The first three weeks of 2023 were encouraging for the African continent’s fight against COVID-19. With cases down 97% year-on-year since the same period in 2022, hospitalizations for severe illness and deaths from the virus decreased significantly, the World Health Organization’s African Regional Office said.

“For the first time since COVID-19 shook our lives, January is not synonymous with a surge,” said Dr Matshidiso Moeti, WHO Regional Director for Africa, adding the continent hopes to transition out of “emergency response mode” as the fourth year of the pandemic kicks off.

But with an ever-growing crop of variants circulating, an uptick in cases in South Africa, Tunisia and Zambia, and the overall drop in reported COVID-19 cases partially attributable to low testing rates, Moeti urged African states to remain on guard against the virus.

“It is important that countries stay alert and have measures in place to effectively detect and tackle any upsurge in infection,” she said.

As the threat of COVID-19 comes under control, new dangers have emerged from a diphtheria outbreak in Nigeria and a cholera epidemic with Malawi as its epicenter. The outbreaks have already taken 38 lives in Nigeria, and 583 in Malawi.

Diphtheria and a mystery flu hit Nigeria

At its weekly press briefing on Thursday, Africa CDC said the diphtheria outbreak had spread to four Nigerian states that do not share borders. Vaccines and treatments exist for the virus, but officials said the rapid spread of the disease constitutes a major public health concern for the African continent.

Diphtheria is a serious bacterial infection that primarily affects the nose and throat. Infection leads to a thick grey or white coating of the tonsils, throat, and nose, making it difficult for infected patients to breathe or swallow. Left untreated, diphtheria causes severe complications such as heart conditions, nerve damage, and death.

Out of 123 confirmed cases, the virus has killed 13% of the people it has infected.

Africa CDC also revealed it is working with its Chinese counterpart and health authorities in Nigeria to investigate the outbreak of an unknown flu-like disease that has infected at least ten Nigerians.

Officials also reported 59 confirmed cases and 23 deaths from Mpox in the first three weeks of 2023. New cases have been reported in the Democratic Republic of Congo, Ghana, Liberia, and Nigeria.

The 2022 cholera outbreak continues

Several African countries continue to suffer the fallout of a cholera outbreak that began on the continent in March 2022.

Africa CDC has pinpointed Malawi as the epicenter of the 2023 outbreak, which accounts for nearly 20,000 new cases and 583 deaths. Burundi, the Democratic Republic of Congo, Kenya and Mozambique have also reported new cases.

Cholera cases in Malawi have increased seven-fold since the same period in 2022. Africa CDC’s acting director Dr. Ahmed Ogwell Ouma said there are heightened concerns about the spread of the outbreak to Mozambique, a neighboring country that has only reported a few cases.

“The outbreak has affected most of the districts in Malawi, and this resurgence of cases in districts where cholera was being controlled is a very big concern for us and the government,” Ouma told journalists.

The mortality rate of Malawi’s outbreak is currently 3.4%.

Omicron remains the dominant variant in Africa

Omicron remains the dominant variant driving Africa’s COVID-19 caseloads. While recent sequences from South Africa and Botswana revealed the presence of the XBB.1.5 variant on the continent, it represents just 23 of the 150,000 genomes sequenced in Africa.

“Despite the detection of new variants, the system for genomic surveillance is still working well and there is currently no concern for an increase in hospitalizations,” said Tulio de Olivera, professor at the Center for Epidemic Response & Innovation at South Africa’s Stellenbosch University.

XB.1.55 has only been detected in Southern Africa — four cases in Botswana and 19 in South Africa. The presence of the variant has not resulted in an increase in infections, hospitalizations or deaths especially in the last two weeks, Olivera said.

Instead, recent data from South Africa showed that transmission levels are decreasing, with an 18.1% drop in the number of cases detected in the third epidemiological week. This decrease, Oliveira said, is not related to lower testing, but rather a high level of population immunity.

Africa CDC reported that 44% of the target population on the continent have been vaccinated, with four countries having surpassed the 70% COVID-19 vaccination target. Of the nearly 1.1 billion doses of vaccines received by public health authorities, 83% – over 895 million doses – have been administered, including 45 million booster shots.

As the continent continues to make progress on immunization rates, Africa CDC encouraged its member states to continue targeted and public vaccination campaigns.

“We really are encouraging our member states to continue with targeted and public campaigns for vaccination, whether it is amongst youths, health workers or those with comorbidities, even the general public. If we do it in a targeted and sustained way, then we can get even more people vaccinated,” Ouma said.