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xGen™ SARS-CoV-2 Amplicon Panel

Targeted sequencing to research SARS-CoV-2 viral genomics

Ready-to-order panel of multiplexed primers that creates 345 overlapping amplicons of SARS-CoV-2 genomic material for NGS sequencing. Resulting data is crucial to research viral variants and improve understanding of virus evolution and transmission.

xGen™ NGS—made for COVID-19 research.


Product details

xGen SARS-CoV-2 Amplicon Panel enables researchers to identify SARS-CoV-2 strains, including variants, by creating next generation sequencing (NGS) libraries. The sequencing data can be used to answer research questions such as: 

  • Which viral strains account for most infections within a local population? 
  • What new strains are emerging?

IDT’s predesigned amplicon panels for COVID research can aid in identifying the extent and pattern of viral spread within a population and allow researchers to quantify the effectiveness of intervention measures.

Workflow of the IDT SARS-CoV-2 Panel

After isolating the genomic material from a research sample and then converting the SARS-CoV-2 RNA into cDNA, the xGen SARS-CoV-2 Amplicon Panel can be used to create an NGS library. The workflow consists of a 2-step PCR amplification that occurs in a single tube (Figure 1). The first PCR reaction amplifies the SARS-CoV-2 cDNA into 345 overlapping amplicons. The second, indexing PCR adds the adapter/index to each end. For research applications where more than one library is multiplexed for sequencing, IDT offers the xGen Normalase™ reagent that can normalize the libraries so each is represented in the final sequence data.

Figure 1. One-tube library prep workflow of the xGen SARS-CoV-2 Amplicon Panel. After RNA extraction and conversion to cDNA, multiplex PCR primers and master mix create 345 overlapping amplicons of the SARS-CoV-2 genome. These amplicons are converted into an NGS library with adapter attachment/indexing PCR, and normalization (optional).

Product data

The IDT xGen SARS-CoV-2 Amplicon Panel includes multiplexed PCR primers that create overlapping amplicons for NGS. The final amplicon library can include up to 1536 UDIs and provides sequence data for 99.7% of the SARS-CoV-2 genome.

Table 1: Summary of xGen SARS-CoV-2 Amplicon Panel.

Recommended Ct value Coverage (%) Contiguous amplicons (count) Coordinates covered UDIs
<33 99.7 345 25–29,853 Up to 1536

Mapping and coverage

The xGen SARS-CoV-2 Amplicon Panel uses overlapping primers to generate 345 amplicons, 116–255 bp in size (average 150 bp), covering 99.7% of the 29.9 kb viral genome. Overlapping primers ensure that novel variants are detected, even if the mutation results in a dropout of one of the amplicons (Figure 2). Comprehensive mutation detection is crucial for research tracking nucleotide variants, and improving the understanding of virus evolution, transmission, and pathogenesis.

Figure 2. The xGen SARS-CoV-2 Amplicon Panel provides 99.7% coverage of the SARS-CoV-2 genome. RNA was isolated from gamma-irradiated and sonicated cell lysate from Vero E6 cultured monkey kidney epithelial cells (ATCC® CRL-1586™) infected with SARS-CoV-2 isolate USA-WA1/2020 (BEI Resources, Cat. No. NR-52287). 100,000 copies of SARS-CoV-2 RNA was converted into cDNA using the SuperScript IV Kit. The resulting NGS library with the xGen SARS-CoV-2 Amplicon Panel and the Additional Genome Coverage Kit and sequenced 2 x 150 bp on a MiniSeqTM System (Illumina). Resulting reads were downsampled to 280k reads per sample for analysis. Genomic coverage for a representative sample is shown.

*RUO—For research use only. Not for use in diagnostic procedures. Unless otherwise agreed to in writing, IDT does not intend for these products to be used in clinical applications and does not warrant their fitness or suitability for any clinical diagnostic use. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations.