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. By combining high accuracy with long read lengths, HiFi sequencing can distinguish variants that may differ by only a handful of SNPs across an entire genome.
Confident and complete resolution of viral diversity
HiFi sequencing provides >99% 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
|Sample & Library Preparation|
|Obtain targeted sequences with flexible sample and library workflows.|
|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.
|Make discoveries using bioinformatics tools in SMRT Analysis or PacBio DevNet.|
Spotlight: 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-19. PLOS Pathogens. 17(4): e1009431.
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, 24(4), 439-453.
Learn how you can use HiFi reads to enable your viral research, from understanding viral genomes to the host immune response.
To learn more about how to resolve your viral populations, contact us.
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- Su, Bin et al. (2019) Detection of pretreatment minority HIV-1 reverse transcriptase inhibitor-resistant variants by ultra-deep sequencing has a limited impact on virological outcomes. The Journal of antimicrobial chemotherapy
- Lui, Wing-Yu et al. (2019) SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection. Emerging microbes & infections
- Jayaraman, Siddharth et al. (2019) Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. PLoS neglected tropical diseases
- Pinzone, Marilia Rita et al. (2019) Longitudinal HIV sequencing reveals reservoir expression leading to decay which is obscured by clonal expansion. Nature communications
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- Tai, Phillip WL et al. (2018) Adeno-associated virus genome population sequencing achieves full vector genome resolution and reveals human-vector chimeras Molecular therapy
- Paulk, Nicole K et al. (2018) Bioengineered AAV capsids with combined high human liver transduction in vivo and unique humoral seroreactivity. Molecular therapy
- Kumar, Venkatesh et al. (2019) Long-read amplicon denoising. Nucleic acids research
- Abrahams, Melissa-Rose et al. (2019) The replication-competent HIV-1 latent reservoir is primarily established near the time of therapy initiation. Science translational medicine
- Qin, Kai et al. (2019) CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection. PLoS pathogens
- Rossenkhan, Raabya et al. (2019) Combining Viral Genetics and Statistical Modeling to Improve HIV-1 Time-of-infection Estimation towards Enhanced Vaccine Efficacy Assessment. Viruses
- Umotoy, Jeffrey et al. (2019) Rapid and Focused Maturation of a VRC01-Class HIV Broadly Neutralizing Antibody Lineage Involves Both Binding and Accommodation of the N276-Glycan. Immunity
- Silver, Zachary A et al. (2019) A Highly Unusual V1 Region of Env in an Elite Controller of HIV Infection. Journal of virology
- Raghwani, Jayna et al. (2019) High-Resolution Evolutionary Analysis of Within-Host Hepatitis C Virus Infection. The Journal of infectious diseases
- Kaplan, Mark H et al. (2019) Structural variation of centromeric endogenous retroviruses in human populations and their impact on cutaneous T-cell lymphoma, Sézary syndrome, and HIV infection. BMC medical genomics
- Nao, Naganori et al. (2019) Consensus and variations in cell line specificity among human metapneumovirus strains. PloS one
- Mehta, Devang et al. (2019) Linking CRISPR-Cas9 interference in cassava to the evolution of editing-resistant geminiviruses. Genome biology
- Pauthner, Matthias G et al. (2019) Vaccine-induced protection from homologous tier 2 SHIV challenge in nonhuman primates depends on serum-neutralizing antibody titers. Immunity
- Paulk, Nicole K et al. (2018) Bioengineered viral platform for intramuscular passive vaccine delivery to human skeletal muscle. Molecular therapy
- Ramsay, Joshua D et al. (2018) Hepacivirus A infection in horses defines distinct envelope hypervariable regions and elucidates potential roles of viral strain and adaptive immune status in determining envelope diversity and infection outcome. Journal of virology
- Huang, Cindy et al. (2018) Towards Personalized Medicine: An Improved De Novo Assembly Procedure for Early Detection of Drug Resistant HIV Minor Quasispecies in Patient Samples. Bioinformation
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- Davidsson, Marcus et al. (2018) Molecular barcoding of viral vectors enables mapping and optimization of mRNA trans-splicing. RNA
- Knyazev, Sergey et al. (2018) CliqueSNV: Scalable reconstruction of intra-host viral populations from NGS reads BioRxiv
- Banga, Riddhima et al. (2018) Blood CXCR3+CD4 T cells are enriched in inducible replication competent HIV in aviremic antiretroviral therapy-treated individuals. Frontiers in immunology
- Yoon, Yeonsoo et al. (2018) Streamlined ex vivo and in vivo genome editing in mouse embryos using recombinant adeno-associated viruses. Nature communications
- Poster: Laird Smith, M. et al. (2016) An improved circular consensus algorithm with an application to detect HIV-1 Drug Resistance Associated Mutations (DRAMs)
- Poster: Hepler, N. Lance et al. (2016) An improved circular consensus algorithm with an application to detection of HIV-1 Drug-Resistance Associated Mutations (DRAMs)
- Poster: Brown, Michael et al. (2015) High-accuracy, single-base resolution of near-full-length HIV genomes.
- Poster: Murrell, Ben et al. (2015) Full-length env deep sequencing in a donor with broadly neutralizing V1/V2 antibodies.
- Poster: Brown, Michael et al. (2015) Sequencing complex mixtures of HIV-1 genomes with single-base resolution.
- Poster: Laird Smith, Melissa et al. (2015) Full-length HIV-1 env deep sequencing in a donor with broadly neutralizing V1/V2 antibodies.
- Levandoski, Michael (2020) Webinar: Geographic and Temporal Mapping of the SARS-CoV-2 Pandemic in the United States
- Ashby, Meredith and Laird-Smith, Melissa and Watson, Corey (2020) Webinar: Understanding SARS-CoV-2 and host immune response to COVID-19 with PacBio sequencing
- Gharbi, Karim (2020) Customer Experience: Advancing UK genomics research with the PacBio Sequel II System
- Schmutz, Jeremy and Conesa, Ana and Gharbi, Karim and Kuo, Richard (2020) Customer Experience: HiFi reads help scientists explore genomes and transcriptomes
- Ashby, Meredith (2020) Webinar: Opportunities for using PacBio Long-read sequencing for COVID-19 research
- (2020) Video: Introduction to PacBio highly accurate long-read sequencing
- Polson, Shawn (2019) User Group Meeting: New genotype to phenotype associations in viral metagenomes enabled by SMRT Sequencing
- Korlach, Jonas (2019) User Group Meeting: Sequencing chemistry & application updates
- (2017) Tutorial: Minor variant analysis [SMRT Link v5.0.0]
- Paulin, Lars (2017) AGBT Virtual Poster: Single-molecule sequencing reveals the presence of distinct JC polyomavirus populations in patients with progressive multifocal leukoencephalopathy
- (2017) Tutorial: Circular Consensus Sequence analysis application [SMRT Link v5.0.0]
- Application Brief: HiFiViral SARS-CoV-2 for COVID-19 whole genome sequencing – Best Practices (2021)
- SMRT Sequencing Brochure: Delivering highly accurate long reads to drive discovery in life science (2021)
- Informational Guide: Understanding accuracy in DNA sequencing (2020)
- Application Brochure: HiFi reads for highly accurate long-read sequencing (2020)
- Infographic: Mapping the interplay of viral and host genomics with HiFi sequencing (2020)
- PacBio Certified Service Providers (2020)
- Product Brochure: SMRT Link – Explore and analyze your data with confidence (2020)