It was not supposed to be this way.

A month ago Joe Biden appeared to have victory over the coronavirus pandemic within his grasp. As tens of millions of Americans got vaccinated, cases, hospitalizations and deaths were falling precipitously.

Not so fast. In the past week alone the highly contagious Delta variant fueled a rise in daily Covid-19 cases of 43% and pushed deaths up by 39%. Republicans such as Ron DeSantis, the governor of Florida, proved all too willing to take the politicization of face masks to new extremes.

Biden is confronted anew by the reality that he is trying to govern a nation cripplingly polarized in politics, media and even science. The US president and his team of experts’ mission to tame the pandemic and heal divisions has collided with the Delta variant and the DeSantis variant.

“They may have underestimated the degree to which vaccine hesitancy would become a Republican party platform position,” said Laurie Garrett, an award-winning science writer and author of The Coming Plague: Newly Emerging Diseases in a World Out of Balance. “They were imagining that they were dealing with people who were individually scared, had concerns based on crazy things they read on the internet, were fearful of getting autism.

“What they didn’t imagine is that there would be this whole deliberate Republican party position of opposition to all things that Biden would put forward about Covid. It’s not just vaccines, it’s masks, it’s social distancing, now it’s going to be vaccine passports. I’m just waiting for the guns to come out.”

Donald Trump’s catastrophic response to the pandemic left hundreds of thousands of people dead and exposed America’s political schisms, but the rapid vaccine development he put in place gave the country a second chance. Biden greatly accelerated vaccine distribution, hit target after target and brought cases down to 10,000 per day.

While careful to avoid declaring “mission accomplished”, the president held an independence day celebration at the White House on 4 July and claimed “we’ve gained the upper hand” and “together we’re beating the virus”. But he was picking low-hanging fruit: people eager for vaccines, often in Democratic-voting areas.

Vaccinations slowed dramatically and Biden missed his goal of getting 70% of all adults receiving at least one shot by 4 July. Meanwhile the Delta variant, which had caused a spectacular surge in India, reached US shores and began cutting a swath through the unvaccinated.

New cases are now averaging more than 70,000 a day, above last summer’s peak. Over the past week, Florida and Texas have accounted for about a third of new cases and more than a third of new hospitalisations nationwide, the White House Covid-19 response team told reporters on Thursday.

Seven states account for about half of new cases and hospitalizations in the past week, despite making up less than a quarter of the American population. They are Florida, Texas, Missouri, Arkansas, Louisiana, Alabama, Mississippi – most of which have low vaccination rates and all of which voted for Trump in last year’s presidential election.

Polls suggest a hardcore of holdouts who insist they will never get the vaccine, with some expressing concerns that the vaccine will insert a microchip in their body or cause infertility. These irrational fears now threaten Biden’s entire “wartime effort” against the virus.

Garrett added: “The White House has really struggled to come up with a strategy to deal with the 20, 25%, virulently anti-vaccine faction. I don’t think they’ve come close to imagining a strategy for that.

“It’s not for lack of trying. They’ve got they’ve gone through the entire cookbook of recipes for, confronting vaccine resistance and refusal.and I think they just are at a loss, just as we are for just about everything else that goes on politically in the United States right now.”

In the pandemic of the unvaccinated, Florida’s hospitalizations have hit a record high, reaching 12,500 on Thursday, with more than 2,500 in intensive care. The state is averaging nearly 18,000 newly confirmed infections per day, up from fewer than 2,000 a month ago. But DeSantis has shown only defiance, banning mask mandates in schools and dismissing new restrictions as threats to “freedoms”.

When Biden this week asked Republican governors to “get out of the way” of efforts to contain the virus, DeSantis retorted: “Why don’t you do your job? Why don’t you get this border secure? And until you do that, I don’t wanna hear a blip about Covid from you, thank you.”

For good measure the pugnacious governor, who is up for reelection next year and widely seen as a 2024 presidential contender, added: “This is a guy who ran for office saying he’s going to shut down the virus. And what has he done? He’s imported more virus from around the world by having a wide open southern border.”

The US-Mexico border is not wide open. On Thursday, after taking an electric car for a spin in the White House grounds, Biden was asked for his response to Governor DeSantis. He replied, “Governor who?”, prompting laughter.

Until now the White House has sought to play down any perception of conflict between Biden and Republican governors in the hope taking the political sting out of the pandemic response and rallying the nation at a moment of crisis. But it is no coincidence that states such as Florida and Texas, both coronavirus hotspots, have styled themselves as bastions of Republican resistance to Biden.

Garrett observed: “It’s pretty clear that the Republican party of Florida is ecstatic about how DeSantis is playing his cards. So it’s not in his interest to suddenly decide that having Floridians survive Covid is more important than he getting elected president of the United States.”

Biden’s presidency was always likely to be judged by historians, and voters, on how he handled the biggest public health crisis for a century. His impressive early momentum on the issue has stalled. In a new Quinnipiac University opinion poll, the share of people who approved of his response to the crisis stands at 53%, down 12 points from May.

But Monika McDermott, a political science professor at Fordham University in New York, said: “I actually think the Biden administration handled it amazingly well, given how much mistrust there was very early on for the vaccine, how non-existent the rollout was under Trump. Everything that Biden had facing him when he stepped into office was against his being able to do a good job on this, and I think he did as well as he could under the circumstances.

“Now, maybe the administration could have addressed the misinformation and the conspiracy theories more directly earlier on. That would be the only thing that I think maybe they missed. I don’t know if that would have made a difference, but those are so firmly entrenched at this point that I don’t know how you’re going to budge them.”

Leslie Dach, who was global Ebola coordinator for the health department under Barack Obama, defended the May decision by Biden and the Centers for Disease Control to advise that fully vaccinated people could go unmasked indoors – since revised for areas where the Delta variant is rampant.

“Guidance is judgment calls and science changes and there were a lot of reasons to try and get the country back to normal,” Dach said. “When they did that, it was the right thing to do but science changes and then you have to move back. And you learn new things about these diseases. We learned a lot of new things about Ebola, unfortunately, because people had Ebola.”

Biden, who reached across the aisle often during 36 years in the Senate, ran for president as an apostle of bipartisanship and continues to work with Republicans on infrastructure spending. But as legal battles over mask mandates rage in cities and states across the country, the stark and deadly schisms could shake his faith in that principle.

Dach, now chair of Protect Our Care, a healthcare pressure group, observed: “Everybody who’s running for president in the Republican party believes that the path forward is to be as Trumpian as they can, and to follow the basic rules, which are: reject the experts, double down when you’re attacked, and play deep to the base. Because everybody, for their politics, wants that.

“Biden has actually tried to build a bigger tent whereas they’ve chosen to always go deeper into the base and that’s what Trump always did. But in this case that means putting their own people in mortal risk because they they never show any willingness to act more reasonable. Instead DeSantis digs deeper, attacks more.”