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Open Access Research article

The mode and tempo of hepatitis C virus evolution within and among hosts

Rebecca R Gray12, Joe Parker3, Philippe Lemey4, Marco Salemi12, Aris Katzourakis5 and Oliver G Pybus5*

Author Affiliations

1 Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA

2 Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA

3 Kitson Consulting, Bristol, BS8 3UL, UK

4 Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Leuven, Belgium

5 Department of Zoology, Oxford University, South Parks Road, Oxford, OX1 3PS, UK

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BMC Evolutionary Biology 2011, 11:131  doi:10.1186/1471-2148-11-131

Published: 19 May 2011

Additional files

Additional file 1:

Table S1: Accession numbers and dates of sampling. Accession numbers and isolate sampling dates of all sequences used in this study.

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Additional file 2:

Figure S1: The G/C content at each codon position for three datasets. Three separate data sets are shown: among host subtype 1a (green), among host subtype 1b (blue) and within-host (red). Separate parameters were estimated for each of 21 partitions spanning the HCV coding region (see genome schematic and partition numbering at top of Figure). The alternating white and grey bars are for visual clarity only.

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Additional file 3:

Figure S2: Absolute rates for the 1st+2nd versus 3rd codon positions for each partition. Three separate data sets are shown: among host subtype 1a (green), among host subtype 1b (blue) and within-host (red). Squares represent the rate of the 1st+2nd positions, circles the 3rd position. The symbols are offset within each partition for visual clarity only. Separate parameters were estimated for each of 21 partitions spanning the HCV coding region (see genome schematic and partition numbering at top of Figure).

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