Early in 2015, an outbreak of HIV-1 infection associated with injection of the prescription opioid oxymorphone was identified in Scott County, Indiana. The investigation revealed that the affected community had a high prevalence of hepatitis C virus (HCV) infection. To characterize the circulating HCV strains, molecular anlaysis of HCV from 492 specimens was conducted.
HCV strains were genotyped using phylogenetic analysis of NS5b sequences. To sample intra-host HCV variants (quasispecies), next generation sequencing (NGS) of the HCV hypervariable region 1 (HVR1) was performed. NGS HVR1 sequences were analyzed using Global Hepatitis Outbreak and Surveillance Technology (GHOST), a recently developed bioinformatics toolkit for inferring genetic relationships among HCV strains and graphically presenting HCV transmission networks.
Of the 492 HCV antibody reactive specimens, 334 (67.9%) were HCV-RNA positive, and the distribution of HCV genotypes included: 1a (69.8%), 1b (2.4%), 2b (5.1%), 3a (22.8%). Among the cases of HCV infection, 23% were co-infected with HIV. Phylogenetic analysis of the NS5b sequences identified one major cluster of genotype 1a strains (n=104) with >93% homology, and 2 clusters of the genotype 3a strains (n=46; n=8) with >94% and 95% homology, respectively. Of the 240 cases tested by GHOST, 70 (29%) were infected with >1 HCV strain, and 46 (19%) were infected with >1 HCV genotype. One person was infected with 5 strains of genotypes 1a, 1b, 3 and 6. NGS analyses identified a total of about 335 HCV strains, with 65% of the strains organized into 19 transmission clusters (median cluster size = 3). One major transmission cluster involved 92 cases (Fig.1: Orange nodes).
Fig.1: Network of transmission clusters identified by Global Hepatitis Outbreak and Surveillance Technology (GHOST). Clusters are color-coded; each node represents a case; size is proportional to HCV HVR1 heterogeneity. Links join cases with genetic distance below the relatedness threshold.
Co-circulation of a large number of HCV strains indicates multiple independent introductions of HCV to the community over a long period of time. Identification of a third of the tested cases infected with >1 HCV strain highlights longstanding endemicity of HCV infection in the community. A complex transmission network genetically detected by GHOST reveals continuous HCV dissemination, and provides a novel tool to supplement public health intervention efforts for identification and disruption o