Tuesday, December 21, 2021

No, 73% of US COVID-19 Cases Aren’t Omicron Yet (Prep.)

Something extremely odd happened this afternoon. The press, including the New York Times, the Washington Post, CNN, the Wall Street Journal, USA Today, and Axios, reported that the CDC had announced that 73% of US COVID-19 cases were now being caused by the Omicron variant, and major public health gurus like Ashish Jha, Eric Topol, Florian Krammer, Eric Feigl-Ding, and Scott Gottlieb circulated the reports at face value. But that’s not really what’s happening. There was some kind of bug in an automated statistical algorithm at the CDC, known as the variant proportions Nowcast. Omicron isn’t really dominant in most of the USA yet (although all evidence continues to indicate it will be soon). And the bug in Nowcast went from a quiet database update on a quiet CDC web page, to a national press sensation, in a matter of hours. 

 What actually happened? No humans at the CDC stood up in front of a podium and announced the 73% number, or wrote a press release. It came from the CDC’s automated COVID data tracker website. But it’s also not a statement of hard data, it’s the output of an algorithm called the Nowcast. The Nowcast algorithm is based on the CDC’s variant proportions data. Every week a small percentage of US COVID-19 cases are subjected to genome sequencing, which identifies them by strain. Right now it’s about 3.6%, but it varies by state. The CDC collates this data to produce weekly reports on the prevalence of each variant in each of ten regions of the continental USA. However, the genomic data takes time to generate and process, then get deposited into genomics databanks, then get analyzed by the CDC, so the newest data is about two weeks old at each weekly refresh (today, sixteen days old; the week ending December 4). 

 To display an estimate of current prevalence, the CDC uses an algorithm it calls a “Nowcast,” to project forward from two weeks ago and give an estimate of current prevalence for different strains. The Nowcast algorithm has been remarkably accurate and useful in the past; I followed it with great interest as Alpha, Gamma, Delta, Mu, and other strains washed across the USA from early 2021 until Delta attained total dominance in the summer. It’s a significant achievement for the CDC, and I celebrate them for it. But something is on the fritz now. In this week’s update, which dropped Monday afternoon, the Nowcast algorithm is presenting results that don’t make sense.