RESEARCH

VISUAL DATA PLOTS PANDEMIC PATH

THE ADVENT OF the COVID-19 pandemic not only ignited medical and economic responses, but saw social scientists working at the Gauteng City-Region Observatory (GCRO) respond with agility to advise in the planning of these responses.

The GCRO is a partnership between Wits University, the University of Johannesburg, and the Gauteng Provincial Government. Years of research around Gauteng made it possible for the GCRO to use a visual analytics platform developed by IBM Research Africa, and collaborate with data scientists, to offer insights into how best to respond to the pandemic. By using a “syndemics approach” the key social forces and structural drivers that may exacerbate the spread of disease were identified — basically, a vulnerability detector in the context of COVID-19.

The GCRO’s COVID-19 Map of the Month was launched as a result. It initially explored two key themes: 1) the multiple risk factors in the maintenance of basic preventative hygiene and social distancing and 2) the risk factors in contexts of major shutdowns and potential outbreaks.

A year on from its inception, the project has rapidly expanded with impressive outputs. Among others, these include COVID-19 in children and adolescents; the impact of COVID-19 on long-term care facilities; household characteristics in relation to COVID-19 risks; the impact of COVID-19 on women; income and household vulnerability; COVID-19 cases in South Africa by province; and COVID-19 risk indices per municipality.

“It is something we put out in a very visual way to try to understand where vulnerable people are. It has kind of stood the test of time. There’s lots we can do to improve on it, but it has proved itself useful. It has also now been picked up to help support a vaccination strategy,” says senior researcher and Wits alumna Gillian Maree (BSc URP 1999).

“It unfolded as the pandemic evolved — we’re paving the road while we’re driving on it. As an organisation we’ve had to be adaptive. I don’t think we quite knew in the beginning the extent to which government was going to engage with this research.”

The research has enabled the GCRO to remain true to its mandate to provide direct policy support (for local and national government) as well as to inform partner officials and clinicians within Gauteng Provincial Government, yielding rigorous peer-reviewed academic scholarship at the same time.

“All of the work is collaborative. Every piece put out has been done with a few people, with a range of skills. It makes it really special. In the short time we’ve had it, we’ve really made use of the wide range of social science skills at the GCRO,” says Maree.

They hope to deepen analysis by exploring the socio-economic impact of COVID-19 through indicators such as gender, age, access to transport and amenities, and making use of clinical data such as hospitalisations and deaths in relation to population density.

The list of collaborative researchers includes Dr Julia de Kadt (PhD 2011), Dr Alexandra Parker (BAS 2005, BAS Hons 2008, MArch 2009, PhD 2014), Graeme Götz (BA 1991, BA Hons 1993), Melinda Swift, Dr Robin Moore, Samkelisiwe Khanyile (BA 2014, BSc Hons 2015, MSc 2016), Christina Culwick Fatti (BSc 2009, BSc Hons 2010, MSc 2013), Yashena Naidoo, Sthembiso Pollen Mkhize, Sandiswa Mapukata (BA 2016, BA Hons 2017, MSc 2019) and Samy Katumba.

Photo: Simon Wolfson

COVID-19 AND WOMEN IN GAUTENG

One output from the GCRO under its Map of the Month series revealed the disproportionate impact of the pandemic on women. More women than men tested positive for COVID-19 in Gauteng between 6 March - 7 August 2020.

The COVID-19 infection data as well as the GCRO vulnerability index point to a double burden for women. Women tested positive at a higher rate than men and have a greater social and economic vulnerability during lockdown.

“There are several possible explanations for why working women may be more exposed to COVID-19 in the Gauteng context. It may be that more women are employed in higher-contact care and frontline service work (such as cashiers, cleaners and nurses). Globally, some 70% of healthcare workers are female and this may be one of the drivers for a higher rate of infection (as could the higher rate of testing of women). It is also possible that because women make up the majority of social grant recipients they are contracting the virus at a higher rate than men while standing in queues for monthly payments,” the study reads.

The drivers for the higher rates of infection include risk factors such as living in a crowded dwelling; dependence on public health care facilities; reliance on public transport; existing health conditions; and access to medical aid.

For more see https://gcro.ac.za/outputs/map-of-the-month/ detail/women-and-covid-19-gauteng/

The GCRO's two risk indices related to COVID-19 vulnerablilities help to understand drivers of the higher rates of female cases. Index 1(top) considers risk factors related to preventative measures. Index 2 (bottom) examines risk factors related to lockdown conditions that are likely to increase health and socio-economic vulnerabilty.

The chart shows that the proportion of female infections is higher for younger working adults (in their twenties) and drops to the average of 56% for older working adults. For cases over the age of 80 the dark orange shows a much higher proportion of female cases in line with international trends and the higher proportion of females in the population at this age. The higher proportion of male infections is really only evident for a few ages under 10 years of age.

