CleanPlex® Respiratory Research Panel

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


Product Description

The CleanPlex® Respiratory Research Panel combines SARS-CoV-2 whole genome amplification with ~80 strategically designed primers to cover characteristic regions that span multiple gene segments for each Influenza A subtype H1N1, H1N2, H3N2, and Influenza B. As a result of more targets, the higher coverage and increased sensitivity make 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 influenza 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 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 Research Panel addresses the need to assay the SARS-CoV-2 and influenza 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 SARS-CoV-2 and Influenza viruses, influenza 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 shotgun metagenomics sequencing methods.
  • High Coverage of Target Regions
    Whole-genome coverage of the SARS-CoV-2 genome and selective coverage of influenza 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 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.

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#718002 – 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 Size114 – 185 bp
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)>97% with 10,000 copies viral input at less than 0.1M PE reads per sample
On-Target Aligned Reads> 97%
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)
Human RNA Primer ControlTBP ( House Keeping Gene)1 (pool1)

Additional Information

Pack Size (Reactions)

8, 96, 384

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