What has happened to the ordinary human-infecting coronaviruses?

These harmless cold-causing viruses appear to have been displaced by Omicron, in much the same way as pre-Omicron SARS-2 lineages displaced influenza.

The CDC helpfully track ordinary human coronavirus infections in the United States. Here is their surveillance since late 2020, expressed by test positivity:

The purple line is what we’re most interested in. That’s OC43, the virus that likely jumped from cows to humans in the later 19th century causing a worldwide pandemic. Now it’s just one of four ordinary coronaviruses that nobody cares about. Note how OC43 infections seem to have collapsed precipitously in May of this year. This ought to have been their peak, if 2021 is any guide. Note furthermore how OC43 is just totally gone now. This used to be the dominant coronavirus in the United States and everywhere else too, but suddenly it’s nowhere to be found.

May 2022 was the peak of the Omicron wave in America. As soon as Omicron surged, OC43 vanished. German surveillance data is much lower quality, but it shows, very roughly, the same pattern:

Our surveillance doesn’t differentiate among the human-infecting coronaviruses, but this doesn’t matter for our purposes. Since May, almost none of the sentinel swabs come back positive for an ordinary coronavirus at all. Through the end of 2021, in the era of Delta, these hCoVs were more common than SARS-2. Now it looks for all the world like SARS-2 has replaced them.

This chart also illustrates another phenomenon that has accompanied Omicron, namely the return of influenza. As soon as the new Omicron strains began replacing the prior Delta lineages, the flu started to creep back. The mystery of disappearing influenza, which has been with us since the earliest days of the pandemic, is no more in the era of Omicron.

Despite its genetic similarity to prior SARS-2 lineages, Omicron is a fundamentally different pathogen. Earlier strains were more severe, because they depended on what is called attendant-mediated transmission. They were adapted primarily to circulate in healthcare institutions. Omicron, on the other hand, circulates primarily via direct contact in the population; this is a different strategy, and one which probably places a firm upper limit on its pathogenicity. If you cast your eyes back over the infection statistics of the past three years, you could even say that we have had two pandemics. The first, consisting of the wild-type, Alpha and then Delta variants, was superseded by a second, very different Omicron pandemic.

The mechanisms of viral interference remain opaque to us, yet it seems clear that the pre-Omicron variants interfered directly with influenza, while leaving the other human-infecting coronaviruses undisturbed. Direct-contact Omicron can suddenly coexist with the flu, but it has displaced the greater part of ordinary human coronaviruses. We’ve added a whole new seasonal pathogen, in other words, and yet the overall respiratory disease burden hasn’t substantially increased.