Viral Whole-Genome Resequencing

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Viral Whole-Genome Resequencing

Although the application of viral genome resequencing is progressing slowly, it can enhance the power of molecular epidemiology and thus accelerate the development of new therapies and vaccines. Here, using short-read (Illumina) and long-read sequencing (PacBio SMRT), CD Genomics is providing a robust and flexible viral genome resequencing service.

Why Need Long Reads to Study Viral Genomes?

Viral mutation clade layout by radial diagram.

The emergence of new viral pathogens poses serious health problems for animals and humans as issues such as globalization and climate change intensify. As intracellular parasites, viruses are characterized by a high replication rate and a high mutation rate in their host. In this way, new genomes containing mutations are continuously generated and selected. Among them, RNA viruses have the highest mutation rate, with an average mutation rate of 10-4 ~10-5 errors per nucleotide copied. Additionally, recombination of genomic parts as another evolutionary driver further increases genomic differentiation of viral populations. Due to the high mutation and recombination rates of many viruses, the population structure can have a dominant variant with only a small percentage of rare variants, or it can consist of a highly diverse set of closely related variants called quasispecies. Thanks to low sequencing background bias and accurate reads mapping, PacBio SMRT sequencing (HiFi reads) allows researchers to fully characterize all variants in the viral population, not just the dominant ones. The identification and monitoring of novel virus variants help to understand viral diversity, which is essential for predicting future transmission risks or possible viral disease outbreaks.

With rapid and accurate sequencing of the viral genome, it is possible to,

  • Track and investigate outbreaks prevalence, and distribution of viruses.
  • Confirm viral transmission routes.
  • Detect and identify all known and new drug-resistant variants.

Sample Requirements

  1. Sample Type: Genomic DNA/cDNA, OD260/280=1.8~2.0, no degradation and no contamination.
  2. Viral DNA amount:
    -Illumina platform: ≥ 1 μg.
    -PacBio platform: ≥ 5 μg.

Viral Whole-Genome Resequencing Analysis Workflow

Viral Whole-Genome Resequencing Analysis Workflow-CD Genomics.

Analysis Contents

Standard Analysis Advanced Analysis
-Assemble viral samples against a reference sequence
-Evaluate variants and export consensus sequences
-Align consensus sequences to known strains
-Viral genetic variant identification, annotation, and statistics
-Comparative Genomics Analysis
-Phylogenetic analysis
-Customized analysis

Application of Our Viral Whole-Genome Resequencing

  • The study of viral epidemiology, including the origin and spread of the virus.
  • The study of viral genome diversity.
  • The study of virus evolution.
  • The investigation of viral genetic association with disease.

Since viruses are fast-evolving, rapid and accurate sequencing of viral genomes is particularly important. Our whole-genome resequencing analysis workflow is robust and available for various viral samples. More importantly, we provide end-to-end and customized services according to our global customers' specific project requirements, cycle time, and budget. For more information about our services, please just complete the inquiry form below.


  1. Houldcroft, C. J., et al. (2017). "Clinical and biological insights from viral genome sequencing." Nature Reviews Microbiology, 15(3), 183-192.
For Research Use Only. Not for use in diagnostic procedures.

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