RETHINKING ORIGINS OF VERTEBRATES

Family portrait: This reconstruction of the Late Devonian estaurine lake at Waterloo Farm captures the life history of a stem lamprey Priscomyzon riniensis. Three individuals representing different ontogenetic stages take a shelter in the meadow of charophyte algae Octochara crassa. Clockwise from right: a yolk-sac-carrying hatchling tucked in the charophyte; a juvenile attached to the substrate in the foreground; and an adult looming over the other individuals and showing its feeding apparatus. Art by Kristen Tietjen

LIKE A FORENSIC detective Wits alumnus Dr Robert Gess (PhD 2011) has found a new clue towards solving the puzzle of the origins of vertebrates.

Based at the Albany Museum in Makhanda and affiliated to the Centre of Excellence in Palaeosciences at Wits, Dr Gess has painstakingly chiselled through around 20% of 100 tons of shale assembled from the 360-million-year-old Waterloo Farm heritage site which was exposed during a road construction in 1985. The shale samples were rescued ahead of further roadworks at the site in 1999 and 2007.

Among thousands of fossils recovered from the shale samples are a growth series of lamprey fossils, of the species Priscomyzon riniensis, illustrating its development from hatchling to adult. The smallest preserved individual, barely 15mm in length, still carried a yolk sac, signalling that it had just hatched before entering the fossil record.

Priscomyzon is the oldest species of fossil lamprey in the world, which he had already described from an adult from the site in an article in 2006. But the seven juveniles, which he has assembled over the subsequent 15 years, are completely unlike what everyone would have expected.

Dr Gess, together with colleagues from the University of Chicago, published their findings in the prestigious journal Nature on 10 March 2021.

“To get to the crux of the story”, explains Dr Gess, “we need to recall how living lampreys have affected biologists’ views of vertebrate origins and why. Lampreys (and their cousins the hagfish) are the only living vertebrates that branched from our shared family tree before we evolved jaws, so since the 1800s they have been intensely studied for insights into early vertebrate evolution. Their larvae, known as ammocoetes, are so vastly different from the adults that until the mid eighteen hundreds they were thought to be a completely different kind of creature.

“Ammocoetes are simple, blind wormlike creatures that burrow into stream beds and filter passing water for microscopic food. They then gradually transform into adult lampreys that are clearly vertebrates, have well developed eyes and swim around looking for other fish to attack. They latch onto them with a special sucker disk that surrounds their mouth, and drink their blood. Since the eighteen seventies it has been widely accepted and taught that this transformation preserves a record of the evolution from invertebrates to our earliest vertebrate ancestors. So, the last invertebrate ancestor of vertebrates is often portrayed as ammocoete-like, and the earliest vertebrate as being lamprey-like. For this to be true both ammocoetes and lampreys would need to have been around for 500 million years, since this event is believed to have occurred.”

The most surprising feature of the recent baby lamprey fossil discovery is that they have almost the same appearance as their adults. The hatchlings were already sighted with large eyes and armed with a toothed sucker, much like the blood-sucking adult phase of modern lampreys.

“This drastically different structure of ancient lamprey infants provides evidence that modern lamprey larvae are not evolutionary relics. Instead, the modern filter-feeding phase is a more recent innovation that allowed lampreys to populate and thrive in rivers and lakes. Therefore, distant human ancestry seemingly did not include a lamprey-larva-like stage. Modern lampreys now appear to be a highly evolved side branch, which shared a common ancestor with us – probably a jawless fish enclosed in bony armour,” says Dr Gess.

The discovery calls for a rewrite of textbooks referring to vertebrate origins. Until now, it was commonly believed that modern lampreys were time capsules that could give insights into the biology and genome of a truly ancient lineage, as well as our own evolutionary heritage. “Lampreys are still really special,” adds Dr Gess, “but the long held evolutionary model based on their development turns out to have been a beguiling myth.”

PRISCOMYZON HATCHLING Image: Tetsuto Miyashita

WHAT ARE LAMPREYS?

Lampreys are primitive, fishlike vertebrates without jaws of which there are about 43 species. Lampreys belong to the order Petromyzontiformes. They live in coastal and fresh waters and are found in temperate regions around the world, except in Africa. These eel-like, scaleless animals range from about 15 to 100 centimetres (6 to 40 inches) long. Like their cousins, hagfishes, they lack bones, jaws, and paired fins —their skeletons consist of cartilage. They feed by latching onto other fish with a sucker around their mouth, securing their grip with circles of teeth and then drinking their victim’s blood after rasping a hole with special teeth on their tongue.

JAB TO CHANGE HIV COURSE

A student from Wits explains the Self HIV Testing Kit. Self-testing and vending machines distributing prescription drugs are two ways that HIV treatment is being automated to reduce stigma in South Africa. Image: Getty Images

WOMEN IN SOUTH AFRICA bear a disproportionate burden of the HIV pandemic. According to UNAids figures, of the more than 7.7 million adults living with HIV in South Africa, 62.7% are women and new HIV infections among young women aged 15-24 were more than double those among young men. Wits University has long been recognised as a global leader in HIV research.

The trial, known as the HPTN 084, was headed by Professor Sinead Delany-Moretlwe (MBBCh 1995), a research professor at Wits and director of research at the Wits Reproductive Health & HIV Institute. Her cochair in the study is Professor Helen Rees.

