As the weather warmed up this year, coronavirus case numbers plummeted, and life in the U.S. started to feel almost normal. But in recent weeks, that progress has stalled.
The vaccination campaign has slowed, and the delta variant is spreading rapidly. And new infections, which had started to plateau about a month ago, are going up slightly nationally.
New, localized hot spots are emerging, especially in stretches of the South, the Midwest and the West. And, according to an analysis NPR conducted with Johns Hopkins University, those surges are likely driven by pockets of dangerously low vaccination rates.
"I think we should brace ourselves to see case increases, particularly in unvaccinated populations," says Jennifer Nuzzo, a senior scholar at the Johns Hopkins Center for Health Security.
The number of people catching the virus has risen in more than half of the states over the past two weeks. And 18 states have greater numbers of new infections now compared with four weeks ago, including Arkansas, Florida, Iowa, Missouri and Oklahoma, where new daily cases have doubled.
"It's an early trend," Nuzzo says. "Unfortunately looking at what's happening in individual states, I do worry we will continue to see national numbers increase."
The number of people getting hospitalized for COVID-19 has also started rising again in nine states, according to Johns Hopkins: Arkansas, Florida, Hawaii, Iowa, Missouri, Nebraska, Texas, Wisconsin and Mississippi.
"I expect that more states would join that list in a few weeks as they continue to see case increases," Nuzzo cautions.
To understand what's driving the small rise in cases at the state and national level, researchers are keeping an eye on county-level trends.
A federal team including the Centers for Disease Control and Prevention does a daily ranking of counties' level of COVID-19 risk and identifies those it considers hot spots. These are places where COVID-19 presents a "high burden" to the community, measured in part by a significant rise in cases as well as increases in case positivity rates.
NPR and Johns Hopkins analyzed the current hot spots from the week of July 1 to July 7 to see how many of them have been in bad shape over a longer period. The analysis found that the vast majority of the CDC's hot spot counties from the last seven days have seen increases in new cases compared with one month ago — 104 out of the 136 counties.
This shows that for many of these hot spot counties, the rise in cases "isn't a blip," Nuzzo says. "That means that they're headed in the wrong direction" in those places.
Many of the places with dramatic rises in cases are rural areas or small towns.
For example, Newton County, Mo., has seen a 182% increase in new infections; Nacogdoches County, Texas, has seen a 632% increase. Ottawa County, Okla., has seen infections soar 828%.
Nuzzo points out that for some of the rural hot spots, the increases may be small in terms of total numbers, but that these communities typically have fewer health care resources to treat even a slight rise in COVID-19 cases.
"The ability to save lives is dependent on there being enough resources to offer lifesaving medical care," she notes. "We could see people die from their infection that otherwise could have been saved."
NPR analyzed counties included in a federal COVID-19 hospitalization dataset and found that COVID-19 hospital admissions rose modestly in one-quarter of these counties last week compared with two weeks ago. Nearly half of the places where hospitalization increased were in Southern states, with Texas, North Carolina and Georgia leading. Another quarter of counties that increased were in the Midwest.
Nuzzo says she's worried about a continued trend of "localized surges" around the country.
"Most of the [hot spot] counties are in states that are also reporting state-level increases, but not all are. In fact, we are seeing counties in states that we haven't really been worrying about — California and Washington state, for instance," Nuzzo says.
Some of the hot spot counties are also in suburban and even urban areas. For instance, Salt Lake City has had new infections rise over the last month, as has Clark County, Nev., home to Las Vegas, and Contra Costa County, Calif., home to some San Francisco Bay Area suburbs.
NPR's analysis with Johns Hopkins illustrates dramatically the impact of vaccination rates on risk for localized outbreaks. Most — 9 in 10 — of the CDC hot spot counties that have seen increasing cases over the last month had lower vaccination rates than the average U.S. county.
Nationally, 47.6% of the U.S. population was fully vaccinated as of July 7. Rates in many of the hot spot counties with sustained outbreaks were drastically lower. For instance, Ottawa County in Oklahoma has only vaccinated about 24% of its population. Utah County, Utah, the second-most populous in the state, has about a 32% vaccination rate. The lowest rate in the list of hot spots was Newton County, Mo., at nearly 17%.
While urban and suburban counties tend to have higher vaccination rates than rural ones overall, NPR's analysis found that hot spot counties, even in more urban areas, tend to have lagging vaccination rates. And across all geographic types, hot spot counties had lower vaccination rates. For instance, among all U.S. counties designated as "small urban" areas, the average vaccination rate was 41% nationally, whereas among the hot spots, it was 33%.
