ArticleBMC genomics2017
GHOST: global hepatitis outbreak and surveillance technology.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
32 citing papers in PubMed, 52 citations in OpenAlex.
- Genomic surveillance uncovers regional variation in HCV transmission networks in rural United States.Nature communications · 2025Article
- Viral Hepatitis Surveillance in the United States: Then, Now, and Looking Forward.Public health reports (Washington, D.C. : 1974) · 2025Article
- A graph homomorphism approach for unraveling histories of metastatic cancers and viral outbreaks under evolutionary constraints.Nature communications · 2025Article
- A healthcare-associated outbreak of hepatitis C virus infections attributable to tampering injectable anaesthetic opioids, South Germany, 2017-2018.Frontiers in public health · 2025Article
- Model-inferred timing and infectious period of the chickenpox outbreak source.BMC infectious diseases · 2024Article
- Widespread hepatitis C virus transmission network among people who inject drugs in Kenya.International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2024Article
- HCV prevalence and phylogenetic characteristics in a cross-sectional, community study of young people who inject drugs in New York City: Opportunity for and threats to HCV elimination.Health science reports · 2024Article
- Validation of dried blood spots for capturing hepatitis C virus diversity for genomic surveillance.Journal of viral hepatitis · 2024Article
- Article
- SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework.Cell systems · 2022Article
- Identification of Genetically Related HCV Infections Among Self-Described Injecting Partnerships.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2022Article
- Primary case inference in viral outbreaks through analysis of intra-host variant population.BMC bioinformatics · 2022Article
- Article
- Next-generation sequencing studies on the E1-HVR1 region of hepatitis C virus (HCV) from non-high-risk HCV patients living in Punjab and Khyber Pakhtunkhwa, Pakistan.Archives of virology · 2021Article
- MicrobeTrace: Retooling molecular epidemiology for rapid public health response.PLoS computational biology · 2021Article
- Transmission Dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 in High-Density Settings, Minnesota, USA, March-June 2020.Emerging infectious diseases · 2021Article
- Hepatitis C Virus Transmission Clusters in Public Health and Correctional Settings, Wisconsin, USA, 2016-2017Emerging infectious diseases · 2021Article
- Epidemiological data analysis of viral quasispecies in the next-generation sequencing era.Briefings in bioinformatics · 2021Review
- Quantitative differences between intra-host HCV populations from persons with recently established and persistent infections.Virus evolution · 2021Article
- Convex hulls in hamming space enable efficient search for similarity and clustering of genomic sequences.BMC bioinformatics · 2020Article
Corrections and comments
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Authors and funding
20 authors at 4 institutions in 1 country.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.