SA's gene genies create Covid database to help save lives around the world

South Africans are once more at the leading edge of Covid science after creating a database that could save the lives of people who may be genetically predisposed to severe infection. 

The Coronavirus Host Genetics South Africa (COHG-SA) database, developed by researchers from the universities of Pretoria (UP) and Cape Town (UCT), can be used as a basis for exploring the influence of genes on Covid outcomes.

Researchers led by Fatima Barmania of the Institute for Cellular and Molecular Medicine at UP said their database could help to unravel the mystery of why some people remain asymptomatic or experience mild symptoms, but others progress to severe disease and death.

“Epidemiological studies have identified risk factors for severe disease, including older age, male sex, and comorbidities such as diabetes, hypertension, obesity, chronic respiratory diseases, cardiovascular disease and cancer,” they said.

“Some otherwise healthy, young individuals, however, also succumb to Covid-19, and ongoing studies are now identifying host genetic makeup as an important contributor to disease outcome.”

The researchers' work, published this week in the European Journal of Human Genetics, coincides with a new global analysis of Covid genomic surveillance, published this week in Nature Genetics. 

It The genomic surveillance found that many countries sequencing SARS-CoV-2 genomes are sharing only a fraction of them in public repositories — and many sequences are missing important information. 

According to the study of 62 countries that report this data, 23 have uploaded fewer than 50% of their sequences from Covid's first four variants of concern, Alpha, Beta, Gamma and Delta.

The researchers believe unshared sequences are probably being held back for political reasons, among other things, including the repercussions of being the first country to report a new variant of concern.

When researchers in SA and Botswana alerted the world to the Omicron variant last November, for example, several countries shut their borders to travellers from Southern Africa.

For South African researchers, sharing vital data is important and the country is in the top category when it comes to performing routine genomic surveillance and making the results available. 

Barmania and her institute's director, professor Michael Pepper, said the database is a compilation of genes that have been linked to Covid outcomes either in terms of susceptibility to infection or the severity of the affects. 

“The Covid-19 pandemic is a global crisis which has highlighted the critical need for collaboration among members of the medical and scientific community,” said Barmania. “The database is tailored for researchers or clinicians who may need to access Covid-19 genetic information to further their research goals.”

She told the Sunday Times that having pertinent information in a single resource will help researchers and clinicians to understand how genetics predisposes people to infection and how their bodies will react. 

“The end goal of such a database would be to create a tailored diagnostic and prognostic platform that can be used to assess individuals who may be predisposed to severity so that appropriate therapeutic interventions can be applied,” she said.

Pepper said the database includes article data, demographics and other useful details, as well as links from studies performed globally that report on any genetic variants associated with Covid susceptibility or severity.

“The database currently consists of more than 30 publications encompassing more than 100 genes. The database is updated frequently and many more published papers are currently being curated for addition,” said Pepper.

The researchers said genome-based studies have provided important contributions to health research, but most participants are of European ancestry.

“The African continent has always been underrepresented in global genome studies, with African participants often being of African-American origin, leaving much of the African continent unexplored.

“The current disparity can cause an imbalance in health research since the outcomes could be less accurate for individuals from African populations.”

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