The COVID-19 pandemic fundamentally transformed how scientific evidence informs public health responses. For the first time, pathogen genomic sequencing was conducted at scale and in near real-time to guide critical decisions from public health interventions to vaccine development. Yet despite the pivotal role this scientific evidence played in pandemic management, surprisingly little was previously understood about how such evidence is effectively generated and integrated into policy decisions during emergency conditions.
Recognising this gap between research generation and policy decision-making as a significant challenge, Wellcome commissioned Research Consulting to investigate this further. We examined ten Wellcome-funded genomic sequencing and surveillance grants as case studies, engaging with 125 researchers who worked at the forefront of COVID-19 surveillance efforts across Africa, Asia, Latin America, and the Middle East.
These researchers revealed how their research systems were severely tested during the pandemic – from funding mechanisms to global supply chains, workforce capacity to data sharing protocols. Their experiences highlight how emergency research success depends not just on scientific expertise but on the resilience of entire research ecosystems.
Through our research, six valuable lessons emerged that can help research funders prepare stronger responses to future public health emergencies.
Lesson 1. Balance speed of funding with accountability in a crisis
When the pandemic struck, traditional research funding models proved unfit for purpose. The normal cycle – developing funding calls, assembling peer review panels, following due diligence processes – had to be dramatically condensed to meet the urgency of a rapidly evolving crisis.
For existing Wellcome grantees, particularly those engaged in major international programmes (like the Africa and Asia Programmes), funds were mobilised relatively quickly through grant supplements and extensions. These institutions could immediately pivot existing resources toward real-time pandemic surveillance, as due diligence processes were already complete and financial management systems aligned with Wellcome’s requirements.
However, new partner organisations – particularly in regions where Wellcome had not previously funded work, such as the Middle East and Latin America – faced significant hurdles. For some institutions, this was their first time receiving Wellcome funding, requiring extensive paperwork and financial documentation at a time when administrative resources were already stretched thin. This created months-long delays to project initiation with real consequences for pandemic response capabilities.
For research funders, the lessons are clear: strategic investments in building regional capacity before emergencies occur pays dividends when crisis strikes, while establishing trusted partnerships during non-emergency periods enables rapid mobilisation when urgency demands it. Additionally, streamlined emergency protocols that allow greater flexibility while acknowledging contextual sensitivities could help deploy vital research funding more effectively when the next crisis emerges. The report specifically recommends developing context-sensitive due diligence frameworks for emergency response and creating more flexible funding mechanisms that accommodate different national regulatory requirements.
Lesson 2: Enable infrastructure resilience when supply chains fail
Even the most well-resourced laboratories encountered significant infrastructure challenges during the pandemic. Global supply chains were severely disrupted, and physical infrastructure was tested by the scale and urgency of surveillance requirements.
Supply chain disruptions affected all funded projects. In normal times, laboratories in low- and middle-income countries already face long lead times (at least three months for essential reagents). During the pandemic, these delays extended beyond four months for critical supplies. The financial impact was also substantial, with labs outside the US and Europe reporting severe import costs and shipping fees – in some cases paying up to seven times more than high-income countries for identical materials.
In remote settings, access to basic physical infrastructure emerged as a critical vulnerability. Cold chain storage, necessary to maintain sample viability during transit, was often inadequate. Teams reported journey times extending from hours to days, resulting in sample degradation. Limited freezer capacity forced teams to prioritise sample retention, often discarding negative samples to preserve positive ones for further analysis.
Equipment failures presented another challenge, particularly in regions without manufacturer service centres. One laboratory reported waiting three months for a replacement robotic arm available only from San Diego, bringing sequencing operations to a standstill.
These findings lead to key recommendations for funders addressing infrastructure challenges. While funders may have limited ability to address global supply chain disruptions directly, they can support models for pooled procurement of consumables and equipment, encourage risk management planning as part of application processes, and help institutions sustain relevant instrumentation and software for sequencing. This may be achieved through developing strategic relationships with NGOs like UNICEF, encouraging the inclusion of research equipment in emergency logistics planning.
Lesson 3: Address the bioinformatics bottleneck by investing in human capacity
The pandemic highlighted both the critical importance of skilled workforce capacity and the global inequities in its distribution. Bioinformaticians – specialists who analyse biological data using computational methods – proved to be particularly crucial, yet scarce, resources during the crisis.
Teams with existing expertise from prior genomic projects had a significant advantage, able to rapidly pivot from malaria, swine flu, or tuberculosis research to SARS-CoV-2 sequencing. This expertise wasn’t built overnight – it represented years of investment in training and capacity building.
To address immediate shortfalls, many funded teams developed innovative training approaches. Some offered accelerated bioinformatics training programmes not only for their staff but also for researchers at partner institutions, public health facilities, and local hospitals. These programmes combined formal instruction with hands-on skill development, creating a pipeline of trained personnel that will strengthen future epidemic responses.
Beyond formal training, researchers benefited from engaging in both formal and informal knowledge-sharing networks. Regular consortium meetings allowed teams to exchange findings and troubleshoot emerging challenges, while established professional relationships enabled rapid ad-hoc knowledge exchange.
