The COVID-19 pandemic introduced a brand-new respiratory virus, SARS-CoV-2. With that introduction, as suspected, lots of things were thrown into disarray. One of those was the circulation of other respiratory viruses, bacteria and fungi. Here we’ll look at influenza viruses.

Background

Some suggested loudly that a rise in cases of other pathogens after the first waves of COVID-19 was due to the disease somehow interfering with our immune response, as with the human immunodeficiency virus. This was not the case.

Yes, like all viruses, SARS-CoV-2 has some tricks that interfere with our responses for a little while. But these aren’t a permanent destruction of our important immune cells. Our body doesn’t lose all of its immune memory, and it quickly replenishes its lymphocyte count after a drop. The snapback in numbers reflected a range of more practical issues related to the global pause in infections, which I’ve covered before in “The “Infection Pause”: because it’s about fewer infections, not an immune debt to repay“. I highly recommend reading that for context.

Influenza

Each year, “seasonal” influenza strikes in epidemic proportions, ticking up from a much lower baseline. Temperate zones see influenza viruses seasonally. The tropics have a higher overall caseload.

We see 3 distinct influenza viruses co-circulate each season (i.e., epidemic period), usually with one winning the “race” and dominating. However, sometimes one will dominate early and be replaced by another later in the season.

Before the COVID-19 pandemic, there were four of these, but our halt on travel- internationally and intranationally knocked out one virus: the Yamagata strain of seasonal influenza B viruses (B/Yamagata). To date, this virus has never returned to the wild and now only exists in laboratory freezers worldwide(😬). Our remaining seasonal influenza viruses are A/H3N2, A/H1N1 and B/Victoria. You may have read about A/H5N1 and many others- those aren’t seasonal influenza viruses. They are animal viruses that rarely spill over into humans, a phenomenon called a zoonosis, due to close contact with infected animals (usually birds).

The pandemic impact on flu

Influenza circulation was massively disrupted by our staying apart and masking, but mainly by slowing down its global travelator. Slowing and stopping external flights effectively halted the distribution of novel variants. In one case, we successfully removed a viral pathogen from humankind. Overall, we essentially stopped seeing seasonal influenza. You can see that period – marked by “Infection Pause” in the image below.

We still tested for the flu (I can assure you, as a lab dog, that is a true fact!). It just wasn’t there because it was so reliant on that variant refresh trvellator mechanism. Many other viruses and bacteria were also knocked down to incredibly low levels, the kind of low which many of us had never seen; such was the strength of the non-pharmacological interventions to prevent COVID-19 transmission until people were vaccinated. This was more successful in a handful of countries that took this approach than in those that chose not to or were too slow to react. Australia and New Zealand were examples of the former.

Then we turned the travelator back on

But, predictably, after the pandemic, respiratory viruses, including influenza, roared back as travel gates- both within countries and between countries- were slammed open and humans mingled once again.

Having never lived through the rapid emergence of a novel and highly transmissible respiratory virus, we only had history to go by – and that history had few of the diagnostic and investigative tools we have today. How long would the disruption to respiratory virus circulation last? Would patterns ever return to “normal”? Would other viruses disappear? How would SARS-CoV-2 fit in? Would virus-virus interactions impact other viruses’ seasons? How?

Initially, we saw large surges in viruses such as respiratory syncytial virus (RSV) and metapneumovirus (HMPV), as well as in bacteria such as group A streptococcus and Bordetella pertussis (cause of whooping cough). And we’ve seen early, huge influenza seasons. Until 2026, all of those, except influenza, had spent two or so years in higher-than-normal-number territory, then settled back down.

It looks like it’s not influenza’s turn.

Flu Season in Australia

Before the COVID-19 pandemic, Australia’s flu season usually peaked just after July, and cases started rising above the baseline in June.

I went into this in “Flu down under is a July thing“, from where this graph originates.

Once SARS-CoV-2 drove people apart and then they came back together again, Australia’s flu season peak shifted to before July for a time, and, more consistently and clearly, it also started much earlier and reached higher peaks (aided by more testing). I think the difference in start and size is pretty clear from the next two graphs.

Firstly, looking at the COVID-19 pandemic period to date, the season began to rise in May, not June, building from a relatively high summer and autumn baseline.

Secondly, if we add back all the years on record, you can see how different it used to be. But what’s notable is 2026. It’s gone against the pandemic pattern and looks like it might be returning it to normal.

In the next graph, you can see that in May, we finally saw a rise in some jurisdictions (New South Wales and Western Australia) compared to the preceding month; the first change to the month-on-month decline pattern we’ve been seeing this year. Flu may now be picking up. Time will tell on this.

So, after big years that have seen two years of A/H3N2 and two of A/H1N1 dominance, perhaps the immune systems of a suitably big chunk of us are somewhat reset? Because influenza vaccination levels are low, I assume this is due to infection for the most part, with those vaccinated contributing their immunity as well, though they are not the majority.

Is two years the magic number to reset an infection pause?

So just to throw this out there: is two years enough time after an event like the COVID-19 response to reset a given pathogen’s immune levels in the majority of the community following an infection pause and return a circulation pattern to normal?

I think that it is.

So this might be another chapter in the pandemic playbook, which was in need of writing.

References

1. The “Infection Pause”: because it’s about fewer infections, not an immune debt to repay
   https://virologydownunder.com/the-infection-pause-because-its-about-fewer-infections-not-an-immune-debt-to-repay/
2. Every flu season is a soup of viruses
   https://virologydownunder.com/every-flu-season-is-a-soup-of-viruses/
3. Flu down under is a July thing
   https://virologydownunder.com/flu-down-under-is-a-july-thing/