CleanPlex® Respiratory Virus Research Panel V2

This amplicon-based Respiratory Virus Research Panel is designed for the detection, research, and surveillance of COVID-19 SARS-CoV-2 virus, Influenza (flu A/B), and respiratory syncytial virus (RSV) (A/B), enabling complete genome sequencing of the SARS-CoV-2 virus and concurrent influenza and RSV sub-typing with highly sensitive detection.

Product Description

The CleanPlex® Respiratory Virus Research Panel v2 combines SARS-CoV-2 whole genome amplification with 149 strategically designed primers to cover characteristic regions that span multiple gene segments for each Influenza A subtype H1N1, H1N2, H3N2, Influenza B, and respiratory syncytial virus (RSV) types A and B. The increased target regions yield a higher coverage, resulting in higher sensitivity and making this panel more suitable for high-throughput screening strategies such as testing multi-sample pools, than qPCR methods with only 1 to 2 targets per subtype. The respiratory virus primers were expertly designed in consideration of over 45,000 viral genome sequences to generate highly specific, but also universally conserved targets for each influenza and RSV subtype to allow confident detection throughout flu seasons, regardless of changes in strain prevalence.

Built upon the CleanPlex SARS-CoV-2 Research and Surveillance Panel, the Respiratory Virus Research Panel v2 addresses the need to assay the SARS-CoV-2 and other respiratory viruses concurrently during the overlapping flu season and the COVID-19 pandemic. The panel utilizes the CleanPlex multiplex PCR-based targeted sequencing technology to provide an easy-to-use, fast, and comprehensive solution for detection and differentiation of these common viruses, influenza and RSV subtyping, and SARS-CoV-2 mutation analysis, tracking, and surveillance for informed infection control through comprehensive sequence information.


  • Significant Cost Savings
    99% reduction in sequencing cost. Only 30K50K reads per sample required v.s. 10M reads required by many metagenomics sequencing methods.
  • High Coverage of Target Regions
    Whole-genome coverage of the SARS-CoV-2 genome and selective coverage of influenza and RSV gene segments for sub-typing
  • Ultra-Sensitive Detection
    Multiplex PCR based method for more sensitive detection of low viral copies. 
  • Fast, Streamlined Workflow
    Generate sequencing-ready libraries in just 6 hours using a rapid, four-step protocol including RT step with minimal hands-on time.
  • Superb Performance
    Prepare high-quality NGS libraries with excellent on-target performance using CleanPlex Technology to enable efficient use of sequencing reads. CleanPlex panels’ on-target rates are usually much higher than those of hybrid captured-based small target enrichment panels.

The CleanPlex Respiratory Virus Research Panel contains the CleanPlex Multiplex PCR Primers and CleanPlex Targeted Library Kit with RT components. CleanPlex Indexed PCR Primers for sample pooling and CleanMag® Magnetic Beads for bead purification and size selection are ordered separately to complete the workflow from input RNA to sequencing-ready NGS libraries.

For a complete solution, please use the following indexed PCR primers and magnetic beads SKUs.earl

Pack Size (Reactions)SKUs for Indexed PCR PrimersSKUs for Magnetic Beads
961 x SKU#716006 – CleanPlex® Dual-Indexed PCR Primers for Illumina® Set A (12 x 8 indexes, 96 reactions)1x SKU#718005 – CleanMag Magnetic Beads (20 mL, ~100 reactions for CleanPlex 2-pool panels)
3841 x SKU#716037-716040- CleanPlex® Plated Unique Dual-Indexed PCR Primers for Illumina®1 x SKU#718003 – CleanMag Magnetic Beads (60 mL, ~300 reactions for CleanPlex 2-pool panels)

1 x SKU#718005 – CleanMag Magnetic Beads (20 mL, ~100 reactions for CleanPlex 2-pool panels)

Storage Temperature

Store at -20 °C.

For Research Use Only. Not for use in diagnostic procedures.

Enrichment MethodMultiplex PCR 
Sequencing PlatformsIllumina®
Amplicon Size105 – 196 bp (150 bp Average)
Number of Primer Pools2
Sample Input Requirement5-11 µL (or ~50ng) of extracted total RNA
Sample TypesSputum, nasopharyngeal and oropharyngeal swabs and aspirate, tissue samples, and other methods for viral RNA sampling.
Total Assay Time6 hours
Hands-On TimeLess than 1 hour
Amplicon Coverage (≥30x)> 92% with 10,000 copies viral input at less than 0.1M PE reads per sample
On-Target Aligned Reads> 95%
VirusesSelective Covered RegionsAmplicon Count
SARS-CoV-2Complete coverage (except 92 bp at the ends of the genome)172 (pool 1) 171 (pool 2)
Influenza A H1N1HA, M1, NA, NP, NS1, PA, PB1, PB218 (pool 1)
Influenza A H1N2HA, M1, M2, NA, NP, NS1, PB1, PB217 (pool 1)
Influenza A H3N2HA, M1, M2, NA, NP, NS1, PA, PB1, PB231 (pool 1)
Influenza BHA, M1, NA, NS1, PB1, PB232 (pool 1)
RSV AG, F, M, N, NS1, NS2, L, SH, M2-121 (pool 1)
RSV BG, F, M, N, NS1, NS2, P, L, SH, M2-130 (pool 1)
Human RNA Primer ControlTBP ( House Keeping Gene)1 (pool1)

Additional Information

Pack Size (Reactions)

8, 96, 384

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