In the midst of a tumultuous back-to-school week underscored by numerous COVID-19 cases that have led to half-empty classrooms, administrators filling in for absent teachers and long testing lines, at least one large school district and some private and charter schools are closing temporarily, and others around the Bay Area are scrambling to keep classrooms open.

West Contra Costa Unified School District announced that it is closing its 54 schools Friday and Monday after almost a fourth of the district’s students missed class this week. The district is also closing its three COVID testing sites on Monday. The district does not plan to offer online instruction during the temporary closure.

Caliber ChangeMakers Academy, a charter school system with two campuses located in Vallejo and Richmond, is closing those schools Friday, Monday and Tuesday. And officials at Bentley School, a private school in Oakland, announced they are closing indefinitely starting Thursday and making a full return to online learning.

San Jose Unified and Palo Alto Unified schools, among others, are keeping classrooms open. But masses of students have already tested or are testing positive for the virus, and some parents are keeping their kids home to be safe, raising questions about what the future holds in districts across the Bay Area.

PINOLE, CALIFORNIA – JANUARY 06: Sixth-grade teacher Lola Ejiwumni does a lesson with her students at Collins Elementary School in Pinole, Calif., on Thursday, Jan. 5, 2021. Due to the new wave of the COVID-19 omicron variant, the school will be closed on Friday and Monday. (Jane Tyska/Bay Area News Group) 

As for what’s next for the nearly 29,000 students in the West Contra Costa district, schools are scheduled to reopen for in-person learning on Tuesday, said spokesman Ryan Phillips. Officials there will only close schools for more days if it is “absolutely necessary,” he said.

The district is continuing to test students and is working with the local health department on contact tracing. District officials are encouraging students and community members who are eligible to get vaccinated right away.

Rachael Weingarten, the head of schools at ChangeMakers Academy, said school leaders are closing the system’s two schools “out of an abundance of caution.”

About one quarter of its 1,800 students missed classes this week, said Markus Mullarkey, a chief operating offer for the Academy. The school system is setting up testing sites for students, staff and families on campuses Monday in an effort to test all students that day, get test results by Tuesday and get kids back to school by Wednesday. It’s also planning to give out laptops and devices to students so they can participate in remote instruction during the closure.

PINOLE, CALIFORNIA – JANUARY 06: Students head to class after lunch at Collins Elementary School in Pinole, Calif., on Thursday, Jan. 5, 2021. Due to the new wave of the COVID-19 omicron variant, the school will be closed on Friday and Monday. (Jane Tyska/Bay Area News Group) 

Those closures are exactly the opposite of what state leaders, school officials and teachers’ unions planned for. Governor Gavin Newsom, State Superintendent Tony Thurmond and members of the state health department sent out millions of test kits to schools ahead of the winter break to local school districts and worked with school leaders across the region on mitigation strategies to keep infected children and staff home and classrooms open.

But instead of the smooth transition to in-person learning they hoped for, chaos ensued. Parents dropped their kids off at school on Monday, but many students arrived to find nearly half of their classmates and their teachers missing. Many teachers and school staff called in sick. Superintendents and school administrators filled in for them, teaching elementary math and science classes and supervising recess. Families rushed kids to school testing centers, and many are still trying to get their kids tested again so they can send them back to class with the required negative test.

Many families still don’t know how long their kids will be home if they test positive and how they’ll learn if more schools close. Others are supporting school leaders who have opted to close campuses and resume online learning before the COVID-19 omicron variant spreads any further.

Juana Saguindel, a mom of a 4th grader and kindergartener at Garin Elementary School in Brentwood, said she wants her district to postpone in-person learning for at least two to three weeks and give her kids paperwork or online instruction assignments to complete. But she said they do not offer that option at Garin Elementary. The district did give her the option to withdraw her children from the school and enroll them into its independent study program temporarily or permanently.

PINOLE, CALIFORNIA – JANUARY 06:Students play during recess at Collins Elementary School in Pinole, Calif., on Thursday, Jan. 5, 2021. Due to the new wave of the COVID-19 omicron variant, the school will be closed on Friday and Monday. (Jane Tyska/Bay Area News Group) 

Saquindel said she is “scared about the spread of the virus” and worries that her kids will catch it if they go back to school but feels limited in her options and doesn’t want them to fall behind. She plans to keep them out of school when classes begin next week.

San Francisco Unified and Oakland Unified schools are open, and officials say they want schools to continue to stay open, but they’re facing major staffing challenges.

More than 600 teachers and 258 instructional aides and other staff were absent from San Francisco schools Thursday, the same day as a planned district-wide sick-out by a group of teachers, according to the school district. Teachers at several Oakland schools also announced a sick-out Friday to protest the lack of safety measures to keep them and their students safe from the virus. Those teachers are demanding a two-week move to remote learning to “reduce community transmission” of the virus.

PINOLE, CALIFORNIA – JANUARY 06: Sixth-grade teacher Lola Ejiwumni does a lesson with her students at Collins Elementary School in Pinole, Calif., on Thursday, Jan. 5, 2021. Due to the new wave of the COVID-19 omicron variant, the school will be closed on Friday and Monday. (Jane Tyska/Bay Area News Group) 

“Oakland schools are facing the greatest crisis in living memory. Hundreds of school staff and students are reporting absent due to COVID infection, exposure, and risk every day. Lesson plans are falling apart because teachers cannot move forward through their curricula with so many students left behind,” according to a press release from a group of teachers calling itself Skyline Sick Out.

Oakland Unified officials aren’t happy about staff sick-outs planned for Friday. They want schools to resume as planned.

“We need to be clear: this action — at whichever schools it occurs — is likely to significantly disrupt basic operation and instruction and will negatively impact the safety of students,” Sondra Aguilera, Chief Academic Officer, and Tara Gard, Chief Talent Officer, wrote in a letter to the families on Thursday.

K-12 school leaders aren’t the only ones closing campuses.

More universities and colleges in the Bay Area are going online. Cal State East Bay and San Francisco State University announced Wednesday they’re going virtual for the start of the semester, joining four other CSU campuses. UC Davis extended remote learning on Thursday by several more weeks of winter quarter, until Jan. 28.

PINOLE, CALIFORNIA – JANUARY 06: Sixth-grade students do a lesson in teacher Lola Ejiwumni’s class at Collins Elementary School in Pinole, Calif., on Thursday, Jan. 5, 2021. Due to the new wave of the COVID-19 omicron variant, the school will be closed on Friday and Monday. (Jane Tyska/Bay Area News Group)