Virus Reproduction Number in South Africa’s Omicron Epicentre is ‘Something We Have Never Seen’
South Africa has increased its vaccination drive in the face of Omicron

The virus reproduction number of the Omicron variant in Gauteng province – the epicentre of South Africa’s pandemic – is 3 – meaning that one infected person will infect three others on average.  That is the highest seen so far in the country’s COVID-19 pandemic history – and testimony to the highly infectious nature of the new SARS-CoV2 variant.

South Africa’s health minister, Dr Joe Phaahla, described this reproductive number as “something we have never seen” at a Friday media briefing.

During the country’s Delta-driven third wave, the number remained below 2. However, in some other countries, Delta’s reproduction number breached five, according to a Lancet study.

South Africa Reproductive Number Dec 2021 (National Institute of Communicable Diseases, South Africa)

Less severe so far – but early days

South African health minister, Dr Joe Phaahla

On the more positive side, Phaahla said that early data from the department’s national hospital surveillance showed that hospitalised COVID-19 patients had shorter stays, and fewer had severe disease, as compared to patients admitted in a similar time frame in the second and third waves. 

Moreover, some 70% of those hospitalised for COVID-19 were not vaccinated, he added.

He defined severity as any patient who developed acute respiratory distress syndrome, received oxygen, ventilation, was treated in high care or ICU or died.

However, he cautioned that severity data “has several limitations at the early phase of the wave when numbers are small”.

“Patients with mild symptoms are more likely to be admitted as a precaution, patients are diagnosed with COVID-19 incidentally when admitted for other reasons, and because there has not been sufficient follow-up time for severity and outcomes to have accumulated, which is typically up to 3 weeks after diagnosis,” explained Phaahla. 

While there had been an initial increase in hospital admissions for children under five (21% of all admissions), this had decreased to 8%. 

Many of the children had been admitted for other reasons and tested positive “incidentally”, stayed in hospital for less than five days and did not show features of severe disease, the Minister added.

Hospital at epicentre

Tshwane Omicron cases

Dr Mathabo Mathubela, head of the biggest hospital at the epicentre of South Africa’s Omicron infection, reported that her COVID-19 patients were displaying less severe symptoms than previous waves.

Of the 42 COVID-19 patients in her hospital on 2 December, nine needed oxygen, three were in high care and two in ICU. However, for 33 of the patients, COVID-19 was “coincidental” to their admission, said Mathubela, CEO of Steve Biko Academic Hospital in the Tshwane area of Gauteng.

Only six patients were vaccinated, with 24 unvaccinated and the status of eight unknown, she added.

WHO warns it’s too early to draw conclusions on severity

South African statisticians also are beginning to observe a reduced rate of hospital admissions in comparison to the total number of new Omicron infections, suggesting that vaccines and previous infections are providing some protection.

In a briefing on Thursday, however, the World Health Organization has warned that it is still too early to draw conclusions from the South African data on the severity of the new variant.

WHO Lead on COVID-19, Dr Maria Van Kerkhove, said that the South African population was young and had a high level of exposure to COVID-19 from previous outbreaks, which might lessen Omicron’s impact.

WHO Chief Scientist Dr Soumya Swaninathan also warned that it is too early to come to any conclusions about the efficacy of vaccines against Omicron as the only available studies showed a “wide variation” and samples were small.

In addition, a small South African study released late Tuesday suggested that people double-vaccinated with the Pfizer-BioNTech COVID-19 vaccine had significantly reduced protection against the Omicron variant, now reported in 57 countries.

On Wednesday morning, however, Pfizer reported that a third booster of its vaccine would provide significant protection against Omicron, according to a laboratory study.

Meanwhile, South Africa’s health minister said on Friday that while restrictions had been effective in the past in stemming the rise in COVID cases, these “have had severe economic consequences, thus a careful assessment of risks is needed”. 

The South African government is still considering mandatory vaccination, which has the support of most business associations and large trade unions.

Image Credits: Gauteng Department of Health.

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