FILE - In this June 13, 2020, file photo, Silver Dollar City employee takes the temperature of guests before they are allowed to enter the park on just west of Branson, Mo. As the U.S. emerges from the COVID-19 crisis, Missouri is becoming a cautionary tale for the rest of the country: It is seeing an alarming rise in cases because of a combination of the fast-spreading delta variant and stubborn resistance among many people to getting vaccinated. (Nathan Papes/The Springfield News-Leader via AP, File)

KANSAS CITY, Mo. (AP) — A highly contagious coronavirus variant that is contributing to a surge of cases in Missouri first gained a foothold in rural areas of the state where vaccinations rates are low, a pattern not seen previously, state health officials say.

The delta variant, first detected in India, is becoming the predominant strain detected in wastewater in some parts of the state, particularly in the southwest corner, where COVID-19 hospitalizations are on the rise. And it is spreading much differently than the alpha variant, which first was detected in the United Kingdom, said Jeff Wenzel, who oversees the wastewater surveillance program for the Missouri Department of Health and Senior Services.

“With the U.K. variant," he said, “we started seeing that in the larger cities and we saw that spread out into smaller communities, and we are seeing the opposite now with this delta variant."

The delta variant also has turned up in wastewater samples in the Kansas City and St. Louis area. But Wenzel said, “In the larger cities, it just doesn’t seem, we just aren’t seeing it as readily as we are in some of the smaller communities."

Officials aren't yet sure why the spread has been so different but are exploring the possibility that lower vaccination rates in rural areas of the state are playing a role.

In St. Louis County, for instance, 48.4% of residents have received at least one dose. But the percentage is half that across a large swath of southwest and northern Missouri, where the biggest rise in cases have been reported, state data shows.

The variant is worrisome because it is not only more contagious, but also more likely to lead to hospitalizations.

Dr. George Turabelidze, the state epidemiologist, said that Missouri was vaccinating about 50,000 people a day in March and April but that the number has since fallen to about 10,000 a day, making the state's vaccination rate among the lowest in the country.

“That is concerning because this new emerging variant is highly transmissible and the primary target is unvaccinated people," he said in a video posted on the health department's website Wednesday night.

Missouri now leads the nation with most new cases per capita. Over the past 14 days, it has recorded 144.9 new cases for every 100,000 residents, according to data from Johns Hopkins University.

Lisa Cox, a spokeswoman for the health department, said the agency is exploring a variety of incentive options at the state level. But she said Thursday that she had no details.

An email message left for Republican Gov. Mike Parson's communications staff was not immediately returned.

Besides inundating hospitals, cases are again causing problems for schools. In St. Joseph, the school district had to shift summer classes online last week at two schools because about 50% of the students were out sick with COVID-19 or another illness, quarantining or vacationing, said Bethany Clark, director of elementary education for the St. Joseph school district.

She said that wasn't what she envisioned when the district was planning for the summer. Case numbers were so low this spring that the district even decided to make masks optional for summer school.

“I really thought, ‘Things are looking good. Summer school is a great option for opening up some of our restrictions. Let’s see how things work and we can return to as close to normal as we can in the fall,'" she recalled thinking. “And then yeah these cases. It was a hard hit because we really wanted, we really want to be post-pandemic."

But the district is in Buchanan County, where just 20.8% of residents have received at least one shot.

“What you are looking at now is, Where is the virus most able to circulate?" said Dr. Bill Powderly, the co-director of the Division of Infectious Diseases at Washington University’s School of Medicine. “Where are the pockets of vulnerability? And the pockets of vulnerability across the United States are those communities with very low vaccination rates because that means they have lots of people who are susceptible to the virus and therefore the virus is much more likely to circulate."

He noted that younger people are more likely to get sick than with earlier strains. But it is unclear whether even that will drive more vaccinations.

“If you are in a rural community where maybe a couple people got infected and nobody got sick, you think it is overblown and your political leaders are telling you it is no big deal,” he said. “You can understand why people start off the way they do, but I don’t want people to die in order to convince the rest of the population that they need to be vaccinated. I so hope that people will start to realize that this is not trivial.”