“It is the long history of humankind (and animal kind, too) that those who learned
to collaborate and improvise most effectively have prevailed.”  Charles Darwin

In 2019, before Covid-19 became a ubiquitous term, another public health scare was dominating news: an explosive measles outbreak in New York’s Orthodox Jewish community.

Public health records documented significantly low rates of vaccination within these concentrated Hasidic neighborhoods. Given its infectiousness, the disease multiplied rapidly in this susceptible community despite the systemic efforts of state and local health officials to contain the spread.

In retrospect, an important piece of the data puzzle had been overlooked – travel patterns. Community members frequently travelled to and from eastern European countries that were experiencing record numbers of measles cases. Had public health records been overlaid with relevant travel pattern data early on, the outbreak could have been predicted, keeping a spark from becoming a fire.

Recent news regarding the emergence of monkeypox in countries around the world shows the virus spreading beyond its typical territory, confirming how critical it is for the global public health community to be more attentive to data surrounding this re-emerging disease, with a focus not only on traditional data – virological and epidemiological – but additional data that can provide new insights into the spread of infectious diseases.

The lack of relevant data collected and shared to date has clearly limited our current knowledge about this virus.

New genetic analysis that has demonstrated the outbreak is being fueled by two different strains now suggests that the virus(es) have been in circulation for some time – undetected.

As this is a global outbreak, improving our knowledge about the monkeypox virus and risk factors that may be driving the outbreak requires trusted communication and coordination across countries. There is much uncertainty about how and why it is spreading and what the response should be, despite the fact that many countries have been sounding the alarm for years. Utilizing better environmental surveillance for detection as well as examining mobility patterns would further inform our understanding of its recent spread. Right now, no one country has enough puzzle pieces to figure out what’s going on.

These examples demonstrate why public health data is important to identifying and combating disease outbreaks and how triangulating data from other sources can provide important insights we might not get from clinical, laboratory and epidemiological data alone. To develop and utilize an effective early warning system to confront the next virus variant or emerging/re-emerging pathogen, we need the perspectives and insights of many.

Foundational to the Pandemic Prevention Institute is the vision of a “network of networks” that connects a range of stakeholders and enables entities across the globe to connect and contribute traditional and nontraditional data in distinct and innovative ways to solve a global health problem. Our networks are built on collaborations that connect data to derive actionable insights.

Working Across Sectors to Drive Insight and Capacity

So far, the Pandemic Prevention Institute has engaged with more than 40 organizations from a diverse ecosystem, forming three types of collaborations: data and analytics partners, policy and advocacy partners, and industry and technology partners. These distinct groups are part of our single, united network of networks.

SARS-CoV-2 Genome Sequencing Workshop held in Stellenbosch, South Africa – Dr. Jennifer Giandhari of CERI takes a group of participating African fellows through the loading of the MinION Flow Cells into the Oxford Nanopore, GridION device.

The most extensive within this nexus are our data and analytics partners, many of which are scientific centers at the forefront of generating research-based evidence, including entities at the leading edge of applying data science to global health.

Our policy and advocacy partners focus on providing public health guidance while simultaneously mobilizing political and financial commitment among global, regional and national stakeholders.

Our industry and technology partners are leading diagnostic and sequencing manufacturers, accelerating the development and availability of our modern data stack platform, tools and models while facilitating automation and helping build capacity in resource-scarce environments.

Our platform is critical to advancing data driven insights to detect and prevent future pandemics and biorisks by connecting and aggregating signals from publicly available and privately acquired global data sets for analysis.

Working across these three sectors, we are creating collaborations in Asia, Africa, Europe, Middle East, South America and within the United States.

African fellows participate in the SARS-CoV-2 Genome Sequencing Workshop, using sample preparation workflow together, as part of their practical training.

Creating Global Opportunities to Increase Access to Timely Data

In India, for example, we’ve been able to quickly unite a consortia of the country’s leading genomics surveillance centers. Our support of these science partners accelerated the sequencing of more than 11,000 SARS-CoV2 clinical samples across key states and established wastewater surveillance in three major cities.

Working with one of our key industry and technology partners Illumina, we were able to facilitate an in-kind contribution of reagent kits that enabled our partners to double their sequencing capacity while simultaneously leading to an almost 50 percent decrease in the time between sample collection and database upload.

This rapidly expanded the representation of India-sourced genomes available through one of our priority data partners, GISAID. The impact of our work via this approach enabled timely tracking of the Delta variant and identification of the first two confirmed cases of the Omicron variant in Bangalorepartners at the National Centre for Biological Sciences.

In Latin America, we are in the process of building a series of global genomic surveillance ecosystem networks for emerging and re-emerging infectious disease discovery, developing partnerships with key international organizations.

In Africa, support to our partner at the Centre for Epidemic Response and Innovation (CERI) in Stellenbosch, South Africa, helped establish the largest genomic sequencing center on the African continent, focusing on expanding the knowledge base and capability for surveillance across Africa.

The CERI has trained over 100 scientists in 21 African countries to conduct genomic surveillance in their local labs and communities. We are also partnering with the World Health Organization to establish mechanisms and processes for collaboration between the human, animal and environmental health sectors.

Each of these initiatives and others underway present the opportunity to advance programs toward sustainable systems for global health security.

Utilizing a Unique Approach to Analyze Data and Generate Insight

These networks bring together global, regional, national and local entities to consistently inform and be informed by our platform and collection of analytic tools. This allows us to provide an open source repository of assets, enabling global user networks to leverage and contribute to an asset library that will catalyze insight sharing.

Senior scientist, Sureshnee Pillay of CERI, takes a team of African fellows through steps of the sample preparation workflow. This training aims to capacitate key scientists from a range of African countries to perform their own genomic sequencing and surveillance of pathogens.

Recognizing that comprehensive data improves lives, we are testing concepts around cloud data systems and analytics layers – such as bioinformatics tools needed to translate wastewater sequences into variant counts – and mobile applications.

With our partners, we are co-creating a modern pandemic surveillance data ecosystem, leveraging a state of the art modern data stack platform that connects disparate data, providing researchers worldwide the ability to survey genomic, syndromic and environmental data for pathogens and variants. The goal of gaining insights from these data is to trigger data-driven actions to prevent outbreaks from becoming a pandemic. If researchers in South Africa had been able to conduct this type of search in 2021, identifying what we now know to be the Omicron variant of SARS-CoV-2, they would have spotted similar genomes already detected in Europe and the U.S., potentially triggering a faster, more data-driven response.

Continuously expanding our global network of partnerships will build our capability to connect and analyze data and enhance global connectivity to inform decision-making. A world that can connect local data in a global context will ensure a world better prepared to prevent the next pandemic. That is our goal.

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