Charts show how coronavirus positive test rates have roller-coastered in Bay Area counties

As California reverses course this week and shutters many reopened businesses in the counties on its coronavirus watch list, one crucial metric guiding health officials’ decisions is the positive test rate.

That figure, which officials refer to as the “positivity rate,” is the percentage of tests conducted that come back positive for coronavirus. The state threshold for counties to reopen faster is 8% over a seven-day period. California’s current positive test rate sits at 7.1%, and the latest 7-day moving average for the U.S. is 8.7%.

Lee Riley, an infectious disease expert at UC Berkeley, said the positive test rate is one of several ways to assess the trajectory of the epidemic, along with hospitalizations and deaths.

“The public should care because if any of these parameters are increasing, they need to know why,” he said. “They need to know who is not wearing masks and what social gathering settings are contributing to the increased spread. Then, these behaviors can be targeted for correction.”

But what does the positive test rate look like across different regions of the Bay Area, where seven counties — Alameda, Contra Costa, Marin, Napa, Santa Clara, Solano and Sonoma — are on the watch list?

We examined what the average positive test rate was over the past two weeks for each county, and compared that to the historical trendline to see how things have changed over time. For a number of counties, the changes are quite stark.

Top of the list: Marin, Solano, Contra Costa

Marin County tops the list right now with an average rate of 12.9%, the third highest in the state over the past 14 days as of Tuesday afternoon. That number includes the outbreak at San Quentin State Prison, which now has more than 1,300 active cases. The prison had zero coronavirus cases through May until the transfer of prisoners from Chino to Marin County on May 30, which led to the rapid spread.

Marin County doesn’t include the prison statistics in its reporting, and instead listed a 14-day average positive test rate of 7.1% as of July 10. But the state and The Chronicle’s Coronavirus Tracker include the San Quentin cases, which are putting a strain on local hospitals and contributing to community spread, since prison workers have also become infected.

Both of those numbers are considerably higher than what Marin was averaging at the end of May, about 3.7%, before the outbreak at the prison. And the county’s rate was just 2% in early May. Marin County has seen outbreaks in skilled nursing facilities, growing cases among essential workers and within the county’s Latino population.

Solano County currently has the next highest positive test rate in the Bay Area, at 6.3% for the 14-day period. The state points to outbreaks among farmworkers who live in Solano County but work at Napa and Sonoma vineyards. Like many other places that are reopening, county officials have tied many cases to more in-person gatherings among individuals who don’t live in the same household.

Contra Costa County is third highest at 5.1% over the past 14 days. The state reports a rise in hospitalizations paralleling the increasing infections. The 7-day average was last reported at 7.8% on July 12, and in May, it never went higher than 3.8%. The county recently implemented a stricter face mask order requiring individuals dining on restaurant patios to keep face coverings on at all times except when actively eating or drinking.

Posting the lowest rates: San Francisco, Santa Clara

San Francisco has the lowest positive test rate of any Bay Area county at 2.1% for the 14-day period. The lowest average rate it has posted on a weekly basis was 1.1% in mid-June, and the highest was 4.3% in early May.

San Francisco has been cautious about reopening, waiting until June 12 to allow outdoor dining and indoor retail. Further expansions planned for late June and early July, including hair salons and indoor dining, have been postponed indefinitely.

“San Francisco was the first county to implement the lockdowns, so it had low rates to begin with,” Riley said. “I think they’ve been able to maintain these low rates also because people have accepted social distancing practices seriously.”

Santa Clara County is the second lowest at 2.5% for the past 14 days. While Santa Clara’s positive rate has remained well below the state threshold and the average rate hasn’t peaked above 3.3%, the county has seen an increase in hospitalizations, which prompted the state to place it on the watch list.

“Many of the cases identified in Santa Clara County are from long-term care facilities, who are more likely to develop severe disease requiring hospitalization,” Riley said. “The overall number of cases is not very high, but the proportion of people developing severe disease may be higher in this county than some of the other counties.”

The county reported its biggest daily case count of the pandemic, 258, on July 8. Essential businesses in food service and construction have recently been tied to outbreaks in the county.

In the middle: San Mateo, Napa, Alameda, Sonoma

San Mateo County’s positive test rate is 3.3% for the 14-day period ending Tuesday. The county has progressed far into reopening, with less risky businesses resuming in May, indoor dining OKd in mid-June, and most other businesses allowed to open by June 19. It was the only Bay Area county still allowing indoor dining as of Monday, when Gov. Gavin Newsom’s statewide order revoked that privilege; others either suspended operations earlier or hadn’t allowed them to reopen yet.

Napa County, with a 3.7% positive test rate over the 14-day period, was the earliest Bay Area county to reopen outdoor and indoor dining, on May 20. For most of June, Napa’s weekly positive test rate was steady at 1.7%, and in late May it was as low as 0.4%. But the state reports social gatherings, an increase in transmission, especially among the Latino community, and the impact on agricultural workers contributed to a recent rise in the rate, which reached 4.7% on July 5.

Alameda County, at 4% for the 14-day period, has been among the slowest in the Bay Area to reopen. But increased social interactions and a spike in cases among essential workers and in nursing facilities prompted the state to place it on the watch list on Wednesday. The county had allowed outdoor dining to resume on June 19, but had to reverse course last weekend because of a state restriction. As of Wednesday, restaurants can reopen for patio dining again. Alameda posted its lowest weekly rate in mid-June at 3.6%. Throughout May it hovered around 5%.

Sonoma County follows with a 4.2% positive test rate over the 14-day period, and saw its highest daily case count since the start of the pandemic on July 12, when 116 infections were reported. Health officials have blamed the rise on more social gatherings, and workplace outbreaks including at skilled nursing facilities. Outbreaks have also occurred among workers at wineries. Past positive test rates are not recorded on the county website, so we were unable to chart the historical trend.

Here is the complete list of positive test rates for all 58 California counties over the 14-day period ending at 4 p.m. Tuesday: