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Distinguish one virus within a crowd

Virus replication and competition produces a complex mixture of variants within each infected host. Resolution of all the variants within a population is critical to understanding evolution, quasispecies dynamics, drug-resistance, and immune escape. Distinguishing variants that may differ by only a handful of SNPs across an entire genome requires both the high accuracy and long read lengths that only SMRT Sequencing can provide.

Confident and complete resolution of viral diversity

Single Molecule, Real-Time (SMRT) Sequencing produces amplicon sequencing reads that average up to 100 kb in length, providing an unprecedented view of complete viral genes and genomes. Highly accurate, single-molecule consensus reads enable direct detection of phased variants, giving you the ability to:

  • Deconvolute complex mixtures into quasispecies and unique haplotypes
  • Track the evolution and phylogeny of viral populations
  • Identify and quantify minor variants
  • Generate complete de novo assemblies of large viral genomes

Workflow: from DNA to resolved viral populations

 

Sample & Library Preparation
Obtain targeted sequences with flexible sample and library workflows.

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Sequencing
Scale coverage based on your project needs and achieve up 500,000 high-accuracy reads per SMRT Cell 1M on the Sequel System.

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Data Analysis
Make discoveries using bioinformatics tools in SMRT Analysis or PacBio DevNet.

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Spotlight: SMRT Sequencing of full-length HIV env reveals complete compartmentalization of variants in brain versus all other tissues

Phylogenetic analysis of high-quality consensus reads shows that brain-derived viruses are compartmentalized and evolutionarily distinct from virus in tissues outside the brain. By generating thousands of full-length HIV env sequences in a single run, the authors definitively show that virus in each of the three brain tissues studied is genetically distinct, whereas variants from all peripheral tissues are dispersed throughpout the tree. Explore this research further:

Brese, R. L., et al. (2018). Ultradeep single-molecule real-time sequencing of HIV envelope reveals complete compartmentalization of highly macrophage-tropic R5 proviral variants in brain and CXCR4-using variants in immune and peripheral tissues. Journal of Neurovirology, ePub ahead of print.

To learn more about how to resolve your viral populations, contact us.

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