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The biggest quake in the region in 25 years jolted many residents out of bed when it hit at 3:20am (local time), centred 10km south of the City of Napa.
Three people were seriously injured, including a child who suffered multiple fractures after a fireplace fell on him, local fire battalion chief John Callahan said. Six fires broke out, including one that consumed six mobile homes, he said.
Queen of the Valley hospital said it had treated 89 patients.
There were no reports of any fatalities but the quake shook up residents, said Barry Martin, community outreach coordinator for the City of Napa, which has a population of 77,000.
"This was a pretty big jolt in Napa, but it certainly is not The Big One," Martin added in comments to local television, referring to fears Californians have of a catastrophic quake.
California, which sits along a series of seismic faults, is forecast to experience a much more powerful earthquake at some point, but scientists do not know exactly when it will come or how strong it will be, USGS geophysicist Don Blakeman said.
"Usually when people talk about 'The Big One,' they're talking about something on the order of a magnitude 9, which of course is tremendously more powerful" than Sunday's quake, he said.
California Governor Jerry Brown declared a state of emergency, putting all state resources at the disposal of his Office of Emergency Services.
Most damage appeared centered around Napa, a famous wine-producing region and a major tourist destination in northern California.
One hard-hit building housing winery tasting rooms had to be closed to tourists, and the floors of many wine stores were stained red from the contents of broken wine bottles.
Tyler Paradise, general manager of Cult 24 wine bar in Napa, estimated his business lost $50,000 worth of bottles. They were shaken out of their holding cabinets and littered the floor.
'TOO TERRIFIED TO EVEN SCREAM'
Brick facades gave way in the historic section of downtown Napa, and bricks fell off a second floor corner of the courthouse, which showed cracks. On the main street, masonry collapsed onto a car.
Callahan said officials had responded to more than 100 calls regarding problems with gas lines and power lines, and on its website the city reported 30 water line breaks and many broken windows and buildings with interior damage.
The quake knocked out power to about 40,000 homes and businesses in Napa and neighboring cities of Sonoma, St. Helena and Santa Rosa, according to the website for Pacific Gas & Electric.
"They say it went for 50 seconds. It felt like 50 minutes. I was just too terrified to even scream," said antique store owner Patricia Trimble, 50. She rushed to her store in central Napa and found the front window blown out, cabinets on their sides and merchandise littering the floor.
As dawn broke, merchants were on the streets sweeping up debris and boarding up windows.
The U.S. Geological Survey (USGS) said the epicenter of the quake was 5 miles (8 km) northwest of the town of American Canyon, on the northern edge of the San Francisco Bay.
'WOKE US ALL UP'
The quake was the largest to hit the Bay Area since the Loma Prieta quake in 1989, which killed 63 people and caused $6 billion in property damage. That quake measured 6.9, while the famous one that leveled San Francisco in 1906 measured 7.8.
Sunday's quake was strong enough to be felt throughout the Bay Area.
"It was long. I think it was the biggest one since I felt the 1989 quake," said Stephanie Martin, 47, a nursing assistant in Oakland, south of the area where the quake was felt more strongly.
"Nothing tipped over, thank God. Rolling back and forth. Just woke us all up," she said.
Aaron Moreno, 18, rushed to Lola's Market, the Mexican grocery store where he works in Napa, right after the earthquake to prevent potential looting and to begin cleaning up the mess. He said there were broken wine bottles and glass everywhere and the store would probably be closed for two days.
The quake was followed by small aftershocks of about magnitude 2, USGS geophysicist Randy Baldwin said.
USGS's Blakeman said there was about a 50 percent chance there would be an aftershock of at least magnitude 5 within the next week.
"That's the thing people need to worry about if their house is already damaged, because magnitude 5 can cause more problems," he said.
President Barack Obama, who is on his last day of vacation at Martha's Vineyard, Massachusetts, was briefed about the quake and would continue to receive updates, the White House said.