African countries are stepping up measures to detect and control the spread of the Omicron variant as weekly new COVID-19 cases in the continent rise by 54% due to an upsurge in southern Africa.

In Africa, the Omicron variant has now been detected in four countries, with Ghana and Nigeria becoming the first West African countries and the latest on the continent to report the new variant. So far, Botswana and South Africa have reported 19 and 172 Omicron variant cases, respectively. Globally, more than 20 countries have detected the variant to date. The two southern Africa countries account for 62% of cases reported globally.

Omicron has a high number of mutations (32) in its spike protein, and preliminary evidence suggests an increased risk of reinfection, when compared with other variants of concern. Researchers and scientists in South Africa and the region are intensifying their investigations to understand the transmissibility, severity and impact of the Omicron variant in relation to the available vaccines, diagnostics and treatment and whether it is driving the latest surge in COVID-19 infections.

Southern Africa has recorded a surge in cases, mostly driven by South Africa. For the seven days leading to 30 November, South Africa reported a 311% increase in new cases, compared with the previous seven days. Cases in Gauteng, the country’s most populous province, have increased by 375% week on week. Hospital admissions rose 4.2% in the past seven days from the previous seven days. And COVID-19-related deaths in the province jumped 28.6% from the previous seven days.

While new COVID-19 cases are rising in southern Africa, they dropped in all other subregions during the past week from the previous week.

Working with African governments to accelerate studies and bolster the response to the new variant, World Health Organization (WHO) is urging countries to sequence between 75 and 150 samples weekly.

“The detection and timely reporting of the new variant by Botswana and South Africa has bought the world time. We have a window of opportunity but must act quickly and ramp up detection and prevention measures. Countries must adjust their COVID-19 response and stop a surge in cases from sweeping across Africa and possibly overwhelming already-stretched health facilities,” said Dr Matshidiso Moeti, WHO Regional Director for Africa.

The emergence of Omicron is rattling countries around the globe and underlines the importance of pandemic preparedness – the focus of a special session of the World Health Assembly that wrapped up this week. Countries agreed to launch a global process to draft and negotiate a convention, agreement or other international instrument under the WHO Constitution to strengthen pandemic prevention preparedness and response.

In South Africa, WHO is deploying a surge team to Gauteng Province to support surveillance, contact tracing, infection prevention and treatment measures. Botswana is boosting oxygen production and distribution, which are essential for the treatment of critically ill patients.

Additional epidemiologists and laboratory experts are also being mobilized to boost genomic sequencing in Botswana, Mozambique and Namibia. WHO has mobilized US$ 12 million to support critical response activities in countries across the region for the next three months.

African countries are also refining operational plans for stronger disease surveillance and investigations.

In Africa, vaccination rates remain low. Only 102 million people, or 7.5% of the population, is fully vaccinated. More than 80% of the population still needs to receive a first dose.

Only five African nations have reached the WHO global target for countries to fully vaccinate 40% of their population by the end of 2021. Botswana could become the sixth if its current vaccination rates are maintained. Just three other African countries have enough vaccine supplies to meet the targets but, at the current pace of uptake, they will be unable to do so.

“The combination of low vaccination rates, the continued spread of the virus and mutations are a toxic mix. The Omicron variant is a wake-up call that the COVID-19 threat is real. With improved supplies of vaccines, African countries should widen vaccination coverage to provide greater protection to the population,” Dr Moeti said.

Operational planning and funding challenges, vaccine delivery as well as communication and community engagement bottlenecks have hindered the efforts to widen vaccinations in some African countries. WHO and its partners are supporting countries to scale up vaccine delivery and uptake, including intensified assistance to roll out more than 5 million doses at risk of expiring by the end of the year due to having been donated with a short shelf life.

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