Transmission of hepatitis C virus infection among younger and older people who inject drugs in Vancouver, Canada

Characterization of Acute HCV Infection and Transmission Networks in People Who Currently Inject Drugs in Catalonia: Usefulness of Dried Blood Spots

BACKGROUND AND AIMS

Accurate identification of recent HCV infections is critical for tracing the extent and mechanisms of ongoing transmission. We aimed to validate dried blood spot (DBS) samples for the assessment of Hepatitis C virus (HCV) genetic diversity and to determine epidemiological parameters including incidence, determinants of acute infection, and phylogenetic clustering in people who inject drugs (PWID).

APPROACH AND RESULTS

HCV nonstructural protein 5B next-generation sequencing was performed from plasma and/or DBS in 220 viremic PWID from the HepCdetect II study. No significant differences were found in consensus sequences or Shannon entropy (SE) intrahost diversity estimate between paired plasma/DBS specimens. SE values were used to identify acute infections with 93.3% sensitivity (95% CI, 0.81-1.06) and 95.0% specificity (95% CI, 0.88-1.02) in a set of well-defined controls. An acute HCV infection (either primary infection or reinfection) was detected in 13.5% of viremic participants and was associated with age ≤30 years (OR, 8.09), injecting less than daily (OR, 4.35), ≤5 years of injected drug use (OR, 3.43), sharing cocaine snorting straws (OR, 2.89), and being unaware of their HCV status (OR, 3.62). Annualized HCV incidence was estimated between 31 and 59/100 person-years. On phylogenetic analysis, 46.8% of viremic cases were part of a transmission pair or cluster; age ≤30 years (OR, 6.16), acute infection (OR, 5.73), and infection with subtype 1a (OR, 4.78) were independently associated with this condition.

CONCLUSIONS

The results obtained from plasma and DBS characterize PWID with acute infection and those involved in ongoing HCV transmission and allow estimating incidence from cross-sectional data. This information is critical for the design and assessment of targeted harm reduction programs and test-and-treat interventions and to facilitate monitoring of HCV elimination in this key population.

"I want to feel young again": experiences and perspectives of young people who inject drugs living with hepatitis C in Vancouver, Canada

OBJECTIVES

People who inject drugs (PWID) are disproportionately impacted by hepatitis C virus (HCV). Despite the availability and efficacy of direct-acting antiviral (DAA) HCV therapies, treatment rates remain low among PWID. Among PWID, those who are young (under age 30) experience high rates of HCV and also face distinct barriers to care. The objective of this study is to identify facilitators and barriers to navigating various facets of the HCV cascade of care, including DAA treatment access, among young PWID.

METHODS

We draw on data from in-depth, semi-structured interviews conducted between May and November 2019 with a sample of 11 young, street-involved PWID who have lived experience of HCV and who live in Metro Vancouver, Canada. Informed by a social constructivist epistemology, data were thematically analyzed using an equity-oriented theoretical framework.

RESULTS

Our analysis yielded two key themes. First, participants described facilitators to HCV care access, including individual factors (e.g., desire to be cured, knowledge of side effects) and healthcare and socio-contextual factors (e.g., peer supports, supportive youth-specific services). Second, participants described a contrasting set of barriers to HCV care access, including concerns over treatment side effects and (in)eligibility, complex healthcare system navigation, substance use- and housing-related stigma, and clinician gatekeeping of DAAs.

CONCLUSION

Findings from this study underscore the need for HCV-related knowledge-building efforts among young PWID and clinicians. Also needed are structural policy interventions to facilitate access to DAAs, including anti-stigma efforts, access to safe housing, and the scale-up of low-barrier youth-specific services and decentralized HCV care.

Will peer-based interventions improve hepatitis C virus treatment uptake among young people who inject drugs?

