SAN FRANCISCO — It was once said that California’s coronavirus pandemic was hitting dense urban areas the hardest.

Now, it’s rural, agricultural areas that are among the most severely affected.

“The epidemic is moving from urban Latino populations to rural Latino populations,” Dr. George Rutherford, epidemiologist and infectious diseases expert at UC San Francisco, said Wednesday. The risk factors are the same: low-income essential workers who live in crowded housing and must leave home to work and earn money and who may be less likely to speak up to call attention to problematic workplace safety conditions.

Earlier in the pandemic, Los Angeles County was one of the hot spots for new infections. By June, it was Imperial County. The rural, agricultural and impoverished county east of San Diego soared up the list as California’s hardest-hit county, in terms of new cases per 100,000 residents over the previous two weeks. Imperial County hit its worst number on June 16, when there were 1,438 cases per 100,000 residents over the prior two weeks.

Now, it’s clear that the virus is hitting the Central Valley the hardest. Kern County, home to Bakersfield, is now recording 1,160 cases per 100,000 residents over the last two weeks. The rate reached its highest point on Saturday, reaching 1,376 cases per 100,000 residents over the prior two weeks — a figure more than nine times as much as it was at the beginning of July, when the county reported 136 cases per 100,000 residents.

In other words, for the seven-day period that ended Sunday, Kern County reported 12,098 cases; just a month ago, the county was reporting only about 1,350 cases a week.

State officials recommend counties have a case rate of no more than 100 cases per 100,000 residents over the prior two weeks. Case rates may be artificially lower due to a glitch in the state’s reporting system.

The Central Valley is among the areas of the nation that federal officials are particularly worried about. Dr. Anthony Fauci, the U.S. government’s top infectious diseases expert, said the big problem is the uptick in the rate at which coronavirus tests are confirming infections.

The 14-day positive test rate climbed to 24% in Kern County on Monday, more than triple the state’s average of 7% on that day.

“This is a predictor of trouble ahead,” Fauci said on CNN on Thursday. A high rate of tests confirming infections, he said, is “a clear indication that you are getting an uptick in cases, which inevitably — as we’ve seen in the Southern states — leads to surges, and then you get hospitalizations, and then you get deaths.”

“Now is the time to accelerate the fundamental preventive measures ... masks, social distancing, avoiding crowds,” Fauci said.

While California’s second surge of coronavirus this summer is showing signs of stabilization, the levels of circulating virus in places like the Central Valley are a source of deep worry among physicians because of how much higher they are now.

“Although L.A. may be looking a bit better, there’s significant movement of virus from Bakersfield all the way up the Central Valley into Stockton,” Dr. Deborah Birx, the White House’s coronavirus response coordinator, said in a recording of a conference call obtained by the Center for Public Integrity.

Of the 10 California counties with the highest infection rates per capita over the last two weeks, eight were in the Central Valley as of Thursday, according to The Times’ coronavirus tracker. Besides Kern County, they were Merced County (656 cases per 100,000 residents over the last two weeks), Kings (568), Colusa (545), Tulare (538), Fresno (497), Stanislaus (440) and Madera (437).

Imperial County also made the top 10 list, with a rate of 415 cases per 100,000 residents, as did San Bernardino County, with a rate of 397 cases per 100,000.

Other rural areas are also seeing a rise in cases, such as the Salinas Valley in Monterey County and fields in Ventura County, Rutherford said.

Los Angeles County is the 18th hardest-hit California county by this measure, reporting 327 cases per 100,000 residents over the last two weeks.

Gov. Gavin Newsom has identified the Central Valley as a region in great need of resources to slow the spread of the coronavirus. Five of the eight medical teams staffed by U.S. Department of Defense personnel and assigned to California have now been sent to the Central Valley, Newsom said; he also asked state lawmakers to approve $52 million to improve testing, tracing and isolation protocols in an eight-county region of the Central Valley known as the San Joaquin Valley.

The region needs it. Kern County reported its highest COVID-19 hospitalization numbers on record on Sunday, when 321 people with confirmed coronavirus infections were in its hospitals.

As with other Central Valley communities, Kern County has also seen a familiar dynamic play out, said Dr. Hemmal Kothary, chief medical officer of Dignity Health’s Central California division: Black and Latino residents and low-wage workers are getting infected at higher rates.

“Kern County has two modes of income,” he said. “It’s agriculture, and it’s the oil industry.”

Workers in those industries tend to live and work in close quarters, many of them in multifamily households, he said. They are also less likely to be able to stay home when they’re sick and more likely to lack protections to speak out about safety concerns at work.

“I think we’re seeing a lot of that when we’re doing these tracings back, that the whole family has been infected,” he said.

Low-income residents are also less likely to have access to healthcare services.