▶ Watch Video: U.S. battles uptick in COVID cases as Omicron spreads

The Omicron variant made up around 95.4% of new COVID-19 cases in the U.S. last week, the Centers for Disease Control and Prevention said in an updated estimate published on Tuesday. Only two regions of the U.S. — New England and part of the Midwest — have yet to reach 90% locally. The Delta variant, which was dominant up until a few weeks ago, makes up nearly all the other cases.

Earlier federal estimates showed Omicron rapidly spreading, but with labs in several states still working on sequencing their first outbreaks of the variant, the precise numbers were hard to pin down.

However, in the weeks since, CDC officials have said the agency has worked to refine its projections of the variant’s growth as more labs have sequenced Omicron cases. The CDC collects data from commercial and local public health laboratories, as well as from its own contractors, to track variants in the country and produce its “Nowcast” estimates. 

For consumers, standard COVID test results don’t distinguish between Omicron, Delta or other variants, but labs are able to sequence the genome of the virus to identify the strain that caused a positive test.

The new estimates come as growing data on Omicron’s spread in the U.S. and abroad has enabled researchers to better predict the course of the current wave fueled by the variant.

In a new round of forecasts released this week from the COVID-19 Scenario Modeling Hub, which compiles data from more than a dozen leading research organizations, most models chart a “sharp and fast” increase in cases expected to peak “before the end of January 2022” in every state. 

The pace of new cases, hospitalizations and deaths are expected to begin to slow through March, but “are projected to remain elevated” compared to the low levels seen in June last year. 

Despite growing evidence of Omicron’s lower individual risk of severe illness, the models suggest the strain remains dangerous enough that the current wave will lead to hospitalization rates topping the Delta variant’s worst days.

“There’s been so much talk of just saying, ‘oh, it’s just so much less severe. It’s cold-like.’ Sure, maybe it’s similar to some of those things in terms of severity. But this virus is so much more transmissible than all of those things,” says Johns Hopkins University’s Shaun Truelove.

Truelove has helped lead the consortium’s work with the Biden administration to coordinate modeling work from across several teams plotting coming waves of the virus. 

“Just by sheer numbers, we’re going to get a lot of hospitalizations,” warned Truelove. 

Also complicating the battle against Omicron: Doctors are facing a shortage of COVID-19 drugs that will work against the highly-mutated variant.

Of the monoclonal antibody treatments currently authorized for COVID-19, only two drugs — one made by AstraZeneca and one from GlaxoSmithKline and Vir Biotechnology — appear to remain effective against Omicron. 

The Biden administration recently lifted curbs on the distribution of monoclonal antibodies from Regeneron and Eli Lilly, pointing to “significant variability” in Omicron’s prevalence around the country and new guidelines published by the National Institutes of Health on prioritizing limited supplies of the drugs. 

Some scientists had speculated early in Omicron’s rise that the U.S. might see “co-circulation” with Delta. However, the CDC’s new estimates suggest the share of cases that would benefit from those monoclonal antibody drugs is quickly shrinking in every part of the country.

In HHS Region 7, which spans Iowa, Kansas, Missouri and Nebraska, Omicron is now estimated to make up 77.4% of new infections through New Year’s Day. In HHS Region 1, which includes Connecticut, Maine, Massachusetts, New Hampshire, Rhode Island, and Vermont, the CDC said Omicron’s prevalence was 82.4%. 

All other regions are above 90%.