Feb 5 Bay Area COVID Update

It has been 2 weeks since I posted my latest update on Facebook. LAter in this post I talk a little bit about the variants.

Over the past two weeks, the clear Bay Area trend looks cemented (log plot, upper left) and new daily case have fallen by nearly a factor of 2. This is somewhat steeper than the decline off the summer high. That summer decline slope has been closely replicated in nearly every US location I have watched during declines in this pandemic, and corresponds to a reproduction rate (R₀) of about 0.8 assuming a 6.5 day reproduction cycle time. (This wikipedia section has a accessible treatment of the basic math of R₀. In those equations, 𝜏 is the cycle time.)

The individual Bay Area counties I track have about the same relative offsets as always. It is interesting to me how LA County and Solano have tracked so closely. I suspect a demographic relationship means people end up having similar amounts of interactions through work, but this is speculative. I have not looked.

I have been providing some hospital tracking data in a couple of counties where friends work in ICUs. I believe Santa Clara County will closely track the Bay Area overall since it is pretty easy to move patients between hospitals in the area. There has always been a lot of scatter in the available ICU bed tracks, and for the first time I think there is a clear uptrend in Santa Clara county and maybe one beginning in Sacramento. Hospitalized COVID cases have declined a lot.

The purple and red dashed lines refer to a metric different levels of state mandated risk management precuations under the “Blueprint for a Safer Economy” system. There are other metrics besides case counts.

The variants of concern case counts continue to climb, but even if I had time phased data there is likely little value in plotting since genetic sequencing of samples is still low (last I heard was around 2300/week in the entire US, which is a huge improvement over the pathetic 250 from 3–4 weeks ago) and is not being performed in any kind of systematic way. Of note since my last update is more B.1.351 lineage (South Africa variant) and now some P.1 lineage. P.1 is a troubling variant which has ripped like wildfire through Manaus, Amazonas Brazil , where an estimated 75% were infected last year, raising concerns about immunity duration.

B.1.1.7 Lineage

Here are my thoughts on the B.1.1.7 from about 3 weeks ago. This is the more transmissible variant that appears to have originated in the UK. I still believe by the end of this month it will start to be clear if this is going to be a problem.

Today (2/7) I came across a preprint on B.1.17 spread in the US. The investigators use a particular gene deletion (SGTF, S-gene test failure) as a proxy for B.1.1.7 lineage detection. A PCR test called TaqPath looks for three segments of the SARS-CoV-2 genome. One of the three is negative in the B.1.1.7 lineage due to a gene deletion. The authors of the preprint on US spread performed whole genome sequencing (WGS) on many samples with the missing gene to see if it is indeed B.1.1.7. They use the ratio as a correction factor to apply to the number of SGTF test results in the otherwise positive samples to turn it into a a proxy test for B.1.1.7.

The authors applied this technique to all the COVID tests processed by Helix between 12/15/20 and 1/30/21 ( ~ 500,000 tests) and they share their results. Just to be careful if proxy test correction factor changes for some reason, they continually recalculate it for each batch of tests. Figure 1from their paper tells the tale. (The orange bar correction factors areinferred from the prior proxy correction factor because of a time lag in getting WGS results.)

The areas that, all things being equal, would have a higher reproduction rate are where the new variant becomes dominant sooner. It reproduces more effectively, so the more overall transmission, the bigger a leg up it gets on other virus lineages. So, Florida can expect B.1.1.7 to be the dominant lineage in early March, and California a month later. March could be rough in Florida….Gotta get those vaccines in arms ASAP.

An interesting note in the paper is an examination of older samples finds B.1.1.7 in the US in mid to late November and at least 6 separate introductions total that are seen in the data today. As usual another rip on the value of travel restrictions. It was already here even as scientists in Britain were onlybeginning to wonder if there was something new going on. It was mid December before they started pulling the picture together, and travel restrictions in the US requiring folks from the UK to quarantine did not go into effect until 12/28, at least a month after it had been introduced to the US.

New Variant Severity

The data is still coming into focus on this. There just have not been enough cases to be sure, but it is starting to look like death is 20–30% more common in older populations in the UK according to the UKs NERVTAG (New and Emerging Respiratory Virus Threats Advisory Group). It looks higher in younger folks too, but too soon to be sure as their death rates are lower so there were not good statistics as of 1/15 when that report was compiled. Any difference will be clear in the UK before anyplace else because nearly all of their cases are B.1.17 now, so better statistics.

I have a background in science. I back up nearly everything science I write with peer reviewed research, or at least preprints and pointers to my data sources