Friday, 24 May, 2024
HomeCoronavirus WatchSo far, milder disease seen with Omicron, with shorter hospital stays —...

So far, milder disease seen with Omicron, with shorter hospital stays — SA hospitals analysis

Although it’s too early to draw definite conclusions, it appears that the Omicron variant might cause less severe infection than previous strains, according a preprint study analysing South African hospital data.

Of 42 people admitted to the Steve Biko/Tshwane District Hospital Complex in Pretoria on 2 December, 29 (70%) of them were not oxygen-dependent, according to a report authored by Dr Fareed Abdullah, director of the office of Aids and TB research at the SA Medical Research Council, which published the report online. Another notable finding was the shorter length of stay compared with earlier waves, at just 2.8 days in the past two weeks compared with 8.5 days over the past 18 months.

Twenty-four of the 38 adults hospitalised in the COVID ward on 2 December 2 were unvaccinated, eight had an unknown status, and six were vaccinated. All nine patients with COVID pneumonia were unvaccinated, including one child, reports MedPageToday.

While the report said most patients aren’t showing respiratory symptoms, and most were admitted to the hospital for other medical reasons, Abdullah said it was still too soon to say the variant causes milder disease. He said the picture would become clearer over the next two weeks.

“What's interesting this time around, and we want to be cautiously optimistic about is, is that most patients in the hospital are what we are calling ‘incidental COVID’,” Abdullah told Newzroom Afrika, a local television station.

“Two-thirds of our [COVID] patients … over the past two weeks are there for another diagnosis,” Abdullah said. “That's unusual, that’s different from previous waves.”

He said at the beginning of all three previous waves, there typically “has only been a sprinkling of patients on room air in the COVID ward and these patients have usually been in the recovery phase waiting for the resolution of a [comorbidity] prior to discharge”, the report stated. “The COVID ward was recogniseable by the majority of patients being on some form of oxygen supplementation with the incessant sound of high flow nasal oxygen machines, or beeping ventilator alarms.”

Other hospitals in Gauteng are having a similar experience with “incidental COVID”, the report stated. On 3 December Helen Joseph Hospital had 37 patients in its COVID ward, with 83% on room air, and Dr George Mukhari Academic Hospital had 80 COVID patients, with 81% on room air.

Of the 13 patients in Tshwane District Hospital Complex who were on oxygen, nine of them had a diagnosis of COVID pneumonia, while the other four were on oxygen for other medical reasons (two were previously on home oxygen, one had heart failure, and one had a diagnosis of pneumocystis pneumonia).

Abdullah’s report also included an analysis of the 166 new admissions at the hospital complex from 14-29 November. While the hospital didn’t do its own genetic sequencing, the South African National Institute for Communicable Disease (NICD) confirmed that nearly all the cases in the Tshwane area were due to the new variant, the report noted.

The age profile of hospitalised patients also differed from previously, and compared with admissions over the past 18 months, 80% of the 166 were under 50 years old.

“We are seeing that probably because in the older age group there are more vaccinated people, so fewer older people getting into the hospital,” said Abdullah.

Some 57% of people over the age of 50 in the province are vaccinated compared with 34% of those in the 18-to-49 age group, the report stated.

Finally, there were 10 deaths in the past fortnight, accounting for 6.6% of the 166 admissions, which was lower than the 17% mortality rate seen over the last 18 months.

The data from the hospital coincide with information released by the national Health Department during a briefing last Friday, that showed younger people are going to the hospital at a higher rate during this wave than with the previous Delta wave.

The health department also had limited data on vaccination status, but of 1,351 hospitalisations, 23% were unvaccinated and 2% were vaccinated (the majority was unknown).

“Until we can get more complete data, I wouldn’t come to sweeping conclusions with this,” Katelyn Jetelina, PhD, MPH, an epidemiologist at UTHealth School of Public Health in Dallas, wrote in a Substack post regarding the health department data. “But it’s welcoming news that the vaccinated aren’t piling up at the hospital.”

Jetelina also called attention to another piece of data, published as a preprint on medRxiv, by a large collaboration of researchers from South Africa’s NICD and several South African universities, which she says informed the World Health Organization’s comments last week.

