The United States has been having one of its biggest influenza (flu) years. Let’s look at how this season’s northern hemisphere flu vaccine, which most Americans most likely didn’t seek out, matches up to the viruses that are around.

What do this season’s flu numbers tell us?

Both seasonal fluA subtypes are dominating about equally: A/H1N1 & A/H3N2 with barely any FluB cases.[1]

The third figure below clearly shows that this is one of the biggest influenza seasons the US has reported in at least 15 years in terms of positive cases per 100,000 population. It looks like it has peaked, but we won’t know that until the next report because late data often still comes in when any report gets published.

What version of A/H1N1 and A/H3N2 are in the wild?

The CDC Report shows the breakdown of different clades (similarly grouped genotypic variants) for the FluAs, as shown below.

Like the SARS-CoV-2 variants we hear so much about, flu viruses evolve constantly. Survival of the fittest means that mutations that convey an edge to newly created virus particles compared to their old-fashioned parents will make those particles more likely to spread effectively to more humans over time. This means the lettering below constantly changes because we need names to talk about “things”.

There are two main clades of A/H1N1 co-circulating – 5a.2a and 5a.2a.1. The C.1.9 and D.5 subclades are the biggest sub-groupings of genetically similar viruses (subclade) after that.

Among the A/H3N2 viruses, the clade 2a.3a.1 dominates, as does subclade J.2.

These data were from Week 5, so I looked at Week 1 to see if there had been a change in the clades or subclades that might explain that strange dip at Week 2 (to 11-JAN), but the virus split is as for Week 5.

These groupings of genetically similar viruses (called clades) are based on how differences in the sequences of the hemagglutinin (HA) gene are represented in tree-like computational comparisons (called phylogenetic trees).

The HA gene’s product is similar to the SARS-CoV-2 Spike protein in that it’s used for attachment to the cell. It’s a viral surface protein to which we mount most of our immune responses. Therefore, there is constant pressure to change so that the virus can escape our virus-killing defences. Because this is evolution, new viruses must contain the changed protein before any escape can happen.

The Northern Hemisphere 2024-2025 influenza vaccine formulation

This season’s northern hemisphere flu vaccine was recommended to contain purified HA antigens (the active ingredients) from the viruses below after considering the nature and fitness of past, present, and predicted future viruses.[3]

Keep in mind that the vaccine components were recommended 23-FEB-024, and then the US FDA met on 05-MAR-2024, and the vaccine was ready in about June for an August release.[4] If you’d like to learn more about the process, there are some links here [6], here [7], and here [8], a great but old infographic here [9] and a newer one here.[10]

So the $64,000 question is, how close to that vaccine formulation are the viruses used to make it compared to the current “wild” A/H1N1 and A/H3N2 viruses infecting people in the United States?

Genetic virus sequences and ferret blood

Remember that a flu vaccine intends to reduce disease severity by getting us to mount an immune response against HA safely. Hence, we’re better prepared to meet a wild version of a virus carrying that gene and studded with that protein. But the wild version’s HA gene will have evolved in the meantime. How much impacts the vaccine’s effectiveness

Sequences

Let’s go to the best open-access influenza virus gene sequence-viewing database, Nextstrain.[5] You can adjust the A/H3N2 landing page to be A/H1N1, or you can also look at the neuraminidase (NA, or the “N” from H1N1, H3N2, H7N8, H7N3, H7N9, H9N2, or H5N1) gene sequences as you like.

A visualisation of the fluA and fluB genomes, which are in pieces (let’s call them genes to keep it familiar).
Flu viruses can swap their genes to create all new strains (antigenic shift).
It’s even possible for two flu viruses with the same name, e.g. H1N1, to contain segments that are different from each other, acquired from different flu viruses, as happened in the creation of the 2009 pandemic H1N1pdm09 virus.
A lot is going on underneath the very cursory name! See here for some background.[13]

Marked on the Nextstrain genetic comparison representations (“phylogenetic trees”) made up of the HA gene sequences from lots of patientsare the A/H3N2 vaccine viruses that were recommended for the 2024-2025 Northern Hemisphere egg-based or cell culture-based vaccines. They are marked with an “X” – as are past and future vaccine viruses. We’ll be referring to this later.

In the next figure, we can see the same style of tree but made up of the HA sequence of A/H1N1 viruses, again using bold X markers for the vaccine viruses.

Now, we’ll add back into a bigger tree the viruses collected from sick people in the US over the last 12 years. The most recent strains are the furthest to the right of the tree in Figure 4 below. The colours indicate the names given to each group of similar genotypes (a “clade”) or their subgroupings (a “subclade”) because naming things matters!

This tree shows that the most recent samples contain viruses clustered into subclades D.3, D.5 and C.1.9, which agrees with the Week 5 CDC report.

Figure 4 still shows the 2024-2025 vaccine viruses – the topmost two X marks (see above for a reminder). These are “near” the subclade D patient viruses. Genetically, they cluster differently and are “away” from subclade C.1.9 viruses.

