Symptoms, vaccine evasion and a new 'offshoot': What we know now about the omicron Covid variant

It’s been two weeks since South Africa reported the omicron Covid variant to the World Health Organization and now it’s spreading around the globe.

In the last fortnight, experts have scrabbled to gain more of an understanding about the new heavily mutated variant, and what kind of symptoms and illness it can cause and whether it undermines the vaccines that have already been developed.

Day by day, more information has emerged regarding the spread, as well as anecdotal evidence and preliminary figures, allowing us to build a bigger picture of its risk profile.

Here’s what we know so far:

As soon as the World Health Organization designated omicron a “variant of concern” on Nov. 26 — just two days after South Africa reported it to the U.N. health agency — the hunt was on for cases of the virus elsewhere, amid concerns that the mutations associated with omicron could make it more transmissible.

The U.S., U.K. and EU, among others, responded to the omicron designation by temporarily suspending flights from southern African countries, or introducing strict quarantines on anyone arriving from the region.

It’s increasingly apparent that omicron is already spreading worldwide, however, and there have been reports of community transmission over the last two weeks, signaling that the omicron variant has likely been circulating more widely, and for longer, than initially thought.

The U.S. CDC said Tuesday that the new variant has now been found in 50 countries and 19 U.S. states.

The first known sample of omicron dates back to Nov. 9 and was found in South Africa. The WHO stated that infections in the country had increased steeply coinciding with the detection of the B.1.1.529 variant, and that phenomenon is being seen elsewhere now.

In the U.K., for example, it’s estimated that 1,000 people a day are being infected by the variant and experts say it’s a matter of weeks, rather than months, before it usurps the delta variant which is globally dominant.

Professor Neil Ferguson of Imperial College, an influential epidemiologist among a cohort of experts advising the British government on Covid, told The Times newspaper Tuesday that early data suggests the number of omicron cases are doubling every “three days or less.” Needless to say, government officials are worried and are preparing for a potential surge of omicron cases as we enter the winter period.

Given the ongoing uncertainty surrounding the Covid omicron variant, experts have been watching the real-world data coming out of South Africa closely, given that it was one of the first countries to spot the variant.

Parts of South Africa have seen an increase in hospitalizations linked to the omicron variant. A report from the South African Medical Research Council, released Saturday, detailing the experiences of several hospitals in the Gauteng province (where omicron was first detected) suggested that the strain is causing milder illness, with fewer patients requiring oxygen or intensive care than seen in previous waves.

In fact, the report noted, the majority of patients on the Covid wards being observed were “incidental Covid admissions,” having been admitted to hospital for another medical or surgical reason.

A majority of patients on Covid wards were unvaccinated and the hospitals reported a higher admission of younger patients and children; age groups with lower rates of vaccination (or none, as children under 12 are not vaccinated in South Africa). The hospitals reported no deaths on the pediatric wards during the two weeks (from Nov. 14 -29) that they were observed.

Experts in the region are investigating what was driving admissions among younger people, who are far more likely to experience less severe Covid infections anyway.

The report also cautioned that “the clinical profile of admitted patients could change significantly over the next two weeks, by which time we can draw conclusions about the severity of disease with greater precision.”

The White House’s chief medical advisor Dr. Anthony Fauci said on Sunday that the preliminary data from South Africa was “encouraging” as it suggested omicron is not as severe as initially feared, but he cautioned that more data is needed to fully assess the risk posed by the variant.

One of the biggest questions for experts, government officials and vaccine makers is whether the omicron variant could undo the work that Covid vaccines have done so far to reduce the risk of severe infection, hospitalization and death. The CEOs of Moderna and Pfizer, who have both created widely-used vaccines, said it could take weeks before they had clarity on whether their shots are effective against omicron.

Early data is not so encouraging, with South African scientists stating Tuesday that omicron significantly reduces the antibody protection generated by Pfizer and BioNTech’s vaccine, according to a small preliminary study. Still, people who have recovered from the virus and received a booster shot will likely have more protection from severe disease, the study showed.

Pfizer and BioNTech said on Wednesday that three doses of their vaccine provide a high level of protection against the omicron variant with a booster shot increasing antibody protection 25-fold compared with the initial two-dose series, according to a preliminary lab study. 

Pfizer’s CEO Albert Bourla told The Wall Street Journal during an interview at the paper’s CEO Council Summit that he expects the number of confirmed omicron cases to surge from dozens to millions over the next few weeks, stating: “We will have a good understanding let’s say before the year-end as to what exactly it means for clinical manifestation.”

Pfizer can develop a vaccine that targets omicron by March 2022, Bourla said, but it’s not clear yet whether there’s a need for a new shot. It will take a few weeks to determine whether the current vaccines provide enough protection against the variant, he said.

Last but not least, testing for omicron is a challenge facing health officials who are trying to gauge the spread of the variant as quickly as possible.

When the WHO first reported the variant, and designated it as one “of concern,” the health agency noted that “this variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs.”

The WHO noted that current Covid PCR tests continue to detect this variant, largely thanks to a quirk in the variant’s genetic structure. “Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as a marker for this variant, pending sequencing confirmation,” the WHO noted.

“Using this approach, this variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage.”

However, there are reports now of a new “offshoot” of omicron that lacks the deletion that allows PCR tests to spot it, making it potentially far harder to track.

The offshoot of omicron has been identified in at least seven genome sequenced cases across South Africa, Australia and Canada, according to the Financial Times, and “no longer possesses this characteristic, meaning full genome sequencing is required to detect it. Researchers have classified the earliest identified form of Omicron as BA.1, while the offshoot has been labelled BA.2,” the FT reported Tuesday.

— CNBC’s Spencer Kimball contributed reporting to this story.