Tuesday, 16 April, 2024
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Next coronavirus variant could cause more illness, SA study finds

As health experts urged government to prepare for the next pandemic, a new South African study has shown that the next coronavirus variant could cause more illness than the current predominant Omicron strain, notes Medical Brief.

The study, using COVID-19 samples from an immune-suppressed individual over six months showed that the virus evolved to become more pathogenic. News24 reports that the study, conducted by the same laboratory that first tested the Omicron strain against vaccines last year, used samples from a person infected with HIV. Over the six months, the virus initially caused the same level of cell fusion and death as the Omicron BA.1 strain, but as it evolved, those levels rose to become similar to the first version of COVID-19 identified in Wuhan, China.

The study, led by Alex Sigal at the Africa Health Research Institute in Durban, indicates that the COVID-19 pathogen could continue to mutate and a stronger, new variant might cause even more severe illness and death than the relatively mild Omicron strain. The study is yet to be peer reviewed and is based solely on laboratory work on samples from one individual.

Sigal and other scientists have previously postulated that variants such as Beta and Omicron – both initially identified in southern Africa – might have evolved in immunosuppressed people, like those infected with HIV.

The delayed time it takes for these individuals to shake off the disease allows it to mutate and become better at evading antibodies, they said.

The study “may indicate that SARS-CoV-2 evolution in long-term infection does not have to result in attenuation”, the researchers said in their findings, which were released last week. “It may indicate that a future variant could be more pathogenic than currently circulating Omicron strains.”

The findings come as three of South Africa’s women leaders in the medical field have highlighted the need for the country to invest in a stronger health system, look into the collateral damage caused by lockdown to people’s lives and keep up and extend investment in research, medical and environmental surveillance systems for the country to be ready for the next pandemic.

The COVID-19 pandemic, they say, has highlighted the urgency to get globally compatible systems in place before the next virus hits, notes Medical Brief.

The response to the next pandemic must start now, urged the trio – Precious Matsoso, Professor Kholeka Milisana and Professor Glenda Gray – during a panel discussion on solutions for the next big pandemic at Daily Maverick’s flagship event, The Gathering.

Hosted by Professor Tim Tucker, founder and CEO of the SEAD public health consultancy and adjunct associate professor at UCT’s school of public health, the panellists said the work to strengthen the response by South Africa and the world to the next pandemic can’t wait until it hits.

Global health experts refer to Pathogen X as the cause of the next pandemic.

“We failed to understand the economic impact of the country’s mitigation strategy,” said Gray, CEO of the South African Medical Research Council (SAMRC), who was also chair of the Research Committee on COVID-19, in reference to the impact that lockdown, for instance, had on schooling and food security.

In its response to COVID-19, the country had also failed to recognise the lack of trust in Western medicine. “We must do a lot more work on culture, mental health, trauma and gender-based violence.”

She added that environmental surveillance would also be crucial as Pathogen X might be the consequence of climate change or a cross-species jump.

The panellists also emphasised the need for South Africa to improve hospital records and for a “unique identifier” system to allow access to patients’ records.  “We need astute hospital records,” Gray said.

While they waited, the virus ravaged

The chairperson of the World Health Organisation’s (WHO) Independent Oversight and Advisory Committee and former director-general of the Department of Health, Precious Matsoso, said a new pandemic treaty was needed as current legal instruments guiding a global health response were too cumbersome.

She said legal instruments available to the WHO in 2020 called for steps to be created, as well as consultation and verification.

“A viral pathogen that moves so fast can’t wait for this process,” she said. “There was delayed movement… Some countries were swift. Some were tardy. Some undervalued health workers. Some played ‘wait and see’. The virus didn’t wait. The virus just ravaged.”

The countries that had done better had engaged communities, and made solid investments in their health workforce.

“You don’t invest in the health workforce during an outbreak. You invest during peacetime. We have pushed for a pandemic treaty that will hold countries accountable.”

Other factors that plagued a successful response to the pandemic included glaring inequities in the distribution of vaccines.

Matsoso added that on the positive side, research and development continued at an unprecedented pace as the world battled COVID-19, and the creation of digital platforms have provided something positive on which to build for the future.

She said global access to lifesaving measures like vaccines must be addressed because it is senseless to support research and development but then neglect global access.

“We have recognised that access must be addressed,” she added, saying one such way was the C-TAP platform (COVID-19 Technology Access Pool) that was created to facilitate faster, equitable and affordable access to COVID-19 health products for people worldwide.

Measures for the equitable distribution of the vaccine had failed and “did not help get vaccines into arms”, and this should be tackled in a legally binding international pandemic treaty.

“It cannot be that in South Africa we fought for antiretrovirals but this time, in the middle of the crisis, we failed.”

Matsoso said the treaty must address governance, equity, systems and financing.

In human health, she pointed out, countless millions who have been affected are not just a statistic. “They are a relative, a friend, a co-worker, a leader and a community member … which will result in a permanent loss, leaving a void not to be filled again. They are also from vulnerable sectors of society.”

She said the pandemic has added to the frailties and fragilities of these groups, compromised access to services and treatments, particularly for the elderly, children, women, people with disabilities, migrants and displaced peoples.

“With the envisaged changes globally, the goal is to prevent these health threats from happening again at such catastrophic proportions and fix the current inadequacies of preparedness and response. Health emergencies are disruptive. They compromise other services and undermine access especially if preparedness plans are absent.

“The assessment of countries, including South Africa, before the pandemic was noteworthy. The shortcomings identified were associated with limited investments in preparedness and response. Using various evaluation tools to help countries assess themselves, it was revealed that only two-thirds of WHO member countries reported having full enabling legislation and financing to support emergency prevention, detection and response.

“The Global Health Security Index revealed that 155 out of 195 countries had not allocated national funds over a three-year period to address epidemic threats.

“Those countries that scored high in these assessments through Joint External Evaluations were not necessarily the best performers. South Africa identified gaps. For instance, the interoperable, interconnected, electronic real-time reporting systems were found to be inadequate, as well as healthcare associated infection (HCAI) prevention and control programmes.

“These could be addressed in a short, medium and long term. There were strengths associated with preparedness and response structures and networks. There were weaknesses with subnational level linkages in some of the countries. This was exposed during the COVID response as the speed at which the coronavirus moved was fast.

“The surveillance and alert systems could not keep up and reaction was slow. This was the case for South Africa and for many other countries, as revealed during assessments and evaluations commissioned by the WHO.”


But Milisana, head of the National Health Laboratory Services, said South Africa’s swift response to the pandemic was one of the things it got right. “Structures were established. The response was scientifically driven.”

A highlight for her was that South Africa already had a laboratory system in the private and public sectors, which meant data could be gathered quickly. The establishment of the Solidarity Fund had also been a positive step.

“Our investment in science paid off,” Gray said. South African researchers who were already engaged in HIV and TB work could move to COVID-19 research when the pandemic started.

Citing examples, she said a platform developed for TB and HIV in 2014 was repurposed for COVID-19 and helped scientists to identify two new variants – Beta and Omicron.

“But the best R750 000 we spent” had gone to a TB researcher to grow a culture of the SARS-CoV-2 virus, which could be used to establish a platform for accurate diagnostics. “This was used in 24 countries, including nine African countries.”

Gray said it was vital to continue investing in diagnostics, as was ongoing collaboration and research and development of vaccines.

“Investing in science is the best way to respond to a pandemic… We need scientists.”

She said the tracking of excess deaths in the country was critical.

‘Weak’ system

Milisana said the health system didn’t cope with the waves of infection caused by the SARS-CoV-2 outbreak – not in infrastructure, supply chain management or human resources.

“The health system is very weak,” she said. “There must be commitment and funding and people with skill to do the work. We have learnt a lot. Now we are in a season between (pandemics). Surveillance will be critical.”

She said South Africa needed a national structure that was well designed, defined and funded and would keep up surveillance work, as well as systems that needed to be kept in place for a response. “Genomic surveillance (the network looking for new variants of the SARS-CoV-2 virus) must be funded and continued.

“We established the DatCov system,” she said, referring to the daily surveillance system measuring admissions and in-hospital deaths and which is used to measure the severity of an outbreak. This system, for instance, provided early indicators in 2021 that Omicron was causing a less-severe form of COVID-19, as could be seen in hospital admissions.

Data integration and links were called for. “It has been a huge challenge for us to establish a unique identifier (a way to identify an individual for records that can be accessed countrywide).”

Gray added that environmental surveillance – including of wastewater – must be prioritised, particularly since the next pandemic might be driven by climate change.

Matsoso said there should also be future investments in increasing the pandemic literacy among the general public, including trustworthy government communications. “We found that in countries that did well the citizens trusted the government.”

Outbreaks start and end in communities, she added.

“Our successes in containment and mitigation will depend on how we build trust, people’s trust, and confidence in health authorities. Engagement of local communities to promote pandemic literacy and understand health communications and working directly with marginalised populations on risk communication policies is a good start.

“Also, health promotion and education can be incorporated to have an integrated approach. South Africa can learn from the experience of countries that dealt with epidemics and performed well.”

The international spread of disease is a global threat, she said. “It has serious consequences for public health, for human lives and livelihoods. It ravages economies and disrupts societal activities. Throughout pandemic many witnessed the gravity of health threats and observed just how vulnerable and fragile our world is.”

Daily Maverick article – Warning – Viruses don’t wait, responding to the next pandemic must start now (Open access)


Daily Maverick article – Pandemic Preparedness – how governments must gear up for global disease threats (Open access)


News24 article – SA lab study shows next Covid strain may be more dangerous (Open access)


See more from MedicalBrief archives:


South Africa’s fixation on Western science worsened its COVID crisis


The demographic face of COVID-19 in South Africa — Johannesburg University


African study finds bulk of COVID-19 variants came from abroad


Zoonotic diseases: Sindbis, Langya and monkeypox outbreaks keep scientists on alert





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