than one drink. A glass of your favourite wine, if you can stomach it, can be a good strategy in the evening before sleep but NOT if you are going to take a nighttime flu medication.

Alcohol in the form of alcohol-based (70% alcohol) hand sanitizers and even ordinary hand soap are very effective in removing the virus from our hands. This might be the most effective strategy of all to avoid getting the flu in the first place, and to avoid infecting others around you when you have it.

Keep in mind that antihistamines (for runny or itchy nose and sneezing) can make you drowsy so avoid driving. Decongestants should be used with caution if you have hypertension (high blood pressure). These drugs enhance adrenaline and adrenaline-like hormones in your body, which restrict blood vessels in your nose and throat, reducing swelling and mucus formation. Vessel restriction also increases your blood pressure, which is a concern if you have heart disease or hypertension. There is new evidence as well that having the flu increases the risk of a cardiovascular event such as a heart attack, an additional reason to treat decongestants with caution. Finally, it appears that over-the-counter decongestant nasal sprays can be physically addictive. Keep in mind too that the adrenaline-like action of a decongestant can keep you from sleeping. That is why this ingredient is left out of nighttime store remedies.

A Few Safe Flu Remedies

Here are some safe flu remedies to consider. Nasal irrigation using saline solution (a neti pot) is a natural and proven method to ease stuffiness. Over-the-counter lozenges, especially those that contain menthol (found in peppermint, eucalyptus and other mints) act to coat and soothe a sore itchy throat and may reduce coughing. A humidifier in the room can help you breathe more easily, especially at night. An old-fashioned saltwater gargle also helps (1/4 to 1/2 teaspoon salt in one cup of warm water) to relieve symptoms and it might even help flush out the virus.

There is much literature online touting the use of vitamin C supplements to boost the immune system and to prevent and treat infections, particularly the common cold. The scientific literature is conflicting. A large analysis of previous scientific studies done by the Cochrane Database of Systematic Reviews in 2013 reveals that those who experience extreme physical stress such as exertion or exposure to cold and who may be deficient in vitamin C can reduce their incidence of colds by about half if they take a daily supplement. Taking a daily supplement appeared in some studies to slightly shorten the duration of colds among adults and children. Like the glass of wine mentioned earlier, vitamin C is an antioxidant. Antioxidants protect cells against damage from free radicals. Both are present naturally in the body. Many foods contain high levels of antioxidants and many dieticians recommend a diet high in citrus fruits, berries and vegetables, which will supply more than enough vitamin C. However, some people believe that taking large daily doses of vitamin C (such as 1000 mg) is beneficial. It is generally harmless to take even large doses of vitamin C (under 2000 mg daily) because the excess is rapidly flushed out of the body by the kidneys. However, there are a number of possible interactions to be aware of. Of particular concern for us are some studies that suggest that a large dose of vitamin C can lower the rate at which acetaminophen is passed from the body in the urine, which means that vitamin C may a dangerous mix with many over-the-counter flu remedies, and even more so if you consume any alcohol as well.

All this cautionary advice might encourage you to seek an herbal flu remedy. According to, there is no hard scientific proof that any herbal remedies work against the flu. Beware that many herbal remedies contain active ingredients and the strength varies from product to product. You should always tell your doctor which herbal remedies you are taking (at any time) because they can interact with prescription medications making them either less effective or too effective.

When to Call The Doctor

This is advice for adults. For children, click for an excellent page on advice. It is published by the Canadian Pediatric Society. Often, a typical run-in with the flu passes in one or two weeks and you don't need to contact your doctor, as long as you don't have symptoms of flu complications as described earlier. Stay home, rest and save others from your nasty germs. But, influenza can quickly turn dangerous, so it is important to monitor your symptoms and contact your doctor if:

1) You have a very high fever, over 39.4°C (103°F), or a moderate fever that doesn't go down after 3 days
2)  You feel unusually short of breath
3) You start to cough up yellow, green or brown sputum
4) You experience a sharp pain in your chest when you breathe in
5) You have a severe ear ache
6) You feel light-headed or faint
7) You have any serious chronic disease (heart, lung, kidney disease or diabetes or you are on immunosuppressant drugs)

 (These guidelines are from Harvard Medical School's site)

A Further Caution: Know Where Your Online Information Comes From

There are now some excellent online reference websites for you to explore for information on influenza and other diseases and conditions. However, when researching health-related information online, one should check to see if the website offers accurate information backed up by peer-reviewed research (there should be links to scientific research papers). This is a task that is difficult for anyone not in a medical field so always trust the advice of your doctor, nurse or nurse practitioner first. These professionals are the real experts and they have your best interest in mind. Most informational websites, even some put out by medical schools and universities, are for-profit. This means that they make money by encouraging readers to buy certain healthcare products or drugs. Even medical advice from, one of the top healthcare websites in the world, and a website accredited by a Washington-based non-profit accrediting organization, should be taken as a supplement to doctor's advice. It is owned by a private equity company and it is publicly traded, which means that it is obligated to its shareholders to make a profit, partly from advertising and partly from sponsorship from private drug companies. The New York Observer and the New York Times each published articles critical of webmd's reliance on drug company sponsors and how those sponsors influence content (see the reference section on its Wikipedia page here).

Types of Flu and How it is Transmitted

Influenza is transmitted by an extremely tiny microscopic particle called a virion. Each spherical or oblong virion is about 100 nanometres wide. To put this in perspective, a human hair is about 100,000 nanamotres wide. A microscopic image of several flu virions is shown below.

CDC/Dr. Terrence Tumpey;Wikipedia
Like the cold virus, the flu virus is an RNA virus. This means that its genetic material is composed of RNA (ribonucleic acid) rather than DNA (deoxyribonucleic acid). Human cells contain both RNA and DNA, following a general rule in genetics that DNA makes RNA that makes proteins. The influenza virus is an infectious agent that replicates only inside the living cells of organisms. It is composed of a strand of RNA (genetic code) housed inside a glycoprotein (a protein that has a carbohydrate attached to it) coat.

