Executive Summary
Why Does This Matter?
The emergence of variants of concern (VOCs) will prevent us from ending the Covid-19 pandemic in a timely manner. If VOCs achieve “viral escape” – when a virus can evade the immunity (T-cell and humoral) generated by a vaccine – new strains of SARS-CoV-2 could infect and kill at a global scale, even after we achieve mass vaccination. Genomic sequencing and surveillance at scale would allow the global community to identify VOCs and their spread earlier so that we can respond rapidly with appropriate vaccines (including boosters), treatments, and policy and public-health measures. Analytic tools, platforms and dashboards enable the viewing of sovereign data and global data to facilitate early public-health interventions, policy planning and decision-making. Genomic sequencing, surveillance and analytic capabilities play a similarly critical role for other infectious diseases, which should be carefully managed as part of emerging global health security priorities.
What Is the Problem?
Despite calls for global cooperation on genomic sequencing and surveillance, three interrelated technology-related problems prevent global coordination on this topic.
There is no turnkey, standardised processing and upload solution for sequencing labs to share data in a common database. The number of sequences collected and shared to date is insufficient. As of the beginning of March, the largest database of SARS-CoV-2 genomic sequences had only amassed one-tenth of the total number of sequences recommended by the World Health Organisation (WHO). Standardised processing of sequence data is critical to enable sharing of data and collaborative research.
Current platforms comparing sequences from multiple geographies to identify and track SARS-CoV-2 VOCs have made significant progress synthesising and visualising genomic evolution, and they have opportunities to further develop to translate this data into actionable research. Additional solutions are needed to rapidly identify when viral evolution would cause a strain to be considered a VOC (i.e., it may result in viral escape) and to allow for transparent governance for data-sharing.
Analytic tools, platforms and dashboards can go further to link genetic mutations and variants to changes in epidemiology, clinical outcomes and effectiveness of vaccines, therapeutics and diagnostics. By linking genetic mutations to these phenotypic changes, genomic surveillance can inform decisions about public-health measures, clinical guidelines and vaccine, therapeutic and diagnostic R&D.
What Is the Solution?
Having the right technology solutions in place, with appropriate governance, can address these problems and enable leaders to better fight the pandemic and VOCs. We need a technology solution complemented by the right governance and incentives that can:
Enable existing and new sequencing labs to rapidly upload and share raw data using standardised processing approaches, including to databases such as GISAID, NCBI and EBI. This solution should protect the privacy of the patient’s data, respect the rights of the lab and sovereignty of the nation whose lab generated the data, and keep the data secure from external threats. Any global cloud-based repository capturing and processing this data should allow for rapid turnaround and return of the consensus genome for download by the user who uploaded the sequence. Nations should have sufficient access to each other’s data to understand global spread of the virus without compromising the ability to control the details of what is shared.
Analyse aggregated, annotated consensus sequences to make key inferences about the pathogen (e.g., emerging lineages or specific mutations) and major phenotypic changes resulting from these genetic mutations (including VOCs).
Translate data about genomic evolution into insights for policymakers about VOCs, specifically their impacts on epidemiology, clinical outcomes, and effectiveness of vaccines, therapeutics and diagnostics. Analytic and dashboard tools should be pragmatic and rapid, with an emphasis on guiding decision-making for combatting the pandemic, including a “variants-to-vaccines and therapeutics” R&D pipeline.
These technology solutions are applicable to SARS-CoV-2, other established diseases and new pathogens. Analytic platforms need to be low-cost and not-for-profit so that they can be readily used around the world, with clear policies and standards (including common data elements). They should have transparent algorithms and processes for users to submit requests so that researchers and users can understand the methodology behind the analytics.
Of course, design and adoption of any technology solution would need to be complemented by appropriate governance, dedicated financing, scientific oversight and sufficient sequencing capacity. Specifically, to complement the technology solution described above, we propose the following broader enablers:
Expanding on-the-ground genomic sequencing capabilities so there are fewer blind spots around the world, complemented by local capacity for clinical phenotyping.
Incentivising the use of common data standards for sharing genomic sequencing data.
Developing international governance for sharing data and designating a custodian for the platform. An international body, ideally convened by the WHO, could set the “rules of the road” for data-sharing and privacy, incentivise global data sharing, and monitor nations’ compliance and participation.
Establishing a scientific advisory committee, ideally convened and chaired by the WHO, to define what counts as wild-type SARS-CoV-2, variants and VOCs, and to determine implications for public-health decisions.
Simplifying and scaling the ability to share genomic sequences of pathogens has broad applications beyond fighting the Covid-19 pandemic. Medical research and drug design depend heavily on the ability to share genomic (and other) data. While the Covid-19 pandemic presents the most immediate use case for truly global coordination of genomic data-sharing, building out this global capability would also unlock genomic data-sharing capabilities for other disease areas, including other infectious diseases, cancer, autoimmune disorders and rare diseases.