It found that the rate of reinfection with Omicron is three times higher than with Delta, based on a national dataset of all positive coronavirus tests in South Africa obtained from March 2020 to 27 November this year.

“In other words,” Jetelina wrote, “infection-induced immunity is not doing a great job of stopping Omicron.”

Study details

Omicron variant increases reinfection risk: Analysis of routine surveillance data from South Africa suggests that, in contrast to the Beta and Delta, the Omicron variant of SARS-CoV-2 demonstrates substantial population-level evidence for evasion of immunity from prior infection.

Juliet R.C. Pulliam, Cari van Schalkwyk, Nevashan Govender, Anne von Gottberg, Cheryl Cohen, Michelle J. Groome, Jonathan Dushoff, Koleka Mlisana, Harry Moultrie

MedRXiv preprint published on 1 December 2021


To examine whether SARS-CoV-2 reinfection risk has changed through time in South Africa, in the context of the emergence of the Beta, Delta, and Omicron variants

Retrospective analysis of routine epidemiological surveillance data

Line list data on SARS-CoV-2 with specimen receipt dates between 04 March 2020 and 27 November 2021, collected through South Africa’s National Notifiable Medical Conditions Surveillance System

2,796,982 individuals with laboratory-confirmed SARS-CoV-2 who had a positive test result at least 90 days prior to 27 November 2021. Individuals having sequential positive tests at least 90 days apart were considered to have suspected reinfections.

Main outcome measures
Incidence of suspected reinfections through time; comparison of reinfection rates to the expectation under a null model (approach 1); empirical estimates of the time-varying hazards of infection and reinfection throughout the epidemic (approach 2)

35,670 suspected reinfections were identified among 2,796,982 individuals with laboratory-confirmed SARS-CoV-2 who had a positive test result at least 90 days prior to 27 November 2021. The number of reinfections observed through the end of the third wave was consistent with the null model of no change in reinfection risk (approach 1). Although increases in the hazard of primary infection were observed following the introduction of both the Beta and Delta variants, no corresponding increase was observed in the reinfection hazard (approach 2). Contrary to expectation, the estimated hazard ratio for reinfection versus primary It is made available under a CC-BY-NC 4.0 International license . perpetuity. preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in medRxiv preprint doi:; this version posted December 2, 2021. The copyright holder for this Page 3 of 43 infection was lower during waves driven by the Beta and Delta variants than for the first wave (relative hazard ratio for wave 2 versus wave 1: 0.75 (CI95: 0.59–0.97); for wave 3 versus wave 1: 0.71 (CI95: 0.56–0.92)).

In contrast, the recent spread of the Omicron variant has been associated with a decrease in the hazard coefficient for primary infection and an increase in reinfection hazard coefficient. The estimated hazard ratio for reinfection versus primary infection for the period from 1 November 2021 to 27 November 2021 versus wave 1 was 2.39 (CI95: 1.88–3.11). Conclusion Population-level evidence suggests that the Omicron variant is associated with substantial ability to evade immunity from prior infection. In contrast, there is no population-wide epidemiological evidence of immune escape associated with the Beta or Delta variants. This finding has important implications for public health planning, particularly in countries like South Africa with high rates of immunity from prior infection. Urgent questions remain regarding whether Omicron is also able to evade vaccine-induced immunity and the potential implications of reduced immunity to infection on protection against severe disease and death.


MedPage Today article – South African Hospital Report Hints at Milder Disease With Omicron (Open access)


Report from Dr Fareed Abdullah (SAMRC) on Tshwane Omicron Patient Profile (Open access)


MedRXiv article – Omicron variant increases reinfection risk (Open access)


Katelyn Jetelina post on Substack – New Concerning Variant: B.1.1.529 (Open access)


See more from MedicalBrief archives:


New variants: Africa needs to strengthen its COVID response


MSF: Support to Livingstone Hospital extended for another month amid Eastern Cape COVID-19 infection surge


How Groote Schuur Hospital’s ICU adapted to the pandemic



MedicalBrief — our free weekly e-newsletter

We'd appreciate as much information as possible, however only an email address is required.