• Pfizer and Moderna say their work on their blockbuster Covid vaccines is far from over, even now that the U.S. has ended the public health emergency.
• The two drugmakers are ushering in a new era for their shots that will elevate the role they play in protecting public health.
• The pharmaceutical companies are also trying to simplify what people need to do to coexist with the coronavirus.

Three years and billions of Covid vaccinations into the pandemic, Pfizer and Moderna say their work is far from over. 

The two pharmaceutical companies, whose Covid vaccines have become household names, are ushering in a new era for their shots that will elevate the role they play in protecting public health, but also simplify what people need to do to coexist with the virus. 

That involves developing new versions of the vaccines that aim to provide broader and longer-lasting immunity against the virus, and combination jabs that protect against Covid and other respiratory diseases in a single dose, among other efforts.

Those plans coincide with a broader shift in the Covid pandemic landscape.

The U.S. and global-level public health emergencies are over, vaccine uptake and sales growth have slowed, and both Pfizer and Moderna will sell their shots directly to health-care providers at around $110 to $130 per dose as soon as the fall, when the federal stockpile of free vaccines is expected to run out.

Neither company provided CNBC with an update on the exact private market price of their shots.

Many of Pfizer's and Moderna's plans for their vaccines may not reach the public for a few more years, and the success of those efforts isn't guaranteed. 

"One of the greatest things about Moderna is the company's willingness to lean in, even if it's not obvious where exactly things will go," Dr. Jacqueline Miller, Moderna's therapeutic area head of infectious diseases, told CNBC.

Here's what Moderna and Pfizer say is next for their Covid shots.

Annual Covid shots

Pfizer and Moderna aim to keep up with a shift in the U.S. toward annual Covid shots rather than frequent booster doses. 

Regulators are transitioning toward a flu shot-like model for Covid vaccines, meaning people will get a single shot every year that is updated annually to target the latest variant expected to circulate in the fall and winter. A panel of independent advisors to the FDA will meet in June to select which Covid strain new vaccines should target when they roll out later this year.

Moderna and Pfizer both told CNBC that messenger RNA technology will allow them to keep pace with new Covid variants each year. 

That technology, which is used in Covid shots from both companies, teaches human cells to produce a protein that initiates an immune response against a certain disease. 

Miller, who helped lead the development of Moderna's Covid shot in 2020, said the advantages of using mRNA became evident earlier on in the pandemic. That includes the ability to rapidly scale up the manufacturing of a shot and easily alter the variants they target. 

"The vaccine became proof of the value of mRNA in a pandemic when you need to make something quickly," Miller told CNBC. "The speed of that platform — it allows us to do things three times as fast." 

Dr. Mikael Dolsten, Pfizer's chief scientific officer, hopes that annual Covid vaccines will improve public sentiment around getting vaccinated. He said the public grew increasingly dissatisfied with health mandates during the earlier stages of the pandemic, and "unfortunately some people see vaccines as part of that." 

An annual schedule may help people view Covid shots as another "very natural part" of protecting their health and encourage more of them to vaccinate each year, according to Dolsten. 

"I think of it like the introduction of seat belts for cars. People didn't want to wear them at first, but over time they realized how much seat belts protect them. Now everyone uses them today," Dolsten told CNBC. "That's kind of how the vaccine story needs to be reimagined." 

'Next-generation' Covid shots

Pfizer's and Moderna's Covid vaccines both deliver robust protection against the virus, but that immunity can start to fade after four to six months. 

Part of Pfizer's strategy for shifting to an annual Covid vaccine schedule is developing "next-generation" versions of the shot, which aim to broaden and extend the protection people get to a full year. 

"Protection is still there but gradually waning, and we're working with two different approaches to make it a bit more like an annual durability for the majority of people," Dolsten told CNBC.  

Pfizer and its Covid vaccine partner BioNTech are working on a shot that will elevate the level of antibodies a person gets after vaccination by "severalfold," according to Dolsten. 

