For weeks, as cases surged in other areas of the country, officials warned that the highly contagious Omicron COVID-19 variant had already reached Humboldt County. Then, with the holidays passed and cases already rising, came a bombshell Jan. 3 report from Public Health: The county had confirmed a record 400 new cases of the virus as well as two cases of Omicron, which dated back to Dec. 19, meaning the variant had likely been circulating for weeks. Then, the following day, the county confirmed another 188 cases. With that, Humboldt County was thrust into the reality already being faced by much of the nation, where cases are surging, hospital capacity is being threatened and people are coming to grips with a new pandemic reality in a new year.

As Humboldt County faces this new chapter, we look at what Omicron is, how it's different and what can be done to mitigate its impacts locally.

What is the Omicron variant and where did it come from?

The Omicron variant was first discovered by scientists in Pretoria, South Africa, who found unusual features in coronavirus samples they were genetically sequencing after noticing a rise in cases in the Gauteng province. They found a dramatically different form of the virus than what was first discovered in Wuhan, China, in 2019, with an estimated 50 mutations.

The prevailing theory is the virus evolved in someone with a weakened immune system. In most people, COVID-19, like other viruses, will be killed off when their full immune responses kick in. But in people with compromised immune systems, the virus can keep replicating for months, with each replication offering the chance for mutations.

What do all those mutations mean?

In Omicron's case, data indicates the constellation of mutations has resulted in a virus that's far more infectious than Delta. While Delta is believed to be at least twice as contagious as the original form of COVID-19 — which is why it quickly surged to become the predominant strain of the virus in the United States and Humboldt County — a study out of Denmark shows Omicron to be 2.7 to 3.7 times more infectious than Delta.

And the variant's rapid rise through other parts of the world — and now the United States — seems to support that, as Omicron has been spreading at a rate comparable to that of the original strain of the virus at the pandemic's outset, when natural immunity was minimal and vaccinations were a distant hope. According to Johns Hopkins University, as of Jan. 4, the United States' seven-day average of new reported cases was more than 480,000, a near doubling of the previous surge mark set around this time last year. While this new surge is certainly fueled by holiday gatherings and travel, Omicron is the driving force, with the U.S. Centers for Disease Control estimating it was already accounting for 95 percent of COVID-19 cases in the country for the week ending Jan. 1.

Why is Omicron so transmissible?

A growing body of data suggests Omicron's incredible transmissibility can be linked to its immune evasiveness. This began to come into focus when researchers dug into a super-spreader event in Norway in late November, when more than 110 people — most of them fully vaccinated — attended a Christmas party at a restaurant with someone who had recently returned from South Africa with Omicron. Ultimately, 70 percent of the partygoers tested positive for the virus.

The more recent Denmark study, published Dec. 22, compared the spread of Omicron and Delta among members of the same household and, as mentioned above, found Omicron to spread far more efficiently, though not across the board. The study found a minimal — about 10 percent — increase in transmissibility among unvaccinated people but that fully vaccinated people (who studies had shown to be far less likely to transmit prior versions of the virus) were twice as likely to transmit Omicron than they were Delta, while people who had been fully vaccinated and boosted were more than 3.5 times as likely to pass on Omicron as they were a Delta infection.

The findings of the Denmark study are preliminary and have yet to be peer-reviewed, but appear to be supported by anecdotal evidence and other preliminary studies, including one from the University of Maryland that found vaccinated people with Omicron were emitting similar amounts of virus into the air while shouting and singing as unvaccinated counterparts earlier in the pandemic.

While breakthrough cases in fully vaccinated individuals certainly occurred with Delta and other COVID-19 variants, they were comparatively rare. But there's a growing body of evidence to suggest Omicron's rise is being fueled by its ability to infect vaccinated people, who then become contagious and shed the virus.

