GHOST: global hepatitis outbreak and surveillance technology

BMC Genomics

Software

Victor Bolet¹  Chris Lynberg²  Yury Khudyakov³  Lilia Ganova-Raeva³  Zoya Dimitrova³  Hong Thai³  Magdalena Medrzycki³  David S. Campo³  Lili T. Punkova³  Sumathi Ramachandran³  Yulin Lin³  Amanda Sue³  Inna Rytsareva³  Pavel Skums⁴  Seth Sims⁵  Atkinson G. Longmire⁶  Thom Sukalac⁷  Silver Wang⁸  Massimo Mirabito⁸  Robin Tracy⁸ 

[1] Centers for Disease Control and Prevention, ITSO Application Hosting Branch, Atlanta, USA;IT Research and Development Office, Centers for Disease Control and Prevention, Atlanta, USA;Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, USA;Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, USA;Department of Computer Science, Georgia State University, Atlanta, USA;Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, USA;Department of Computer Science, Georgia State University, Atlanta, USA;Northrop Grumman Corporation, Falls Church, USA;Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, USA;Northrop Grumman Corporation, Falls Church, USA;NCHHSTP Informatics Office, Centers for Disease Control and Prevention, Atlanta, USA;NCHHSTP Informatics Office, Centers for Disease Control and Prevention, Atlanta, USA;Northrop Grumman Corporation, Falls Church, USA;

关键词: HVR1;    HCV;    Liver cancer;    Threshold;    Transmission;    Outbreak detection;    Surveillance;    Public health;    Cloud;    Virtual diagnostics;   

DOI  :  10.1186/s12864-017-4268-3

来源: Springer

【 摘 要 】

BackgroundHepatitis C is a major public health problem in the United States and worldwide. Outbreaks of hepatitis C virus (HCV) infections associated with unsafe injection practices, drug diversion, and other exposures to blood are difficult to detect and investigate. Effective HCV outbreak investigation requires comprehensive surveillance and robust case investigation. We previously developed and validated a methodology for the rapid and cost-effective identification of HCV transmission clusters. Global Hepatitis Outbreak and Surveillance Technology (GHOST) is a cloud-based system enabling users, regardless of computational expertise, to analyze and visualize transmission clusters in an independent, accurate and reproducible way.ResultsWe present and explore performance of several GHOST implemented algorithms using next-generation sequencing data experimentally obtained from hypervariable region 1 of genetically related and unrelated HCV strains. GHOST processes data from an entire MiSeq run in approximately 3 h. A panel of seven specimens was used for preparation of six repeats of MiSeq libraries. Testing sequence data from these libraries by GHOST showed a consistent transmission linkage detection, testifying to high reproducibility of the system. Lack of linkage among genetically unrelated HCV strains and constant detection of genetic linkage between HCV strains from known transmission pairs and from follow-up specimens at different levels of MiSeq-read sampling indicate high specificity and sensitivity of GHOST in accurate detection of HCV transmission.ConclusionsGHOST enables automatic extraction of timely and relevant public health information suitable for guiding effective intervention measures. It is designed as a virtual diagnostic system intended for use in molecular surveillance and outbreak investigations rather than in research. The system produces accurate and reproducible information on HCV transmission clusters for all users, irrespective of their level of bioinformatics expertise. Improvement in molecular detection capacity will contribute to increasing the rate of transmission detection, thus providing opportunity for rapid, accurate and effective response to outbreaks of hepatitis C. Although GHOST was originally developed for hepatitis C surveillance, its modular structure is readily applicable to other infectious diseases. Worldwide availability of GHOST for the detection of HCV transmissions will foster deeper involvement of public health researchers and practitioners in hepatitis C outbreak investigation.

【 授权许可】

CC BY   
© The Author(s). 2017