The Illumina Respiratory Virus Enrichment Kit allows researchers to obtain whole-genome next-generation sequencing (NGS) data for over 40 important respiratory viruses including SARS-CoV-2 and influenza A/B viruses. This kit enables the identification of targeted viruses present, identification and tracking of variants, and viral surveillance on a wide array of sample types.1
Target enrichment through hybrid–capture methods allows for highly sensitive detection without requiring the high read depth necessary with shotgun metagenomic sequencing. Additionally, this method allows for near-complete whole-genome sequence data acquisition of viral targets and provides flexible solutions for a wide variety of different applications. Compared to other targeted resequencing methods, such as amplicon sequencing, enrichment-based hybrid capture allows for dramatically larger probe panels with a more comprehensive profiling of many different viral targets in a single experiment. Additionally, oligo probes used for hybrid–capture remain effective even within highly mutagenic regions, allowing for the targeting of rapidly evolving viruses, such as influenza viruses and other RNA viruses.
This comprehensive workflow integrates library preparation, target enrichment, sequencing, and data analysis. The workflow is intended to enrich viral targets from extracted total nucleic acid since both RNA and DNA viruses are targeted with this enrichment panel.
Reverse transcription of extracted RNA, library preparation, and enrichment are performed using the well-established, robust Illumina RNA Prep with Enrichment reagents and protocol in conjunction with the Respiratory Virus Oligo Panel v2 provided within the kit. After sequencing on an Illumina NGS system, data analysis can be performed using the DRAGEN Microbial Enrichment App on the BaseSpace Sequence Hub.
| Illumina Respiratory Virus Enrichment Kit | 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 |
| Description | A streamlined workflow for detecting and analyzing SARS-CoV-2 and other common respiratory viruses using Illumina RNA Prep with Enrichment reagents combined with the Respiratory Virus Oligo Panel v2 for library prep and enrichment, Illumina sequencing, and simplified data analysis using the DRAGEN Microbial Enrichment App. | 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 influenza virus strains and SARS-CoV-2. The panel includes probes to human targets as a quality feature, and therefore detects those human targets in every sample assayed. | Detects respiratory pathogens (180+ bacteria, 50+ fungi, and 40+ viruses, including SARS-CoV-2) and antimicrobial resistance alleles (1200+). |
| System Compatibility | MiniSeq, MiSeq, NextSeq 1000, NextSeq 2000, 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. | ||||
Application Note | PDF < 1 MB
Surveillance of infectious disease through wastewater sequencing
Application Note | PDF < 1 MB
Application Note | PDF < 1 MB
A high-performing, fast, and integrated workflow for sensitive applications such as human whole-genome sequencing.
Achieve rapid, targeted interrogation of an expansive number of target genes with exceptional capture efficiency and coverage uniformity.
NextSeq 1000/2000 reagent kits contain a reagent cartridge, flow cell, and resuspension buffer. Multiple flow cell configurations offer adjustable output based on project needs.
Provides a reproducible, economical solution for sequencing RNA from FFPE tissues and other low-quality samples. Accuracy from as little as 10 ng total RNA.
A fast, integrated workflow for a wide range of applications providing targeted resequencing for custom panels, fixed panels, and whole-exome enrichment.
This panel allows for characterization of at least 200 known coronavirus genera for surveillance of animal reservoirs and sequencing of known coronaviruses.
