Covid in Wisconsin

Amateur analysis of our local Covid data.

Variants

20 Feb 2021

This week three additional cases of the B.1.1.7 coronavirus variant were detected in Wisconsin. What is this variant, and what does it mean for Wisconsin?

The manxome foe

Beware the Jabberwock, my son!
   The jaws that bite, the claws that catch!
Beware the Jubjub bird, and shun
   The frumious Bandersnatch!*

The original coronavirus was bad enough (the Jabberwock = “Covid Classic”, obviously). But as soon as we thought we might have that one handled, new variants of the virus have sprung up to afflict us.

The first important variant is B.1.1.7, which became dominant in the U.K. and is thought to be more transmissible and possibly more deadly than Covid Classic. The second is B.1.351, which emerged in South Africa and is thought to less affected by existing Covid immunity. This means that people who have already had Covid can be more easily reinfected, and that the existing vaccines appear to be less effective to some degree.

(Clearly the Jubjub bird is B.1.1.7, since as a bird it travels more easily, and the Bandersnatch is B.1.351, “frumious” meaning “less affected by existing immunity.”)

So far B.1.1.7 is the larger concern. Since it is more transmissible, once introduced it should gradually out-spread Covid Classic. If B.1.351, in contrast, is not inherently more transmissible but is somewhat more able to reinfect those with immunity, this is not immediately as great an advantage. Once most people have some natural or vaccinated immunity, this variant will probably become the bigger concern. (Although Moderna and other vaccine makers are talking about preparing booster shots for it.)

He took his vorpal sword in hand;
   Long time the manxome foe he sought—

How common are these variants right now? The CDC tracks all known cases in the United States by state. There are hundreds of known examples of B.1.1.7, but only a few of the others. California and Florida each have a few hundred known cases, and the other states only a smattering. Wisconsin has only had 5 known cases of B.1.1.7, and none of the others.

A recent preprint estimated the prevalence of B.1.1.7 in the United States and how fast it is displacing Covid Classic. They estimated that at the end of January, B.1.1.7 accounted for 2% of cases in the United States, and its share of cases was growing at 7% per day, which implies that it is about 40% more transmissible than Covid Classic.

A growth rate of 7% per day corresponds to a doubling time of 10 days, which sounds alarming. But it is important to note that this is the growth in share, the proportion of all Covid cases that are from this variant. The overall numbers of Covid cases will follow the Classic trend - which is decreasing - until the variant becomes a substantial fraction of total cases. At that time, we could see another wave as the variant’s increased transmission outweighs the our current resistance.

An uffish thought

So rested he by the Tumtum tree
   And stood awhile in thought.

To see how this might play out in Wisconsin, I made a very simple model pictured below. I eyeball-fit a decreasing exponential curve to Wisconsin’s case trend since mid-January. (Decreasing 3.8% per day, or a reproduction factor of R=0.81, with a 5-day transmission interval.) I then assumed that prevalence of B.1.1.7 was 2% at the end of January, and that its transmissibility was 40% higher (so R=1.1, or increasing 2.7% per day). The sum of the two models the total Covid cases per day over time. Under these assumptions, the case rate would level off at the beginning of April and then begin to rise again, reaching a level comparable to today by June.

WI variant estimate

This is not a prediction, but an illustration of what might happen if current trends just continued indefinitely. The most important observation, I think, is that it shows that we probably still have many weeks before any return to increasing cases. In that intervening time, we have our own weapons to wield.

One, two! One, two! And through and through
   The vorpal blade went snicker-snack!

First, every week almost two hundred thousand vaccines are getting administered. Over 10% of Wisconsin residents have had at least one dose so far, and if we maintain this pace another 10% should have one or two doses by the end of March. This will include a majority of people over 65. There will still be a long ways to go, but this is enough vaccination to further reduce transmission and to prevent a large proportion of the worst outcomes.

Second, I believe the virus must have a strong seasonal change in transmissibility, higher in winter and lower in summer. Every week that passes brings us closer to spring and lower transmission.

Finally, the B.1.1.7 prevalence may not even be as high as 2% in Wisconsin. The paper’s prevalence estimate for the United States did not include any samples from Wisconsin, because it was based on a single company’s data. But Wisconsin has been doing its own decent amount of coronavirus sequencing. We have found 5 cases of B.1.1.7, but that is out of thousands of samples. This article from mid-January reports 4400 samples; presumably it is higher now. A total of 5 positives out of probably more than 5000 samples would suggest a prevalence more like 0.1% at the moment, not 2%. That buys us even more time.

So overall I am optimistic that vaccines and seasonality will win the race against B.1.1.7 in Wisconsin, and things will be mimsy again…although of course there is still much uncertainty.

’Twas brillig, and the slithy toves
   Did gyre and gimble in the wabe:
All mimsy were the borogoves,
   And the mome raths outgrabe.

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