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 | |
|---|---|---|
| Assay Time | < 9 hours library prep time | < 9 hours library prep time |
| Automation Capability | Liquid Handling Robots | Liquid Handling Robots |
| Content Specifications | Targets and characterizes ~40 common respiratory viruses, including SARS-CoV-2. | |
| Description | A streamlined workflow for detecting and analyzing SARS-CoV-2 and other common respiratory viruses using RNA Prep for Enrichment combined with Respiratory Virus Oligo Panel for library prep, proven Illumina sequencing, and simplified data analysis using the DRAGEN RNA Pathogen Detection App or Explify RVOP Software on BaseSpace Sequencing Hub. | A streamlined workflow using Respiratory Pathogen ID/AMR Panel (RPIP) with Illumina RNA Prep with Enrichment, sequencing on Illumina desktop systems, and powerful analysis using Explify RPIP Software allows researchers to identify respiratory infections and co-infections, identify antimicrobial resistance, and perform strain typing of critical pathogens (SARS-CoV-2 and Flu A/B viruses) to study viral evolution and transmission. |
| Hands-on time | < 2 hours library prep time | < 2 hours library prep time |
| Input Quantity | 10-100 ng | 10-100 ng |
| Multiplexing | Up to 384 samples in a single run with unique dual indexes | Up to 384 samples in a single run with unique dual indexes |
| Species Category | Human, Virus | Bacteria, Fungal, Virus |
| Species Details | Detects common respiratory viruses, including recent flu strains and SARS-CoV-2. Includes human probes as a quality feature, human probes are included in every sample. | Detects respiratory pathogens (180+ bacteria, 50+ fungi, and 40+ viruses, including SARS-CoV-2) and antimicrobial resistance alleles (1200+). |
| System Compatibility | MiniSeq, MiSeq, MiSeq, NextSeq 550 | MiniSeq, MiSeq, 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. | ||||
Application Note | PDF < 1 MB
Surveillance of infectious disease through wastewater sequencing
Application Note | PDF < 1 MB
Application Note | PDF < 1 MB
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