Can NGS fight disease transmission in Africa? A new program thinks so.

Next generation sequencing (NGS) can play a critical role in the fight against infectious diseases by enabling experts to identify and characterize the genomes of the pathogens that can cause them—which serves as a crucial first step in the ability to diagnose and protect against novel viruses, including insight into transmission, virulence, and antimicrobial resistance.

Advanced Molecular Detection Program

In 2014, the United States launched the Advanced Molecular Detection program, seeking to integrate pathogen genome sequencing with infectious disease surveillance. That effort could eventually lead to more precise and efficient clinical diagnostics, and even replace traditional microbiology processes with just one workflow that can accommodate a number of pathogens.pat

Now, a similar effort is underway in Africa.

In November, a broad coalition of groups joined to announce a $100 million, four-year partnership to expand next generation sequencing (NGS) tools to strengthen public health surveillance and create a network of labs in Africa.

Contributors include the African Union Commission, the Africa Centres for Disease Control and Prevention, Microsoft, the Bill & Melinda Gates Foundation, the U.S. Centers for Disease Control and Prevention, and two private NGS companies.

African Pathogen Genomics Initiative

The new African Pathogen Genomics Initiative will use pathogen genomic sequencing to build a continent-wide disease surveillance and lab network, according to Microsoft.

Infectious diseases like AIDS, tuberculosis, cholera, and malaria have wreaked havoc on Africa. Tuberculosis, for example, claimed more than 400,000 lives in Africa in 2016, according to the World Health Organization. HIV/AIDS claimed 470,000 Africans in 2018, and cholera claims tens of thousands annually.

“Strengthening genomic surveillance systems is key for early notification and control of disease outbreaks,” said Dr. John Nkengasong, director of Africa CDC. “Use and integration of advanced technologies such as next generation sequencing into surveillance and emergency response programs facilitates public health decision-making for better outcomes as evidenced in two Ebola virus disease outbreaks and the current COVID-19 pandemic.”

As Illumina points out, any novel pathogen can be devastating to a region, but that devastation is amplified when the region’s genomics and bioinformatics infrastructure can’t identify, monitor, or slow its spread.

“In resource-limited environments, public health officials struggle to allocate precious medical commodities such as diagnostics or vaccines,” the company said in a press release. “Africa needs information in real-time, and in high fidelity. Next generation sequencing of pathogen genomes can provide these insights, mitigating the potential loss of life.”

But more than just helping Africans, next generation sequencing efforts in Africa can help everyone. That’s because the broad genetic diversity in Africa can provide global insights into human evolution and common diseases.

Genome sequencing in Africa

Genome sequencing has yet to arrive in Africa due to high up-front equipment costs, a lack of trained lab workers needed to perform the sequencing, minimal infrastructure for data analysis, and ongoing immediate public health emergencies that tend to sap the ability and energy needed to embark on long-term, distant-horizon projects.

As a whole, Africa is underrepresented when it comes to genetics research, though a few projects have begun to make inroads.

For example, researchers in 2019 analyzed newly generated whole genome sequences from 52 Africans spanning a broad range of backgrounds, including groups that have practiced subsistence living, and found that population structure was shaped to a large degree by geographic distances and language. The first study found a “remarkable correlation” between genetic diversity and geographic distance. The second delineated genetic splits in early African populations and determined that the “San genetic lineage is basal to all modern human lineages.”

A study in Nature, this one from 2017, used whole genome sequencing to better understand genetic variation in South Africa.

The South African study is key because it was based on findings from the Southern African Humane Genome Programme. The program, which launched in 2011, would develop the capacity for genomic research in the region, establish a repository and database, and translate genetic information and knowledge into improvements. The group, composed of scientists, ethicists, lawyers, and industry representatives, has more recently been superseded by the Human Heredity and Health in Africa Initiative, which is based at the University of Cape Town.

That initiative is already breaking ground in this field. One of the early works to come out of it, published recently in Nature, presented a baseline of genetic data for African populations. The research sequenced 426 genomes, with 320 analyzed at high depth, to accurately and quantifiably examine rare genetic variants as well as some more common variants which had been studied previously.

Could those earlier programs provide a direction for this new African genomic project? The African Pathogen Genomics Initiative will work continent-wide, with a special focus on capacity building in about 20 countries. It will be a part of the Institute of Pathogen Genomics, which was launched by the Africa CDC in 2019 to work closely with national public health institutes, academic institutes, and public and private labs for prevention, detection, and response to current and emerging public health threats on the continent, with next generation sequencing as an early focus.

While South Africa has so far been a leader in genetic research on the continent, Nigeria is slowly edging into the spotlight, reports an article in Nature. A new venture called 54Gene is leveraging Silicon Valley backing and the need for precision medicine to build a biobank—the first step, already underway, is sequencing and analyzing the genomes of 100,000 Nigerians.

Such “ambitions would have been unthinkable a decade ago, when most universities and hospitals in Nigeria lacked even the most basic tools for modern genetics research,” wrote Nature. 54Gene “is riding a wave of interest and investment in African genomics that is coursing through Nigeria.”

Other Nigerian projects include a $3.9 million genomics center and a revamp of the National Reference Laboratory to analyze the DNA from 200,000 blood samples stored in the lab’s new biobank.