Mini-XT, a miniaturized tagmentation-based protocol for efficient sequencing of SARS-CoV-2.

Area of Science:

• Genomics
• Virology
• Public Health

Background:

• Whole genome sequencing (WGS) of SARS-CoV-2 is crucial for tracking viral spread and variant evolution.
• Existing high-throughput sequencing protocols require optimization for cost-effectiveness and sustainability.
• The COVID-19 Genomics UK (COG-UK) Consortium has sequenced nearly one million SARS-CoV-2 genomes.

Purpose of the Study:

• To develop a miniaturized, cost-effective library preparation protocol for SARS-CoV-2 WGS.
• To reduce consumable use and costs associated with high-throughput sequencing.
• To maintain sequencing quality while improving efficiency.

Main Methods:

• Development of the 'Mini-XT' tagmentation-based library preparation protocol.
• Utilized acoustic liquid transfer to reduce reaction volumes and tip usage.
• SARS-CoV-2 RNA amplification via ARTIC nCov-2019 multiplex RT-PCR.
• Sequencing performed on an Illumina MiSeq platform.

Main Results:

• The Mini-XT protocol reduced reagent volumes eightfold and halved tip usage.
• Sequenced 4384 SARS-CoV-2 samples from N. Ireland with a 97.4% COG-UK QC pass rate.
• Maintained comparable sequencing quality and consistent lineage/SNP calling against standard protocols and nanopore technology.

Conclusions:

• The Mini-XT protocol offers significant cost savings and improved efficiency for SARS-CoV-2 WGS.
• This miniaturized protocol facilitates more efficient high-throughput sequencing of viral isolates.
• Enables sustainable and cost-effective pathogen WGS for future public health applications.