For the third week in a row, nearly every Bay Area county remained in the orange “substantial” category of coronavirus transmission, as defined by the U.S. Centers for Disease Control and Prevention.

Rates in San Francisco notably have risen sharply in recent weeks. The 7-day rolling average of new cases hit 11 per 100,000 residents this week from an autumn low of 4 per 100,000 in the last week of October. Most of the cases are among unvaccinated residents.

With people expected to travel, gather with friends and spend more time indoors over the next few weeks, officials are concerned the region could soon head for another surge.

“This increase started after Halloween and paralleled the increase we saw during the 2020 winter surge,” Colfax said Wednesday, attributing the uptick to colder weather and increased activity.

Other counties have experienced a similar trajectory or seen cases plateau with a high virus load in circulation. Santa Clara County has held at 9 cases per 100,000 residents since September, while Sonoma County has hovered around an average of 13 cases per 100,000.

“We should expect increasing cases in the coming weeks and months,” said Jorge Luis Salinas, an infectious disease expert at Stanford. “To me, it’s more about, are we prepared?”

Some health care facilities are already under stress from pandemic-related delays in clinical procedures and visits, he said. With the arrival of the cold and flu season, a continued uptick in COVID-19 cases could lead to a shortage of beds and medical staff.

“I don’t think the Bay Area is in critical condition at the moment,” Salinas said. “Things can get there.”

So far, the region’s high vaccination rates have helped prevent the intensive care unit bed crisis the state experienced last year.

But public health officials are worried that the vaccines’ effectiveness at preventing symptomatic infection wanes over time, even though they still help avert the most severe outcomes of infection.

“This disease is not taking the winter off. It’s coming back in force,” Gov. Gavin Newsom said at a briefing Tuesday at a vaccination clinic in Kings County.

California’s case rate has leveled off at about 15 cases a day per 100,000 people over the past month, with breakthrough infections more common than previously thought.

That’s why county health departments are urgently pushing booster shots ahead of the holidays for all adults six months after completing a Pfizer or Moderna vaccination series, or two months after receiving the single-dose Johnson & Johnson jab. Officials are also expanding vaccination opportunities for children ages 5 to 11.

“We are doing well in terms of our booster uptake, but we need to do better,” Colfax said, adding that the confusion around scheduling the shots would clear up as the city and state updated their appointment sites to reflect expanded eligibility.

He said only about 43% of the city’s older population has received an additional vaccine dose, even though many received their initial shots last winter.

Bracing for the winter surge, state officials are already taking measures to bolster the state’s health care system and surge staffing.

Newsom has extended California’s COVID-19 state of emergency declaration through March, which waives some bureaucratic requirements for out-of-state workers and gives county health officers the ability to implement a variety of virus mitigation measures.

About 30% of children in the younger age group in San Francisco have received their first vaccine dose, helping push the total of the city’s eligible population having received one dose to 87%.

That’s better than the national average. The White House said on Wednesday that about 10% of children 5 to 11 have received a dose of the Pfizer COVID-19 vaccine since its approval for their age group two weeks ago.

Even though the more contagious delta variant of the virus is now the dominant strain, that robust vaccination uptake should help stem a potential ICU crisis in local facilities.

“A surge in cases shouldn’t translate in the same severity of previous surges,” said Salinas. “That is the role of vaccines. They protect you exceedingly well from getting ill and dying.”

As of Wednesday, Alameda County was the only county in the Bay Area region in the CDC’s yellow “moderate” transmission risk category.

“We’re in a little better position to absorb cases in the hospitals this winter,” Nicholas Moss, the health officer of Alameda County, told the Board of Supervisors on Tuesday.

In the meantime, officials are urging people to delay travel until fully vaccinated, get a flu vaccine and keep their holiday activities outdoors as much as possible.

Statewide, about 67% of the total population is fully vaccinated, and another 8% are partially vaccinated.

More than 25 million Californians are eligible for booster doses. But only about 4 million have received their additional doses so far.

“My belief is, if we can get those vaccination rates another 5 to 10%, we’ll be in a completely different place,” Newsom said.

Bay Area health officers are unlikely to roll back the indoor mask mandate or other pandemic mitigation measures before the end of the year “based on the numbers we are seeing,” Colfax said.

“I recognize the fear many of us have as we now enter into the winter, where if past is prologue, we should anticipate an increase of cases. An increase in hospitalizations. An increase in people in ICUs,” Newsom said. “And, tragically, the likelihood if we don’t take seriously this moment, an increase in the number of people that will lose their lives.”

Chronicle staff writer Catherine Ho contributed to this report.

Aidin Vaziri is a San Francisco Chronicle staff writer. Email: avaziri@sfchronicle.com