The study enrolled 3 223 cisgender women at research sites in Botswana, Eswatini, Kenya, Malawi, South Africa, Uganda, and Zimbabwe. Fifty-seven percent of the participants were under the age of 25, the average age of participants was 26 years, 82% were not living with a partner, 55% reported two or more partners in the past month, and 34% reported having a primary partner who was living with HIV or had an unknown HIV status. “The intepretation of this study is that cabotegravir is 89% more effective than Truvada in preventing HIV in women,” says Prof Delany-Moretlwe.

The HPTN 084 results, along with the recent positive opinion of the dapivirine ring by the European Medicines Agency, represent a real opportunity to change the course of the HIV epidemic for women in sub-Saharan Africa.

The HPTN is a worldwide collaborative clinical trials network that brings together investigators, ethicists, community members and other partners to develop and test the safety and efficacy of interventions designed to prevent the acquisition and transmission of HIV. It has collaborated with more than 85 clinical research sites in 19 countries. It has more than 50 trials ongoing or completed with over 161 000 participants enrolled and evaluated.

Professor Delany-Moretlwe is also an advisor to the South African National Department of Health technical working group and serves on several WHO and other advisory committees. She was recently profiled by Forbes Africa as one of the key women leading the charge through the COVID-19 pandemic. “For Wits, it has been important that we’ve had this trial led by women and my co-chair is also a woman from the continent. At times in the trial, it was incredibly important to reflect the voices of the people who would use these products. Women and women from Africa had to reflect the context in which these products would be delivered, so that we make sure that they are able to eventually reach the people who need them,” she says.

AGILE HUNTER IN BULKY BODY

A live reconstruction of Anteosaurus attacking a herbivorous Moschognathus.

A NEW STUDY ON Anteosaurus — a premammalian reptile that roamed the African continent 263 to 260 million years ago — found that it would have been able to outrun, track down and kill its prey effectively, despite its bulky size.

Anteosaurus is not a dinosaur but belongs to the dinocephalians — mammal-like reptiles predating the dinosaurs. Much like the dinosaurs, dinocephalians’ fossilised bones are found in many places in the world. They stand out by their large size and heavy weight.

The Anteosaurus’s skull was ornamented with large bosses (bumps and lumps) above the eyes and a long crest on top of the snout which, in addition to its enlarged canines, made its skull look like that of a ferocious creature. However, because of the heavy architecture of its skeleton, it was previously assumed that it was a rather sluggish, slow-moving animal, only capable of scavenging or ambushing its prey, at best.

By carefully digitally reconstructing the skull of the Anteosaurus using X-ray imaging and 3D reconstructions, a team of researchers investigated the internal structures of the skull and found that the specific characteristics of its brain and balance organs were developed in such a way that it was everything but slow-moving.

“Agile predators such as cheetahs or the infamous Velociraptor have always had very specialised nervous systems and fine-tuned sensory organs that enable them to track and hunt down prey effectively,” says Dr Julien Benoit of the Evolutionary Studies Institute at Wits.

The team found that the organ of balance in Anteosaurus (its inner ear) was relatively larger than that of its closest relatives and other contemporaneous predators. This indicates that Anteosaurus was capable of moving much faster than its prey and competitors. They also found that the part of the brain responsible for coordinating the movements of the eyes with the head was exceptionally large, which would have been a crucial trait to ensure the animal’s tracking abilities.

“In creating the most complete reconstruction of an Anteosaurus skull to date, we found that overall, the nervous system of Anteosaurus was optimised and specialised for hunting swiftly and striking fast, unlike what was previously believed,” says Dr Ashley Kruger (BSc Hons 2012, MSc 2014, PhD 2017) from the Natural History Museum in Stockholm, Sweden.

“Even though Anteosaurus lived 200-million years before the famous dinosaur Tyrannosaurus rex, Anteosaurus was definitely not a ‘primitive’ creature, and was nothing short of a mighty prehistoric killing machine,” says Benoit.

BIG BRAINS ACT AS HEATERS

Image: Dr Olga Shpak

SCIENTIFIC EVIDENCE SHOWS specialised features in the large brains of whales and dolphins are adapted for heat production.

Whales and dolphins have the largest brains on the planet, some of them weighing over eight kilograms, six times heavier than the average human brain.

Scientific evidence from a study led by Professor Paul Manger from the School of Anatomical Sciences at Wits indicates that whales’ and dolphins’ large brains lack the diversity, flexibility and adaptability in their mental processes and behaviour that humans have, and that their large brains instead evolved to keep warm in icy oceanic temperatures. This research has been published in the journal Scientific Reports.

“In water, mammals lose heat to the environment 90 times faster than we do to the air,” says Manger. “The brains of all mammals produce heat independently of the heat-producing mechanisms of the body. This heat is required to keep their neurons warm enough to function efficiently.”

Whale and dolphin brains became exceptionally large around 32 million years ago, 20 million years after they became fully aquatic and around the time when there was a major drop in oceanic water temperatures across the planet.

“Knowing how central water temperature is to their survival may allow us to understand what will happen to certain species of whale and dolphin during the inevitable rise in oceanic temperatures associated with human-induced climate change,” says Manger.