But there's also some evidence to suggest other aspects of Omicron contribute to its transmissibility. While the research is preliminary, data from animal tests suggests Omicron is more efficient than other COVID-19 variants at infecting cells in people's nose and upper respiratory system, though less efficient at moving into the lungs than the Delta variant. Because the virus seems to concentrate in the upper respiratory system, some researchers believe it may result in more of it shedding in the aerosols people emit while breathing and talking.

How do the vaccines hold up against Omicron?

Like everything with Omicron at this early stage, the data here is preliminary. But it's also decidedly mixed.

As noted above, there's a growing body of evidence to suggest Omicron is far more capable than other variants of infecting the fully vaccinated and that they are also then more capable of transmitting it to others. That's the bad news. The good news is data suggests the vaccinations remain very effective at preventing severe illness and death with Omicron.

A report released Dec. 31 by British health officials analyzed more than 1 million COVID-19 cases in recent weeks and found fully vaccinated individuals with Omicron were 65 percent less likely to be hospitalized than their unvaccinated counterparts, while those who had also received a booster shot were 81 percent less likely to be hospitalized compared to unvaccinated people.

While that's certainly encouraging, Nicholas Davies, an assistant professor of mathematical modeling at the London School of Hygiene and Tropical Medicine, cautioned the data is very preliminary, telling The New York Times the Omicron wave there has largely hit a younger mix of patients.

"It's important to bear in mind that we don't have much data on risks in older people yet," he told the paper.

In the United States, anecdotal evidence in the areas so far hardest hit by Omicron also suggest the vaccinated are well protected from severe illness and death.

Craig Spencer, an emergency room doctor in New York who also serves as the director of Global Health in Emergency Medicine at Columbia University Irving Medical Center, took to Twitter on Dec. 26 to provide an update on what he's seeing as Omicron cases surged in his ER.

"Every patient I've seen with COVID that's had a third 'booster' dose has had mild symptoms," he wrote. "By mild I mean mostly sore throat. Lots of sore throat. Also some fatigue, maybe some muscle pain. No difficult breathing. No shortness of breath. All a little uncomfortable, but fine.

"Most patients I've seen that had two doses of Pfizer/Moderna still had 'mild symptoms,' but more than those who had received a third dose," Spencer continued. "More fatigued. More fever. More coughing. A little more miserable overall. But no shortness of breath. No difficulty breathing. Mostly fine."

Spencer wrote that patients who'd received a single dose of the Johnson and Johnson vaccine fared worse overall, saying they "felt horrible," feeling weak and tired, with some shortness of breath and coughing, "but not one needing hospitalization, not one needing oxygen." The unvaccinated, he said, faced far more severe illness.

"Almost every single patient that I've taken care of that needed to be admitted for COVID has been unvaccinated," he wrote. "Every one with profound shortness of breath. Every one whose oxygen dropped when they walked. Every one needing oxygen to breathe regularly."

How is Omicron impacting hospitals?

At this stage, it seems clear Omicron is resulting in less severe illness than Delta, though it's difficult to pinpoint exactly why or to what degree. Certainly, the fact that a larger portion of the population is fully vaccinated and boosted is reducing hospital admissions and, as noted above, there is evidence Omicron is less effective at invading the lungs — and then other organs — than Delta, lessening the risk of severe disease. But substantive studies on the comparative risks of Omicron and Delta for unvaccinated people have yet to be conducted.

But it's very clear Omicron still poses a very significant threat to hospitals, many of which have already been running thin with staffing shortages and burnout caused by nearly two years of treating pandemic patients. Health officials worry that even with lower rates of severe illness, Omicron is spreading so fast that it will overwhelm hospital capacity, which is already being seen in some areas of the country. The U.S. Department of Health and Human Resources reported that 78 percent of the nation's intensive care unit beds were full as of Dec. 31, and that was before the country recorded a record of more than 1 million new infections Jan. 3.

In Humboldt County, the hospital census has held fairly steady at around 10 or so COVID-19 patients daily for several weeks, down from its Delta-fueled peak of 42 in early September. But local capacity is fragile and dependent on staffing, and, as we learned during the peak of Delta, outside reinforcements are unlikely to come amid a national surge.

Even before the confirmation of Omicron's presence in Humboldt, there was evidence cases were poised to surge after the holidays, as they did last year. Recent weeks have seen confirmed cases — as well as the potentially more telling test-positivity metric — trend upward. Then came the Jan. 3 report of 400 new cases, which represent a whopping 3.5 percent of the county's cumulative case count to date. With COVID-19, hospitalizations always lag behind confirmed cases and since the start of the pandemic, roughly 4.2 percent of local confirmed COVID-19 cases have resulted in hospitalization. If this current surge results in even half that rate, that will mean eight new patients hospitalized as a result of the Jan. 3 report alone, offering an indication of how quickly capacity can become overrun.

Are kids safe back in school?

It was likely a jolt for many local parents that news of 400 new COVID-19 cases and Omicron's presence in Humboldt County came the same day their kids returned to local classrooms after the winter break. Across the state and the nation, officials have made it a priority to keep children in schools for in-person learning. And at least in areas where masks are required, most have been able to do so with minimal impacts on transmission rates.

In addition to threatening hospital capacity in some areas and infections causing staff shortages in others, prompting some districts to pivot back to online learning in other parts of the country, the Omicron surge has seen record numbers of hospitalized children. But officials caution that rates of severe illness in children remain far, far lower than those for other demographics. Rather than Omicron presenting an elevated risk of illness for children, officials say the overall transmission rates of the variant are simply leading to higher hospital admissions of children, with those under the age of 5 still ineligible for vaccinations.

Locally, districts made rapid at-home tests available to families before the Jan. 3 restart of school, with district staff in all areas of the county showing up on campus this past weekend to help distribute them. County Superintendent of Schools Michael Davies-Hughes said the Humboldt County Office of Education was notified by the California Department of Public Health on Dec. 23 that it would be receiving rapid tests the next week, and the office immediately began planning so when the tests arrived Dec. 30, they were quickly distributed to local districts.

Additionally, Humboldt County Public Health received 9,000 rapid tests the week before Christmas and distributed 5,000 to local schools, with the remainder going to daycares, family resource centers and homeless outreach services, spokesperson Heather Muller said.

Davies-Hughes said HCOE has not received any new guidance specific to Omicron but continues to work with districts to implement mitigation measures, including masking policies, testing programs and increased ventilation of indoor spaces. But, he added, everyone has a role to play in keeping schools open.

"To prevent and mitigate the impact of this disease on our community we encourage everyone who is eligible to get vaccinated, to mask appropriately and to undergo regular testing," he said.

How do we mitigate the spread of Omicron in Humboldt?

It appears — even more so than with other iterations of the virus — there is no silver bullet to stopping, or even slowing, the spread of Omicron, locally or anywhere else. In his podcast In the Bubble, Andy Slavitt, the former administrator of the Centers for Medicare and Medicaid Services and senior advisor to the Biden administration's COVID-19 response coordinator, urged people to take a layered approach to Omicron.

Describing mitigation measures as "Swiss cheese," Slavitt said they all have holes. In and of itself, masking is only so effective, and Omicron is proving that vaccination alone won't prevent infection or transmission, while there are limits to what physical distancing and ventilation can do. But if we layer those measures on top of one another — getting vaccinated, masking, distancing, etc. — we are more likely to form a cumulative barrier that prevents the spread.

With a fragile local hospital system that's already stretched and battered — as well as 7,000 children under the age of 5 who are too young to get vaccinated and scores of others who are immune-compromised or live with co-morbidities that make them inherently more at risk of severe illness — it seems Humboldt County's ability and willingness to embrace that Swiss cheese approach will determine Omicron's impact locally.

Thadeus Greenson (he/him) is the Journal's news editor. Reach him at 442-1400, extension 321, or thad@northcoastjournal.com. Follow him on Twitter @thadeusgreenson.