Identification of Genetically Related HCV Infections Among Self-Described Injecting Partnerships

Abstract

Background: The current opioid epidemic across the United States has fueled a surge in the rate of new hepatitis C virus (HCV) infections among young persons who inject drugs (PWIDs). Paramount to interrupting transmission is targeting these high-risk populations and understanding the underlying network structures facilitating transmission within these communities.

Methods: Deep sequencing data were obtained for 52 participants from 32 injecting partnerships enrolled in the U-Find-Out (UFO) Partner Study, which is a prospective study of self-described injecting dyad partnerships from a large community-based study of HCV infection in young adult PWIDs from San Francisco. Phylogenetically linked transmission events were identified using traditional genetic-distance measures and viral deep sequence phylogenies reconstructed to determine the statistical support of inferences and the direction of transmission within partnerships.

Results: Using deep sequencing data, we found that 12 of 32 partnerships were genetically similar and clustered. Three additional phylogenetic clusters were found describing novel putative transmission links outside of the injecting relationship. Transmission direction was inferred correctly for 5 partnerships with the incorrect transmission direction inferred in more than 50% of cases. Notably, we observed that phylogenetic linkage was most often associated with a lower number of network partners and involvement in a sexual relationship.

Conclusions: Deep sequencing of HCV among self-described injecting partnerships demonstrates that the majority of transmission events originate from outside of the injecting partnership. Furthermore, these findings caution that phylogenetic methods may be unable to routinely infer the direction of transmission among PWIDs especially when transmission events occur in rapid succession within high-risk networks.

Keywords: deep sequencing; hepatitis C virus; injection drug use; molecular epidemiology; phylogenetic.

Figure 1.

Overview of the study population within the UFO partnership study. In total, 101 partnerships were enrolled and denoted as lines between individuals. Black lines represent those injecting partnerships in which the at-risk partner did not seroconvert. Red lines between study participants reflects those where a new HCV infection was observed in the at-risk partner. Abbreviations: HCV, hepatitis C virus; UFO, U-Find-Out.

Figure 2.

Maximum-likelihood phylogenetic tree showing phylogenetic clusters within the UFO partnership study for (A) Core-NS2 and (B) NS5B. Phylogenetic clusters defined by bootstrap analysis and genetic distance threshold are highlighted by a dashed line and labeled C1–14. Bootstrap supports values are only shown for nodes over 70%. Genotypes and subtypes are labeled respectively. Scale bar indicates the number of nucleotide substitutions per site. Abbreviation: UFO, U-Find-Out.

Figure 3.

Deep sequence phylogenetic data from injecting partnerships. A, Histogram shows the distribution between injecting partnerships of the minimum subgraph distance obtained using phyloscanner, this analysis included data from 19 self-described partnerships and 3 newly identified putative partnerships. Majority of clustered participants had minimum subgraph distance <0.05 substitutions per site (indicated with a dotted line). B, Subgraph distances calculated from deep sequencing phylogenies for Core to NS2 stratified in those phylogenetically linked and unlinked partnerships. Subgraph distances (y-axis) summarized for all analyzed deep sequence phylogenies for 19 self-described injecting partnerships in which index and at-risk partners have Core to NS2 or HVR sequence data available. Dotted line indicates the distance threshold of 0.05 substitutions per site to define those partnerships classified as phylogenetically close and linked and those phylogenetically distant and unlinked. RM0295 is not depicted as deep sequencing data was not available. Three clusters denoted as putative links as found in Figure 2 are also shown.

Figure 4.

Time between collection of index and partner samples among 32 sequenced self-described partnerships. Blue dots indicate those partnerships that are shown by phylogenetic means to be unlinked; red dots indicate those partnerships that are phylogenetic linked. Data are plotted in days between the collection time of the index and partner samples.

Figure 5.

Network representation of the UFO partnerships in which a new HCV infection occurred. Circles and connecting lines denote an injecting partnership in which a new infection occurred. Colored circles denote stage of infection (baseline RNA status) at time of enrollment; blue indicates that the participant was in the chronic stage of infection; red indicates that the participant was in the acute infection window as defined by anti-HCV negative and HCV RNA positive test results; and black indicates that the participant was HCV negative upon study enrollment. Colored lines denote different category membership; red indicates that an injecting partnership was confirmed by sequencing and phylogenetic analysis; black indicates that an injecting partnership was not confirmed by sequencing and phylogenetic analysis; gray lines indicate that an injecting partnership could not be evaluated due to a lack of sequence data for a participant. Phylogenetically defined clusters are labeled as indicated prior and correspond to those as depicted in Table 1 and Figure 2. A, Dyadic injecting partnerships in which HCV-infected individuals are only enrollment with one at-risk partner. B, Larger injecting networks in which infected individuals are linked to multiple index and partners. Abbreviations: HCV, hepatitis C virus; UFO, U-Find-Out.

Figure 6.

Phylogenetic relatedness of injecting partnerships, cluster size and sexual relationship. A, Proportion of injecting partnerships comparing those PWIDs who are in a dyadic relationship and those that share more than two at-risk partners plotted as a function of their phylogenetic status (linked vs unlinked). B, Proportion of injecting partnerships comparing whether an index and at-risk partner are engaged in a sexual or non-sexual relationship and their determined phylogenetic status. Abbreviation: PWID, person who injects drugs.