On early-warning systems


By Lara von der Brelie, GCPPP Staff, December 14th 2021

If only we had known sooner – or could know in time on the next occasion. Putting in place early-warning systems for future dangerous pathogens promises to be a key mission for public policy and above all for preparedness at an international level. But how? Political and practical obstacles make such a mission far from straightforward. This ANALYSIS builds on a previous Policy Monitor on the risk of Zoonotic disease transfers – viruses jumping from animals to humans – to look at the steps that could be taken, both in an ideal world and in our own far-from-ideal one.


The problems and needs are becoming widely recognised. A panel, the Global Preparedness Monitoring Board, set up by the World Health Organisation (WHO) and the World Bank, produced a report in October which concluded, among other things, that the current surveillance ecosystem “is not fit for purpose and needs major reform”.

Moreover, according to pandemic expert Dr Dennis Carroll, the slow response to Covid-19 was partly caused by the failure of current monitoring capabilities to track viruses they hadn’t previously encountered. “Our surveillance is essentially waiting for a bad thing to happen,” he told us. As Chair of the Global Virome Project (GVP), a US-based collaborative scientific initiative dedicated to the issue, and previously as Director of USAID’s Pandemic Threats Unit, Dr Carroll is a leading proponent of early-warning systems.

Some early-warning systems are already in operation but remain limited in scope. The chief example is OFLLU. This collaboration between the World Organisation for Animal Health (OIE) and the UN’s Food and Agriculture Organisation (FAO), supports efforts by the WHO’s Global Influenza Surveillance and Response System’s (GISRS) to find and monitor new strains of influenza. The project reports new variations of the virus which it finds in animals to help the GISRS keep tabs on strains which might be transmitted to humans.

Such programmes are good, but are far from sufficient. There are currently about 25 viral families and 500,000 individual viruses with the potential to harm humans. For an early warning system to have a real impact on threat mitigation, viral discovery on a larger scale is needed, says Dr Carroll.

Before the pandemic, the GISRS was testing people and animals for new influenza strains, but found many illnesses it was not equipped to explain. According to Dr Carroll, approximately 80% of human patients being tested for flu-like symptoms in the years before the pandemic did not have the flu,  leading investigators to conclude  that at least one or more significant infectious diseases were being missed by monitoring systems.


Ideally, large-scale, well-resourced early-warning systems would help health agencies better anticipate pandemic threats and strengthen surveillance by identifying potentially harmful viruses before they reach humans rather than once they do, as now. However, opinion is split over whether this is feasible at the required scale, demanding both the support and involvement of many governments all over the world and a set of adequately funded and empowered international institutions. Today, political divisions, especially between the West and China, stand in the way and institutions are under-funded or disempowered.

The task is clear enough. Early-warning systems should monitor diseases by sequencing viral threats while they are still circulating in wildlife. This process of viral discovery would enable researchers to keep tabs on previously unknown diseases and develop medical and physical countermeasures before they become a problem.

In a perfect world, viral discovery programmes would complement current surveillance mechanisms by forming a global monitoring structure with three tiers.

The first tier would be a large-scale, decentralised programme to detect new viruses in domestic animals and in wildlife around the world. Researchers operating on the ground would take samples from humans, local wildlife and domestic animals and analyse them using a technique known as consensus Polymerase Chain Reaction.

This process screens unknown viruses and compares them to known viral families such as influenza, corona and filo to determine how much of a threat they might pose to humans. Data on microbes found to be dangerous would then be shared with local authorities, as well other participating states and institutions, through an open data platform.

To manage costs, wildlife samples could be taken only from those animals with the most frequent human contact – mainly rats, bats, and non-human primates — mammalian species displaced from their traditional habitats and able to survive in human settlements.  While some additional training and resources would be required to bring local laboratories up to speed, Dr Carroll says health capabilities in many regions already provide a good basis for such testing.

The second tier would take the form of more intensive risk-based surveillance projects focused on places deemed zoonotic ‘hotspots’, because of frequent interactions between wildlife, livestock and humans. Using information gathered and distributed thanks to viral discovery, routine testing in places such as live animal and bird markets would check for newly ‘discovered’ microbes (as well as known diseases) in local human and animal populations.

This in turn would work in conjunction with a third tier, event- and indicator-based surveillance, incorporating systems to track local information from clinics and hospitals about patient symptoms for any signs of a previously identified infectious disease.

Event-based surveillance monitors unstandardised information such as local reports, rumours and stories for any indications of a new public health risk or disease outbreak. Indicator-based surveillance uses information from healthcare providers such as laboratory reports to track signs of an emerging threat. Both would be made more effective  in conjunction with  a proactive early warning system . It would enable these surveillance programmes to not only look out for known viral threats which have already infected humans, such as the Ebola virus, but also for its viral ‘cousins’  residing in wildlife.


Prevailing conditions are far from ideal. Organizational and funding shortcomings exacerbated by political divisions make the building of such a comprehensive and ambitious network currently too daunting.

