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Approximately 20% of hepatitis C virus (HCV) infected individuals clear the virus. Host factors that influence the course of HCV infection are still under investigation, and the data on the association of human leukocyte antigen (HLA) alleles and HCV clearance are scarce and controversial. The aims of this study were to investigate whether HLA alleles are associated with clearance of HCV infection in a highly admixed Brazilian population and whether these associations could be influenced by ethnicity and route of infection. HLA-A, -B, -C, -DRB1 and -DQB1 genotyping were performed in 135 HCV-infected Brazilian patients among which 45 cleared HCV infection (cases) and 90 had persistent viral infection (controls). Controls were matched by sex, ethnicity (withes and non-whites) and route of infection (high infectious dose or low infectious dose). No significant association was identified between HLA alleles and the outcome of HCV infection when analyzing the sample as a single group. However, a new protective association of HLA-DQB1*04 (P = 0.006; Pc = 0.030) and a rarely described association of HLA-DRB1*08 (P = 0.004; Pc = 0.048) were found only among white patients. The DRB1*11 allele, previously reported in homogeneous population, was associated with HCV clearance (P = 0.020) only among patients with expected high-dose exposure. These findings confirm the influence of ethnicity on the associations of HLA with spontaneous viral clearance of HCV infection and emphasize the possible influence of route of infection in this process.