A validated genomic sequencing pipeline for SARS-CoV-2

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This blog post is authored by Dr Junko Takata. She presents the findings of her recent preprint “A validated cloud-based genomic platform for co-ordinated, expedient global analysis of SARS-CoV-2 genomic epidemiology” January 27, 2025 — Dr Junko Takata

The COVID-19 pandemic demonstrated the transformative power of whole-genome sequencing in shaping public health policies. From tracking the emergence of new variants to guiding vaccine development, sequencing became the foundation of our global response. However, while sequencing technologies have advanced rapidly and become more accessible, a persistent challenge is the bioinformatic expertise to analyse and interpret the data produced, - especially in resource-constrained settings, where the need for accessible and efficient tools is most acute

To address this gap, the Modernising Medical Microbiology (MMM) group at the University of Oxford has been working on developing cloud-based sequencing pipelines with the aim of addressing such bottlenecks. In 2021, we first developed a sequencing pipeline for SARS-CoV-2, commissioned by the UKHSA for use during the pandemic. While this initial version served its purpose effectively, we have since significantly upgraded the pipeline into the Tiled Amplicon Pipeline (TAP)—a secure, cloud-based tool capable of processing uploaded FASTQ files and delivering actionable results, such as lineage identification and genetic relatedness, in about 20 minutes.

In this preprint, we present the development and validation of the pipeline. To illustrate its capabilities, we processed and analysed over 5,000 SARS-CoV-2 sequences from clinical samples collected across seven countries during the same two-week period. This large-scale analysis demonstrated how a cloud-based tool such as TAP can coordinate data sharing, enhance collaboration, and facilitate global genomic surveillance.

Although TAP was initially designed to address the specific challenges posed by SARS-CoV-2, its potential applications could extend beyond this virus. The pipeline’s design allows for adaptation to other viruses that utilise tiled amplicon sequencing methods.

By simplifying the analytical process and making genomic data more accessible, a tool such as TAP can empower researchers and public health professionals to integrate genomics into their workflows more seamlessly. We hope that this will contribute to the widening of access to genomics and facilitate global collaboration – which, in turn, will help us prepare for the next pandemic.

TAP has now been deployed on the EIT Pathogena platform as the “SARS-CoV-2” pipeline and is currently freely accessible for use.