ArticleBioinformatics (Oxford, England)2018
QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 83 citations in OpenAlex.
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- Tracking cryptic SARS-CoV-2 hospital outbreak through quasispecies analysis.Virology journal · 2024Article
- Incipient functional SARS-CoV-2 diversification identified through neural network haplotype maps.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data.Nature communications · 2023Article
- Reconstruction of Viral Variants via Monte Carlo Clustering.Journal of computational biology : a journal of computational molecular cell biology · 2023Article
- Evaluating the potential of whole-genome sequencing for tracing transmission routes in experimental infections and natural outbreaks of bovine respiratory syncytial virus.Veterinary research · 2022Article
- Quasispecies Fitness Partition to Characterize the Molecular Status of a Viral Population. Negative Effect of Early Ribavirin Discontinuation in a Chronically Infected HEV Patient.International journal of molecular sciences · 2022Article
- Molecular source attribution.PLoS computational biology · 2022Article
- SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework.Cell systems · 2022Article
- Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification.PLoS computational biology · 2022Article
- Primary case inference in viral outbreaks through analysis of intra-host variant population.BMC bioinformatics · 2022Article
- The evolutionary dynamics and epidemiological history of hepatitis C virus genotype 6, including unique strains from the Li community of Hainan Island, China.Virus evolution · 2022Article
- Bacterial genomic epidemiology with mixed samples.Microbial genomics · 2021Article
- Scale-Free Spanning Trees and Their Application in Genomic Epidemiology.Journal of computational biology : a journal of computational molecular cell biology · 2021Article
- Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction.Nucleic acids research · 2021Article
- Precision Tracing of Household Dengue Spread Using Inter- and Intra-Host Viral Variation Data, Kamphaeng Phet, Thailand.Emerging infectious diseases · 2021Article
- Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts.PLoS pathogens · 2021Article
Corrections and comments
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Authors and funding
16 authors at 5 institutions in 1 country.
Funding
Abstract
Motivation: Genomic analysis has become one of the major tools for disease outbreak investigations. However, existing computational frameworks for inference of transmission history from viral genomic data often do not consider intra-host diversity of pathogens and heavily rely on additional epidemiological data, such as sampling times and exposure intervals. This impedes genomic analysis of outbreaks of highly mutable viruses associated with chronic infections, such as human immunodeficiency virus and hepatitis C virus, whose transmissions are often carried out through minor intra-host variants, while the additional epidemiological information often is either unavailable or has a limited use. Results: The proposed framework QUasispecies Evolution, Network-based Transmission INference (QUENTIN) addresses the above challenges by evolutionary analysis of intra-host viral populations sampled by deep sequencing and Bayesian inference using general properties of social networks relevant to infection dissemination. This method allows inference of transmission direction even without the supporting case-specific epidemiological information, identify transmission clusters and reconstruct transmission history. QUENTIN was validated on experimental and simulated data, and applied to investigate HCV transmission within a community of hosts with high-risk behavior. It is available at https://github.com/skumsp/QUENTIN. Contact: pskums@gsu.edu or alexz@cs.gsu.edu or rahul@sfsu.edu or yek0@cdc.gov. Supplementary information: Supplementary data are available at Bioinformatics online.
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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.