VirScan: PhIP-Seq Antibody Profiling

Human virome epitope-level antiviral antibody profiling service via T7 phage display and immunonprecipitation sequencing

VirScan: PhIP-Seq Antibody Profiling

Human virome epitope-level antiviral antibody profiling service via T7 phage display and immunonprecipitation sequencing

THE ENTIRE UNIPROT HUMAN VIROME IN A SINGLE ASSAY

The collection of viruses found to infect humans (“the human virome”) can have profound effects on health. In addition to directly causing acute or chronic illness, viral infection can alter host immunity in more subtle ways, leaving an indelible footprint on the immune system.

ANTYGENVirScan™ service, developed by CDI’s Scientific Advisory Board Members Steve Elledge and Ben Larman, provides an unparalleled way to assay a patient’s viral history by comprehensively analyzing antiviral antibodies to a phage library displaying peptides from 206 species and over 1000 strains of viruses every virus annotated to have human tropism in the UniProt database. This product is available as a service to both academic and industry customers.

VirScan™ technical details.

The original VirScan PhIP-Seq library was created by downloading viral protein sequences from UniProt, using software to tile overlapping sequences, tuning tiled sequences for translation by the phages and their bacterial hosts, and then ordering the sequences as synthetic oligonucleotides from a vendor as described (Xu, et al, 2020). This oligonucleotide library was PCR-amplified with adaptors for cloning and inserted into a T7 phage display vector that was expanded in E. Coli. The expanded T7 phage library quality is confirmed by sequencing to have >90% of the library within one log of overall average clonal frequency. An aliquot from this library is then reacted with diluted patient serum or other antibody-containing fluid. Bound antibodies are immunoprecipitated with protein A/G beads, the precipitate amplified by PCR, and the sequences quantified by a next-generation sequencing and analysis pipeline that compares patient-sample IP read counts to negative controls with no antibody input (mock IPs) in the context of overall clonal frequency of individual peptides in the parent library. Output data are then created at both the peptide and whole-protein level. A more detailed description of this process is available (Mohan, et al, 2018).

VirScan™ service details & data deliverables.

A typical VirScan™ service involves case and control serum or plasma samples. These are heat deactivated and undergo a protein A/G pulldown assay, PCR amplification, and next-generation sequencing. Raw sequence data are run through a normalization and quantitation pipeline as previously described (Mohan et al., 2018).  Raw pipeline outputs are then provided to customers as normalized read counts data tables for both whole proteins and individual 56mer peptides.

VirScan™ service sample requirements.

Human serum or plasma only: Send two 20μL aliquots per sample.

Ten sample minimum.

Note: VirScan™ and HuScan™ assays can paired together in a single-well assay at a reduced cost.

VirScan™ service sample requirements.

Human serum or plasma only: Send two 20μL aliquots per sample.

Ten sample minimum.

Note: VirScan™ and HuScan™ assays can paired together in a single-well assay at a reduced cost.

Sample shipping & sample return.

We will include shipping details in your quote – you must cover the cost of shipping samples to CDI. Typically, after you receive your report, CDI keeps the remaining samples for two months and then disposes of them. When shipping to us, please let us know if you want the remaining samples returned after the study is complete. We will charge for return shipping.

Contact us to learn more.

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