Omicron’s XBB.1.5 is 10% of local cases

The transmissible Omicron subvariant XBB.1.5 now accounts for 10% of coronavirus genomes sequenced in SA, but there is no sign of a new wave of infections, says one of SA’s top scientists. XBB.1.5 has caused concern among scientists and health authorities because it is the most transmissible coronavirus strain detected to date.

The transmissible Omicron subvariant XBB.1.5 now accounts for 10% of coronavirus genomes sequenced in SA, but there is no sign of a new wave of infections, says one of SA’s top scientists.

XBB.1.5 has caused concern among scientists and health authorities because it is the most transmissible coronavirus strain detected to date and has rapidly displaced less infectious variants in many parts of the world. It now accounts for nearly half the cases in the US, and has been detected in more than two dozen countries.

A total of 23 cases of XBB.1.5 have so far been detected in genomes sequenced from Southern Africa, of which 19 were from SA and four from Botswana, said Tulio de Oliveira, director of the Centre for Epidemic Response and Innovation at Stellenbosch University.

There has been no increase in the number of infections, hospital admissions or deaths recorded in SA since its first case of XBB.1.5 was detected in early January, he said during a virtual news briefing hosted by the World Health Organization (WHO). In fact, the latest SA data shows the weekly death rate has begun to decline, he said.

WE ARE CONFIDENT ... WE ARE STILL DOMINATED BY OMICRON, AND HAVE NOT SEEN ANY NEW VARIANTS OF CONCERN IN AFRICA

There were 1,506 new Covid-19 cases and seven deaths in the week to Wednesday, according to government figures.

SA’s high level of population immunity has blunted the impact of XBB.1.5, De Oliveira said. Most people living in SA now have a degree of protection against Sars-CoV-2, the virus that causes Covid-19, thanks to prior infection, vaccination or a combination of the two.

“We are quite confident that at the moment we are still completely dominated by Omicron, and have not seen any new variants of concern emerging in Africa or other parts of the world,” he said.

De Oliveira spearheaded the creation of the Network for Genomic Surveillance in SA (NGS-SA), a collaborative effort between SA universities and the National Health Laboratory Service that works closely with other African countries to monitor the evolution of Sars-CoV-2.

Early detection of new variants has been a vital part of SA’s response to the disease, De Oliveira said. The identification in late 2021 of the Omicron variant, which drove SA’s fourth wave, gave authorities time to prepare hospitals and secure oxygen supplies before cases surged, he said.

The expertise in genomic surveillance that has been built across African institutions during the coronavirus pandemic could be applied to other diseases, he said. “We need to be sure we can quickly detect and characterise new pathogens and new variants in real time.”

WHO Africa head Matshidiso Moeti said Africa is emerging from the new year travel season without a significant increase in Covid-19 cases for the first time since the pandemic began.

A total of 20,552 new cases were recorded in the first three weeks of January, a 97% decline on the same period in 2022 despite an uptick of cases in SA, Tunisia and Zambia in the past fortnight. While the drop in new cases is partly due to lower testing rates, the number of new hospital admissions and deaths has fallen significantly, she said. There were 88 Covid-19 associated deaths reported in Africa in the three weeks to January 22, compared to 9,096 in the corresponding period in 2022.