Next, I used the tools on Nextstrain to rejig the tree to present “antigenic advance” (Figure 5). The vaccine virus HA sequences are still the topmost Xs, as I understand this, regarding how the immune system sees them. More red means a bigger change to the proteins that matter for antibody recognition compared to the first pandemic A/H1N1 virus sequence from 2009. Blue indicates less change. For A/H1N1, there isn’t a massive change among the main subclades circulating in the US. A step change occurred around the 2018-2019 season when clade 5a.2 emerged (not shown here).

Moving on to A/H3N2, I’ve just used the antigenic advance tree. The vaccine virus sequences are the second and third distinct Xs from the top next to the J subclade label. Most of the A/H3N2 viruses being detected in the wild during the 2024-2025 season are more often genetically and a bit antigenically distant from the vaccine virus. Viral changes play a significant role in how effective (the word means use of real-world human patient data rather than trial data) a vaccine can be. In addition, there’s been a drop in US vaccine uptake, at around 40%, down from 50% pre-pandemic (much better than AUstralia’s rates, by the way😒).[10]

But do these pretty colours, trees, and genetic changes mean anything to the battlefield inside our bodies?

Testing vaccinated ferret antibodies against cultured wild flu viruses

The CDC immunise ferrets with the current vaccine and collects their blood for its newly made antibodies. They also culture a small sample of representative flu viruses from the current season’s patients to see how well the vaccine-made ferret antibodies block the contemporary human flu viruses. A laboratory method called haemagglutination helps here.[11]

The Week 5 report showed that A/H1N1 viruses reacted well with antibodies from the blood of immunised ferrets. This means that if you were vaccinated and become immune, you should be protected from severe disease due to A/H1N1 infection. There are exceptions, of course. Something about your history of flu infections (called an imprint) may interfere with producing vaccine antibodies. Also, ferret antibodies may not tell a story as accurately as human antibodies.

If you weren’t vaccinated, you obviously have no chance of getting protection from a vaccine!

For A/H3N2, though, the vaccinated ferret antibodies only did well, recognising about 42% of patient viruses. So there’s a decent chance that even though vaccinated, you could still get decently ill due to A/H3N2 viruses that have significantly evolved between when the vaccine viruses were decided upon in February and when you got a shot around August or later. If you take a close look at the legend of Figures 5 and 6, you will see that the H3N2

2024-2025 is a big season

For whatever reason(s), both seasonal FluA viruses are having a big year in the US. This may impact the southern hemisphere’s flu season. Hence, it’s interesting to note that the A/H3N2 vaccine virus recommendation for the southern 2025 winter vaccine is for a different virus than was used in this season’s northern hemisphere flu vaccine.[12] This brings it closer to the action in subclade J.2 (see top Xs in Figure 6 – there are actually two of them, egg and cell culture).

The flu vaccine’s effectiveness has never been great (see below; [14]) and can be a lot worse some years compared to others, but it is still the safer way to get immunity. But keeping up with the rapidly evolving viral target is something we’ll be able to do better once we move on to “universal” flu vaccines in the future.

References

1. https://www.cdc.gov/fluview/surveillance/2025-week-05.html
2. https://virologydownunder.com/flu-genes-clades-and-h3n2/
3. https://www.who.int/publications/m/item/recommended-composition-of-influenza-virus-vaccines-for-use-in-the-2024-2025-northern-hemisphere-influenza-season
4. https://www.cdc.gov/flu/whats-new/trivalent-vaccines-2024-2025.html
5. https://nextstrain.org/seasonal-flu/h3n2/ha/2y
6. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/covid-19-vaccines/explainers
7. https://www.cdc.gov/flu/vaccine-process/?CDC_AAref_Val=https://www.cdc.gov/flu/prevent/how-fluvaccine-made.htm
8. https://www.niaid.nih.gov/diseases-conditions/influenza-vaccine-production-and-design#:~:text=The%20most%20common%20method%20used,%E2%80%9D)%20recommended%20flu%20vaccine%20virus
9. https://backslashcoding.com/work/old_ifpma/resource-centre/the-exciting-journey-from-flu-virus-to-vaccine/
10. https://www.cdc.gov/flu/whats-new/2024-2025-flu-activity-vaccine.html#:~:text=Flu%20vaccination%20coverage%20is%20about,same%20time%20point%20(40.6%25)
11. https://virologydownunder.com/influenza-virus-haemagglutination-a-sticky-technique-that-does-a-lot-of-lifting/
12. https://www.who.int/news/item/27-09-2024-recommendations-announced-for-influenza-vaccine-composition-for-the-2025-southern-hemisphere-influenza-season
13. https://virologydownunder.com/an-influenza-virus-is-the-sum-of-its-parts/
14. https://academic.oup.com/cid/article/76/3/540/6758391?login=false