After many months with little to suggest that SARS-CoV-2 was evolving to transmit more readily or evade immune responses, we are now concerning variants such as B.1.1.7 emerge and spread, as worrisome mutations such as N501Y, E484K, and L452R repeated evolve in disparate locales.

While I'm surprised at this turn of events, in retrospect I don't think there's much a mystery here. At first glance it might seem as if something has shifted in the way the virus is evolving. But I don't think this is what is happening.

Two key facts come into play.

First, in the US and throughout much of the world, genomic surveillance is very limited. We don't pick these changes up when they first begin to spread. We see them once they get common. So these functional mutations have been arising for some time.

Second, the total number of worldwide COVID-19 cases has been increasing almost exponentially since last Spring. This means there has vastly more opportunity for dangerous new variants to arise over the past few months. About half of all COVID cases have occured since November!

More cases occurred in September and October than in all months previous. And so forth.

I think that we are now seeing the consequences of allowing SARS-CoV-2 to continue spreading at ever-increasing pace.

Combinations of mutations that had not arisen yet in Spring or Summer arose once or several times in Autumn, and we're just now picking these strains up as the become prevalent in different regions of the world.

So it's not that the fundamental dynamics of the virus have changed. It's that we gave it enough rein to explore the so-called "fitness landscape" and find mutation combinations that make it more transmissible.

The other thing to keep in mind is the lag in detecting these variants. Until we have adequate genomic surveillance, we'll never know what is about to hit us.

Just as this autumn we didn't know about the more transmissible strains that were beginning to spread in our midst, there is every reason to expect there are now a number of more recent mutations of concern that arose this winter but we have yet to detect.

And because the total number of cases continues to grow exponentially, it is not hard to argue that more variants of concern arose this winter and remain undetected than arose in fall and now are on our radar.

In short, we need powerful genomic surveillance programs immediately.

Addendum: there are a few skeptics in the replies who doubt my assertion of near-exponential increase. Of course I checked it before making the claim. We see a linear increase on a semilog plot (below) since late summer, and near-linear since testing ramped up in spring.