For research funders, the research highlights the importance of investing in human capacity, particularly in specialised fields like bioinformatics, to build resilience for future emergencies. By fostering ongoing training programmes and enabling knowledge exchange across institutions, funders can help address the global inequities in workforce distribution that became so evident during COVID-19. Importantly, these investments yield benefits beyond emergency preparedness, strengthening research capacity for ongoing health challenges as well.
Lesson 4: Maintain data quality and openness for global benefit
The pandemic exposed tensions between the imperative for rapid global data sharing and competing priorities including equitable scientific credit, national sovereignty concerns, and quality assurance needs.
GISAID emerged as a primary platform for sharing SARS-CoV-2 sequence data, particularly popular among researchers in low- and middle-income countries, because it allowed depositors to retain rights over their data and receive credit for subsequent use. However, requirements imposed on data reuse through GISAID created delays when scientists needed to aggregate and reanalyse sequencing data alongside other datasets.
Many countries developed national repositories to navigate this complexity and protect sovereignty over health data. In India, for example, the INSACOG network emerged to coordinate national sequencing efforts before data was shared internationally.
Teams also implemented interim solutions to share data with key stakeholders before public release. This included restricted sharing with trusted collaborators and direct communication channels with policymakers, allowing critical information to inform urgent decisions while navigating complex approval processes.
Metadata quality and completeness emerged as significant challenges, particularly in routine healthcare facilities rather than dedicated research settings. Incomplete or inconsistent metadata prevented or delayed the open sharing of many genomic sequences.
Our research findings suggest several approaches for funders to improve data management and sharing. This includes recognising the importance of credit for data generators while finding ways to ensure data is openly available. It also highlights the need for clear protocols for tiered data sharing that prioritise rapid information flow to critical decision-makers while working toward full public release. Additionally, funders should provide clear guidance on sharing anonymised data associated with sequence information to improve metadata collection.
Lesson 5: Bridge the science-policy divide by empowering local voices
The effectiveness of research uptake during the pandemic was significantly shaped by local contexts, including governance structures, historical experience with disease outbreaks, and existing relationships between research and policy communities.
Pre-existing relationships between research institutions and government agencies proved invaluable for translating scientific evidence into policy action. Countries with experience managing infectious disease outbreaks, such as Uganda and Vietnam, integrated COVID-19 surveillance into established emergency response frameworks more effectively.
Policy briefs emerged as crucial tools for communicating complex genomic data to decision-makers. These concise, non-technical documents with executive summaries and visual aids helped bridge the gap between scientific findings and policy needs. Technical working groups and specialised task forces formed vital mechanisms for information sharing, providing authoritative platforms where scientific evidence directly informed national decision-making.
Local leadership in policy engagement proved more effective than having foreign researchers take prominent roles, recognising the importance of cultural context and avoiding perceptions of external interference. Similarly, community engagement strategies were most successful when carefully tailored to local contexts, using appropriate communication channels from radio programming in Africa to televised discussion forums in Nepal.
For research funders looking to enhance the impact of funded work, the report highlights the importance of building researcher capacity for policy engagement. Pre-existing relationships between research institutions and government agencies proved invaluable during the pandemic, demonstrating that these connections (which can be cultivated during routine research activities) create resilience and impact pathways that become critical during emergencies. Funders should encourage and support the development of these relationships as an integral component of all research, rather than as a separate emergency preparedness activity.
Lesson 6: Recognise the invisible research environment
The pandemic revealed numerous hidden processes and pressures that significantly impacted researchers’ ability to conduct their work effectively. These ranged from psychological impacts like fear for personal and family health, to increased workloads, to administrative challenges and communication barriers. In some cases, senior team members felt solely responsible for project success, creating additional mental burden.
The consultation found that activities like shared meals and team sports helped build morale, while implementing shift-working patterns helped manage limited lab access under lockdown restrictions. Finally, transparent communication from project team members helped to increase certainty during worrying times.
For research funders, acknowledging and addressing these hidden aspects of the research environment is crucial. Supporting researchers’ wellbeing, recognising extraordinary efforts, and building flexibility into grant structures can help maintain both scientific productivity and researcher resilience during high-pressure emergency responses. Funders should consider how their processes and expectations might inadvertently add to researcher burden during crisis situations.
The path to building resilient global health systems
The path to building resilient global health systems requires strategic investment before emergencies occur, flexible approaches during crisis periods, and systematic learning afterward. By addressing challenges across the entire ecosystem – from funding mechanisms to human capacity, infrastructure to data sharing, and research-policy connections – funders can help ensure that scientific evidence effectively informs public health action when future emergencies arise.
These lessons from COVID-19 sequencing efforts demonstrate that resilience comes not just from technological capacity but from the strength of human networks, institutional relationships, and adaptable systems that can respond to unprecedented challenges. Most importantly, they highlight how strategic investments in building regional capacity before emergencies occur are a critical preparation for when crisis strikes.
The full report is now available and provides comprehensive findings, detailed case studies, and expanded recommendations.
