• Two years ago, the CDC confirmed the first known case of coronavirus in the U.S.
• A 35-year-old traveler had returned from Wuhan, China to Washington state and tested positive.
• The virus has killed more than 860,000 people in the U.S. and infected more than 69 million.
• With the emergence of omicron, the future course of the pandemic is unclear as experts struggle to understand how new variants emerge.

A 35-year-old man returned to the U.S. from Wuhan, China on Jan. 15, 2020 and fell ill with a cough and fever.

He had read an alert from the Centers for Disease Control and Prevention about an outbreak of a novel coronavirus in Wuhan and sought treatment at an urgent care clinic in Snohomish County, Washington four days later.

On Jan. 21, the CDC publicly confirmed he had the first known case of coronavirus in the U.S., although the agency would later find the virus had arrived on the West Coast as early as December after testing blood samples for antibodies.

The man said he had not spent time at the Huanan seafood market in Wuhan, where a cluster of early cases were identified in December. He was admitted to isolation unit at Providence Regional Medical Center in Everett, Wash. for observation.

After confirming the Washington state case, the CDC told the public it believed the risk "remains low at this time." There was growing evidence of person-to-person transmission of the virus, the CDC said, but "it's unclear how easily this virus is spreading between people."

Then President Donald Trump told CNBC the U.S. had it "totally under control."

"It's one person coming in from China. We have it under control. It's going to be just fine," Trump told "Squawk Box" co-host Joe Kernen in an interview from the World Economic Forum in Davos, Switzerland.

However, Dr. Anthony Fauci would confirm the public's worst fears on Jan. 31: People could carry and spread the virus without showing any symptoms. Dr. Helen Chu's research team at the Seattle Flu Study started examining genomic data from Wuhan. It became clear early on that person-to-person transmission was happening, Chu said. By using the flu study's databank of nasal swab samples, the team was able to identify another Covid case in a 15-year-old who hadn't recently traveled, indicating it was spreading throughout the community.

In late February, a senior CDC official, Dr. Nancy Messonnier, warned that containing the virus at the nation's borders was no longer feasible. Community spread would happen in the U.S., she said, and the central was question was "how many people in this country will have severe illness."

In the two years since that first confirmed case, the virus has torn through the U.S. with a ferocity and duration few anticipated. The human toll is staggering, with more than 860,000 people dead and more than 69 million total infections. Hospitals around the nation have been pushed to the breaking point with more than 4 million admissions of confirmed Covid patients since August 2020, when the CDC started tracking hospitalizations. The hospital admissions are an undercount because they do not include the wave of cases that first hit the U.S. in the spring 2020 when hospitals were caught flat footed and testing was inadequate.

Though the U.S. now has effective vaccines and therapeutics to fight Covid, the future course of the pandemic remains uncertain as the virus mutates into new variants that are more transmissible and can evade vaccine protection. The highly contagious omicron variant has pushed infections and hospitalizations to record highs across the globe this month, a shock to a weary public that wants a return to normal life after two years of lockdowns, event cancellations, working from home and mask and vaccine mandates.

The rapid evolution of the virus and the dramatic waves of infection that would follow, from alpha to delta and omicron, came as a surprise to many elected leaders, public health officials and scientists. Dr. Michael Osterholm, a top epidemiologist, said the Covid mutations are the big unknown that will determine the future course of the pandemic.

"We don't yet understand how these variants emerge and what they are capable of doing," Osterholm, director of the Center for Infectious Disease Research and Policy in Minnesota, told CNBC. "Look at how omicron caught us as a global community surprised by the rapid transmission, the immune evasion. Look at delta and all the impact it had on disease severity," he said.

As new infections started to decline in the spring of 2021 and the vaccines became widely available, the U.S. began to let its guard down. The CDC said the fully vaccinated no longer need to wear masks indoors. President Joe Biden proclaimed on July 4th the U.S. was closer than ever to declaring independence from the virus.

However, the delta variant was taking hold in the U.S. at the time and would soon cause a new wave of infection, hospitalization and death as vaccination rates slowed. Public health leaders have struggled for months to convince skeptics to get the shots.

More than a year after the first vaccine was administered in the U.S., about 67% of Americans older than 5 are fully vaccinated, according to CDC data. Tens of millions of Americans still have not gotten their shots, despite the fact that data has proven them to be safe and effective at preventing severe illness and death.

"We had no sense in January of 2020, the divisive politics and community reaction to this that were going to occur," Osterholm said. "Who would have imagined the kind of vaccine hesitancy and hostility that's occurred."

Delta was more than twice as transmissible as previous variants and research indicated it caused more severe disease in unvaccinated people. The CDC would reverse its loosened mask guidance and encourage everyone, regardless of vaccination status, to wear masks indoors in public in areas of substantial transmission as delta spread.

The vaccines took a hit when omicron emerged in November. Though they still protect against severe illness and death, they are less effective at preventing infection from omicron. Chu said the U.S. relied primarily on vaccines to prevent transmission of the virus without equally emphasizing widespread masking and testing, which are crucial to controlling a variant like omicron that can evade immunity.

"We now know that, proportionately, you can be repeatedly infected, you can have vaccine breakthroughs, and that this virus will just continue to mutate and continue to evade us for a long time," Chu said.

Katriona Shea co-leads a team of researchers who bring together models to forecast the trajectory of the pandemic. In their latest update, the omicron wave of cases and hospitalizations will likely peak before the end of the month. However, their most optimistic projection shows anywhere from 16,000 to up to 98,000 additional deaths from the omicron wave by April 2.

Currently, the U.S. is reporting an average of more than 736,000 new infections per day, according to a seven-day average of Johns Hopkins data analyzed by CNBC. While that is still far higher than previous waves, average daily infections are down 8% from the previous week. The U.S. is reporting more than 1,800 deaths per day as a seven-day average.

"It's really, really frustrating and tragic to see people dying from a vaccine preventable disease," Chu said.

The implications of omicron for the future course of the pandemic are unclear. In in the classic view, viruses evolve to become more transmissible and less severe, making it easier to find new hosts.

"There are lots of reasons to believe that might not be true because the jump to omicron was so massive, it suggests that there's lots of space for it to change quite dramatically," said Shea, a professor of biology at Pennsylvania State University. Omicron has more than 30 mutations on the spike protein that binds to human cells. The shots target the spike protein, and the mutations make it more difficult for vaccine-induced antibodies to block infection.

Doctors and infectious disease experts in South Africa, where omicron was first identified, said the variant peaked and started to declined rapidly, demonstrating a significantly different trajectory than past strains. The researchers also said ICU admissions and deaths were lower at Steve Biko Academic Hospital, indicating decreased severity.

"If this pattern continues and is repeated globally, we are likely to see a complete decoupling of case and death rates, suggesting that Omicron may be a harbinger of the end of the epidemic phase of the Covid pandemic, ushering in its endemic phase," the researchers wrote.

Over time, the virus could become less disruptive to society as mutations slow and it becomes mild as greater immunity in the population limits severe disease, according to Jennie Lavine, a computational investigational biologist at the biotech company Karius.

However, the head of the World Health Organization, Dr. Tedros Adhanom Ghebreyesus, cautioned earlier this week that the pandemic is "nowhere near over," warning that new variants are likely to emerge as omicron rapidly spread across the world.

"Everybody wants to get to this thing called endemic. I still don't know what the hell that means," Osterholm said, noting that he has 46 years of experience as an epidemiologist. "With variants, we can go for a period of time with relatively low activity, like we've seen in many places in the world, and then a new variant could change all that overnight. We don't really understand our future yet."