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31 octobre 2020
- doi: 10.3390/v12111241
- issn: 1999-4915
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info:eu-repo/semantics/altIdentifier/doi/10.3390/v12111241
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info:eu-repo/semantics/altIdentifier/pmid/33142675
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info:eu-repo/semantics/altIdentifier/eissn/1999-4915
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info:eu-repo/semantics/altIdentifier/urn/urn:nbn:ch:serval-BIB_D73F11FC1FB68
info:eu-repo/semantics/openAccess , CC BY 4.0 , https://creativecommons.org/licenses/by/4.0/
Mots-clés
genetic variation; hepatitis C virus infection; infection recency; sequence analysis; viral genomicsSujets proches
Infectious diseasesCiter ce document
L.A. Carlisle et al., « HCV Genetic Diversity Can Be Used to Infer Infection Recency and Time since Infection. », Serveur académique Lausannois, ID : 10.3390/v12111241
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Résumé
HIV-1 genetic diversity can be used to infer time since infection (TSI) and infection recency. We adapted this approach for HCV and identified genomic regions with informative diversity. We included 72 HCV/HIV-1 coinfected participants of the Swiss HIV Cohort Study, for whom reliable estimates of infection date and viral sequences were available. Average pairwise diversity (APD) was calculated over each codon position for the entire open reading frame of HCV. Utilizing cross validation, we evaluated the correlation of APD with TSI, and its ability to infer TSI via a linear model. We additionally studied the ability of diversity to classify infections as recent (infected for