NGS capacity mapping
Page last updated 22 Jul 2021
Mapping global next-generation sequencing capacity for SARS-CoV-2
Next-generation sequencing (NGS) technology forms the cornerstone of SARS-CoV-2 genomic surveillance. NGS is being used around the world to monitor the spread and evolution of SARS‑CoV‑2. The emergence of novel SARS-CoV-2 variants of concern, which can be more transmissible or associated with more severe disease, has accelerated the need for a coordinated global plan to enhance NGS and surveillance capabilities.
As of July 2021, the GISAID genomic repository has received over 2.25 million submissions of SARS‑CoV‑2 genomes. While this is a significant achievement, there is a huge geographic disparity in global coverage of the data, with only four countries accounting for 66% of all submissions. For more than 180 countries, most of which are low- and middle-income countries (LMICs), the GISAID genomic data represents only 0–1% of the total positive SARS-CoV-2 cases.
Access to sequencing capacity in LMICs is essential for genomic surveillance and tracking of SARS-CoV-2 variants around the world. To this end, FIND has carried out a systematic mapping exercise to assess existing global capacity for SARS-CoV-2 genome sequencing, with input from the World Health Organization (WHO) and other global health stakeholders. Our mapping exercise looked at available data on diagnostic testing capacity, NGS capacity and ongoing in-country SARS‑CoV‑2 sequencing. Available data for each country were graded to evaluate capacity according to the criteria outlined below.
Overview of data sources and classification methods for NGS capacity mapping
Country classification framework based on NGS capacity
Based on the NGS capacity mapping data, we have developed an action-oriented framework to classify LMICs into one of four archetypes, with associated actions needed to operationalize SARS-CoV-2 genomic surveillance:
|Country archetype||Description||Action needed|
|Test||Insufficient or unreliable diagnostic or molecular testing capacity for SARS-CoV-2||Establish sufficient diagnostic testing capacity for SARS-CoV-2|
|Connect||Sufficient diagnostic capacity for SARS‑CoV‑2, but no existing NGS capacity identified||Set-up sample referral networks to utilize regional NGS capacity or build NGS capacity from scratch|
|Leverage||Sufficient diagnostic capacity for SARS‑CoV-2 and existing NGS capacity identified, but not deployed for SARS‑CoV‑2 genomic surveillance||Perform situational analysis to identify potential ways to leverage or repurpose existing NGS capacity for SARS-CoV-2 genomic surveillance|
|Strengthen||Sufficient diagnostic capacity for SARS‑CoV‑2 and existing NGS capacity being utilized for SARS-CoV-2 genomic surveillance||Expand existing genomics capacity to scale-up ongoing SARS-CoV-2 genomic surveillance|
The specific actions or activities start with ensuring that countries have sufficient diagnostic testing capacity for COVID-19, performing a needs assessment for NGS capacity building or a situational analysis to understand and close gaps in utilization, ensuring technical and operational readiness (laboratory setup and equipment procurement, protocols, bioinformatics), providing training and technical support and, most importantly, linking sequencing capacity with existing molecular testing and surveillance networks. In addition, certain overarching activities need to be carried out across all archetypes, such as improving genomic data sharing tools, infrastructure, standards, and establishing mechanisms to rapidly assess the impact of new variants on existing diagnostics and vaccines.
The classification framework based on NGS capacity has potential utility across a variety of areas, including guiding countries in prioritizing activities to strengthen global genomic surveillance, resource allocation, and the routine monitoring of progress in genomic surveillance strengthening at global and regional levels. The framework could also support in-country planning and implementation of sequencing-based surveillance, and assist global health agencies, ministries of health, donors, and implementers to coordinate investments and identify partnerships to strengthen sequencing for SARS-CoV-2, and other important pathogens.
The NGS capacity mapping dashboard is an online visualization tool that provides access to the country classification framework for NGS capacity in LMICs and includes functionality to explore source data at the country level. While the current country classification system aims to understand NGS capacity and needs in LMICs, source data from high-income countries have been incorporated when available.
Although the classification system is not designed to change frequently, we will monitor and update the data on a monthly basis to accommodate any shifts in the underlying data sources. Future versions of the dashboard will incorporate new data and variables, such as the location and ongoing usage of NGS in countries, information on surveillance capacity for influenza-like illness/serious acute respiratory infection, and the burden of respiratory disease.
Click HERE to view in full screen.
The NGS capacity map can also be viewed in a tabular format, which includes information on the current archetype and supporting quantitative data for countries grouped by geographical region.
We envision the country classification framework and accompanying dashboard as important tools to help visualize information from global stakeholders on NGS capacity in LMICs. The tools can also be used to identify market opportunities and potential partnerships, and coordinate investments that can support the design of country-focused action plans to operationalize and expand SARS‑CoV‑2 genomic surveillance. We encourage all relevant stakeholders to utilize the online capacity mapping dashboard and share data that can be used to refine country‑specific information on diagnostics, NGS, and surveillance capacity. Feedback on the online dashboard and query tools can be provided here.
The ACT-Accelerator and Genomic Surveillance Working Group
This work was carried out as part of the Access to COVID-19 Tools (ACT) Accelerator Genomic Surveillance Working Group established in April 2021, co-led by WHO and The Rockefeller Foundation and coordinated by FIND, as the overall co-convener of the ACT-Accelerator. The ACT-Accelerator is a global collaboration designed to rapidly leverage existing global public health infrastructure and expertise to expedite the end of the COVID-19 pandemic. The objective of the Genomic Surveillance Working Group is to harmonize, coordinate, and accelerate priority activities and investments across partners to:
- strengthen and integrate genomic surveillance into routine surveillance systems;
- enhance access to sequencing tools to build capacity and improve information sharing in countries for rapid identification and monitoring of variants of concern to inform real-time outbreak response; and
- support global efforts for rapid assessment of the impact of variants of concern on existing and future diagnostics, vaccines, and therapeutics.
We are grateful to the data contributors who shared the data used in this Web Application via the GISAID Initiative*: the Authors, the Originating Laboratories responsible for obtaining the specimens, and the Submitting Laboratories that generated the genetic sequences and metadata.
*(a) Elbe, S., and Buckland-Merrett, G. (2017) Data, disease and diplomacy: GISAID’s innovative contribution to global health.
(b) Shu, Y., McCauley, J. (2017) GISAID: From vision to reality.
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