Next-Generation Sequencing Center for GHOSTing Hepatitis C Virus: Transforming Community Based Molecular Surveillance and Outbreak Investigation

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PROJECT SUMMARY: The United States is in the midst of an enormous opioid epidemic. In 2015, more than 52,000 American's died due to a drug overdose, over 60% of which were associated with prescription or illicit opioid use. Given that injection drug use remains the major risk factor for HCV transmission, concomitantly the US has observed a striking >150% increase in the incidence of HCV between 2010-2013, and a 364% increase in new HCV infections between 2006 and 2012 in four Appalachian states, most notably in rural areas. As such, there is urgent need to more strategically detect, prevent, treat and control HCV on a national level. This U24 application proposes to develop a centralized GHOST laboratory to generate high-quality, high- throughput HCV NGS data for the CDC's GHOST center and accompanying clinical research sites to aid in the identification of HCV transmission links among persons who inject drugs (PWID); manage the collection and storage of serum samples from HIV- and HCV-infected participants from the clinical research sites under RFA- DA-17-014; and ship specimens to the CDC for syphilis testing and phylogenetic mapping for HIV and HCV. This proposal builds on the investigators' strong track record in generating large-scale Sanger and next- generation sequencing (NGS) data for highly variable pathogens such as HCV and HIV, development and maintenance of robust SOPs for reducing contamination and sample mix-up in large-scale NGS projects, and the development of robust NGS analysis platforms to enable real-time curation and storage of NGS data, downstream variant calling, and phylogenetic analysis. Dr. Allen's laboratory at the Ragon Institute of MGH, MIT and Harvard has been sequencing the highly variable pathogens HIV, HCV and SIV over the last 15 years during which time he has developed a well-established physical laboratory to support all stages of the laboratory process. He has also served as the PI of several viral sequencing cores on NIH/NIAID U01, U19 and P01 project grants during this time, thus providing extensive experience related to the cost-effective generation, curation, analysis, and deposition of sequence data for viral pathogens.