You may have heard about how fast flu viruses mutate. By the time a new vaccine is formulated, one or more of the target viruses may have already mutated into a different form, making that vaccine less effective or even ineffective. Their RNA is the reason flu viruses can do this. Influenza viral genomes, as a group, have the highest mutation rates of any genome. Compared to DNA viruses (they cause cold, warts, herpes, chicken pox, etc.), RNA viruses tend to have higher mutation rates, and single-stranded RNA viruses (such as flu viruses) have the highest mutation rates of all. Within DNA viruses, DNA-directed RNA polymerase (part of the cell's RNA-making machinery) can proofread and fix code errors in newly replicated RNA. RNA polymerases in RNA viruses lack this proofreading step. A lack of genetic proofreading would lead to life-threatening cancers in complex organisms like us but it is actually a boon to the flu virus. It allows constantly occurring minor point mutations in the genetic code to make coat proteins that subtly but constantly change, enough to fool antibodies, like a thief choosing a new mask all the time. This high mutation rate also allows it to stay one or more steps ahead of virologists desperately trying to predict each year's new vaccine cocktail.

There are three types of flu virus: Type A, Type B and Type C. These three types, or genera as they are called taxonomically, can cause influenza in many different classes of vertebrates, including humans and other mammals such as pigs, dogs, seals birds, etc. Influenza A is of most concern. This type of flu virus mutates the fastest and it is the only type associated with past flu epidemics, including the devastating 1918 Spanish flu pandemic, the 2009 swine flu pandemic, the Asian flu of the 1950's and various bird flu outbreaks. Some of subtypes of influenza A, such as H1N1, can be highly pathogenic and/or highly virulent, which means they have a high ability to cause disease and they have a high ability to infect a host, respectively. In other words, they spread quickly and they have a high mortality rate. Not all viruses of subtype H1N1 are so dangerous. Some strains of this subtype cause only mild seasonal flu. Virus phylogeny consists of type, divided into subtypes, which are further divided into strains.

The H1N1subtype is of particular interest to virologists. It is one of three subtypes that are always part of the flu vaccine cocktail. It was responsible for the deadly "Spanish" 1918 flu and for the 2009 "swine" flu pandemics, as well as others. There is currently (January 2018) a deadly epidemic of a new H1N1 strain in Pakistan that mutated from the sine flu. An epidemic is an outbreak of disease that attacks many people at the same time in the same general location. A pandemic occurs when an epidemic spreads throughout the world.

Other strains of the H1N1 subtype are commonly found in small numbers during every annual flu season. Each subtype comes in numerous different and always-evolving variants or strains. One strain of H1N1 might produce an average short-lived isolated flu outbreak. Another might only infect pigs and not humans at all, while a third could be as dangerous at the 1918 Type A H1N1 strain.

Type B influenza only infects humans and seals. Fewer hosts (fewer animal reservoirs of the virus) and a mutation rate that is 2 to 3 times lower than Type A influenza means that Type B is less dangerous. Unlike influenza A, Type B is broken down directly into strains and lineages rather than subtypes. There are only two lineages currently in circulation in the world. Each year's flu vaccine contains Type B virus. Type B flu virus can cause flu epidemics as well, but sufferers tend to have less severe flu symptoms than those from Type A viruses. Type C influenza infects humans and pigs. Outbreaks of type C are rare and they tend to cause only mild flu symptoms but there have been local epidemics. This type of virus is more difficult to isolate and study so much less is known about it than the other two types. The good news is that by the time we are 10 years old, most of us have been exposed to type C flu and have antibodies against it. It is the slowest virus type to evolve and it doesn't present a serious threat to humans.

Influenza Virion Structure

The influenza virus is crafty. It probably evolved for many millennia infecting humans and various animals, spreading back and forth between these vectors, although the first reliable evidence of an influenza outbreak was a pandemic in Asia, Africa and Europe, recorded in 1580. Technically the virus is not a living organism because it needs a living host to survive and reproduce, but has evolved many strategies to carry on its progeny from one host to the next over the millennia, adapting to new hosts and changing conditions during the process.

The diagram below helps to explain how a particular virion is labeled (for example, H1N1). A Fujian flu virus (a type A virus) is used as the example. Types A, B and C flu viruses are structurally and compositionally very similar to one another.

The squiggly purple lines inside the circle represent enclosed RNA genetic material. The glycoprotein coat is shown in red. In flu viruses, this coat is composed of two large glycoproteins: hemagglutinin (the small red "lollipop" structures, H) and neuraminidase (the rectangle-shaped structures, N. The arrow is a bit off.). Hemagglutinin, denoted as H left but elsewhere in this article shortened to HA, allows the virus to recognize and bind to its target cell. Neuraminidase (N or NA) enables new viruses made inside the target cell (or host cell) to be released. Both HA and NA are viral sites that antiviral drugs target. HA and NA are also antigens that our antibodies target during an immune response to the virus. Each antibody made by our immune system targets a specific antigen, like a lock and key mechanism, and binds to it (shown below left). Different antibodies have many different functions. Those that attack flu and other viruses usually block part of the (virus's) antigen's surface, rendering it ineffective.

Two glycoproteins, HA and NA, distinguish which subtype the virus is. H3N2 is another particular subtype of flu virus Type A. The flu vaccine almost always contains a strain of this subtype as well.

HA molecules on the surface of the flu virus envelope identify and bind to corresponding receptor sites on the membrane of an epithelial cell in the host's respiratory system. Once attached, the viral envelope fuses with the host cell membrane. The viral RNA genome then enters the host cell and commandeers its RNA-making and protein-making machinery to make new virus proteins and RNA. This process gradually weakens or kills the host cell while it sheds multitudes of new viruses into the respiratory system. See the diagram below showing how a virus attaches to and enters a host cell and how it uses the host cell's machinery to make new viruses that bud off the host cell to infect new host cells.

User:YK Times;Wikipedia
Glycoprotein coat-making machinery is on the left in the cell and RNA-making machinery is in the center, inside the cell nucleus. Steps 1 through 7 are described in detail here (under "summary").

The flu virus can be transmitted in three main ways. First, transmission occurs when viruses within the saliva and mucus (such as in a sneeze by an infected person) land directly on a new victim's eyes, inside the nose or inside the mouth. This is direct transmission. It can also take an airborne route, where someone later inhales virus-laden air sneezed or coughed out by an infected person. Third, someone can pick up the virus by touching a surface that was infected by a sick person or through skin-skin contact such as shaking hands. The flu virus can live outside the body for up to 24 hours on a hard surface and for more than a week in mucus. The simple message to wash your hands often and well if you are sick and if you are around people who are sick is a very effective method to avoid the getting and spreading the flu. A single sneeze or cough can spray up to half a million viral particles into the air. Two methods you can use to stop this transmission route are to sneeze or cough into the crook of your elbow or to sneeze or cough into a tissue, then throw that tissue into the garbage and then wash your hands.

Why Do I have These Symptoms?

During the first day or two after exposure to the virus, your immune system is already responding by churning out antibodies and T cells (the immune system's "soldiers"). If you got the flu shot and it matches the strain of flu you caught or if you've previously been exposed to this strain, your body already has a stockpile of antibodies. They provide an immune shortcut, a kind of a one-up on the virus. Antibodies will recognize that viral strain and stop it in its tracks, preventing illness. If your flu shot does not match but is similar to this strain or if you were already exposed to a similar but non-matching flu in your past, you likely still have a advantage; your flu will likely be milder than it would have been otherwise.

By around day three or four after being infected with the flu virus, your immune system, good as it is, is no longer keeping up with the viral onslaught. You go from feeling normal to feeling like you've been hit by a train, often over a period of hours. You have a fever, chills, headache and all of your muscles feel like you just did some kind of beast race. The root cause of your exhaustion, fever, headache, chills and muscle aches is your immune system. It's gone into code red emergency mode, creating a body-wide inflammatory response, with these unpleasant symptoms as side effects.

Your entire body is now in flu-fighting mode and that is why it is wise to rest and fuel it for the war it is waging against the viral invasion. Dead epithelial cell debris clogs up your breathing passageways - you develop a dry cough. Your throat is sore; your nose is red, itchy and runny. The flu essentially blows infected epithelial cells apart. These are the cells that normally protect your respiratory tract. The virus causes tissue damage, felt as soreness, swelling and inflammation. It is this damage to the lining of the respiratory tract, and the detritus left behind, that can set up the stage for complications from the flu such as a possible secondary bacterial infection such as bacterial bronchitis or bacterial pneumonia.

Although it isn't much of a concern for healthy adults infected with mild to moderate seasonal flu, you should seek medical help if you start to feel worse after you've already started feeling better. Bacterial pneumonia comes on slower than flu symptoms do. Serious chills, serious sweating, a high fever, trouble catching your breath, faster breathing and faster pulse are signs that you may have pneumonia as a complication of the flu. Go to emergency because it is a potentially very dangerous and rapidly evolving situation.

It is going to take about a week before your immune system starts to get the upper hand. In the meantime, there is a risk that bacteria and other viruses can invade you in your weakened state. It usually takes about two weeks before you can confidently feel recovered, and during this whole time, your body continues to shed the flu virus, although at a constantly decreasing level after the first few days when viral shedding peaks. This means that you are contagious throughout the whole time you are sick, and you are particularly contagious even before your first symptoms.

How the Flu Virus Makes Us Sick (Its Pathophysiology)

One factor that makes it hard to contain the transmission of flu is the simple fact that you are contagious before the symptoms hit you. The virus has entered your nose, throat and lungs. It is getting right to work taking over the cellular machinery in your epithelial cells lining these airways so that it can copy itself and multiply. At this point you are contagious but you don't know it yet. Every sneeze and cough hurls new viruses into the air, and onto surfaces around you, and onto your hands as you politely try to cover your mouth and nose. A deeply ingrained regular hand-washing habit can avoid having others around you come down with the flu too.

When a flu virion enters the respiratory tract, its hemagglutinin, the glycoprotein on its surface membrane, recognizes and binds to sialic acid-containing receptor proteins on the membranes of epithelial cells. Once the virus binds to the epithelial cell, the cell engulfs it as well as the bit of cell membrane that was stuck to it, to make an endosome inside the cell that is filled with the virus. An endosome is depicted in the right side of the cell in the cell diagram earlier. The cell then does what it is programmed to do when a foreign body enters it. It acidifies the inside of the endosome and then begins to digest the contents. However, the virus is quite ingenious. As soon as the pH falls below 6, the HA molecule partially unfolds, releasing a peptide that acts like a grappling hook. Then the HA molecule refolds into a new low-pH-stable structure. It uses the "grappling hook" peptide to come up to and fuse its endosome membrane with the epithelial cell's inner membrane. Once done, it spills its contents, including its RNA, into the cell's cytoplasm and gets to work using the cell's replication machinery.

There are at least 18 different subtypes of HA: H1 through H18. Several of these only infect specific animal species. H1, H2 and H3 are human viruses. Of each subtype there are numerous continually evolving strains. Antibodies made in the body usually attack the specific subtype/strain hemagglutinin that the virus presents on its surface. Hemagglutinin (HA) is a lollipop-shaped structure. It has a head, which binds to sialic acid on target epithelial cells. It also has a distinct stalk. The head structure changes subtly but continuously thanks to frequent mutations in the RNA coding for it. Most antibodies bind to the HA near its "lollipop head," preventing it from attaching to sialic acid receptors on the epithelial cells. To a lesser extent, antibodies are also made to recognize and attach to the stem part of the HA molecule instead. These antibodies stop the virus by inhibiting the membrane fusion machinery, most of which is located in the stem part. The stem will become important later on in this article.

Why Are Some Flu Epidemics So Deadly?

Each subtype of flu (such as H1N1, for example) can come in many different strains. A specific strain of H1N1 caused the deadly 1918 flu (about 50 million deaths) pandemic while another strain of H1N1 is currently a mild seasonal flu. Some strains are far more pathogenic than others. Viruses that contain avian (bird) hemagglutinins, such as H1, H6, H7, H10 or H15, appear to cause low-pathogenicity illnesses in birds but when these particular genes for the HA glycoprotein cross over into human strains of flu, they can potentially do far more damage in human lungs and they can be far more deadly than they are in birds. Avian subtype flu viruses also seem to cause a far more intense inflammatory immune response in humans, a physiological response that, in itself, can be deadly. In a 2014 study by Li Qi et al., mice (with respiratory systems and epithelial cell receptors very similar to humans) injected with H1, H6, H7, H10 or H15 avian HA viral subtypes rapidly lost weight and some died from primary viral pneumonia (pneumonia caused by the flu virus itself) within a week. Other (non-avian) subtypes (H2, H3, H5, H9, H11, H13, H14 and H16) caused no significant disease in the rodents.

The 1918 flu appears to have been one of these avian/human crossovers. Normally, the immune system is immediately activated after exposure to a mild seasonal flu virus. Cells of the immune system (white blood cells) such as macrophages, cytotoxic T cells and neutrophils recognize, target and kill virus-infected cells. This 3-minute video animation describes how these and other immune cells carry out an immune response:

However, for not entirely understood reasons, avian-like flu viruses, such as the 1918 epidemic virus, stimulate an exaggerated immune response that can be as damaging as the virus itself. Even healthy cells of the respiratory tract are targeted and killed, leading to life-threatening events such as acute respiratory distress syndrome and multiple organ dysfunction syndrome. These events can kill a person within hours of infection with the virus. The 1918 flu virus, and other avian-type flu viruses appear to target not just pulmonary epithelial cells but also the cells lining the alveoli deep in the lungs. The body has epithelial receptors for this particular avian-like strain of HA glycoprotein not only in the nose, throat, and upper respiratory tract but the lower tract as well.

By attacking not only the throat and nose but also deep inside the lungs, infection with the 1918 viral strain led to serious consequences such as rapid fluid and dead cell detritus buildup in the lungs. Unlike mild to moderate seasonal outbreaks, the 1918 flu targeted young healthy 20-35 year olds (although illness rates were highest among school age kids). This flu was contagious but not unusually so. Still, those who were infected with it suffered greatly. Within hours some victims experienced intense fatigue, and a cough violent enough to tear abdominal muscles. They turned blue as they coughed up foamy blood and many victims suffocated to death within two to three days of getting sick. It is important to note, however, that most victims died later on, approximately a week after getting sick and they died from secondary bacterial pneumonia, rather than the deadly acute immune reaction just described.

The types of casualties revealed a puzzle. Previously healthy victims with robust immune systems died partly because their immune system turned against them. In most 40 year olds, the immune response begins to weaken and it is simply unable to match such deadly intensity, and in the very young the immune system is not yet completely developed. Careful studies of the victim's histories also revealed another clue. These young healthy victims were not exposed to a similar flu in their youth, but older people living then were exposed, and some researchers suspect that this prior exposure is what saved many in the older group. Antibodies to a similar flu virus will lessen the severity of a flu infection. People born before 1875 were around 43 when the epidemic hit. These people had been exposed to a variety of subtypes of influenza A that some researchers suspect that exposure led to partial immunity against the 1918 flu strain. This, in addition to a less robust immune system that cannot run amok, might have offered older people some protection.

Understanding the unusual pathophysiology of the 1918 flu epidemic offers clues about how to avoid a similar flu deadly pandemic in the future. Knowing how our immune systems evolve over time, how different strains attack the body, where in the world and in what species new strains could originate from, and how previous exposure to past similar flu strains can moderate our immune response all help the world's health organizations zero in on what to watch out for as each new season takes shape.

 Avian Flu Cross-Over: A Concern for the Future


While the 1918 deadly H1N1 flu strain appears to have been a cross-over from an avian flu virus, this and similar strains may be much less likely to cause a future deadly pandemic. In recent years, outbreaks of H1N1 have been fairly mild and it makes the rounds often enough that most humans have antibodies against at least a few strains of this subtype. Those who get the flu shot will also have antibodies against various strains of the H1N1 subtype. Virologists now have their eye on a different avian flu subtype, H5N1, a subtype commonly called "bird flu" (even though there are many subtypes of avian influenza, see above). It is currently one of two most likely candidates for a future deadly flu pandemic. Even though mouse studies, exposing mice to avian H5N1, did not result in serious illness, it doesn't mean that this virus has not been deadly in humans.

Bird flu is largely a south Asian disease of birds but it can infect a wide range of other hosts species as well such as pigs, cats and humans. There are low pathogenic (LP) strains of H5N1 (these are also found in North America) and high pathogenic (HP) strains of H5N1. Virologists are particularly concerned with a high pathogenic strain called HPAI H5N1. It was discovered in China in 1996, isolated in a goose, and the first human outbreak of this strain was in 1997. The rate of infection has been increasing since then, with several hundred cases of this strain in humans now reported to the WHO (World Health Organization). WHO announced that between 2003 and 2013, 630 cases have been confirmed and of those, more than half, 375 people, have died. H5N1, at least currently, doesn't easily spread from birds to humans but when it does, the disease is often unusually pathogenic, and deadly. In a 2006 outbreak, limited human-to-human transmission was confirmed as well, which is even more worrying.

What makes all avian influenza subtypes a concern is where they tend to attack the body. As mentioned earlier, viral HA recognizes and attaches to sialic acid receptors in respiratory epithelium cells. There are two kinds of sialic acid receptors: 2,3 linked and 2,6 linked. Flu viruses that originate in birds tend to prefer the 2,3 linked type of sialic acid receptor, while flu viruses that originate in humans tend to prefer 2,6 linked receptors. 2,6 linked receptors are mostly found in the upper respiratory tract, such as in the throat, the nose, and in the upper trachea. Humans also have 2,3 linked receptors and these tend to be most numerous deep in the lungs. This means that when avian-type viruses infect humans, there is a higher risk that deadly primary viral pneumonia can set up deep in the lungs, and this accounts for its high mortality rate. An upside to this is that because the site of attack is deeper in the body it is more difficult to sneeze or cough out viruses, making these infections less likely to spread through airborne contact. So far, there has been no recorded instance of a highly pathogenic avian influenza outbreak that is transmitted through airborne contact. However, a  2008 study found evidence that the H5N1 subtype, in addition to infecting deep lung tissues, can infect the gastrointestinal tract, the brain, the liver, the blood cells, and in one case it even crossed the placenta into the fetus of a pregnant woman, which means it could cause damage to and weaken various regions of the body.


Another avian influenza Type A virus, H79N, has recently also appeared on WHO's radar, and this subtype might be considered even more worrisome than H5N1. There have been about 1200 confirmed cases of H7N9 so far, and about 40% of those have died. Not as much is known about the transmission and pathology of H7N9, but it also appears to attack the lower respiratory tract, leading to viral pneumonia. It also appears to overload the immune system causing a cytokine storm, which in some cases led to acute respiratory distress or multiple organ dysfunction syndrome. A cytokine storm acts like a dangerous positive feedback loop. It occurs when various immune cells are activated in large numbers. These cells release cytokines, which in turn activate even more white blood cells.

In 2013, virologists reported that it did not transmit easily from birds to humans and that person-to-person transmission was unlikely. Therefore it was unlikely to cause a pandemic. However, since then they walked that back. While H5N1 causes illness in birds, making it fairly easy to identify and monitor, H7N9 doesn't appear to cause any visible signs of disease in birds. This makes it virtually impossible to monitor in bird populations such as poultry farms. Since birds don't get sick, it also means that there could be a large sustained pool of the virus in the bird population. There is no evidence yet for person-to-person spread of this subtype, but there is concern that the virus could mutate and gain that ability.

The Flu Shot: What Does It Do and Is It Worth It?

The annual flu vaccine typically reduces your risk of getting the flu by about 50% on average year over year, and if you do get the flu, the symptoms tend to be milder. Aside from taking antiviral drugs, it is the only action you can take to prevent the flu. Here in Alberta, the annual flu shot is provided free of charge through Albert Health Services. They provide it through immunization clinics or you can get it at your local pharmacy (like I do every year). It is generally available at the start of flu season, some time in October. Protection starts about two weeks after you get the shot. In the United States and In Canada, the flu shot is recommended for everyone aged 6 months and older. Vaccination rates in Canada have been steadily increasing over the past two decades. According to a Canadian report released four years ago (2014), about 30% of all Canadians got the flu shot annually, with a high of about 67% for seniors and a low of about 20% for people between 12 to 17 years old. By 2016, vaccination rates increased to about 42% for all Canadians, 59% of which were children aged 6 months to 17 years. Every accredited medical website I checked online recommends that you get the annual flu shot.

A unique flu vaccine is formulated each year to protect against three or four of the most likely virus strains to show up. These strains are determined by the World Healthcare Organization (WHO), usually some time in February, for each upcoming year.

What's In the Flu Vaccine? Is it Safe?

I know a lot of friends and family who resist getting the annual flu shot, and the reason varies from a fear of needles to a belief it is ineffective to worries about the safety of the vaccine. Side effects from the flu shot can occur and that is why you are told to wait 15 minutes after your shot before leaving the pharmacy. The side effects are usually minor, with the most serious possibility being an allergic reaction, and that is primarily what the pharmacist watches for during those 15 minutes. Symptoms such as swelling around the eyes or lips, hives, a racing heart beat, dizziness or trouble breathing indicate that you are having an allergic reaction to the flu shot. Severe allergic reactions to the flu shot are very rare (there are just 1.31 reported cases of anaphylaxis per million doses given, according the CDC in the United States). If you have a severe allergy to eggs you should talk to your doctor before getting the flu shot. However, the flu shot is recommended even for those with moderate egg allergies, provided they are monitored after the shot for symptoms. Most flu shots and the nasal spray are manufactured using chicken eggs so they contain a small amount of egg protein such as albumin.

Another possible avenue for allergic reaction is thimerosal, a preservative that is added to multi-use vials of flu vaccine. Prefilled syringes and the nasal spray do not contain it. Thimerosal exposure can trigger rare and mild allergic symptoms such as itchiness, redness and swelling around the injection site. Thimersol is also present in make-up, soaps, some contact solutions and ointments. Thimerosal contains ethylmercury and some people worry about mercury exposure. Our body eliminates ethylmercury so it cannot build up in our tissues and cause damage. Methylmercury, however, does build up in the body (it is the molecule that builds up in fish tissues and can be toxic). You can choose a thimerosal-free vaccine dose if you are concerned.

The vaccine also contains stabilizers such as sucrose (table sugar), sorbital (artificial sweetener) and monosodium glutamate (MSG). These additives prevent the vaccine from losing potency when exposed to heat and light. Even if you are diabetic or are sensitive to sorbital or MSG, the amount in your dose is far too small to cause any reaction. Antibiotics are also added to the vaccine, again in extremely small amounts. A small amount of emulsifier, polysorbate 80, is also added. This is the stuff in purchased salad dressings and sauces. The shot vaccine also contains formaldehyde, which is used to deactivate the virus. Formaldehyde, found in wood glues and adhesives, can cause eye and throat irritation and it is a carcinogen with long-term large-dose exposure. As a water-soluble gas, almost all of it is removed from the vaccine before packaging. The amount that is left in the vaccine is less than the amount found in your body naturally, and so is not a concern.

The flu vaccine causes approximately one in one million elderly people to get Gullian-Barré syndrome. This is a very rare disorder in which your immune system attacks your nerve cells, and it can occasionally lead to paralysis. You are more likely to get the syndrome after the suffering from the flu itself than from the flu vaccination. People with a history of Gullian-Barré syndrome after receiving a previous flu shot, however, should talk to their doctor before getting the current season shot.

If you do not feel well, you should talk to your doctor before you get the shot. You want to have a robust immune reaction to your flu shot to maximize antibody production. If your immune system is already taxed, your body is less likely to develop good immunity against the flu strains in it.

Shots and Nasal Sprays

As you suspect, the flu shot contains the flu virus, or viruses to be precise. Side effects from the flu shot include soreness, redness or swelling at the injection site, headache, mild fever, nausea and muscle aches (I usually experience a sore arm, the most common side effect, for a few days). You might experience a runny/stuffy nose for a few days after the nasal spray. These symptoms might sound familiar after reading this article. They are symptoms of the flu itself, albeit much milder. They are far easier to live with than the symptoms of the full-on flu itself. It is important to note that the vaccine viruses themselves DO NOT cause these symptoms. These are signs that your immune system is being activated. They are the immune response to the disease but not the disease. You CANNOT get the flu from the flu shot or the nasal spray.

The flu viruses in the flu shot are inactivated (dead). Formaldehyde inactivates the virus, while leaving the surface HA glycoproteins intact to trigger an immune response. The viruses in the nasal spray are live but they are attenuated, or weakened. First made available in 2003, some American studies have recently shown it to be less effective in reducing cases of the flu, and the reasons for that are not yet understood, which is unfortunate for children and others who fear needles. In the United States, the CDC did not recommend the nasal spray for this flu season (2017/2018) while Canada's National Advisory Committee on Immunization still recommends it, based on Canadian studies that show that it works. That being said, Alberta and Saskatchewan stopped offering the nasal spray for free last fall, although it is available at a cost.

Because the nasal spray contains a live (but weakened) virus, it can cause a mild flu infection. The virus in this case is grown in a cold setting, which means it can survive and reproduce in the cooler nasal passages but it cannot live elsewhere in the warmer (deeper) respiratory tract. Sniffles and a stuffy nose means that it is triggering an immune response and making antibodies. You DO NOT actually get the flu. It is not the cascade-like invasion of virus that is the hallmark of a bout of influenza. However, the nasal spray could lead to complications in people with already weakened immune systems. Wikipedia lists those who should not get the flu nasal spray here. People who receive the nasal spray may also shed small amounts of live virus for about a week afterward, which means it could lead to transmission of the viruses in the vaccine, although it is a very minimal risk.

Soreness, redness or swelling at the injection site, headache, mild fever, nausea and muscle aches are all good signs that your immune system has recognized the viral invaders and is launching a counter-attack. Your immune system will remember those flu strains. If it encounters any of those strains in the future it will be able to attack the virus without delay.

How Long Does Immunity Last?

How long does immunity last against a particular flu strain? You need a flu shot every year not primarily because your immunity wears off but because flu viruses mutate into new strains every year. Each year, a new collection of three or four of the "worst and most likely" viruses is used to make vaccine. One or more of these viruses can and often will mutate before the vaccine is manufactured and distributed, which will make the vaccine less effective or even ineffective against that particular strain. It's a frustrating game of Russian roulette or maybe whack-a-mole.

Is there a side benefit from the yearly shot, such an ever-increasing arsenal of antibodies and memory B cells against various flu strains? I would like to think this is a bonus of getting the shot every year, but the evidence for this is not yet solid. It is unclear whether yearly vaccination produces a strong enough immune response to provide a lasting year-over-year memory B cell population that is large enough to provide strong immunity to each strain we receive. However, there are hints that this could be the case, at least for past exposures to wild strains of the flu. Evidence from studies on the 1918 flu pandemic suggests that antibodies to a similar viral strain can reduce the severity of a current infection. That work also suggests that memory B cells created in response to a flu infection, especially while the immune system is young and robust, can lead to decades and perhaps even a lifetime of immunity against that strain as well as similar future strains.

How long you retain antibodies and memory B cells depends on how powerfully your immune system reacted to the virus. For the best antibody production you need a healthy and mature immune system. A baby is born with an immature but highly adaptive immune system. It acquires immune memory in the form of long-term memory B-cells as the child grows and comes into contact with various antigens over the years. Memory B-cells migrate to the bone marrow after an immune response, where they live for up to several decades. These are the cells that produce (shorter-lived) antibodies in response to a repeat invasion of foreign material such as a virus. B lymphocytes make antibodies to an antigen (the naive B cell shown below). At the same time, they also make memory B cells, which remember that antigen and launch a faster antibody response the next time the body is infected with virus "A."

As you get older you develop an expanding repertoire of memory B-cells to various antigens. Your immune system reaches its peak function at around age 30 and then goes into slow decline. At around 50, we have noticeably weaker immune systems in general but our overall health at this age makes a big difference. Although memory B-cells persist, the immune response in general declines with age as fewer immune cells are made after exposure. The equilibrium of the immune system is also weaker after around 50. Tolerance to self-antigens goes down, which means we experience more autoimmune diseases, our bodies experience increased overall inflammation, and our systems no longer recognize and eliminate cancerous cells as efficiently.

All of this suggests that exposure to many strains of flu virus when we are young and healthy could build up a good arsenal of memory B-cells to help protect us against various strains of flu well into our declining years. It might mean that starting the yearly shot with its ever-changing cocktail of viruses as young as possible (at six months for the shot) and getting immunized every year might be the best long-term strategy against the flu. A couple of studies, however, show just the opposite - that getting the yearly shot might actually diminish one's immunity against the flu, a perplexing finding. One possibility for this is negative interference. For example, if identical or very similar viral strains are present in the shot two years in a row, the antibodies produced in year one might neutralize the virus in the year-two vaccine before it can trigger a full immune response. In this case, infection with the strain in year two must rely on a two-year-old repository of antibodies/memory B cells to attack it. While the presence of antibodies should lessen the severity of the flu, they might not be as effective as antibodies made more recently. In other years, the opposite (positive interference) might occur, which could provide enhanced protection instead. Researchers need to determine if negative interference exists and what to do about it. One possible solution is a higher dose vaccine in year two, which would elicit a stronger response.

Some of my friends/family claim it might be better for kids to actually contract the flu each year rather than to get the shot or spray. It is possible that a full-blown bout of the illness could elicit a more robust immune response than the shot or spray, making a better arsenal of antibodies for the future, and some researchers suspect this is the case but there is a price. Getting a full-blown flu is massively unpleasant and it has significant risk associated with it, and vaccination does not. The yearly shot, I think, is the more logical and kinder strategy for your kids, and it might add that bonus of a broadening immunity against the flu.

I have found conflicting evidence in various research papers about how long the flu shot affects future immunity against the flu. One study, based on the 2009 H1N1 outbreak, for example, suggests that after immunization, immunity against that strain was lost within a year. Another study suggests that we could gain immunity against a strain of the flu that could last a lifetime. Importantly I think, this was based on a prior infection with the flu, not exposure from vaccination. 90 years after the deadly 1918 flu epidemic, 32 elderly volunteers still contained memory B cells circulating in their blood that readily secreted antibodies after exposure to hemagglutinin (HA) glycoprotein from the same strain.

Even though questions remain about how long immunity from the flu shot or nasal spray lasts, evidence that the annual flu shot offers some protection against the flu is clear. Even during years when the shot's effectiveness is low, it may still offer protection by reducing the severity of the illness, and therefore reducing the risks associated with serious and sometimes deadly flu complications.

The first flu vaccines were developed in the 1930's. Flu vaccines have been widely administered throughout the world for well over 50 years, but there is still much to learn about how the vaccine works and how to maximize its effectiveness. Researching the effectiveness of flu vaccines is very difficult. The pool of test subjects is almost impossible to control for. Individuals have unique and highly variable immune system function, which depends on health history, exposure history, sex and age. The effectiveness of the flu shot varies based on two central things: how closely it matches current circulating viral strains, which are always in the process of changing, and second, on the particular immunity of the person being vaccinated (which can often be a black box).

How The Flu Vaccine Is Made

Over a hundred national influenza centres across over more than a hundred countries collect flu data all year long. They monitor which strains are making people sick and how those strains are spreading, and then they pass that data along to the World Health Organization (WHO) and other centres. The data is gathered and analyzed to determine which strains are most likely to spread and cause illness during the year ahead. Usually three strains and sometimes four are selected: most often they are an H1N1 strain, an H3N2 strain and a B strain. This link lists the viral compositions of past (back to 2010) and present WHO-recommended flu vaccines.

Egg-based Flu Vaccine

The egg method has been used since the first flu vaccines were made, and it is still the method almost exclusively used. Each strain in the flu vaccine is produced separately in fertilized chicken eggs that are 11 to 12 days old. The following brief 2-minute video from McMaster University in Hamilton, Canada illustrates the basic procedure:

This fairly low-tech method is currently how most live attenuated and inactivated vaccines are made. This 2015 article outlines the protocol very clearly and is easy to follow. The candidate viruses are injected into eggs and incubated for two days so that the viruses can replicate. Then the virus-containing fluid is collected. The viruses are inactivated (for the shot), and then purified and tested before they are released. Attenuated viruses are also manufactured using eggs but the process is different and relies upon some modern genetic tools. In this case, a universal master donor virus is used. This master virus is made to be cold-adapted and temperature-sensitive by being cultured at progressively colder temperatures. It is then used as a vehicle to combine with the genes for the current virus, and then it is attenuated. Specifically, the genes used are those that encode the virus strain's unique hemagglutinin (HA) surface glycoprotein.

Although it has been used for many decades, the egg system in general is not a perfect system for several reasons. One problem with egg incubation is that it takes a long time. Even though the actual viral replication time is short (a few days) the entire process from start to end takes several weeks to obtain a sufficient amount of virus. Growing human viruses in an avian environment also presents a problem. Recent research reveals that it prompts the (human-adapted) virus to adapt to its foreign (avian) environment. This means that by the time the viruses are harvested, there is a chance that the immunologically important HA structure has mutated away from that of the original virus. The altered-HA virus in the vaccine now matches a different antigen, not the one causing people to get sick. This is a problem found especially with H3N2 strains of type A virus, and there are some questions about this happening with H5N1 as well. These two subtypes are part of most yearly vaccines. The H3N2 subtype in particular, for unclear reasons, grows poorly in eggs. Some years the virus grows so poorly that egg incubation fails altogether. When it does grow, it often means that its HA glycoprotein has mutated to help it replicate better (another function of this HA molecule). In this case, the HA either no longer matches the original antigen or its mutation reduces the ability of our antibodies to attach to it. Either mutation makes the vaccine less effective against H3N2 viruses. A fourth problem is that the timeline between virus identification and vaccine availability is 4-6 months, plenty of time for the "wild" virus itself to mutate within the human population so that the vaccine no longer targets it. A fifth worry is that because these are avian-type viruses that could also make chickens sick and die, a sudden pandemic of a virulent H5N1, H3N2 or other avian-type virus could come on scene without a ready supply of eggs. These are the primary reasons why we sometimes get frustratingly low success rates with the yearly flu vaccine, and why we need a better method soon.

Cell-based Flu Vaccine

In 2012, Flucelvax was the first flu vaccine manufactured using cell culture technology to be approved by the FDA in the United States. In this case, the virus was cultured in mammalian (dog kidney) cells) instead of a chicken egg, an environment that is more similar to a human host environment. Dog kidney cells (a cell line called MDCK) are a uniquely suitable epithelial cell substrate for culturing the influenza virus. Not only are they very similar to human epithelial cells, avoiding mutation pressure, but the virus also replicates readily in these cells. You might wonder why human cells aren't used. The canine version of an interferon-induced protein doesn't resist viral replication as it would in a human cell line.

Using mammalian cell culture technologies has several advantages over the egg method. There is hope that viruses cultured in mammalian cells do not experience as much pressure to adapt and mutate during culture. Importantly, while egg technology depends on having an egg supply (millions upon millions of eggs) ready, these culture cells can be frozen and banked, immediately ready for use, when a vaccine is needed quickly such as during a pandemic of a new strain. It also avoids possible allergic reactions against egg proteins and, finally, cell lines such as MDCK can be grown in a (supplemented) synthetic medium rather than commonly used fetal bovine serum. By avoiding bovine serum, the accidental transmission of some diseases such as spongiform encephalitis can be avoided. Since this method has been established now for a few years, why aren't most or all vaccines made this way, I wonder. Pharmaceutical companies appear to be reluctant to invest in switching over their technology.

DNA-based Flu Vaccine

A new and exciting approach currently underway goes even farther. The idea here is to isolate part of the particular virus's genetic code and inject that into the body, rather than the virus. The code will also contain special DNA code that allows it to enter our cells and direct them to make a flu antigen. Rather than a whole virus, this antigen could be the HA receptor itself or another viral segment. This approach would mean isolating a particular segment of the viral RNA and replicating it in large numbers in a cell culture. Like the cell-based method, this high-tech process takes much less time than isolating the virus and growing it in chicken eggs. Because the isolated genetic code remains identical to the virus's original RNA code throughout the process, there is no longer any problem with genetic drift (mutation away from the original). The vaccine is always an exact match to the virus. As long as the "wild" virus doesn't mutate in the human population during manufacturing time, it will match the virus making people sick. This shorter process reduces the window of time when that can happen as well. One problem encountered so far, however, seems to be getting the body to make a strong enough immune response. For unknown reasons, isolated parts of the flu virus (such as the HA receptor glycoprotein) do not stimulate as vigorous a response as an invasion of the whole virus does.

A Universal Flu Vaccine

Flu viruses are notorious for their mutation rate. This is probably the biggest hurdle faced when each yearly vaccine is created. By the time the vaccine is made, the virus has changed again. Some parts of the virus mutate at faster rates than other parts, and this can be exploited to make a universal flu vaccine. Our immune system naturally recognizes the HA receptor glycoprotein as an antigen and makes antibodies against it. As mentioned earlier, the HA receptor has two parts - a head and a stalk. Both the head and the stalk contain antigenic proteins but the immune system prefers to focus on the immunodominant head and makes antibodies against it. The problem is that head part of HA receptor mutates very often, meaning that antibodies induced by a flu vaccination often miss the mark. The stalk part, however, doesn't change much over the years. These proteins are encoded by conserved components of the viral genetic code.

In 2009, researchers discovered that the body also makes antibodies against the HA stem but not in as high a titre. The stem contains most of the virus's membrane fusion machinery. An antibody that binds to it blocks it and prevents the infection of epithelial cells, stopping the flu infection in its tracks.

If one can make a DNA vaccine against this conserved part of the virus, one can target the flu virus no matter what new strain it has mutated into. That is how a universal vaccine can be made against all influenza strains. The trick is to get the body to make a lot of stalk antigen and then to make a lot of antibodies against it, which it doesn't naturally do. The immune system tends to go for the HA head and ignore the stalk. One approach being investigated is to attach part of the stem to another protein called ferritin. The ferritin serves as a kind of glue that sticks a bunch of stem parts together and highlights their presence to the immune system. Another approach is to chop off the heads of the HA molecules and modify the stem so antibodies can attach to it more effectively.

A robust immune response against the flu viral HA stalk means the body will launch a rapid offensive against any future flu virus it encounters. If the researchers are lucky, it could even be a one-time vaccination if the production of memory B cells against it is robust enough, doing away with the hassle, significant expense and uncertainty of coming up with new yearly vaccines. Perhaps most importantly, it could protect us from the next highly pathogenic "pandemic" virus to come along, saving countless lives. It is frustrating for us to sometimes come down with the flu even after we've been vaccinated and to worry about the next inevitable deadly flu epidemic. It may seem that too little is being done to improve things but there are many lines of research underway that are focused on a new and better flu vaccine. It takes time, however, because each promising approach must be tested in preclinical (test animal) trials and if they show promise, and are proven to be safe, they can move on to clinical (human) trials, a process that generally takes several years. Still, what I've read makes me hopeful. I can imagine a day when my personally dreaded "Christmas flu" (even more dreaded than fruitcake) will be just a story from the scary old days. More importantly for all of us, we may soon never have to worry about a horrifyingly deadly pandemic like the1918 Spanish flu ever again.