H3N2 is 50 years old and still going strong

The highly variable H3N2 influenza viruses which seem to cause us the most trouble, heartache and headlines have only been with us since 1968. These tiny droplets of dread emerged 50 years ago, causing a pandemic but their constantly evolving offspring continue to cause the world trouble in 2019.

A schematic influenza A virus virion highlighting the exposed surface proteins (NA, HA and M2), the internal proteins (M2, PB1, PB2 and PA), the lipid layer stolen from the host cell as the virus leaves and the gene segments that make the proteins. In reality, there is more complexity to the packing of and contact between various components in the virion; this is a guide only.

Where did A/H3N2 come from originally?

Flu A/H3N2 first emerged in Hong Kong in 1968.[1,2] Before this, there were no human A/H3N2 viruses. A/H3N2 resulted from the mixing of 6 genetic segments donated by 1957’s pandemic human A/H2N2 with 2 from an avian A/H3N2 (PB1 and HA).[2] The emergence of this new virus led to a global epidemic (pandemic) which killed at least a million humans.[2]

A timeline of human influenza virus discoveries
Source: Virology Down Under

Where in the world a new flu virus emerges can be important in moulding its characteristics.[1] Also important is how a population moves about and, once immune, how a population forces change upon a newly adapting virus in order for that virus to escape population immunity.

Today A/H3N2-dominated seasons are associated with more death and higher rates of hospitalisation among older age groups than are A/H1N1 or fluB dominated years.[8,9]

Where are A/H3N2 viruses coming from today and what modifies their impact?

East, South and Southeast Asia produce most of the newest globally transmitting A/H3N2 variants.[1] These new versions have emerged through mutations that help them spread. The mutations change the viruses enough that they can avoid pre-existing human immunity from past H3N2 infections.

Seasonality is a factor in virus emergence and restriction but so is population size in a region.[1] Large host numbers allow emergent viruses to take hold and for rare mutations to have a better chance of expanding or being worked around if deleterious to the virus. Population age is also important – the regions listed above host birth rates that are higher than in some temperate regions.[1] Younger and less immune populations can encourage viral diversity because of the large number of susceptible human hosts an emerging virus can use to refine aspects of its game as it moves among them relatively unhindered.

Where is A/H3N2 going?

The viruses that comprise A/H3N2 continue to transmit among us, evolving genotypes (genetic variants) that are fitter and/or better able to evade the immune response we mount against them or the version we were previously infected with. A/H3N2 viruses often dominate big and severe flu seasons.[2]

The haemagglutinin (HA) protein and the
gene that encodes it, highlighted in yellow

It starts with a bond

A lot of how flu viruses trouble us revolves around them first attaching to our cells. The focus of this part of the infection is the exposed virus protein called haemagglutinin (HA for short).

Part of the HA protein interacts with sugar chains called sialic acids or glycans. Glycans decorate the ends of our cell surface and secreted proteins and lipids.[10,11] Many of the important antibodies we make to defend us from future flu virus infection target the head and stem of the HA proteins.[3]

Flu viruses evade our defences when they evolve mutants that both retain their necessary HA function and ability to grow and transmit, but still change enough to successfully slip out from under the pressure our immune system exerts.[4]

Figure Influenza A H1 haemagglutinin model. The model highlights the protruding head of one of the 3 HA molecules that form a trimer embedded in the virion. The head protrudes from the viral envelope and sits atop a stalk region called the stem. The HA head is under more pressure from our immune system and changes more frequently than the stem. Change helps the virus evade B-cell produced antibodies. Image adapted from Raymond et al, PNAS (2018) 115(1) 168-173 [5]

A/H3N2 viruses are known to change key antigenic sites on their exposed proteins during their forced switch from growing in us to growing in the eggs used in vaccine production.

H3N2 is 50 years old and still going strong and over that time, these flu viruses have changed the pattern of glycans attached to their own HA proteins. Addition of glycans can shield antigenic sites while loss of glycans can reveal new sites.[8,12] A/H3N2s have also altered their receptor binding preferences for our glycans, grown less well in a range of lab cells and had neuraminidase (NA), another of its exposed proteins and changed their agglutination of red blood cells (RBCs; a problem for detection that has reduced the number of animal species which can provide RBCs).[2,3]

The airways suffer from seasonal viral traffic jams

We’re constantly encountering viruses via inhalation and splatter. A/H3N2 has to contend with competition from other viruses seeking our cells to use as virus production factories. What happens in that space? Virus interference.

