SARS-CoV-2 coronavirus NGS reagents

Studying virus genomes with next generation sequencing (NGS) can provide valuable information about viral spread and evolution. Targeted NGS is a valuable tool for both detection and characterization of viruses. Using very sensitive and accurate assays, we can monitor virus evolution, infection progression, and immune response. Hybridization capture and amplicon sequencing are both NGS techniques that are being used to fight SARS‑CoV‑2. We offer solutions to get researchers started using targeted NGS, featuring high performance and reproducibility, fast turnaround time, and endless customization and scalability.

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Amplicon sequencing

Amplicon sequencing is a type of targeted next generation sequencing that uses PCR to create sequences of DNA called amplicons. It is simple, fast, and has a variety of applications.

Tools to sequence the virus are available through ARTICnetwork, a network of researchers that are developing a system for processing virus samples to generate public health information [1–3]. ARTIC provides a detailed protocol to quickly and accurately sequence SARS‑CoV‑2, featuring a set of primers for amplicon sequencing. We have partnered with ARTIC to produce a bulk set of these primers, which ensures availability and reproducibility.

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.
Dr Joshua Quick, University of Birmingham, ARTICnetwork

For more information about ARTIC's work on SARS‑CoV‑2, click here.

The rhAmpSeq™ amplicon sequencing system is another amplicon sequencing method that enables rapid and accurate detection of viral genomes. The rhAmpSeq system’s combined specificity and multiplexing capabilities can be used to identify viral infection and study viral mutations.

Hybridization capture

RNA viruses like SARS‑CoV‑2 acquire slight mutational changes during the transmission cycle. These mutations can be tracked using very sensitive xGen™ hybridization capture sequencing to investigate viral spread and evolution. xGen hybridization capture is a targeted NGS method that uses long, biotinylated oligonucleotide baits (probes) to hybridize to regions of interest. It is particularly helpful for enriching viral genomes when sequencing a sample that also contains genetic material from the host and other microbes.

SARS‑CoV‑2 is being tracked by a team of researchers from NYU Grossman School of Medicine, lead by Dr Adriana Heguy.

DNA baits are essential to our work, helping us capture human exome sequences and other specific targeted areas of the human genome. From the beginning, as we were designing the library prep and sequencing strategy for the SARS-CoV-2 viral genome sequencing, we sought to use specific baits to fish out this viral genome from our patient samples. IDT has been an invaluable partner in this research effort to ‘capture’ this viral genome, accelerating our sequencing efforts and making them more cost-effective.
Dr Adriana Heguy, NYU Grossman School of Medicine

To learn more about how Dr Adriana Heguy is researching SARS-CoV-2, click here.

Preferred sequencing provider

Washington University in St Louis (WashU) is a part of the IDT Align℠ Preferred Partner Program. Through the McDonnell Genome Institute (MGI), WashU has been a long-standing collaborator with IDT and is committed to bringing you quality data and services. With multiple sequencing platforms at their disposal and access to all IDT NGS products, WashU is standing by to provide sequencing and preparation services for researchers, using their highly efficient, scalable research pipeline.

To learn more about WashU services, click here.

References

  1. Fauver JR, Petrone ME, et al. (2020) Coast‑to‑coast spread of SARS‑CoV‑2 in the United States revealed by genomic epidemiology. medRxiv: 2020.2003.2025.20043828.
  2. Lu J, Plessis Ld, et al. (2020) Genomic epidemiology of SARS‑CoV‑2 in Guangdong Province, China. medRxiv: 2020.2004.2001.20047076.
  3. Itokawa K, Sekizuka T, et al. (2020) A proposal of alternative primers for the ARTIC Network’s multiplex PCR to improve coverage of SARS‑CoV‑2 genome sequencing. bioRxiv: 2020.2003.2010.985150.