The European Union has agreed to return millions of COVID vaccines doses partially produced in South Africa back to the African continent.
South Africa’s Aspen Pharmacare operates the plant that is partially producing Johnson & Johnson vaccines, where vaccine substance from Europe is sent to be bottled and shipped.
The plant is supposed to produce 400 million doses for the AU’s African Vaccine Acquisition Trust through 2022, to be purchased by African nations using World Bank financing. Shipments started in August, with 6.4 million doses delivered to countries, but they have been limited due to the manufacturing plant’s production capacity.
The announcement came as Africa struggles to immunise its population against COVID, partly due to a lack of supply resulting from wealthier countries buying up most vaccines, and also from widespread vaccine hesitancy.
“All the vaccines produced at Aspen will stay in Africa and be distributed to Africa,” said Strive Masiyiwa, special African Union envoy. “This issue has been corrected and corrected in a very positive way.”
The announcement came after a meeting in Berlin between South African President Cyril Ramaphosa and European Commission President Ursula Von der Leyen, he said, adding that the first supplies were expected this month.
“In addition, the Europeans committed to give us 200 million doses before the end of December,” Masiyiwa said at the briefing by the Africa Centres for Disease Control and Prevention.
About 2.93% of people who have been fully immunised against COVID, said Africa CDC director John Nkengasong. The World Health Organization meanwhile warned that eight out of 10 African countries were likely to fall short of the “crucial” goal of vaccinating the most vulnerable 10% of their populations against COVID by the end of the month.
Codivir, a new antiviral drug with promising effects against COVID, will be trialled in South Africa.
Following on from the phase I study’s successful completion, Code Pharma, a Dutch pharmaceutical company developing Codiviir, is starting phase II double-blind controlled study in Spain, Brazil, South Africa and Israel.
Codivir is a short synthetic 16 amino-acid peptide, originally derived from HIV peptides. Code Pharma discovered the peptide’s direct antiviral effect against SARS-CoV-2 after in vitro studies at the British virology research laboratory, Virology Research Services in London.
Codivir was tested in a phase I trial in São Paulo, Brazil, where researchers found that Codivir had a high safety profile while significantly suppressing viral replication in most of the fully assessed patients. All treated patients recovered quickly and no side effects often associated with COVID infections were seen. The results also indicated that Codivir might have a similar beneficial effect on other RNA viruses such as influenza.
Lead researchers from the Department of Medicine at Hadassah Medical Center, Dr Yotam Kolben and Dr Asa Kesler said the antiviral drug had potential for improving the current therapies for COVID.
“The pre-clinical data and the results of the clinical trial support the safety of Codivir administration in humans and suggest its significant anti-COVID effect,” the researchers said.
Professor Shlomo Maayan, director of the Infectious Disease division at the Barzilai Medical Center, said Codivir had a very good safety profile and an impressive antiviral effect, both in the lab and in the phase I clinical trials.
“We eagerly await the results of the double-blind studies using Codivir. It may be a breakthrough in the field of antiviral therapy for COVID patients,” said Prof Maayan.
An article by the Daily Maverick reveals that a wave of suspensions in the Department of Health are impending as a result of the investigation into the Digital Vibes contract, which prompted the resignation of Dr Zweli Mkhize.
Minister of Health Dr Joe Phaahla said that he received a letter from the Special Investigations Unit (SIU) which he would have to act on.
Dr Phaahla said that “in the next few days and weeks there will unfortunately be some action and that will have some impact also on our capacity as a department”, adding that “when wrong things have happened and investigations have led to findings, then people have to be held answerable”.
However, Dr Phaahla said it was regrettable since “it will have an impact on our capacity, because from what I have seen, a number of people will have to be on suspension, pending charges.” He said it would be difficult for the vaccination programme as management staff were already stretched thin, but “it’s a consequence which must follow”.
Drs Buthelezi and Pillay denied any knowledge of suspension, though the Daily Maverick has found out that referral for disciplinary action have been sent to the presidency.
The details of the SIU’s investigation have not been made public yet, although the Daily Maverick was able to tease out some details from an affidavit to set aside the Digital Vibes contract and to seeks to reclaim up to R150 million that was paid for the contract.
