Kenyan ministry of health medical workers prepare to take swabs from truck drivers in Namanga, Kenya. File/Reuters

The UN health agency warned that the coronavirus pandemic would be lengthy and could lead to "response fatigue", as the case count in South Africa topped half a million.

Six months after the World Health Organization declared a global emergency, the novel coronavirus has killed more than 680,000 people and infected more than 17.5 million, according to an AFP tally.

South Africa is by far the hardest hit country in Africa, accounting for more than half of diagnosed infections, although President Cyril Ramaphosa said the fatality rate is lower than the global average.

Health authorities had been expecting a surge in cases after the gradual loosening of a strict lockdown that was imposed at the end of March.

World Health Organization's logo. Image only for representation.

Nigeria on Saturday also announced it would ease a lockdown in the commercial capital Lagos, allowing churches and mosques to reopen next week.

An emergency WHO committee reviewing the pandemic "highlighted the anticipated lengthy duration of this COVID-19 outbreak, noting the importance of sustained community, national, regional, and global response efforts".

"WHO continues to assess the global risk level of COVID-19 to be very high," it said in its latest statement.

The agency also said the effects of the pandemic "will be felt for decades to come".

A boy stands in front of a graffiti promoting the fight against the coronavirus in Nairobi, Kenya. File/Reuters

Mexico overtook Britain to become the third hardest hit country in virus deaths -- after Brazil and the United States -- with more than 46,600 fatal cases.

Although many Latin American countries have begun relaxing stay-at-home measures, the virus is still spreading quickly across much of the region, which has now recorded more than four million cases and almost 200,000 deaths.

Half of them are in Brazil, where President Jair Bolsonaro said he believes "nearly everyone" will catch the virus eventually, after himself recovering from it.

The US, the hardest-hit country in the world, has now tallied more than 4.6 million cases and 154,319 deaths.

Agence France-Presse