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As Africa embraces genomics in the post-Covid era, quality assurance is critical

As Africa embraces genomics in the post-Covid era, quality assurance is critical
Alan Christoffels, Sarah Mwangi and Emma Griffiths
By Alan Christoffels, Sarah Mwangi and Emma Griffiths
22 Oct 2023
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Scientists and institutions in Africa must address numerous challenges if the continent is to bring its genomics capacity on par with global standards. The rush to put that capacity in place during the Covid-19 pandemic led to certain lapses.

It wouldn’t be hyperbole to suggest that Africa enjoyed a genomics boom over the Covid-19 pandemic.

This is in no small part due to Covid-19 and the labours of organisations like the Africa Centres for Disease Control and Prevention (Africa CDC) and the World Health Organisation Regional Office for Africa (WHO Afro).

They and others rolled out next-generation sequencing (NGS) – the gold standard for large-scale genomic work these days – equipment, reagents and training at scale over the pandemic, boosting the continent’s ability to produce invaluable genome sequences of – its initial focus – the SARS-CoV-2, the virus responsible for Covid-19.

But this overnight leap in capacity and quantity of genome data didn’t always go hand in hand with a commensurate uptick in quality assurance. NGS is methodologically and technically complex, as is the analysis of its outputs and results. Both demand the strictest oversight, especially if they are going to be applied broadly in public health contexts and in efforts to contain the spread of disease.

Not all data are created equal


The potential for pathogen genomics – unravelling the genetic makeup of disease-causing organisms – to save lives is, most would agree, boundless. Pharmacogenomics, for instance, is a powerful application that has led to the development of a host of new and improved treatments.

But to tap into these benefits, scientists and institutions in Africa are going to have to address numerous challenges if the continent is to bring its genomics capacity on par with global standards. The rush to put that capacity in place led to certain lapses.

Quality assurance in pathogen genomics takes on many dimensions. Some have already highlighted a number of prominent challenges, like ill-equipped facilities, poor access to research centres, lack of expertise and a supportive environment.

But there are also countless technical obstacles. Consider the issue – a global one – of identifying reliable computational tools to fill in the gaps in genomic sequences. Some tools simply fill in missing segments with reference data, which is highly problematic. (The concept of gap filling was popularised in the film Jurassic Park, where genetic material from frogs was used to fill the gaps in degraded dinosaur DNA, with unintended but deadly consequences.)

Then there is the contamination of sequences by “foreign sequences” which can occur anywhere between the securing of a biosample to the processing of data.

And so on and so on.

So what is quality genomics?


The good news is that a veritable cornucopia of tools has been and are still being developed to tackle these issues. The challenge for Africa is to adopt these – making sure they get the right ones – as genomics matures in practice around the continent.

It helps that Africa is not entirely a genomics novice. Over the past years, organisations like the Public Health Alliance for Genomic Epidemiology (PHA4GE), the Human Heredity and Health in Africa Consortium (H3Africa), the Africa CDC pathogen genomics initiative (Africa PGI), the African Genomic Medicine Training (AGMT) Initiative – a project of the African Society of Human Genetics (AfSHG) andH3Africa – and many more have sought to apply their minds to these challenges.

They have put in place training programmes, have identified gaps in infrastructure and international cooperation agreements, and are developing tools that are easily accessible to and implementable in a variety of low-resource contexts.

And in some cases there will be no need to reinvent the wheel. In a paper published in August this year, for example, a team of Australian scientists affiliated to PHA4GE laid out the need for the accreditation of public health laboratories, pointing out existing standards developed by the International Organisation for Standardisation (ISO).

There is other work that we are engaged in at PHA4GE to ready Africa for its unqualified admission to the world’s genomics community. We are developing a score of tools and resources, working hand in hand with the African science community to ensure that these tools are fit for purpose and context.

In a paper we published in 2022, for instance, we released publicly available standards for the recording of essential “contextual data” like the type of biosamples used in the sequencing, clinical outcomes and the kinds of tests that were conducted.

In another recent paper, currently in preprint, PHA4GE members looked at the development of descriptive quality control “tags” that can be used to flag pathogen sequence data with known quality issues.

All this will feed into the development of what will, funding forthcoming, become the first pan-African platform for the sharing of genomics data, as I and others outline in a paper published in March this year. This shared platform will further cement collaboration and improve quality assurance.

The four-year-old PHA4GE will host its inaugural conference (in Cape Town at the end of October) where scientists from around the world will highlight challenges, solutions and strategies to bring Africa up to par with the rest of the world.

The bottom line is…


In fact, we would argue, Africa can learn from the mistakes the developed world made in not always heeding the data they had at hand. 

Genomics-data-enriched public health surveillance served as a powerful warning system to identify variants of concern and predict looming waves over the Covid-19 pandemic.

Here on the African continent, more than 100 disease outbreaks are reported annually. Each outbreak results in hitting the brakes on our development aspirations.

As such, genomic surveillance based on high-quality data could help change the narrative of disease impacts. DM

Prof Alan Christoffels is professor of bioinformatics and director of the South African National Bioinformatics Institute (SANBI) at the University of the Western Cape. He is also the chairperson of the steering committee for the Public Health Alliance for Genomic Epidemiology (PHA4GE), which will host its inaugural conference in Cape Town from 30 October to 1 November 2023. 

Dr Sarah Mwangi is an implementation science expert at the Africa Centres for Disease Control and Prevention (Africa CDC), the public health arm of the African Union (AU).

Dr Emma Griffiths is a research associate at Simon Fraser University in Canada, and chairperson of the data structures working group with PHA4GE.

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