(Published - 18 May 2020)
As microbial sequencing becomes more routine, access to sustainable bioinformatics capacity has become one of the most critical emerging needs for public health throughout the world – and is proving crucial to tracking and tracing the ongoing coronavirus pandemic. The newly-launched Public Health Alliance for Genomic Epidemiology (PHA4GE) aims to develop the standards that will meet these needs – on a global scale.
“It’s about bringing public health and bioinformatics closer together,” says Professor Alan Christoffels of the South African National Bioinformatics Institute (SANBI) at the University of the Western Cape (UWC). “In addition to the social determinants of health, and health economics, we need to incorporate the genetic component of public health as well. And for global pandemics like COVID-19, we need international collaboration and coordination.”
That Is why PHA4GE, a global coalition, was awarded $840,000 (over R14-million) from the Bill & Melinda Gates Foundation, to develop an open source, community-supported ecosystem for bioinformatics in public health.
The PHA4GE programme was launched at the Global Grand Challenges meeting in Addis Ababa in Ethiopia. As of 1st May 2020, this global programme brings together the following partners: the Africa CDC in Addis Ababa; the Broad Institute in Boston, USA; the Fred Hutchinson Cancer Research Centre in Seattle, USA; Global Emerging Pathogen Treatment Consortium, Lagos, Nigeria; H3Africa Bioinformatics Network, Cape Town, South Africa; the National Healthy Research Authority in Zambia; the National Institute for Communicable Diseases in Johannesburg, South Africa; Oxford University, England; Institut Pasteur de Dakar, Senegal; University of Birmingham, England; University of British Columbia (BC) and BC Centre for Disease Control, University of Cape Town, South Africa; University of Melbourne, Australia; University of the Western Cape, South Africa; US Centers for Disease Control and Prevention (CDC), Atlanta, USA and University of Washington, Seattle, USA.
SANBI-UWC will serve as secretariat for the global programme, and will form part of the steering committee to be formed this month to provide oversight for the various PHA4GE activities.
With a growing participation of more than 70 international scientists and public health practitioners, PHA4GE is working to establish consensus standards, to document and share best practices, to improve the availability of critical bioinformatic tools and resources, and to advocate for greater openness, interoperability, accessibility and reproducibility in public health microbial bioinformatics.
What does this mean?
“Take the current Covid-19 pandemic, as an example,” Prof Christoffels explains. “Ideally, you want to be able to analyse virus samples and share the data to better understand the spread of disease to inform an appropriate intervention. Unfortunately, much of this technical skill sits in academia and not in public health centers where policy is being shaped. We want to more closely align academic analytical tool development with policy makers and implementers.”
Or consider one of South Africa’s biggest problems: multiple drug-resistant tuberculosis (MDR-TB).
“Currently, if you get tested for TB, the first test is to test your sputum. Then, if we want to test for MDR-TB, you have to get a particular test done by a specific laboratory in the country - testing for particular drugs and their effects. But what if we could simply take the TB bacterium, sequence their DNA, and then look at that DNA and determine whether there are MDR-TB bacteria, based on that?” says Prof Christoffels.
“People are doing things like that in the research space. Unfortunately, there are limited global standards and protocols, or best practices for public health practitioners - but PHA4GE can change that.”
PHA4GE is modeled on the Global Alliance for Genomics in Health, which represents a “policy-framing and technical standards setting organisation that enables responsible data sharing within a human rights framework”.
The scope of its effort is broad, including public health infectious diseases bioinformatics development and data management efforts, throughout the world - and a focus on the ethics of data (and technology) sharing.
“Public health isn’t just about dealing with the crisis in front of us now - we have to be thinking about the future,” says Prof Christoffels. “If we learn anything from this pandemic, it's that Global South and the Global North are more connected than ever – and we can come together to build a better, and healthier, world.”
To find out more about PHA4GE visit: