Groundbreaking Omicron research in South Africa has revealed promising insights but also some serious concerns about the variant that is sweeping the world. 

Real-world preliminary analysis by the South African Medical Research Council (SAMRC) and South Africa's largest health insurer, Discover Health, reveal infections are now dominated by the Omicron variant with higher reinfection and breakthrough infections than waves seen in the past. 

Scientists warn Omicron is a highly transmissible variant with rapid community spread and has "displaced" the Delta variant, now dominating infections. 

Effectiveness of Pfizer has dropped under Omicron. Graph / Discovery Health Insights 

They say despite the lower severity, health systems could still be over-run by the sheer volume of cases, considering Omicron's rapid community spread. 

During the first three weeks of the Omicron wave between November 15 and December 7, cases saw a "much steeper increase" in new cases compared to Delta, however admissions and deaths are not increasing as rapidly. 

By December 2, eight days after the first report of the variant, a 250 per cent increase in reinfection was reported for Omicron relative to prior variants in South Africa. 

Effectiveness of the Pfizer vaccine has also reduced significantly while Omicron has "eroded" protection provided by a prior infection. 

Researchers studied more than 211k positive test results between September 1 and December 7 (only three weeks of Omicron cases) and found symptoms are similar to other mutations; scratchy, sore throat, nasal congestion, lower back pain and fever for 2-3 days but seem to resolve quickly with recovery after 3 days. 

Some of the research released by South Africa. Photo / NICD / Discovery Health Analysis 

Epidemiological tracking shows a steep trajectory of new Covid-19 infections, higher reinfections and breakthrough infections than other waves, including the vaccinated. 

However, a flatter trajectory of hospital admissions is proving promising, indicating "likely low severity of the variant". A shorter incubation period of 3-4 days was also noted. 

Researchers say Omicron has "materially reduced vaccine effectiveness against new infections, potentially compounded by waning durability". 

Effectiveness of Pfizer has dropped under Omicron. Graph / Discovery Health Insights 

The Pfizer vaccine is only 33 per cent effective in adults over 18 at reducing Omicron-related infection, and dropped to 70 per cent effective in reducing Omicron-related hospital admissions. 

"Real world effectiveness of the Pfizer-BioNTech vaccine against hospitalisation has reduced from 93 per cent in the Delta [pre-Omicron] wave to 70 per cent in the Omicron wave". 

However, researchers noted, the vaccine continued to "provide substantial protection against hospital admission". 

Most hospitalisations are unvaccinated people and there are a higher number of infections among children, who are at 20 per cent more risk. Children present with a sore throat, nasal congestion and fever for 2-3 days, and tend to complain of a headache. 

Primary diagnoses in children on admission for Covid-19 related disease in Omicron wave are bronchiolitis and pneumonia. 

Patients are facing less respiratory distress on presentation and a significantly lower proportion of admitted patients require oxygen support. Those who do are mostly unvaccinated with only 16 per cent in ICU vaccinated. 

"The vaccine is still the most effective way to prevent further infections," Prof Glenda Gray, CEO SAMRC said. 

"Despite vaccine effectiveness decreasing, other measures like social distance and PPE are more needed than ever." 

Deaths are still significantly lower than previous waves. 

Only three weeks of Omicron data were included in the study and while results are promising, experts warn more data is needed to fully understand the variant. 

South Africa has shared the data with the US CDC, leading SA and UK scientists and others but also warned other countries that they do not know if the findings will translate. 

'Mutations occurred in the same individual' 

Meanwhile, Carlos del Rio, MD, a professor of medicine in the Division of Infectious Diseases at Emory University School of Medicine, has told a panel of experts in the US "it's pretty clear that all these mutations occurred in the same individual or in the same host". 

The panel met last week as Omicron crept into the United States, with an associate professor of medicine at the University of Michigan Medical School's Division of Infectious Diseases describing experts were "struck" by the sheer number of mutations in Omicron's spike protein. 

"Mutations affect how well the virus spreads," Dr Adam Lauring said. 

"Spike is also important as a target for our monoclonal antibodies and for the vaccines. So I think that raised alarm bells appropriately and is why we're all paying attention to it," he told a panel of experts. 

Lauring said that while there are still problems to solve, he predicted we could see the end of the pandemic by 2022. 

"I know that with Omicron it feels that everything has started over again. But we are so much farther than we were at the beginning of the pandemic. 

"We've got highly effective vaccines. We've got drugs coming out. Even though there's a lot of big problems to solve, we really have made tremendous improvements. 

"It feels a long way away, but I think we're going to get to that magic endemic point that everyone talks about. It may be late 2022, but we're going to get there. We're moving in that direction."