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ARTIC SARS-CoV-2 Amplicon Panel

Multiplex PCR panel for SARS-CoV-2 amplicon sequencing

The ARTIC panel consists of two primer pools that amplify SARS-CoV-2 viral genomes from complex samples for research. The sequencing data can elucidate the presence of mutations consistent with known variants or identify new variants in research studies.

xGen NGS—made for COVID-19 research.

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Product details

Using next generation sequencing (NGS) to analyze SARS-CoV-2 can help researchers understand COVID-19. IDT, in partnership with the ARTIC Network, is offering their latest design of the ARTIC SARS-Co-V-2 Amplicon Panel to support global availability of this important research tool.

The ARTIC network—a group of researchers who are developing a system for processing different virus samples to generate public health information—has developed primer sequences, experimental recommendations, and bioinformatic resources to facilitate NGS analysis of the SARS-CoV-2 genome. Their primer design pipeline (PrimalSeq), previously deployed for other infectious disease sequencing, was especially useful early in the SARS-COV2 pandemic [1].

ARTIC provides a detailed experimental protocol featuring a set of primers for amplicon sequencing to quickly sequence SARS-CoV-2 [2]. They also maintain a resource that alerts researchers to updates in the design [3]. An adaptative protocol that allows for sequencing on Illumina sequencers have been developed by others [4].

The sequence of the SARS-CoV-2 genome can enable research in many areas, including:

  • Origin identification
  • Mutations and viral evolution rates
  • Transmission routes of variants
  • Population surveillance, such as wastewater-based epidemiology.
Dr. Joshua Quick
University of Birmingham
ARTICnetwork
The ARTIC network is delighted to be partnering with IDT to produce primer pools for SARS CoV 2 genome sequencing. The ARTIC nCoV 2019 amplicon sequencing protocol has been widely adopted across the world, and the genome data is critical to understanding and tracking the outbreak. Our mission is to put genomics at the heart of outbreak response and having this resource available will help more groups establish genome sequencing capabilities in their own labs in a cost-effective and reproducible way.

Workflow

The ARTIC SARS-CoV-2 Amplicon Panel workflow includes cDNA synthesis, amplicon generation, and cleanup. The final amplicons average 400 bp require 2 x 250 bp read lengths on either the NovaSeq™ or MiSeq™ sequencers (Illumina).

Table 1. Specifications for the ARTIC SARS-CoV-2 Amplicon Panel

Recommended Ct value Coverage Contiguous amplicons Coordinates covered
<30 99.7% 99 50-29,827

Product data

Figure 1. The ARTIC SARS-CoV-2 Amplicon Panel’s genome coverage for Omicron variants. Two nasopharyngeal swab samples (Cts 28.4 and 13.6) were subjected to the protocol using the ARTIC v4.1 primer pool to create amplicons, then the xGen DNA Library Prep MC Library Prep Kit to adapt the amplicons to create an NGS library. Libraries were sequenced on a MiSeq™ (Illumina) with 2 x 250 bp PE reads. Data was down sampled to 100,000 reads. Alignment was then performed using the Burrows-Wheeler Alignment (BWA) Tool [4] and a consensus file uploaded to Pangolin for lineage calling. High genomic coverage for the BA.1 lineage was observed (IGV screenshot above) indicating the compatibility of the panel with Omicron variants.

Table 2. Sequencing metrics for ARTIC v4.1 libraries created from nasopharyngeal swabs.

Sample Ct Reads aligned On-target Coverage uniformity % Genome >10X Lineage
Sample 128.4100,00099.785.997BA.1
Sample 213.6100,00099.797.6100BA.1

Sequencing metrics for NGS libraries originating from nasopharyngeal swabs. Libraries were created with the ARTIC v4.1 primer pool and the xGen DNA Library Prep MC Library Prep Kit. Libraries were sequenced on a MiSeq™ (Illumina) with 2 x 250 bp PE reads. Data was down sampled to 100,000 reads. Lineages were called with Pangolin.

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