We know little about how distinct A/H3N2 viruses play with other respiratory viruses of which there are a couple of hundred. Could some help A/H3N2 infections while others hinder them? And to what extent are A/H3N2 and bacteria interacting to makes things worse (think secondary infection and disease complications), or better (think microbiome)?

Timing and intensity of flu seasons may be impacted by concurrent respiratory virus epidemics, but more research is needed to explore this area.

Past infection, immunity, age and imprinting

To make things a lot more confusing we have… immunity.

We know that the immune response we develop to our earliest symptomatic flu infections influences our immune responses for later life; they leave an imprint. This early priming influences how our immune response reacts to subsequent infections by related viruses and to vaccines containing components of those flu viruses. But our responses aren’t as simple as “hey, I’ll mount a full-blown attack with memory and everything” for each and every flu virus infection. Variability in our immune responses also affects how we react to flu vaccine components. Immune imprinting and flu have a published history that dates back to the 1950s and the field of research remains an area of relevance, study and ongoing refinement.[13]

For example, those over 55 years of age may have been imprinted by A/H2N2 (around from 1957) or A/H1N1 (around from 1918) viruses whereas young children may not yet have been imprinted by any symptomatic influenza infection.

A study from Canada

A recent paper by Skowronski and colleagues really highlights how important even the smallest A/H3N2 variations are when considered in the context of our past infections.[12] They can really mess with our current response to flu vaccines.

On rare occasions, a component of a flu vaccine doesn’t protect us well against a contemporary infection or even, as was the case in Skowronski’s Canadian study of the 2018/19 flu season, priming may increase the chance of illness after infection by a virus of this or that clade of A/H3N2 in among the vaccinated.[12] Intriguingly, this can come down to changes in just one or two amino acids.

The 2017/18 imprinting issues with clade 3C.3A A/H3N2 viruses centred on just 2 amino acids that have changed constantly over the decades. This figure shows the percentage of worldwide A/H3N2 viruses with specified amino acid residues at haemagglutinin protein positions 159 and 193, by year.
Source: Figure 3 from ‘Paradoxical clade- and age-specific vaccine effectiveness during the 2018/19 influenza A(H3N2) epidemic in Canada: potential imprint-regulated effect of vaccine (I-REV)’. Euro Surveill. 2019;24(46):pii=1900585.

Keep in mind that this was a specific event that required a particular A/H3N2 clade to rise in dominance, a particular vaccine formulation to have been developed during a particular season. A similar negative protective effect for this component was seen elsewhere.[14]

Skowronski and colleagues noted that this issue didn’t have the same impact on the other 3 viral components (A/H1N1, B/Yamagata and B/Victoria) of that season’s quadrivalent flu vaccine; vaccination was still much more effective than not have any vaccine, overall.[12]

The rise of the A/H3N2s

Yet another really interesting thing about A/H3N2 is apparent from the work of Bedford and crew, shown in the image below. It’s the way that this thing many of us mostly think of as “a” virus seems to be settling out into perhaps what might simply be called, a few viruses.

Since the late 1990s, H3N2 viruses have come and gone, usually hanging around as distinct “viral entities” (let’s just call them genotypes) for about 3 years.[6] Within that pattern, the genetic change is fairly constantly moving along while the change that our immune systems recognises – the antigenic change – stops and starts in a stepwise manner.[6] Maybe think of it as the motion of a caterpillar – the overall motion is advancing forward, but within that, the front has to wait for the back to catch up.

A/H3N2s: Behaving differently since 2015?

Then came 2015 and from then onwards (see the figure below), there seem to have developed 4 or so distinct, co-circulating genotypes of A/H3N2. These have all stuck around for longer than usual. Change continues but each of these genotypes seems to have put down some roots. The eldest of these A/H3N2 genotypes have roots that are perhaps 5 years old and they seem to be still hanging on.

An edited version of Slide 10 from Trevor Bedford’s (@trvrb) talk at the International Society for Influenza and Other Respiratory Virus Diseases (ISIRV) Optison X conference in Singapore, 28 August – 1 September 2019.
I’ve added a line to highlight the normal timespan during which approximately 3-year lifespan of H3N2 viruses (black line) and boxed the unusual change to this pattern seen from about 2015 onwards.
Source: https://bedford.io/talks/flu-forecasting-options-2019/

Is this expansion playing a role in what seems to be bigger A/H3N2-dominated flu seasons in recent years? It surely must be contributing to the specific underperformance of the A/H3N2 component of flu vaccines (as a virus, as a vaccine component and related to the immunity it induces).[7,8] As we saw above, it takes very little antigenic (and genetic) change for an A/H3N2 to escape vaccine-induced immunity.

Are we seeing more genotypes co-circulating each season and, for some reason, are they settling into some level of stability we haven’t seen before? Will each of these from a platform from which future reassortments will jump and ongoing mutation can continue to spin out new versions?

Why do A/H3N2 viruses seem to be worse for older people?

The other flu viruses aren’t generally so fast-moving. Trees for these viruses, made in the same way as the A/H3N2 one above, aren’t so tightly pruned; they have more upright trunks and more numerous branches. The non-A/H3N2 viruses seem relatively more settled.

There are a couple of main issues here. A/H3N2 viruses keep changing at such a rate that it “looks”, to our immune system anyway, like a different virus each season. We respond to that difference with inflammation which is what results in “the flu”.

Then there’s infection history. A/H3N2 viruses have only existed as distinct viruses since 1968 onwards so people born before and around this time won’t have received their first flu illness from them. And there’s also imprinting which we discussed above. This isn’t just a problem for vaccines; it’s a problem for wild-acquired infections too. Older people may have been imprinted by A/H3N2 viruses that increase their risks of illness following infections. They may also have been infected by A/H2N2 virus which passed its HA gene on to the new A/H3N2 and so could be less susceptible.

Going strong while we watch and wait

What does the future hold for H3N2? That’s a tough question to answer for flu…because flu.

The illness, the viruses that cause it and the hosts that transmit it are each complex things. I watch the outputs of the nextstrain crew closely. This lineup of experts has a great way of using imagery to show us what has happened in flu’ville, what is happening (usually more quickly than any public health entity) and what might happen in the future.

To do that, keep the following pages on frequent refresh:

We can also watch the A/H3N2 trees for expansion or retraction; the impact this has on vaccine selection and effectiveness and we can also hope that an entirely different flu virus doesn’t jump out at us while we’re watching A/H3N2.

H3N2 is 50 years old and still going strong; changing, peaking and killing. One day we’ll hopefully have some improved vaccine approaches which more effectively deal with these troublesome members of the influenza virus family, but it is not this day.


  1. Explaining the geographical origins of seasonal influenza A (H3N2)
  2. H3N2 influenza viruses in humans: Viral mechanisms, evolution, and evaluation
  3. Conserved Neutralizing Epitope at Globular Head of Hemagglutinin in H3N2 Influenza Viruses
  4. Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants
  5. Conserved epitope on influenza-virus hemagglutinin head defined by a vaccine-induced antibody
  6. Mapping the antigenic and genetic evolution of influenza virus
  7. Improving Influenza Vaccine Effectiveness: Ways to Begin Solving the Problem
  8. Influenza Vaccine Effectiveness: Defining the H3N2 Problem
  9. Hospitalizations associated with influenza and respiratory syncytial virus in the United States, 1993-2008
  10. Sialic acid tissue distribution and influenza virus tropism
  11. Sialic acids in human health and disease
  12. Paradoxical clade- and age-specific vaccine effectiveness during the 2018/19 influenza A(H3N2) epidemic in Canada: potential imprint-regulated effect of vaccine (I-REV)
  13. The ghost of influenza past and the hunt for a universal vaccine
  14. Spread of antigenically drifted influenza A(H3N2) viruses and vaccine effectiveness in the United States during the 2018-2019 season

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