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xGen™ Respiratory Virus Amplicon Panel

A panel consisting of primers designed to cover >98% of the RSV A, RSV B, Influenza A H1N1, Influenza A H3N2, Influenza B, and SARS-CoV-2 genomes. These primers obtain high levels of genome coverage from as low as 10–100 viral copies. xGen Amplicon Technology uses overlapping primer sets to provide comprehensive coverage in a single-tube, 2.5-hour workflow.

xGen NGS—made for respiratory virus research.

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The IDT xGen Respiratory Virus Amplicon Panel provides a single-tube, two-step PCR amplification workflow with primer sets designed to create amplicons across the entire genome.

  • >98.7% genomic coverage of 6 respiratory viruses
  • Super amplicons result in increased coverage, even in changing or diverse genomes
  • Sequence data from viral titers as low as 10–100 viral copies
  • cDNA to sequencer in 2.5 hrs
  • Up to 1536 UDIs
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Product details

DNA-to-sequencer in 2.5 hours

Figure 1. xGen Amplicon Panel workflow. A dual-index library is prepared from viral samples in three main steps: 1) multiplex PCR, 2) adapter attachment with indexing PCR, and 3) an optional Normalase™ step to produce equimolar library pools.

Table 1. Features of the xGen Respiratory Virus Amplicon Panel.

FeaturesSpecifications
Design coverage and panel information
  • 1199 amplicons, sized 92–255
  • Primers designed to target RSV A (OP890336), RSV B (OP965707), Influenza A H1N1 (A/California/7/2009), Influenza A H3N2 (A/New York/392/2004), Influenza B (B/Malaysia/2506/2004), SARS-CoV-2 (Wuhan-1)
  • Customize it here
Input Material
  • 1st or 2nd strand cDNA
  • Minimum 10–100 viral copies
Time2.5 hours viral DNA-to-library
Multiplexing capabilityUp to 1536 UDIs
Compatible with other indexes?Yes
Recommended depth

200K reads per library, PE150

Product data

The xGen Respiratory Virus Amplicon Panel offers a streamlined (DNA-to-sequencer in 2.5 hours), single-tube NGS workflow for studying respiratory syncytial virus (RSV) subtypes A and B, influenza A (H1N1 and H3N2), influenza B, and SARS-CoV-2. This Predesigned xGen Amplicon Panel built with xGen Amplicon technology includes amplicon tiling and creation of super amplicons to ensure comprehensive genome coverage and provide resistance to future viral mutations that may fall on a priming site, thus enabling future identification of novel variants. Identify the unidentified by using IDT’s solution for achieving comprehensive coverage of respiratory virus genomes RSV A, RSV B, Influenza A H1N1, Influenza A H3N2, Influenza B, and SARS-CoV-2.

Figure 2: The xGen Respiratory Virus Amplicon Panel provides a high level of coverage for various respiratory virus genomes. Examples of panel coverage are shown here for different genomes. For all libraries, cDNA was created using the SuperScript™ IV Kit (Thermo Fisher Scientific) with 10 ng of universal human reference (UHR) RNA. The resulting NGS libraries generated with the xGen Respiratory Virus Amplicon Panel was sequenced on a MiniSeq™ (Illumina) with 150 bp paired-end (PE150) sequencing . Resulting reads were downsampled to 1M reads per sample for analysis. Example data for one replicate per respiratory virus genome are shown in panels A-F. (A) RSV A coverage. 5 µL of BEI NR-43976 was used into RT . The input genome, JX069800, has 96.25% ID to the designed primers. (B) RSV B coverage. 5 µL of BEI NR- 48831 was used into RT. The input genome, AF013254, has 96.7% ID to the designed primers. (C) Influenza A H1N1 coverage. 50K copies of Twist RNA control 103001 was used into RT. The input genome, A/California/7/2009, matches the designed primers. (D) Influenza A H3N2 coverage. 50K copies of Twist RNA control 103002 was used into RT. The input genome, A/New York/392/2004, matches the designed primers. (E) Influenza B coverage. 5 µL of BEI NR-10048 was used into RT. The input genome, B/Malaysia/2506/2004, matches the designed primers. (F) SARS-CoV-2 coverage. 50K copies of BEI NR-52287 was used into RT. The input genome, USA-WA1/2020, matches the designed primers.

Table 2: xGen Respiratory Virus Amplicon Panel NGS metrics.*

RSV ARSV BInfluenza A H1N1Influenza A H3N2Influenza B  SARS-CoV-2
% mapping86%93.60%99.20%99.40%99.50% 98.50%
% on-target (base)97.20%96.70%96.50%96.30%96.60% 97.20%
% base uniformity67.40%70.10%93.20%93.10%77.80% 92.90%
% genome >10x coverage94.50%98.90%100%100%100% 100%

*Sequencing metrics are shown for the libraries described in Figure 2.

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