Using the Respiratory Virus Oligo Panel with Illumina RNA Prep with Enrichment allows researchers to obtain next-generation sequencing (NGS) data that can confirm the presence of SARS-CoV-2 and advance variant analysis studies. The agnostic design allows for widespread identification of pathogenic respiratory viruses.
Target enrichment through hybrid–capture methods allows for highly sensitive detection, without requiring the high read depth needed for shotgun metagenomic sequencing. Additionally, this method allows for near-complete sequence data of targets and opens up applications such as variant analysis for viral evolution or viral surveillance.1
Compared to other targeted resequencing methods, such as amplicon sequencing, enrichment through hybrid capture allows for dramatically larger probe panels with more comprehensive profiling of the target regions. Additionally, the oligo probes used for hybrid–capture protocols remain effective even within highly mutagenic regions, allowing targeting of rapidly evolving viruses, such as RNA viruses.
This comprehensive workflow integrates sample preparation, library preparation, target enrichment, sequencing, and data analysis. The workflow is intended to enrich viral targets from total nucleic acid extraction.
Reverse transcription of extracted RNA and library preparation is performed using Illumina RNA Prep with Enrichment, followed by enrichment with the Illumina Respiratory Virus Oligo Panel. After sequencing on an Illumina NGS system, data analysis proceeds using the DRAGEN Pathogen Detection pipeline and IDbyDNA Explify Platform.
| Respiratory Virus Oligo Panel | Respiratory Pathogen ID/AMR Enrichment Panel Kit (Powered by Explify) | |
|---|---|---|
| Automation Capability | Liquid Handling Robots | Liquid Handling Robots |
| Species Category | Human, Virus | Bacteria, Virus |
| System Compatibility | MiniSeq, MiSeq, NextSeq 550 | MiniSeq, MiSeq, NextSeq 550 |
In a titration experiment with 1000 down to two copies of virus spiked into human saliva RNA, Illumina RNA Prep with Enrichment resulted in detection of viral reads from as low as two copies of SARS-CoV-2.
| System | No. of cycles | Reads (M) | Run time (hours) | Samples per run (1M reads per sample) |
|---|---|---|---|---|
| NextSeq 550 System (high output) | 150 | 400 | 18 | 400 maxa |
| NextSeq 550 System (mid output) | 150 | 130 | 15 | 130 |
| MiSeq System (v3 chemistry | 150 | 25 | 21 | 25 |
| MiniSeq System (high output) | 150 | 25 | 17 | 25 |
| a. Indicates that the number of samples per run exceeds the available number of indexes. | ||||
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Surveillance of infectious disease through wastewater sequencing
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Achieve rapid, targeted interrogation of an expansive number of target genes with exceptional capture efficiency and coverage uniformity.
This high-throughput next-generation sequencing (NGS) assay detects mutations from the SARS-CoV-2 virus.
This NGS panel targets >280 respiratory pathogens (including SARS-CoV-2) and 2000+ antimicrobial resistance alleles, with data analysis powered by Explify RPIP.
Optimized chemistry to increase cluster density and read length, and improve sequencing quality scores, compared to earlier MiSeq reagent kit versions.