Rapid and collaborative SARS-CoV-2 analysis

Validated with over 5000 samples across 7 global sites

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SARS-CoV-2: Ongoing challenges of monitoring, evolution, and global impact

SARS-CoV-2, the virus responsible for COVID-19, continues to circulate globally without clear seasonality, leading to ongoing infections and severe acute disease. As of November 2024, over 776.8 million confirmed cases and more than 7 million deaths have been reported across 234 countries (source: WHO) .
The impact of COVID-19 varies by country, and the World Health Organization's ability to monitor circulation, severity, and virus evolution is challenged by reduced surveillance, testing, sequencing, and limited integration into long-term prevention programs. Changes to COVID-19 surveillance over the past five years have been consistent, but integration is variable across regions (source: UKHSA Research Portal)

The virus's unpredictable behaviour, including unexpected surges and declines, complicates the forecasting and preparedness efforts. Additionally, the emergence of new variants, underscores the virus's evolving nature, necessitating continuous monitoring and adaptation of public health strategies.

Quality and Speed

  • Validated with over 5000 samples across 7 global sites

  • Like-for-like the fastest genomic analysis pipeline: Run a batch of 100 samples in 20 minutes.

  • Using an amplicon-aware assembler, Viridian, our assemblies are more accurate, due to reduction in errors at primer binding sites and improved indel detection.

  • Faster Phylogenetic Insights: Identifies samples within 3 SNPs for outbreak detection and patient linkage.

  • Faster and less resource intensive than ARCTIC- ILM and ARCTIC-ONT.

EIT Pathogena’s Bioinformatics Analysis Pipeline for SARS-CoV-2

The SARS-CoV-2 analysis includes consensus genome assembly, pangolin lineage assignment, and identification of related isolates for samples sequenced using tiled amplicon sequencing.

Fastest like-for-like genomic analysis – batch of 100 samples in 20 minutes. Robustly tested with over 5,000 genomes sequenced (pre-print paper).

Configured to support multiple amplicon schemes, with flexibility to incorporate new schemes in the future.

This pipeline operates within an Oracle-secured environment, ensuring data privacy. It allows for data storage and management, with easy access and control over results. Outputs include automated reports and intermediate files.

Supported NGS Technologies: Illumina and Oxford Nanopore Technologies.

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HOw it work - SARS

How the pipeline works

Upload and Human Read Removal

Upload: The upload process for Gzip FastQ files is incredibly simple using our drag and drop interface.

Select your amplicon scheme: Select which amplicon scheme you have used. We also have an experimental option for automatic amplicon scheme detection.

Human read removal: The pipeline is built with data privacy and security at its core. To protect patient information and to avoid encumbering downstream analyses with off-target sequences, the first step when using the pipeline is human read removal. This step is performed using Hostile, developed by our partners, Moderinising Medical Microbiology, from The University of Oxford. Hostile has been demonstrated to be faster and far more sensitive than NCBI’s Human Read Removal Tool (HRRT). Demonstrated to remove 99.6% of human read, including short reads.

For added security, you also have the option to remove human DNA before leaving your network, when using the command-line interface.