The affidavit further reveals that Dr Mkhize allegedly pressured the previous Director-General, Precious Matsoso, to employ Tahera Mather to be contracted for communication.
Precious Matsotso was replaced after an unblemished ten years by Dr Anban Pillay, who had been Deputy DG. Dr Pillay then became the active facilitator for the Digital Vibes contract, the affidavit suggests — a matter in which the DIU has also referred to the National Prosecuting Authority.
The current DG, Dr Sandile Buthelezi, who replaced Dr Pillay, is also noted as approving payments to Digital Vibes, though the DIU states it is not seeking any relief against him other than setting aside of relevant agreements.
The situation still has a way to run, with disciplinary inquiries, the Special Tribunal hearing and NPA investigations all ongoing.
However, the Daily Maverick warns that it is clear that this critical government department is in “freefall” and will not have the capacity to deal with South Africa’s health challenges in the months and years to come.
A preliminary study recently uploaded on the medRxiv preprint server, researchers detail the detection and characteristics of the C.1.2 variant of SARS-CoV-2, which has not yet been assigned a variant of interest (VOI) status, but which could potentially have increased transmission and immune escape potential.
The researchers describe how they identified a new SARS-CoV-2 variant, C.1.2. The first detection of this variant was during the third wave of infections in South Africa from May 2021 onwards, and has also been detected in seven other countries around the world.
New SARS-CoV-2 variants are commonly associated with new waves of infection. Like several other variants of concern (VOCs), C.1.2 has accumulated a number of substitutions beyond what would be expected from the background SARS-CoV-2 evolutionary rate. This suggests the likelihood that these mutations arose during a period of accelerated evolution in a single individual with prolonged viral infection through virus-host co-evolution. Deletions within the N-terminal domain have been evident in cases of prolonged infection, further supporting this hypothesis.
C.1.2 contains many mutations that have been identified in all four VOCs (Alpha, Beta, Delta and Gamma) and three VOIs (Kappa, Eta and Lambda) as well as additional mutations. Many of the shared mutations have been associated with improved ACE2 binding or furin cleavage, and reduced neutralisation activity, raising concern about the transmission potential of this variant. The next step is determining the functional impact of these mutations and to find out if they give it a replication advantage over the Delta variant.
The C.1.2 lineage is continuing to grow, and as of 20 August 2021, there were 80 C.1.2 sequences in GISAID, and the variant has now been detected in Botswana and in the Northern Cape of South Africa. Note that this study is yet to have the peer review process completed.
SARS-CoV-2 viruses (yellow) infecting a human cell. Credit: NIH
Dr Shankara Chetty, a general practitioner with a natural science background in genetics, advanced biology, microbiology and biochemistry, has been critically reviewing information that has arisen from observations of the COVID pandemic from around the world. Knowledge gained from a broad natural science background convinced him that there was a missing element in these reports. This is a summary of an article published in Issue 5 of Modern Medicine in 2020.
“A wealth of knowledge of hospital presentations, pathology and investigations has been generated, but there has been a distinct lack of information regarding initial presentation, progression and pathogenesis,” said Dr Chetty. Type 1 hypersensitivity reaction When COVID arrived in South Africa, Dr Chetty isolated himself so as to limit interactions with family and the public and erected a tented field clinic in his practice parking so as to be able to examine and follow up on every COVID patient without risk to his other patients. According to him he had a theoretical understanding of the possible pathogenesis but needed to verify his suspicions.
“From the examination, treatment and follow up of over 200 symptomatic COVID patients, it is my opinion that COVID illness has two aetiologies. It is initially a respiratory viral infection with typical symptoms, progression and outcomes over the initial 7 days. On around day 7, a Type 1 hypersensitivity reaction is triggered in those that are sensitive, leading to the sequelae typically seen on admission.
“This reaction causes the release of chemical mediators in the ling, resulting in inflammation, oedema, and in time, massive cell damage. The resultant cellular disruption is what triggers the ‘cytokine storm’ in an attempt to repair damaged cells and remove debris. This release of cytokine produces the variety of pathologies that are seen,” said Dr Chetty.
Rapid response to treatment His treatment protocol included the use of hydrochloroquine, azithromycin and doxyclcline to combat the viral component and antihistamines, leukotriene receptor antagonists and steroids, amongst others, for the Type 1 hypersensitivity reaction. This protocol produced consistent outcomes, no sequelae, and rapid recovery of all patients. In all, they had no deaths, no hospitalisations and recover of all patients, regardless of age, within 14 days.
“Outcomes of identifying and treating a Type 1 hypersensitivity reaction were most telling in the more severe dyspnoiec patients, with saturations below 85% on presentation that had improvement to over 95% in 24 hours, with outpatient management on room air, negating the need for oxygen or hospitalisation,” said Dr Chetty.
According to Dr Chetty, the rapid response to these medications used to treat Type 1 hypersensitivity reactions confirmed its existence. This could have some serious implications for the future management of the COVID pandemic. Monitoring for a hypersensitivity reaction and prompt treatment would decrease morbidity and mortality significantly.
A review of surveys towards COVID vaccines in South Africa has revealed that there are multiple factors at work, with an underlying scepticism towards vaccines in general that appears to be growing in the very face of the pandemic.
The findings, published in Expert Review of Vaccines, highlight the multi-faceted and unique aspects of vaccine hesitancy in South Africa, such as men being more likely to reject a vaccine.
Vaccine hesitancy is not new; two years before the emergency of COVID the World Health Organization identified it as a top ten threat to health, underscored by outbreaks of preventable diseases such as measles.
A previous review of 126 surveys in 2020 found a global decline of COVID vaccine acceptance from 70% in March to 50% by October. Vaccine hesitancy has been an obstacle in South Africa for a long time: it was a factor in various measles outbreaks from 2003 to 2011, and it became more apparent during the nation-wide school HPV vaccination programme begun in 2014.
The researchers searched for surveys on COVID vaccine hesitancy in South Africa up until 15 March 2021, with sample sizes ranging from 403 to 75 518.
Unlike elsewhere, men are more hesitant In a survey by Ask Africa, men were more likely to distrust vaccines (39%) than women (26%). Of the women who would refuse, there was a higher percentage who would However, women were more likely to take the vaccine even if they thought it was unsafe. The authors cautioned that this result should be interpreted with caution; however, Department of Health deputy director Dr Nicholas Crisp also recently pointed this out, suggesting that more recent survey data helped inform his opinion. Curiously, this is in contrast to other COVID studies and other vaccine studies in general, which indicate that women are more hesitant than men when it comes to vaccines in general.
Age, race, education, geographical location Three of the studies found that age may be important, with older adults having less concerns and/or being more accepting of COVID vaccination.
The COVID-19 Democracy survey found that people 55 or older were more likely to take the vaccine (74%) compared to those 18 to 24 years old (63%). The same survey found that white adults were the least likely racial group to accept vaccination, with only 56% willing to be vaccinated compared to 69% of black African adults. Education was another factor, with just 59% of tertiary educated people willing to be vaccinated compared to 72% of this who did not complete high school.
Council for Medical Schemes (CMS) survey found that vaccine acceptance was higher (83%) in urban suburban settings compared to other settings (73% and 78%).
Doubts about safety significant Three rounds of Ipsos survey data showed a huge drop in acceptance from 64% in July/August and 68% in October to 53% in December. Of those not accepting, concern about side effects as a reason rose from 30% in October to 65% in December.
The Ask Afrika survey indicated that stopping the roll-out of the AstraZeneca vaccine early this year reduced both levels of trust in vaccine safety and confidence in the process.
Of particular concern were several surveys indicating South African antipathy to all vaccines; in the Ipsos surveys, about a quarter refusing COVID vaccines were also opposed to vaccines in general. Thus, this hesitancy to COVID vaccines, the authors suggest, is just the tip of the iceberg of South African vaccine hesitancy. Indeed, the Africa CDC survey indicated that at least one in five South Africans were less likely to get vaccinated in general than before the pandemic.
More research and targeted messaging needed Overall, the authors found about a third of the adult South African public is hesitant towards COVID vaccines. Age, race, education, geographic locations and possibly gender all influence the social nature of vaccine acceptance in South Africa.
The authors conclude that responding to vaccine hesitancy, including COVID vaccine hesitancy, requires a better understanding of the often complex and multi-layered issues influencing vaccination views and practices, and tailoring interventions accordingly. Individualistic, decontextualised, and ‘one-size-fits-all’ approaches are unlikely to have great success.
As the official COVID death toll in South Africa passes the 80 000 mark, the Department of Health is now shifting focus to addressing flagging vaccine demand.
The department said this will include making access easier, such as vaccinating at shops or places of work.
Another change would be providing transportation to vaccine sites to help those in underprivileged areas. One option being looked into is the introduction of home vaccinations and ‘pop-up’ sites in rural areas where travel is harder to come by and at busy commercial areas such as shopping centres.
The government also hopes for assistance from the religious sector, with the possibility of churches offering vaccines on a Sunday. Mosques, synagogues and other places of worship would also offer a ‘familiar environment’ where people feel comfortable receiving a vaccine.
Public awareness Social media will be heavily employed for vaccine promotion, and could incude online influencers and ambassadors to encourage vaccination. This could extend to identifying ‘apolitical’ vaccine champions relevant to the target group who have also great influence, such as celebrities and traditional leaders.
A number of awareness initiatives are being considered, including making use of channels such as social media and teachers to provide information to young people and counteract misinformation, as well as more traditional media efforts such as radio slots and signage.
Vaccine skepticism high in men Department of Health Deputy director-general Dr Nicholas Crisp, pointed out that South Africa has a particular problem with men not wanting to be vaccinated.
“This is not good,” Dr Crisp said. “It means that men are going to end up very sick and in hospital, and we don’t want that to happen just before Christmas.”
Mandatory vaccinations on the cards Health minister Dr Joe Phaahla warned of a very long road ahead as new cases continue to spike.
The ministerial advisory committee on COVID is now discussing the possibility of mandatory vaccination for certain groups of people, which could include healthcare workers and those professions spending time indoors with other people, according to the Sunday Times.
Scientists and health activists told the paper that the right to refuse a vaccine is outweighed by the health hazard of the pandemic.
The country would then be able to reopen and operate in a way as close as possible to the pre-COVID era, said leading vaccinologist Professor Shabir Madhi.
“In these settings, if people choose not to be vaccinated, they should be compelled to undergo testing every three or four days at their own expense,” he said.
While vaccinations don’t confer complete COVID protection, it is still significant, and more impactful if a greater proportion are vaccinated, Prof Madhi said.
In a digital media briefing, Western Cape Premiere Alan Winde said that the province had still not exited its third wave of COVID infections.
With an R value of 0.9, this was the first time in the third wave that the value was below 1. However, this could be due to testing delays caused by the long weekend. Indeed, a sharp daily increase in national COVID cases has been recorded as of Thursday’s latest data, with the NICD reporting a 90% jump to 14 271. Overall case positivity still hovers above the 20% mark at 22.52%.
Cases continue to spike While overall cases in the Western Cape are plateauing, spikes in certain areas are seeing higher case rates than in the peak of the second wave. Oxygen is still being used as fast as it can be produced in the province, being supplemented by an additional 22 tonnes per day by truck deliveries from other provinces. A total of 3665 patients are in acute hospitals, with 99% occupancy in Metro areas. The Metro area is seeing a week-on-week case rise of 7%, which points to a plateau.
Vaccines proving effective – even against beta The Johnson & Johnson vaccine however is proving effective, with 91-95% protection against death and 65-66% protection against hospitalisation. With regard to variants, the vaccine confers 67% protection against hospitalisation when beta is dominant and 71% where delta is dominant.
The Western Cape’s vaccination programme remains on track, with 287 000 doses of Pfizer and 28 800 J&J doses to arrive today, Friday 13th.
Elsewhere, with 31.2 new cases per 100 000 people, KwaZulu-Natal may be becoming a COVID hotspot.
A further 473 people have died from COVID, bringing the official death toll to 76 247.
