Resolve viral populations

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.

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Confident and complete resolution of viral diversity

HiFi sequencing provides 99.9% accurate reads from amplicons up to 20 kb, enabling direct detection of phased variants and giving you the ability to:

  • Deconvolute complex mixtures into quasispecies and unique haplotypes
  • Track the evolution and phylogeny of viral populations in a host, within a community, or across geographic regions
  • Identify and quantify minor variants linked to immune evasion or drug resistance
  • Generate complete de novo assemblies of large viral genomes

Workflow: from DNA to resolved viral populations

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Sample + library preparation

Obtain targeted sequences with flexible sample and library workflows.

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Scale coverage based on your project needs with the Sequel II System

  • Achieve 1.25 – 3 million HiFi reads per SMRT Cell 8M on a Sequel II System, depending on amplicon size
  • Maximize output and turn-around-time with adjustable run parameters
  • Choose 10 – 30 hr movie times based on amplicon or insert size

*Read lengths, number of reads, data per SMRT Cell, and other sequencing performance results vary based on sample quality/type and insert size, among other factors.

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Data analysis

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

Read our SMRT Analysis Barcoding Overview


HiFi reads reveal emergence of SARS-CoV-2 minor variants during acute infection

A longitudinal study of a person who ultimately recovered showed that spike variants resistant to autologous neutralizing antibodies arose transiently before being displaced by the original strain ahead of virus clearance. Application of the method to more diverse cohorts may reveal circumstances under which variants capable of immune escape emerge and persist.

Ko, S. H., et al. (2021) High-throughput, single-copy sequencing reveals SARS-CoV-2 spike variants coincident with mounting humoral immunity during acute COVID-19PLOS Pathogens. 17(4): e1009431.

Ko_2021_Plos Pathogen Figure 5a - PacBio


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 throughout 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, 24(4), 439-453.

Brese 2018

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Mapping the interplay of viral and host genomics with HiFi sequencing

Learn how you can use HiFi reads to enable your viral research, from understanding viral genomes to the host immune response.


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