Omicron Now Accounts For The Majority Of New COVID Cases In The US

“The capacity for superspreading events is really extraordinary,” one expert said.

Nycshooter / Getty Images

People wait in line outside a COVID-19 testing site in Times Square.

Go get a vaccine and a booster shot. Unless you want COVID.

That’s the clear message sent by the Omicron coronavirus variant, uncovered only a month ago and now racing around the globe.

The variant is now the dominant strain in the US, quickly toppling the long predominant Delta variant. First reported in November, the variant of the novel coronavirus caused 94.5% of US cases in samples reported in the last week — most strikingly in the northeastern US, where it caused 98% of cases — according to CDC figures released late on Jan. 4.

On Nov. 26, the World Health Organization and US government both designated the Omicron the fifth “variant of concern” of the coronavirus. More than 75 countries have reported cases caused by the variant, marked by around 50 mutations total, many more than earlier ones. It was only discovered in Botswana and South Africa last month.

“The reality is that Omicron is probably in most countries, even if it hasn’t been detected yet,” said WHO Director-General Tedros Adhanom Ghebreyesus, speaking at a briefing on December 15.

Omicron is among the most contagious pathogens on the planet, with exponential rises in cases in UK, SA. We should expect similar surges in US and globally. We need more data on serious disease & how to prevent disease progression. We have good reason to be concerned & to prepare

Twitter: @LawrenceGostin

When the discovery of Omicron was first announced, scientists and health officials warned us not to panic, cautioning that it would take weeks to know how Omicron would change the COVID game.

Three weeks have now passed since the WHO’s initial announcement. In that time, a near-daily deluge of scientific analyses and case reports have answered some early questions about the variant — it sure looks more contagious — while leaving others, like where it picked up all its mutations, still hanging. Here’s a rundown of what we do and don’t know:

Transmissibility

A Nov. 26 Christmas party in Oslo was an eye-opener on the contagiousness of the Omicron variant. Of 111 people who attended the party, 80 came down with COVID-19, according to a Norwegian Institute of Public Health report that concludes the variant is the most likely culprit. More than 60 other people who ate at the same restaurant that evening also got sick.

“The capacity for superspreading events is really extraordinary,” said Emory University biostatistician Natalie Dean.

Early indications are that the Omicron variant may more readily attack the mouth, nose, and throat, the initial beachhead of an infection, compared to other variants. A University of Hong Kong study, for example, suggests that Omicron infects and multiplies in cells there 70 times faster than the Delta variant now dominant worldwide, as well as the original version of the virus.

“We are seeing patterns overseas, in the UK, in Norway, that point squarely to things looking like they will get worse,” Dean said. Omicron cases appear to roughly double every two days, according to the CDC (the Delta variant at this stage in its first advent, in June, doubled once every two weeks). The United Kingdom’s Health Security Agency predicts that Omicron cases will reach parity there with Delta cases by the middle of the month, as a result. More than 73% of mid-December cases in London were caused by the new variant.

NEW: here’s a chart showing daily cases by specimen date in London, broken down by variant. This is what is coming to ~every country across the world in the coming weeks.

Twitter: @jburnmurdoch

The expectation is that the US will see a similar increase in Omicron cases, starting with New York and then to other well-traveled cities. Despite travel bans meant to buy time, according to National Institute of Allergy and Infectious Diseases chief Anthony Fauci, the variant has clearly already spread within the US. Only about a third of the first 43 US cases reported by the CDC were people who had traveled overseas. He calls a winter surge “inevitable” for the US.

“I see right now as the lull before the storm,” said Dean, who added she was seeing relatives ahead of potentially having to button down for the holidays. CDC Director Rochelle Walensky has suggested that January might see a peak of cases in the US.

It is worth noting that the US is still in the midst of an increasing Delta surge, with an average of about 1,200 people a day dying of COVID-19. Many hospitals are already reporting they are overstressed, with 78% of ICU beds now occupied, according to federal data — and all of this is happening before Omicron has really spread enough to make an impact.

With hospitals already full, scientists are warning that nothing good can come of a variant that transmits with the speed that Omicron appears to.

