The role of positive selection in hepatitis C virus. 
Hepatitis C virus (HCV) is a major health problem worldwide, infecting an estimated 170 million people.  In this study, we have employed a large data set of sequences (14,654 sequences from between 25 and 100 clone sequences per analyzed region and per patient) from 67 patients infected with HCV genotype 1 (23 subtype 1a and 44 subtype 1b).  For all patients, a sample prior to combined therapy with alpha interferon plus ribavirin was available, whereas for some patients additional samples after 6 or 12 months of treatment were also available.  Twenty-seven patients responded to treatment (12 subtype 1a and 15 subtype 1b) and forty patients did not respond to treatment (11 subtype 1a vs. 29 subtype 1b).  Two regions of the HCV genome were analyzed, one compressing the hypervariable regions (HVR1, HVR2 and HVR3) of the envelope 2 glycoprotein and another one including the interferon sensitive determining region (ISDR) and the V3 domain of the NS5A protein.  Previously (Cuevas, J.M., Torres-Puente, M., Jiménez-Hernández, N., Bracho, M.A., García-Robles, I., Wrobel, B., Carnicer, F., del Olmo, J., Ortega, E., Moya, A., González-Candelas, F., 2008b.  Genetic variability of hepatitis C virus before and after combined therapy of interferon plus ribavirin.  Plos One 3 (8), e3058), several amino acid positions in both regions analyzed were detected to be under positive selection.  Here, we have compared the amino acid composition of each positively selected position between responder and non-responder patients for both subtypes.  If we exclude some non-conclusive cases, no clear differences were detected in any case.  In conclusion, identifying specific positions as completely discriminatory of treatment response seems to be a difficult task.  Our results, in concordance with previous studies, suggest that HCV evasion strategies are more likely based on a global increased variability, which would yield combinations of mutations with an increased resistance, than on the fixation of specific amino acids conferring resistance to antiviral treatment or immune response.  In this sense, the particular systemic response from each patient could play an essential role in determining the outcome of the antiviral treatment.