Two Omicron variants fastspreading in South Africa

South Africa’s daily coronavirus test positivity rate neared a record, rising above 30 percent on Saturday for the first time in almost five months as two sublineages of the Omicron variant spread rapidly ahead of the nation’s winter season.

There were 8,524 new Covid-19 cases identified, representing a 31.1% positivity rate of those tested, the National Institute for Communicable Diseases said in a statement on its website. That’s the highest rate since the 32.2% recorded on Dec. 15, when a record 26,976 cases were recorded. The surge means South Africa is close to its highest positivity rate yet. The record so far was 34.9% on Dec. 14.

The positivity rate is taken as an indicator of how fast the disease is spreading through the community as many cases go undetected.

Still, only five deaths were recorded in the last 48 hours and just over 2,600 people are in the hospital with the disease. At the peak of the wave in mid-2021 when the Delta variant was rampant, hundreds of people were perishing daily and hospitalizations peaked at about 16,000.

South Africa, which together with Botswana identified the Omicron variant in November, was the first country to experience a wave driven by the strain and the way it played out was seen as an indication for what could happen elsewhere. Last month South African scientists identified two Omicron sublineages, BA.4 and BA.5, and laboratory experiments have since shown that those strains can reinfect those who have already had the original Omicron strain.

The current surge in infections and positivity shows that even though previous waves have been caused by the emergence of new variants the sublineages are now having the same effect, Tulio de Oliveira, who runs gene sequencing institutes in South Africa said on Twitter.

Long Covid risk

The risk of lingering symptoms after Covid-19 appears influenced by the strain of coronavirus that caused the infection, according to an analysis from the UK, where an estimated 1.8 million people reported experiencing long Covid in early April.

The odds of reporting fatigue, shortness of breath, difficulty concentrating and other persistent symptoms were 50% lower following infections likely caused by the Omicron BA.1 variant than those likely caused by the Delta strain, the Office for National Statistics said in a report Friday. The difference was only found among adults who were double vaccinated when infected. Among those who were triple vaccinated, the difference wasn’t statistically significant.

Among triple vaccinated adults, the odds of reporting long Covid were higher following infection with the Omicron BA.2 variant than the BA.1 variant, the analysis found.

More than two-thirds of those with self-reported long Covid, or 1.2 million people, said their symptoms adversely affected their day-to-day activities, and almost a fifth said their symptoms limited them a lot, according to the statistics bureau.

Most long Covid symptoms don’t seem to be life threatening, but things like shortness of breath or fatigue can be disabling. The US Government Accountability Office said in a March report that long Covid could affect the broader economy through decreased labor participation and an increased need for use of Social Security disability insurance or other publicly subsidized insurance.