Vaccines

One of the bad news stories of Omicron has been its ability to seemingly run roughshod over immunity from past infections and vaccines: The “vast majority” of the people at that superspreading Norwegian Christmas party, for example, were fully vaccinated, according to the investigation of the incident. Of those first 43 US cases, 34 were fully vaccinated and 14 had received a booster or extra shot.

Overall, where the widely used Pfizer-BioNTech vaccines were still looking around 70% effective against infection from older variants, they only look around 33% effective against infection from Omicron, Fauci said. The AstraZeneca vaccine widely used worldwide is negligible in its effectiveness, according to a British study. Experiments with antibodies from people with vaccines suggest they are 20 to 40 times less active against Omicron, compared to other variants. That’s below levels seen as protective against first catching the virus.

However, antibodies are not the immune system’s only defense against COVID-19. Other parts of the body’s immunity strengthened by the vaccines appear to remain protective. The significant good news about vaccines and Omicron is that the shots, while they don’t prevent contracting COVID caused by Omicron, appear to remain effective against severe disease and hospitalization. This appears to be true for the J&J shot, as well as the more widely used mRNA ones.

“If you are vaccinated, you could test positive, but if you do get COVID, your case will likely be asymptomatic or mild,” said White House pandemic czar Jeff Zients, speaking Friday.

What’s more, a booster shot seems to restore much of the vaccine’s protection against infection, with antibody levels restored after about a week or more to protective levels. However, only about 40% of eligible adults in the US have received a booster, so far.

Disease Severity

Some early studies seemed to suggest that the Omicron virus more often produces mild cases of disease. But serious questions hang over these preliminary findings. The first is: Are they true? Early evidence from South Africa, where the variant was first observed, suggested that it led to fewer hospitalizations and oxygen use in the hospital, on average, than in past surges. Most of the Omicron patients at the Steve Biko/Tshwane District Hospital Complex in Pretoria, remarkably, came in for problems other than COVID-19.

The catch is that those patients were mostly younger people, who are naturally more likely to have mild illness from the coronavirus. And in South Africa, they are more likely to have had previous infections, which offer some protection against serious disease. The same goes for prior vaccination. A Danish study of 785 Omicron cases — three-quarters of them in people who were vaccinated or boosted — reported only nine hospitalizations, with just one case in the ICU among them. Whether the variant or the vaccination mostly caused this low severe illness rate is unclear.

This is part of a bigger problem in assessing the severity of disease caused by Omicron: It will reinfect more people with some immunity, either from vaccines or past infections, than with any prior variant, noted a report out this week from Harvard’s William Hanage and his colleague, Roby Bhattacharyya, of Massachusetts General Hospital.

graphic displaying the risk of different populations to Omicron and Delta COVID variants
Harvard Center for Population and Development Studies

A chart depicting the difficulty of assessing variant severity among different populations with and without some immunity (from either vaccination and/or prior infection)

What’s more, hospitalization and deaths typically lag behind initial case reports by about two to three weeks, making any initial assumptions about a variant that’s only been loose in the world for a few months naive.

Still, over the holidays more evidence arrived in early hospitalization rates that the new variant is less likely to cause severe severe disease, especially for vaccinated or boosted patients. "All indications point to a lesser severity of Omicron versus Delta," said National Institute of Allergies and Infectious Diseases chief Anthony Fauci in a White House briefing on Dec. 29.

The second question is whether it matters: Even if Omicron produces more mild cases on average, in a rapidly doubling surge the variant could still produce enough severe cases to overwhelm already stressed US hospitals.

The pandemic has shown a strong relationship between overcrowded hospitals and high death rates in the US, in Israel, and in Europe. This is raising concerns of a terrible January surge in states where the number of vaccinated people is low and hospitals are already strained.

“For the unvaccinated, you are looking at a winter of severe illness and death,” Zients said. “Get vaccinated.”

UPDATE

This story has been updated with Jan. 5, 2022, variant figures from the CDC, and a Dec. 29 comment from Anthony Fauci.

UPDATE

This story has been updated with Dec. 28, 2021, variant figures from the CDC.

UPDATE

This post has been updated with Dec. 20, 2021, variant figures from the CDC.