How HIV expertise is helping South Africa tackle coronavirus

South Africa has spent the last two decades fighting against its deadly HIV and TB epidemics, and many of its HIV researchers are now mustering their expertise to battle the Covid-19 pandemic.

The scientific community has “galvanized” to investigate the novel coronavirus and the disease it causes, says Jinal Bhiman, principal medical scientist at the National Institute for Communicable Diseases.

The country—which has more than 1,300 confirmed cases and has recorded its first Covid-19 deaths in the last week—is on physical lockdown. The government is scrambling to contain the SARS-CoV-2 virus, which can lead to the Covid-19 disease.

While one of the most developed countries in sub-Saharan Africa, South Africa has the highest number of HIV infections in the world, with about 7.7-million people living with the disease. In response to this devastating HIV epidemic, South Africa has one of the most prolific HIV research bases globally. After the United States and the United Kingdom, the country’s researchers produce the most academic papers describing and understanding HIV. “There are a lot of similarities [between the two viruses] that mean that a lot of the folks who’ve been working on HIV for the last 15 years are able to step in and study SARS-CoV-2,” says Penny Moore, a research chair in virus-host dynamics at the University of the Witwatersrand in Johannesburg. “Understanding the virus and sequencing local strains is something we’ve done for years for HIV.”

The National Institute of Communicable Diseases (NICD), which has been advising the government and spearheading its testing and surveillance response to Covid-19, has already sequenced the full genome of SARS-CoV-2 in a local case.

Acquired from someone who had recently returned from Italy, “this genome clusters with other European strains”, says Bhiman. “However, an analysis of over 2,000 sequences collected from around the world shows them to be highly similar indicating that this virus is not evolving significantly despite its rapid spread.”

However, if the virus does mutate in the local population, tests will need to be for those specific strains.

“Tests and assays have to be for the South African [version of the] virus, so we need to know where and how it is different to the European one,” Moore says.

And, because of HIV, South Africa’s scientific community has vast experience in tracking and studying viruses.

Glenda Gray, head of South Africa’s Medical Research Council and a HIV expert, thinks that the country’s existing research capacity is vital in shaping its response to the Covid-19 epidemic. “There is so much we don’t know about the natural history of Covid-19 in Africa,” she says – from how it moves in the country’s closely-packed townships to whether some population groups are more susceptible to it.

This is where the HIV community’s expertise in immunology, tracking disease spread, and clinical trials can be marshaled to fight Covid-19.

Moore’s laboratory specializes in people’s immune response to HIV. “Using the same technologies, [we can see] what happens in SARS-CoV-2 and what is considered a good immune response within people [whose immune systems] are clearing the virus,” she says. “We’re repurposing things that have been up and running for 15 years.”

While she doesn’t expect the immune response between a South African and an Italian, for example, to be different, “from a clinical point of view, it’s likely to be different [because our population has] a lot of HIV and tuberculosis”. About 60% of the country’s HIV-population also has TB, a bacterial infection that mainly targets the lungs.

Meanwhile, large swathes of the country’s infectious disease machinery—from researchers to public health officials – have turned to tracing the spread of the virus and testing those suspected of being infected.

South Africa has tested more than 44,000 people for the virus, but officials and experts are concerned about the availability of tests. “Real-time surveillance is paramount for your response and [in South Africa] that is curtailed by the lack of test availability,” says Gray.

This is a major focus of local researchers—to try and develop tests that could be manufactured locally. “There’s been a push in South Africa to do that for HIV,” says Moore, “and there’s a drive to accelerate that to try and get [coronavirus] antibodies.”

But one of South Africa’s major contributions to HIV research has been as a site for clinical trials—although they are often funded from outside of the country. In fact, the country is already gearing up for a landmark Covid-19 treatment trial.

“South Africa is well geared up to run vaccine trials,” says Gray, who is a principal investigator on the international HIV Vaccine Trials Network. “We have the capacity, 34 sites that have done HIV vaccine trials from phase one to three. These sites are staffed, have pharmacies, and have infrastructure that could really respond to evaluating vaccines.”