SAN FRANCISCO (KPIX 5) — Transit agencies around the Bay Area have struggled during the pandemic. BART and Muni are both facing budget disasters as riders stay home. But now Caltrain may have jumped to the top of the endangered list, in part because of something very few people saw coming.

“Yeah, we got a tip at the beginning of the meeting, after the meeting started,” says Adina Levin, founder of Friends of Caltrain. “It was a total shock.”

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Even for those who follow transit issues closely, it came as a surprise when San Francisco supervisors decided not to advance a November ballot measure for a Caltrain-dedicated sales tax.

“Caltrain is operated by SamTrans, which means San Francisco voters and San Francisco leadership don’t actually make the decisions as to what happens,“ San Francisco District 10 Supervisor Shamann Walton said during a conference call Wednesday.

“We were never hot about a sales tax,” added District 3 Supervisor Aaron Peskin.

Explaining their decision Wednesday, the supervisors pointed to the longstanding rift over how the system is managed and funded.

“San Mateo County has saved Caltrain multiple times,” countered Charles Stone, a Caltrain Board Member who represents San Mateo County. “We’ve stepped up the money when San Francisco and Santa Clara County didn’t want to.”

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Stone said the three-county sales tax that was drawn up to modernize the system is now needed to save it from the pandemic.

Without the sales tax support, “It may well just mean the end of Caltrain as we have come to understand it,” said Stone.

“Why would you have a power struggle in the middle of a pandemic that is causing so much destruction,” asked Levin. “Why would you take action to make the destruction worse?”

That is the worry, that any further damage to the wounded system might be lasting. Now the unexpected standoff has transit advocates on the peninsula trying to change minds at San Francisco city hall.

“That is our Bay Area original sin,” Levin said, “trying to manage our regional assets by local control. What we really need is leadership.”

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San Francisco supervisors could reverse their decision, but they would likely have to do it with an emergency meeting before the end of this month.