Full-Genome Analysis of Hepatitis C Virus in Japanese and Non-Japanese Patients Coinfected With HIV-1 in Tokyo

Background: Acute hepatitis C virus (HCV) infection is increasing among HIV-1-infected individuals in Tokyo. Appropriate clinical management is needed. Setting: To delineate the epidemiological status of HCV transmission, we analyzed stocked plasma samples of HCV/HIV-1-coinfected patients seen at the largest referral center for HIV care in Tokyo. Methods: HCV full-genome sequences were amplified and determined using next-generation sequencing. HCV genotyping and phylogenetic and phylodynamic analyses of thus obtained sequences were performed and combined with the analysis of HIV-1 reverse transcriptase sequences. Results: HCV phylogenetic analysis identified 3 dense clusters containing cases of men who have sex with men (MSM) and injection drug users (IDUs). Most of the confirmed acute infection cases were included within these clusters, indicating that the clustered viruses are currently being actively transmitted among HIV-1-infected MSM and IDU. Phylodynamic analysis indicated population expansion of one of these clusters from 2006 to 2008, during which the largest number of HIV-1-infected MSM was diagnosed in Tokyo. HIV-1 reverse transcriptase sequences of HCV-coinfected patients included in the same clusters did not converge together and did not form clusters, but rather diverged in the area of subtype B in the phylogenetic tree, indicating that they acquired HCV infection from individuals different from those from whom they had acquired HIV-1 infection. It is considered that these MSM changed their sexual partners and that IDU changed their drug use groups. Conclusions: The results warrant careful monitoring of high-risk groups including MSM and IDU and early introduction of HCV treatment to prevent HCV epidemic.