This zip archive contains a fasta-formatted file of 2922 aligned half- and quarter-genome HCV sequences from 17 acute and 14 chronically infected study participants. The alignment file format is Nexus with MacClade extensions.
Hui Li, Mark B. Stoddard, Shuyi Wang, Lily M. Blair, Elena E. Giorgi, Erica H. Parrish, Gerald H. Learn, Peter Hraber, Paul A. Goepfert, Michael S. Saag, Thomas N. Denny, Barton F. Haynes, Beatrice H. Hahn, Ruy M. Ribeiro, Alan S. Perelson, Bette T. Korber, Tanmoy Bhattacharya, and George M. Shaw.
Elucidation of Hepatitis C Virus Transmission and Early Diversification by Single Genome Sequencing. In review, 2012.