COVID-19 cases are accelerating in some parts of Africa and governments should step up preparations for a second wave, the Africa Centres for Disease Control and Prevention said on Thursday.

Over the past four weeks, cases have increased by 45 percent per week on average in Kenya, by 19 percent in the Democratic Republic of Congo and by 8 percent in Egypt, the African Union-run organisation's head John Nkengasong said.

"The time to prepare for a second wave is truly now," he said, urging governments "not to get into prevention fatigue mode."

The continent of 1.3 billion people has so far managed better than widely expected in terms of containing the epidemic, with a lower percentage of deaths than other regions, partly due to strict lockdown measures imposed in March.

There have been 41,776 deaths among the 1.74 million people reported infected with the virus, according to a Reuters tally based on official data as of Thursday morning.

Beginning in August, many governments eased restrictions, however, and a trend of decreasing cases has flattened, Matshidiso Moeti, Africa director for the World Health Organization (WHO) said in an online press conference on Thursday.

In Kenya, the government allowed bars to reopen on September 28 and cut the nightly curfew by two hours. Schools partially reopened on October 12.

Some easing was justified to help economies in the region to start recovering, Moeti said.

However, "we will need to be dealing with some of these upticks. What is important is to contain them."

Kenyan President Uhuru Kenyatta on Wednesday announced a November 4 summit to review the surge in infections, and urged Kenyans to wear face masks properly and practice social distancing to avoid "losing hard-fought for ground" in the fight against the disease.