Three charts show South Africa’s Covid crisis as omicron takes hold

A health worker packages a coronavirus swab test at a Testaro Covid-19 testing site in the Goodwood district of Cape Town, South Africa, on Thursday, Dec. 2, 2021.

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Since the omicron Covid variant was first detected in South Africa in November, the world has been watching the country closely to see how the heavily-mutated variant impacts case rates, hospitalizations and vaccine efficacy.

Early indications are mixed, with preliminary data out of South Africa suggesting that omicron is more transmissible than the globally dominant delta variant, but causes less severe illness.

The effectiveness of Covid vaccines against the variant is also being investigated, with vaccine maker Pfizer-BioNTech releasing results from an initial lab study which showed that the effectiveness of the initial two-dose vaccination series fell significantly against omicron, but that a booster shot restored protection.

The World Health Organization declared the variant “of concern” two days after South Africa reported it on Nov. 24. Since then, it has been identified in 57 countries across the world.

CNBC has compiled charts reflecting case rates, hospitalizations and the degree of Covid vaccine protection in South Africa as omicron takes hold.

Cases soaring

The Covid infection rate has surged in South Africa since the second week of November, with 62,021 new cases reported between Nov. 29 and Dec. 5, a 111% increase compared to the previous week, according to the WHO’s latest weekly report published Tuesday.

It’s not possible to tell if all those cases are omicron, although the variant is reported to be dominant in the country right now.

WHO added in its report that there have also been “very large increases” in the weekly incidence of Covid cases in some countries neighboring South Africa with Eswatini seeing a 1,990% surge from the week before, Zimbabwe seeing a 1,361% increase, Mozambique seeing a 1,207% increase with Namibia (681%) and Lesotho (219%) also recording increases to a smaller degree.

The WHO has cautioned that “while drivers of these increases remain unknown, it is plausible that [the] spread of omicron in combination with enhanced testing following the declaration of a VOC [variant of concern], play a role, together with the relaxation of public health and social measures and sub-optimal immunization coverage.”


South Africa has reported a rise in hospitalizations but such data is only starting to feed through, given the lag between contracting the virus and a possible hospitalization.

Early evidence from the country, both anecdotal and based on small studies, suggests that patients are experiencing far milder symptoms and illnesses compared to previous waves.

One report published earlier this week, and based on a small number of patients in several South African hospitals, found that the patients on its Covid wards had been admitted for other reasons, and on routine testing on admission to hospital, were then found to have Covid (the report presumed most of the infections were caused by omicron, given the spread of the variant). Far fewer patients on the Covid wards were oxygen-dependent or needed intensive care either.

However, the report noted that: “What is clear though is that the age profile is different from previous waves.”

Analyzing 166 patients admitted to the hospital between Nov. 14 and 29, the report found that “the age profile differed markedly from the previous 18 months,” with far more younger adults and children being admitted to the hospital.

“In the last two weeks, no fewer than 80% of admissions were below the age of 50 years. This is in keeping with the age profile of admissions in all public and private hospitals in Tshwane and throughout the Gauteng Province in the last two weeks … Nineteen (19) percent were children aged 0-9 years and the highest number of admissions was in the age group 30-39 years, making up 28 percent of the total,” the report noted.

It added that the increase in younger admissions to the hospital could be a result of lower vaccination rates in this age group, stating, “it may be that this is a vaccination effect as 57% of people over the age of 50 have been vaccinated in the province compared to 34% in the 18-to-49-year group.” The majority of the Covid ward patients were unvaccinated.

The report cautioned that the patient information it had presented only represented the first two weeks of the omicron wave in the Tshwane district (in the Gauteng province where omicron was first detected) and 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.”

As for fatalities, the report noted there was no “significant increase in in-hospitals deaths in relation to the dramatic rise in the case rate for the Gauteng Province as a whole. This may be due to the usual lag between cases and deaths and the trend will become clearer over the next few weeks.”


Covid vaccines have been proven to withstand other variants of Covid, such as alpha or delta, and vaccines help to greatly reduce the risk of severe infection, hospitalization and death. Experts and vaccine makers have been trying to determine in the last few weeks how omicron could affect inoculation.

In South Africa, around 17.2 million adults (or 43%) are fully vaccinated out of an eligible adult population of almost 40 million, official data shows. In the 18-34 age group, only 29% of adults are vaccinated. Almost 681,000 in the 12-17 year age bracket have also been at least partially vaccinated.

Countries with lower vaccination rates, like South Africa, could be in a more vulnerable position as a more transmissible variant takes hold, and that could push hospitalizations up further.

Botswana, for example, has a much higher vaccination rate and has not seen a rise in Covid hospitalizations, its health minister said Wednesday, with 71% of its 1.3 million eligible population now fully vaccinated, according to Reuters.

“Currently we only have one person in ICU (intensive care). But there is a trend that we have noticed which is that those that get seriously ill have not been vaccinated,” Health Minister Edwin Dikoloti told a news conference, the news agency reported.

Omicron poses a challenge not only to vaccine makers but to governments who are racing to vaccinate as many people as possible. A lack or sluggish supply of vaccines in developing countries coupled with vaccine hesitancy, as in South Africa, poses extra challenges.

Pfizer and BioNTech released an initial lab study Wednesday showing that a third dose of its vaccine is effective in fighting the omicron variant, but the effectiveness of the initial two-dose vaccination series fell significantly.

Pfizer’s CEO Albert Bourla said on Wednesday that people might need a fourth Covid-19 shot sooner than expected. That’s easier said than done. Our World in Data reports that 55.4% of the world population has received at least one dose of a Covid vaccine but only 6.3% of people in low-income countries have received at least one dose.

While many countries are racing to roll out third booster shots in order to beat omicron, others, like South Africa, are still trying to vaccinate their populations with a first set of shots.

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