If you're getting a little confused and dizzy by the back-and-forth with the CDC's color tiers and the COVID status of Bay Area counties, you're not alone. But rest assured that while cases seem to be leveling off, transmission of the virus remains fairly low in San Francisco.

The Chronicle blared the headline last week that "Entire Bay Area is back in CDC's orange and red tiers for COVID spread," and while true, this was a somewhat misleading and panicky proclamation. San Francisco County and others nearby have bounced in and out of orange- and red-tier territory for weeks now. The reason is just that, unlike the state color-tier system that we got used to last year, which had a two-week lag time, this system updates daily, and a slight shift in positive COVID tests can push a county in or out of a tier in just a day.

To explain the system: The CDC is adding up all the COVID tests over the previous seven-day period, and calculating the rate of new cases per 100,000 residents, every day at 8 p.m. ET, Monday to Saturday, as well as the test-positivity rate.

In San Francisco as of Saturday, we had 404 cases over the previous seven days, which comes out to 45.83 cases per 100,000 — with 50 being the threshold between the yellow or "moderate" tier and the orange or "substantial" tier. The test-positivity rate remains low, at 1.48%. San Mateo County is doing similarly, with a new case rate of 47.09 per 100,000, and a positivity rate of 1.22%. Both counties are now in the yellow tier again, after being briefly in the orange tier last week.

As you can see in the map below, one California county is showing up in the blue or "low" transmission tier, and that is Alpine County, because it reported zero new COVID cases over the previous week. This is misleading though, because Alpine County has only 1,039 residents, so if it even had one case it would automatically jump into the orange tier.

The latest CDC county-level map showing San Francisco, San Mateo, and Monterey counties in the yellow tier. The rest of the Bay Area is in the orange tier.
Data via CDC

If San Francisco continues bouncing between the yellow and orange tiers for a while, that is not necessarily cause for concern. As Stanford immunologist Dr. Robert Siegel told the Chronicle last week, "As long as there’s virus in the population, as we increase our risk behaviors, we will see more infections." And where we are reaching now is what experts consider a "tolerable risk level" based on the community's behavior, which leads to a certain, steady number of new cases but still very few deaths.

Mass vaccination of the Bay Area's kids ages 5 and up will lead to still lower case numbers and less community spread of COVID. However as adults' immunity wanes from vaccines received early this year and previous infections, if most people don't seek out boosters, there will continue to be spikes in cases, says Dr. Bob Wachter of UCSF.

Wachter laid out the two sides of the equation for endemic COVID, and the equilibrium we may be reaching between forces driving cases up and forces driving them down, on Twitter. "Today's Covid situation is a version of the one we'll live with for at least next 1-2 years... perhaps moderately better or moderately worse (will vary by region), but unlikely to be massively better or worse," Wachter writes, adding, "It's not great."

In the good-news column, boosters and widespread vaccination including kids will continue to help, and as oral anti-virals get approved to treat COVID, we should see less and less hospitalization.

But because the disease has largely not been tamped down in wide swaths of the country, we still risk seeing a "nastier" variant come along to replace Delta. But, Wachter says, optimistically, "Delta's bad, but at least nothing worse is on the horizon." Not yet, anyway.

UCSF epidemiologist Dr. George Rutherford points to the fact that deaths in San Francisco have remained very low in this pandemic — and the number of deaths during the 1918-19 flu pandemic were five times higher than in this one, during a time when the city's population was much smaller.

"In the Bay Area, we’ve handled this better than anybody,” Rutherford told the Chronicle. “We’ve handled this as best we can."

Meanwhile, conservative parts of the country where there are high numbers of Republican voters who refuse to get vaccinated, and where there's hostility to mask-wearing, continue to see much higher mortality rates from COVID. As the New York Times reports, the red-state vs. blue-state gap in COVID deaths is widening each month, and in October, 25 out of every 100,000 residents died from COVID in counties that voted for Trump, a rate more than three times higher than in Biden-supporting counties.

The gap seems to have peaked, however — and it seems likely that in heavily red counties where little pandemic precaution has been taken, there is a growing level of natural immunity from previous COVID infection that is far higher than in liberal counties where people have followed all the public-health rules. Thus, the two kinds of immunity, from vaccination and from previous infection, are beginning to even out the mortality rates across the political divide.