The vaccine won't work too differently from the company's current shot, which teaches cells how to make harmless copies of Covid's spike protein. The immune system detects that protein and creates protective antibodies that help fend off the virus but decrease over time.

The main difference is that the next-generation shot will teach cells how to make copies of an "enhanced" spike protein, which will generate a far higher level of antibodies that could last for an entire year. 

"If we're elevating antibodies, let's say threefold, that means they will last and protect for a year," Dolsten said. 

The company is working on a second vaccine that aims to boost T-cells, another form of protection that targets and destroys cells infected with Covid. 

In addition to antibodies, Pfizer's existing shot triggers the creation of T-cells against the spike protein. T-cells wane slower than antibodies, meaning they offer longer-term protection against the virus. 

Pfizer is adding another strain of mRNA in its new shot that will broaden that T-cell response. 

The strain will specifically trigger an increase in T-cells against other parts of the coronavirus called non-spike proteins. Those T-cells, in addition to the ones generated against the spike protein, will provide protection against "all corners of Covid's viral landscape," according to Dolsten. 

Non-spike proteins also mutate slower than the spike protein, which means that any T-cells generated against them will likely protect against a wide range of Covid variants. 

Dr. Paul Burton, Moderna's chief medical officer, said the company has its own "next-generation" Covid vaccine, which aims to improve how shots are stored and administered. 

The company's current shot must be kept in ultra-cold storage. Once thawed, the vaccine can be stored in the refrigerator for up to 30 days, according to Food and Drug Administration guidance.

Burton said Moderna's new shot will be "refrigerator stable," meaning it would have a longer refrigerator shelf life. The company will accomplish that by shortening the length of the mRNA strand in the vaccine, according to Burton. 

The shot could increase the number of vaccine providers around the world, especially in developing countries that may not have freezer capabilities. 

Moderna is studying the shot in a phase 3 trial, Burton said. The company's existing Covid shot is its only commercially available product. 

Combination shots

Pfizer and Moderna are both banking on a new slate of combination vaccines, expected to provide robust protection against Covid and certain respiratory diseases in a single dose. 

Dolsten said there's an increasing need for that kind of shot because certain shifts in society are creating a "more thriving environment" for infections. 

Climate change is driving up the Earth's temperature. Populations are living longer but becoming more vulnerable to disease as they grow older. A growing number of people are moving within countries and across borders. 

Dolsten said those factors have contributed to the spread of different diseases, sometimes at the same time. The U.S., for example, experienced a so-called tripledemic of Covid, respiratory syncytial virus and the flu last winter. 

Dolsten said people may not remember or even feel comfortable taking three different shots for those respiratory diseases on an annual basis. So creating a shot that will help people fight more than one of them at once will "simplify life for them," he said. 

Pfizer and BioNTech are developing a vaccine that targets both Covid and the flu. The companies started a phase 1 trial for the shot in November and said they expect to launch it in 2024 or later. 

Dolsten said the drugmakers are also conducting clinical trials for another shot targeting Covid and RSV. Pfizer first hopes to win FDA approval of its RSV vaccine for older adults later this month, he noted. 

Meanwhile, Moderna's shot targeting Covid and the flu is in early clinical trials. Another shot that protects against the flu and RSV is also in that early stage. Moderna is also developing a triple combination shot, which would target Covid, the flu and RSV all at once. 

Burton said Moderna's combination vaccines could be available by 2025 at the earliest, noting that the company still needs the FDA to approve its individual flu and RSV shots.

The public health benefit of combination vaccines will be "tremendous globally" since Covid, RSV and the flu can be deadly, according to Burton. He added that the convenience of those shots could encourage more people to take it. 

"To have to get three different shots for each and go to a pharmacy chain a couple of times, it can be burdensome for people," Burton told CNBC. "So to be able to get a single 3-in-1 or 2-in-1 shot – we know that compliance and adherence are huge with a single administration."