The record confirms this, Covid-19 the latest example. UN bodies have so far failed to convince countries to collaborate fully on disease prevention, mitigation, and even  data sharing. There is a huge disparity between countries’ public health systems. The UN’s Global Preparedness Monitoring Board (GPMB) concluded in its October report that the World Health Organisation lacks the resources and authority needed to lead a pandemic preparedness initiative. Within China, in 2019 information was slow to percolate from doctors to health officials and to government, let alone internationally. Information flow was restricted, not encouraged.

Some countries have evinced concern over perceived security risks involved in sharing information about their populations with other states. Others see no incentive for sharing data given the uneven distribution of resources for tackling infectious disease. Some poorer states believe an improved monitoring system would benefit only those able to afford countermeasures.

Clearly, creating a more coordinated global disease strategy will be an uphill struggle. Nevertheless,  progress is possible. Building an international consensus is a feasible first step, along the lines established for climate policy, albeit with the same drawbacks and limitations. This is being tried in several ways for disease surveillance.

The US-based Milken Institute recently published a report outlining some of the steps which need to be taken for viral discovery to be integrated into current surveillance strategies. Written following a series of workshops with pandemic experts, the report explored how governance could be shared between local, regional and international organisations. Local centres would collect data, analyse it for immediate public health policy, and share it with regional counterparts. Regional hubs would be responsible for transferring information between local and global centres, establishing community buy-in, and ensuring that enough resources are distributed to localities. International headquarters would in turn analyse and share data, develop methodology, and disseminate critical information to decision-makers across the world.

The Institute of Pathogen Genomics set up by the Africa Centres for Disease Control is an already established example of one such network. Local laboratories across Africa manage disease-surveillance programs and share their results with a cross-continental network of laboratories, as well as the CDC Institute. The Institute leads this network, providing tools and training to help local health experts collect and sequence potential viral threats in their respective regions. Naturally, it could do more with more funds.

But would China take part? Before the pandemic hit in 2019-20, the Chinese government had been poised to allow the Global Virome Project, intended to create a global viral discovery network managed at the national level but coordinated internationally, to operate in China. Whether and how  this willingness may be resuscitated is a major question.

The GVP Chair, Dr Carroll, believes that the best way to make a globally coordinated early warning system possible would be for it to operate outside of the United Nations. “Senior leadership at WHO and the UN’s Food and Agriculture Organization (FAO) both stated that, for [the GVP] to be effective, it couldn’t sit within WHO or FAO,” he says, “it couldn’t sit within the UN, but the UN would need to be actively engaged in it”.

Not everyone agrees: the GPMB report suggested working from within the UN to improve early warning systems and disease surveillance. It advised policymakers to use a Tripartite+ alliance between the WHO, FAO, the World Animal Health Organisation (OIE) and the UN’s Environment Programme (UNEP) to create a more comprehensive monitoring system.

The difficulty is that while UN institutions may offer standards and convening powers, they are often constrained by geopolitics and their own bureaucracies. That is why some global health organisations work at arm’s length from the UN. For example, GAVI, the vaccine alliance created in 2000, works in partnership with WHO and UNICEF, but is governed independently as a public-private partnership.

Managing a global data platform also needs country buy-in and trust. Chatham House has proposed seven general principles, including transparency practices for data usage, accommodation for national legal restrictions, and an articulation of the comparative benefits of data collection despite a loss of rights. An influenza data-sharing platform now active also for Covid-19, GISAID, has succeeded in addressing many of these points. The programme, in operation since 2008, provides open access genomic data on viruses free of charge to any individual who identifies themselves and agrees to its Database Access Agreement.


Past efforts to build early-warning systems have suffered a number of false starts, often for lack of funding. For example, USAID’s pioneering viral discovery programme, PREDICT, had its funding stopped in 2019 by the Trump administration after more than decade. The project had operated across 30 countries, sampled more than 80,000 animals and conducted over 400,000 viral discovery tests. Dr Carroll, who was the project’s director, believes PREDICT showed the potential. Realising that potential requires funding to be sustained and secure.

A number of proposals relating to funding have been advanced. The Milken Institute report suggested following the multi-stakeholder model used by the Coalition for Epidemic Preparedness Innovations (CEPI). The foundation was set up in 2017 by the governments of Norway and India, the Bill & Melinda Gates Foundation, the Wellcome Trust and the World Economic Forum, to finance research on vaccines through donations from public, private, philanthropic and civil society organisations.

The UK government recently set up the Infection Innovation Consortium (iiCON), a £171 million ($225 million)collaboration between the government and private firms (such as Unilever), based in Liverpool, to fund research and development projects for pandemic preparedness.

The GPMB in its October report proposes that the World Bank establish a new collective financing mechanism to fund improved disease monitoring. This could be akin to the Global Environment Facility, set up under the World Bank’s wing but independent of it.


We cannot be certain about  what would have happened differently had adequate early-warning systems been in place before Covid-19. But we do know that earlier discovery was possible: viral discovery might have found the virus in bats and shared the information with Wuhan health officials; Wuhan’s live animal market could have been designated as a zoonotic ‘hot spot’ and placed under heavier disease surveillance; and researchers might even have been able to identify the first cases of Covid-19 in the local human population much sooner. Knowing this much makes it inexcusable not to try to prepare more effectively for next time.

Photo by Jody Confer on Unsplash

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