Prior to the winter flood, much of the Bay Area celebrated low coronavirus transmission rates, which allowed for easy restriction of opportunities for fun, work, and life in general.

Now, on the other side of that spike, case rates have fallen again, and San Francisco has reported the lowest case rate since very early in the pandemic – a year ago when the city was in lockdown mode. That was before a summer spike made the numbers skyrocket before dropping to lows in early October.

The picture in the Bay Area is mixed, however, and some counties are still a long way from achieving the lower levels seen last fall. And even as we near the lows, experts are concerned about the possibility of a fourth spike in the coming weeks.

The lowest reading in San Francisco, just before the winter flood, was a 7-day average of 2.8 infections per 100,000 people recorded on October 1. Last week the city hit a fall rate of 2.6 on Thursday, although the rate has since ticked up to 3. San Francisco last had a lower case rate of 2.4 on March 20, 2020.

San Mateo County reported a fall rate of 3.95 last week, down from the 4.35 rate it hit in mid-October before the winter flood began. The district has also seen an increase to 6.5 from Sunday since last week.

In Sonoma County, which was struggling with high transmission even before the winter surge, infections dropped below 7 for the first time since June 30, the county reported a case rate of 6.5 on Sunday, well below 8.2 Pre -Surge low on September 15th.

Overall, the infection rate in the Bay Area is falling near the lowest transmission level seen in the fall. As of Sunday, the 7-day average of daily new cases per 100,000 people was 5.9, just above the low of 5.2 set on October 17.

Despite the good news, some counties are still not near their pre-winter lows. Napa County reported a rate of 6.8 on March 16, but it rose to 8.7 by Sunday, much higher than the Labor Day rate of 3.5.

Some counties, including Napa, don’t report data on weekends or holidays when the chances of reporting outliers are greater. Gaps in reporting can result in artificially low numbers for certain days and inflated numbers on days when reporting catches up. State reporting errors could also contribute to these daily lows if they create gaps for a few days without new cases being reported.

Marin County had a case rate of 2.5 per 100,000 on October 3, but it didn’t drop to 3.9 on Thursday before rising to 5.2 on Sunday. San Mateo, Contra Costa, Alameda, and Solano counties have all seen similar patterns.

This “honeymoon period” of falling fall rates after an increase has feared some experts that at the end of March or beginning of April a fourth increase could be on the way, which is fueled by the coronavirus variants, namely the B.1.1.7 variant originates from UK and is 50% transferable. A few variants from California are rapidly gaining ground in the state as well.

Lessons also remain from the time the state introduced a new color-coded tier system in late August that links reopening to progress metrics against the virus. Most of the Bay Area started in the orange row. Less than two months later, most were downgraded to purple after easing restrictions came with a relapse in progress.

While it is unlikely to trigger such a dramatic spike as the winter months, the variants and resident complacency could push the curves back up before much of the population is vaccinated. The U.S. Centers for Disease Control and Prevention has repeatedly raised this concern as worrisome variants spread and many states relax COVID-19 restrictions.

“Increasingly, a growing proportion of their COVID-19 cases in states are being traced back to variants,” said CDC Director Dr. Rochelle Walensky during a White House briefing on Monday. “I worry that if we don’t take the right measures now, we will see another preventable increase – as we are seeing in Europe right now and are just so aggressively stepping up vaccination.”

Mike Massa contributed to this story. Dan Kopf designed the graphics for this article.

Kellie Hwang is a contributor to the San Francisco Chronicle. Email: [email protected]