Researchers had long feared places with low vaccination rates would end up being at risk for outbreaks, says Dr. David Rubin, director of PolicyLab at Children's Hospital of Philadelphia, which has been tracking the pandemic in the United States. And now that pattern is proving true, he says.
You can see this play out vividly in the different parts of Missouri, he notes. For example, St. Louis County in the metro St. Louis area has a vaccination rate of 47% of the total population and is seeing a small increase in new infections of 17% over the last 30 days. In Greene County, home to Springfield, Mo., the vaccination rate is more than 10 points lower and has seen a 275% increase in new cases.
"The emergence of the delta variant is going to mean for those areas with low rates of vaccination that they're very much at risk to see significant increases in transmission, with potentially even exponential growth," he says.
Some regions may fall prey to a scattering of new outbreaks, while others may stay relatively unscathed, Rubin says. For instance, he points to New York and Massachusetts, which have high vaccination rates, and so far, few new infections. "It's like a wall has formed in the upper Northeast with regards to transmission," he says.
But, as Nuzzo notes, localized flare-ups in unvaccinated areas could spread regionally.
"One of the things that we keep forgetting about this pandemic is that something that happens in one state is not isolated from something that will happen in another state," Nuzzo says. "So as long as we keep seeing case increases in any part of the country, it remains a national crisis."
The troubling rises in cases and hospitalizations are stirring worries that the country may be on the cusp of yet another national surge that could continue into the fall.
Ali Mokdad, a researcher with the University of Washington's Institute for Health Metrics and Evaluation, says the delta variant is a "game changer" for the group's forecasting models.
"The delta variant has changed all our projections," he says. "It's more likely to be transmitted, makes the vaccines less effective; previous infections are not protective. We will see a rise in cases."
And that rise is likely to occur in the summer instead of the fall, as the group had previously projected. That's in line with forecasts from a group of modelers organized by the CDC.
Deaths could start going up again too, by mid-August, Mokdad says. The Institute for Health Metrics and Evaluation projects that deaths could rise from their current rate of around 200 a day to up over 1,000 by fall.
And the burden of the pandemic, Mokdad predicts, will not be evenly shared.
"We're going to see a divide in the country," he says. Places that have high vaccination rates may still see small surges, he says, but "it will be much worse in these locations with low vaccination coverage."
Things may worsen in the fall, in part because that's when more people will be heading indoors as a result of cold weather.
No one is predicting things will get anywhere close to as bad as last winter. But researchers emphasize that any increase in deaths is a travesty, given that COVID-19 has essentially become a preventable disease.
Mokdad notes that among recent COVID-19 deaths, "the majority, 97[%] to 99% of the deaths, are among people who are not vaccinated."
"It's so sad for me on a daily basis to look at the number of deaths in the United States, knowing that these mortalities could have been prevented. No one — no one — should die from COVID19 while we have an effective vaccine."
Researchers are hoping these early hot spots will be a wake-up call to communities with lower vaccination rates.
"They should be heeding the warning that's coming out of Missouri and Arkansas and recognizing that they need to boost their vaccination rates," says Rubin of PolicyLab at Children's Hospital of Philadelphia.
Nuzzo agrees. "There's a lot more that we can do to stop the spread of this virus and to prevent people from being hospitalized or dying from it," she says.
Alyson Hurt and Duy Nguyen of NPR and Emily Pond of the Johns Hopkins Center for Health Security contributed to this report.
To categorize hot spots, NPR analyzed daily updates of all counties' rankings on the Area of Concern Continuum from July 1 to July 7, provided by the Centers for Disease Control and Prevention. Sustained hot spots and hot spots were marked as such if they achieved that ranking at least once through the week.
Among these hot spots, Johns Hopkins compared 30-day averages of new COVID-19 cases to see where cases have seen sustained increases this month compared with the previous month.
Vaccination data comes from county-level counts of fully vaccinated people as of July 7 provided by the CDC and the Texas Department of State Health Services. NPR excluded Georgia, Vermont, Virginia and West Virginia, because fewer than 80% of their vaccination records included a person's county of residence. NPR used the National Center for Health Statistics 2013 Urban-Rural Classification Scheme to calculate average vaccination rates by county type, weighted by county population, both for all counties and for the hot spot counties.
NPR calculated per-capita county hospitalization rates using seven-day counts of confirmed COVID-19 hospital admissions for the weeks ending June 26 and July 3. This data is provided in Community Profile Reports published by the White House COVID-19 team.