Let's bring together countries and corporations to grow global pathogen surveillance

Responding to an infectious disease outbreak is a complex and hurried operation. Countries must have the right people with the right tools at the right locations. A critical early step in this highly coordinated process is understanding what pathogen (virus or bacteria) is at the root of the problem. This level of detailed insight can be gained through genome sequencing, a powerful way to track how viruses form new variants and a necessary tool for developing effective diagnostics and vaccines.

Yet, many countries are unable to sequence pathogens. As the US approaches its billionth COVID-19 sequencing test, some countries have performed only a handful. But, across Africa, countries that used to struggle with sequencing are now able to track viruses, a development that many hope will spread globally through public-private partnerships.

African countries have a long history of responding to disease outbreaks, including Ebola, Lassa Fever, Marburg and the recent COVID-19 pandemic. To better anticipate and respond to disease threats, including epidemics, the African Union launched the Africa CDC in 2017. After assessing all 55 African member states and their capacity for sequencing, analysing and sharing genomic data, the Africa CDC formed the Institute of Pathogen Genomics in November 2019, just before the first reported global case of COVID-19.

Over the next three years, Africa’s ability to detect, track and respond to the rapidly evolving COVID-19 pandemic dramatically improved. In October 2020, the Africa Pathogen Genomics Initiative (Africa PGI) was launched to mobilise resources, advance sequencing capabilities, train workforces and update policies. In 2018/19, only seven countries had next-generation sequencing capacity within their public health laboratories (Figure 1). By 2022, that number grew to 31, while over 410 individuals were trained to perform viral sequencing, enabling the continent to produce and share nearly 140,000 total genomes.

But COVID-19 is not the end of the story. Many pathogens have come before and many will spread after. The United Nations Environment Programme warns of the growing risk of zoonotic diseases, infections that spread between people and animals. This is due to increased urbanisation, the rapid expansion of cities and industrialised agriculture. Building a continent-wide pathogen surveillance system that is versatile and adaptable is a vital part of managing these risks and a core part of the PGI vision.

This is why the Africa CDC assembled representatives from all 55 African countries and 31 companies and organizations in Addis Ababa, Ethiopia for a symposium entitled Beyond COVID-19: Pathogen Genomics and Bioinformatics for Health Security in Africa. This event was hosted by the Africa CDC in collaboration with the African Society for Laboratory Medicine (ASLM) and with support from the Bill and Melinda Gates Foundation, the Africa CDC Saving Lives and Livelihoods Program and the Robert Koch Institute. At the side of the symposium, the Africa CDC and the World Economic Forum held a partner session to coalesce public-private support for the continent-wide pathogen surveillance initiative. The eclectic group of attendees sought to carry momentum built during the COVID-19 pandemic into monitoring other health burdens, such as Malaria, emerging diseases, antimicrobial resistance and others.

Realizing Africa CDC's bold vision will not happen in isolation. In fact, the creation of PGI came out of partnerships with the Bill and Melinda Gates Foundation, CDC and notably Illumina and Oxford Nanopore, DNA sequencing companies.. This type of multi-sector collaboration with global funders and industry will be necessary to overcome the technical, logistical, political and economic hurdles common across low- and middle-income countries. Industry involvement must span several impact areas, from supply chain and logistics to data and bioinformatics.

To improve access, alongside developing innovative technologies fit for emerging markets, companies must work with entities, such as Africa CDC, to create new business models to bring down costs, collaborate regionally to match supply and demand and update policies to promote the cross-border exchange of materials and data.

And, while Africa remains a focus area for building out genome sequencing capacity, gaps exist across the globe. The Bill and Melinda Gates Foundation is expanding Africa PGI’s model to Asia, where Dengue, Salmonella Typhi and V. cholerae are imposing significant health burdens. These regional initiatives must ultimately learn from each other and grow towards a global pathogen surveillance network – a long-term vision that will help authorities from country to international levels prevent the next pandemic. An African proverb uttered in the halls of the African Union captures the ethos of global partnerships and the spirit of collaboration: “If you want to go fast, go alone. If you want to go far, go together.”

This article originally appeared in This Day.