title: Inference with viral quasispecies diversity indices: clonal and NGS approaches.
abstract: Given the inherent dynamics of a viral quasispecies, we are often interested in the comparison of diversity indices of sequential samples of a patient, or in the comparison of diversity indices of virus in groups of patients in a treated versus control design. It is then important to make sure that the diversity measures from each sample may be compared with no bias and within a consistent statistical framework. In the present report, we review some indices often used as measures for viral quasispecies complexity and provide means for statistical inference, applying procedures taken from the ecology field. In particular, we examine the Shannon entropy and the mutation frequency, and we discuss the appropriateness of different normalization methods of the Shannon entropy found in the literature. By taking amplicons ultra-deep pyrosequencing (UDPS) raw data as a surrogate of a real hepatitis C virus viral population, we study through in-silico sampling the statistical properties of these indices under two methods of viral quasispecies sampling, classical cloning followed by Sanger sequencing (CCSS) and next-generation sequencing (NGS) such as UDPS. We propose solutions specific to each of the two sampling methods-CCSS and NGS-to guarantee statistically conforming conclusions as free of bias as possible.
  
  
  
  josep.gregori@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
authors.affiliation: Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain.
authors.forename: Josep
authors.initials: J
authors.lastname: Gregori
authors.affiliation: Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain.
authors.forename: Miquel
authors.initials: M
authors.lastname: Salicrú
authors.affiliation: Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain.
authors.forename: Esteban
authors.initials: E
authors.lastname: Domingo
authors.affiliation: Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain.
authors.forename: Alex
authors.initials: A
authors.lastname: Sanchez
authors.affiliation: Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain.
authors.forename: Juan I
authors.initials: JI
authors.lastname: Esteban
authors.affiliation: Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain.
authors.forename: Francisco
authors.initials: F
authors.lastname: Rodríguez-Frías
authors.affiliation: Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain Liver Unit, Internal Medicine Lab Malalties Hepàtiques, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035 Barcelona, Spain, Roche Diagnostics SL, 08174, Sant Cugat del Vallès, Spain, Statistics Department, Biology Faculty, Barcelona University, 08028, Barcelona, Spain, CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco, 28049, Madrid, Spain, Bioinformatics and Statistics Unit, Vall d'Hebron Institut Recerca (VHIR-HUVH), 08035, Barcelona, Spain, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain and Biochemistry Unit. Virology Unit/Microbiology Department, HUVH, 08035 Barcelona, Spain.
authors.forename: Josep
authors.initials: J
authors.lastname: Quer
mesh_terms: D019295:Computational Biology; D014644:Genetic Variation; D016174:Hepacivirus / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D012367:RNA, Viral / Q000235:genetics; D017423:Sequence Analysis, RNA
chemical_list: D012367:RNA, Viral