In an article published in the South African Medical Journal, Shabir Madhi, Professor of Vaccinology at Wits, argues that COVID variants have made the initial goal of attaining herd immunity no longer feasible, even for well-resourced countries. However, vaccine protection against severe COVID seems a more realistic path to normalcy.
In low and middle income countries (LMICs), the official COVID case estimates are likely grossly underestimated, Prof Madhi writes, due to a lack of testing coverage. Even in South Africa, the true number of COVID cases is likely in the region of 10 times the 2.39 million recorded through testing. The true number of COVID-related deaths in India is also estimated as 3.4–3.9 million, again 10 times the official count, and in South Africa it is likely three times the official figure of 70 388 in July 2021.
While New Zealand researchers have suggested that COVID eradication is feasible, it is likely a very long term goal if at all attainable. The herd immunity goal can be considered with the equation (p1 = 1 – 1/R0), where p1 is the proportion of immune individuals who will also no longer transmit the virus, and R0 is the reproduction rate, ie the number of susceptible individuals a single infected person can further infect. However, this ignores key aspects of the virus.
The problem is that the proportion of people that would need to be immunised to achieve herd immunity was initially calculated at 67%, based on an assumed R0 of 3, derived from the Wuhan strain’s R0 of 2.5 to 4. However, the Delta variant has an R0 of 6, meaning that to reach herd immunity, 84% of the population would need to be vaccinated. In South Africa, this would be 100% of the population aged over 12.
The emergence of SARS-CoV-2 variants, especially the Beta variant with the E484K mutation, showed that existing vaccine protection, including the Pfizer variant, can be degraded to an extent.
Studies have strongly suggested that neutralising and antibody titers are associated with mild to moderate COVID protection, while protection from severe COVID may be mediated by T-cell immunity.
Real world data showed that in Israel, with a world best immunisation of 61.6% using the Pfizer vaccine which produces the greatest antibody response, herd immunity appeared to be successful until an outbreak of the more transmissible Delta variant combined with waning vaccine effectiveness.
However, in the UK, excess death data showed that, even with a resurgence of cases caused by the Delta variant, there was a significant decoupling of deaths from cases. This points to the effectiveness of vaccines in preventing severe illness, as opposed to reaching herd immunity.
Vaccine rollouts have therefore not interrupted COVID transmission. Prof Madhi concludes that, based on an estimated R0 of 6 for the Delta variant, “it is unlikely that any country could have a sustainable strategy for durable high level of protection against infection by the delta variant. Mutations of the SARS-CoV-2 genome are likely to continue resulting in enhanced transmissibility, infectiousness and resistance to neutralising activity.”
He observes that the “UK approach seemingly concedes that the goal of herd immunity, even in a highly resourced setting, is unattainable.”
He adds that aspiring to reach herd immunity by wealthy countries comes at the cost of exacerbating vaccine inequality, which he says “is immoral.” Antibody dynamics modelling suggests that a booster would be required every 2–3 years to protect against severe COVID, and every 6–9 months to protect against moderate disease. This is a challenging goal, and likely unattainable for most LMICs, especially given the slow rate of vaccination in those settings.
Western Cape premier Alan Winde said that the province is at the peak of its third wave of COVID infections.
“We are beginning to see the flattening of the curve at our peak as new case infections start to plateau again,” he said in a briefing on Thursday. “This happened after an initial plateau two weeks ago, and then a subsequent increase the week thereafter.
“This is largely explained by a disruption in testing caused by the taxi violence in the Cape Metro during that time.”
Winde supplied the following information:
The ‘R’ number is currently 1.1 and the test positivity rate is 41.5%. New hospital admissions are at 339 per day, with a slight downturn. Deaths have increased, with about 108 deaths per day and will be the last indicator to fall.
Winde said that provincial authorities are simultaneously monitoring the number of trauma admissions to hospitals to ensure that there is sufficient capacity in the province’s hospitals and that it can proactively identify any risks so that they can be addressed. Senior CSIR researcher Ridhwaan Suliman, PhD, who was been analysing COVID data tweeted an update on Friday night, indicating that there was still no sign of the peak passing just yet:
