Biospecimen Analysis

The Biospecimen Analysis Core (BAC) of our Vanderbilt-coordinated human Virome Characterization Center (V2C2) is designed to enable the composition and complexity of a host-contextualized human virome (replicating and integrated) to be rapidly and cost-effectively generated with high-quality across multiple tissue types. In Aim 1, the BAC will receive and characterize the virome across a range of biospecimen types from our Biospecimen Collection Core (BCC). This process will include viral sequencing (whole metagenomics/metatranscriptomic sequencing), validation studies (digital PCR and capture-based methods, among them), and host response characterization, including tropism studies (via bulk and single-cell RNA-seq approaches, in vitro infection studies) and assessments of host inflammatory state (targeted proteomics). In Aim 2, the BAC will establish standard operating procedures for metadata, analytics, and quality control and assessment, including consortium-wide benchmarking and reproducibility of critical assays to investigate and limit variability from the collection point to the final analysis. The BAC will synergize with all other V2C2 cores via (1) scientific counsel to the administrative core and the wider HVP on the development of new technologies based on HVP results to enable viral screening at the epidemiologic scale; (2) enabling collaborative projects with other HVP efforts (e.g., tropism studies with Functional Interactions projects; RFA-RM-23-017), augmenting essential human translational biology in the HVP. Our BCC has several fundamental strengths that ensure success, including: (1) leadership structure with extensive expertise in large epidemiologic efforts: Dr. Simon Mallal (a renowned physician-scientist who works on viral-host co-evolution and genetic interactions, Director of the Vanderbilt VANTAGE sequencing core), Dr. Jane Freedman (a leader in sequencing and proteomics and large NIH studies, including Common Fund efforts), and Dr. Suman Das (a human molecular virologist with extensive experience in methods development and discovery in human virology), all of whom have a track-record of collaboration in large NIH-funded human studies; (2) deep expertise in viral sequencing: Dr. Das and Mallal have sequenced many classes of human viruses (e.g., influenza, RSV, HIV, HCV, HBV, EBV, enteroviruses, rotavirus, norovirus, Ebola, Zika, coronaviruses, resulting in >400K Genbank accessions); (3) expertise in methods development in metagenomics: in this process, they have developed many new laboratory and computational methods enabling capture of the human virome (replicating eukaryotic RNA/DNA viruses and phages) and host integration; (5) rapid assessment of host response characteristics (including mucosal immunity, relation with other commensal microbial flora, and emerging types for characterization [e.g., extracellular vesicles, platelets, proteomics]); (6) large, NIH-funded core laboratory structures that enable cost-efficient BAC conduct (e.g., NHLBI TOPMed 2.0 Core; Vanderbilt resources led PD Mallal/PI Das). Successful completion will provide HVP with a comprehensive host-viral characterization for consortium-wide integration.