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Delta variant dominates Gauteng and is spreading to rest of SA

The highly contagious Delta variant of the Sars-CoV-2 virus is the driving force behind the large increase in COVID-19 cases in Gauteng and is spreading to other parts of South Africa, as well causing havoc elsewhere on the continent, reports MedicalBrief.

The National Institute for Communicable Diseases (NICD), which has been performing genomic surveillance for SARS-CoV-2, confirmed on Wednesday (30 June 2021) that the Delta variant is now dominant in Gauteng.

A new record – 11,777 new cases in a day in Gauteng alone – was reported on Friday. The Gauteng rolling seven-day average is 10,092 cases a day, although the Tuesday infection figure dipped to 8,927 new cases.

More than half of 11,149 COVID-19 patients in hospitals nationwide are in Gauteng – over double the crest of the second wave of 5,526 hospitalised.

The USA is donating 1m doses of the Pfizer/BioNTech vaccine to SA, arriving within the next few weeks. The bilateral donation is part of the 500m doses the US previously announced it would purchase from Pfizer to donate to other countries, primarily through the international vaccine financing agency, Covax, and the African Union.

However, with less than 5% of South Africans having received at least one dose of a vaccine, scientists are concerned that the problem is not a shortage of vaccines but the slow rollout.

Professor Francois Venter, an expert in communicable diseases at Wits University said that within a week or two, “Gauteng will look like India.” Professor Koleka Mlisana, co-chair of the Ministerial Advisory Committee on COVID-19, warned that an increase in infections in other provinces will be seen in a “matter of days”.

Private hospitals under pressure

SA’s three biggest private hospital groups have all recorded significantly higher admissions for COVID-19 in Gauteng during the current wave, forcing them to transfer small numbers of patients to facilities in other provinces.

Netcare CEO Dr Richard Friedland told Radio 702 that Gauteng should be subject to Level 5 lockdown restrictions and all schools should close. He said hospitals had to work since last week as if they were dealing with a “mass trauma event” such as a train accident.

Friedland said Netcare was treating more than 2,600 COVID-19 patients across its hospitals in Gauteng. “This is 45% higher than the 1,792 patients we had at the peak of the second wave, and almost 100% higher than the 1,377 patients admitted during the peak of the first wave in Gauteng.”

In the absence of a completed vaccine rollout, South Africans must rely on the strictest possible non-pharmaceutical preventive measures. Of the more than 33,000 Netcare frontline workers vaccinated [with the Johnson and Johnson vaccine], he said only 206 (or 0.6%) have experienced a breakthrough infection and only seven required hospitalisation.

Netcare was making plans to deal with an expected surge in coastal areas. “We have already started scaling down on non-urgent surgery and medical admissions in our coastal hospitals, and some have suspended such surgery to rapidly create capacity for the expected increase in COVID-19 patient numbers. To free beds for COVID-19 patients, only medically necessary, time-sensitive surgeries will continue, as well as emergency admission of non-COVID-19 patients.”

Plans were also in place to convert Medicross day theatres and other facilities to accommodate COVID-19 patients if needed. Netcare had secured more than 1,000 more mobile oxygen concentrators and another 100 ventilators. This includes 40 transport ventilators, which can be used by emergency medical services personnel when transporting patients who need oxygen.

NICD genomic data

The NICD said in a statement that data from the UK show that the Delta variant is 97% more transmissible than the original lineage. COVID-19 vaccines remain highly effective in preventing severe disease after Delta variant infection, with the Pfizer-BioNTech vaccine showing 96% efficacy after two doses.

“It is important to be mindful that reinfection with the Delta variant is possible after a Beta infection, due to waning of immunity,” said Prof Adrian Puren, the NICD’s acting executive director. Limited data are available on whether different symptoms result after Delta infection, and preliminary data from the UK suggest that the Delta variant can potentially cause more severe disease.

Genomic data, generated by the Network for Genomic Surveillance in South Africa (NGS-SA) from sequenced COVID-19 specimens during May 2021, show that 70% of 680 genomes were the Beta variant. However, in June 2021 genomes (n=541) sequenced from samples revealed a 31% drop in the Beta variant to 39%, with the Delta variant increasing and accounting for 45%.

Gauteng, the epicentre of the resurgence, presently accounts for an average of 65% of daily new cases. In this region, 64% of 244 genomes sequenced from May 2021 are attributed to the Beta variant, while in June this dropped to 37%. In contrast, during June, 53% of genomes (n=341) from Gauteng being the Delta variant.

Delta variant is becoming the dominating COVID-19 variant across the world. Currently, 85 countries have now confirmed the presence of the Delta variant, reports the World Health Organization.

A bleak picture elsewhere in Africa

Elsewhere in Africa, the picture is similarly bleak, with the Delta variant rampaging across at least 20 countries. “The Delta variant is aggressively taking over from other variants and crowding them out, not just in Uganda but in other countries such as the DRC,” said Africa CDC director Dr John Nkengasong at his weekly COVID-19 briefing on Thursday.

New deaths rose 19% from the previous week’s update, and have gone up 7% during the past month. More than 5m cases have been reported on the continent. Another challenge in the third wave is that younger people are getting sicker with COVID-19 than they were in the first two waves.

“For the first time (in the pandemic) there are reports that hospitals are being overwhelmed. Yesterday, the ministry of health in Zambia said they were completely overwhelmed. The DRC president said their hospitals are overwhelmed. Uganda is overwhelmed,” said Nkengasong.

“So many people are dying because of the basic lack of oxygen. Yesterday that was the experience of Zambia, where oxygen had run out completely.”

Namibia had the second highest number of new cases per million population in the past week at 548, after Seychelles at 1,013.

Overall this month, new infections have risen on average by 23%, with only West Africa staying stable (1% decrease), and the other four regions showing sharp increases: Southern Africa (40%), Central Africa (25%), East Africa (15%) and North Africa (1%).

Rapid vaccination at scale is the solution to the worsening pandemic, said Nkengasong. “Unfortunately the numbers speak for themselves: 1% coverage is far, far removed from the target where we expected to reach.”

Countries like the UK have fully vaccinated 47% of their population and the US has 45% COVID-19 vaccine coverage. On the positive side, said Nkengasong, African countries had used up 80% of the vaccine doses they acquired, getting them into the arms of their people. SA was lagging behind on this.

Seychelles is one of Africa’s most vaccinated countries, relying on Chinese-sourced vaccines, yet infections in the island state are climbing, prompting the Africa CDC to investigate.

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