People who inject drugs (PWID) are disproportionately affected by hepatitis C virus (HCV) and have low rates of direct-acting antiviral (DAA) treatment uptake, despite universal coverage of the medication in most Canadian settings. Investigation into peer-based interventions as a means of improving treatment uptake has yielded promising results in adult PWID populations. In this commentary, we discuss the benefits and considerations of integrating peer-based interventions into HCV care for adolescent and young adult PWID living with HCV. Given that young PWID experience high transmission rates and account for most new infections, improving strategies for youth engagement with DAA treatment is critical. We describe how peer-based interventions can feature the unique importance of peer relationships in this period of life and provide a low-barrier way of delivering health promotion messages. In particular, we discuss the ability of peer-based interventions to reshape the narrative of HCV care in young PWID peer networks by empowering youth to share experiences and knowledge with others. We conclude by addressing knowledge gaps in the literature which must be filled in order to strengthen the impact of peer-based interventions on treatment uptake rates among young PWID.

HCV incidence is associated with injecting partner age and HCV serostatus mixing in young adults who inject drugs in San Francisco

BACKGROUND

HCV incidence is increasing in the US, notably among younger people who inject drugs (PWID). In a cohort of young adult (age<30 years) PWID in San Francisco we examined whether 'injecting partner mixing' factors, i.e. age of partner and knowledge of their HCV serostatus, were associated with HCV transmission.

METHODS

In 448 susceptible PWID studied prospectively. All participants were asked to report characteristics and behaviors they engaged in with up to 3 injecting partners defined as "people whom you injected the most with" in the past month". These partnerships did not specify that drugs or injecting equipment was shared. HCV incidence was estimated by age of up to 3 injecting partners, categorized as: (i) all <30; (ii) mixed-age (<&≥30); and (iii) all ≥30 years and perceived knowledge of the HCV status of participants' injecting partners' HCV status. Interaction was evaluated between partnership age categories and perceived HCV status of partners.

RESULTS

Between 2006-2018, overall HCV incidence (/100 person years observation [pyo]) was 19.4 (95% CI: 16.4, 22.9). Incidence was highest in those with mixed-age partnerships: 28.5 (95% CI: 21.8, 37.1) and those whose partners were all <30 (23.9; 95% CI: 18.8, 30.4), and lowest if partners were ≥30 (7.5; 95% CI: 4.8, 11.8). In a multivariable analyses adjusting for age, sex (of index), injection frequency, and injection partnership 'monogamy', we found evidence for an interaction: the highest HCV incidence was seen in PWID whose partners were all <30 and who knew at least one of their partners was HCV-positive (58.9, 95% CI: 43.3, 80.0; p<0.01).

CONCLUSIONS

Younger injectors are more likely to acquire HCV from their similarly-aged peers, than older injecting partners. Protective seroadaptive behavior may contribute to reduce incidence. These findings can inform new HCV prevention approaches for young PWID needed to curb the HCV epidemic.

Phylogenetic Methods Inconsistently Predict the Direction of HIV Transmission Among Heterosexual Pairs in the HPTN 052 Cohort

BACKGROUND

We evaluated use of phylogenetic methods to predict the direction of human immunodeficiency virus (HIV) transmission.

METHODS

For 33 pairs of HIV-infected patients (hereafter, "index patients") and their partners who acquired genetically linked HIV infection during the study, samples were collected from partners and index patients close to the time when the partner seroconverted (hereafter, "SC samples"); for 31 pairs, samples collected from the index patient at an earlier time point (hereafter, "early index samples") were also available. Phylogenies were inferred using env next-generation sequences (1 tree per pair/subtype). The direction of transmission (DoT) predicted from each tree was classified as correct or incorrect on the basis of which sequences (those from the index patient or the partner) were closest to the root. DoT was also assessed using maximum parsimony to infer ancestral node states for 100 bootstrap trees.

RESULTS

DoT was predicted correctly for both single-pair and subtype-specific trees in 22 pairs (67%) by using SC samples and in 23 pairs (74%) by using early index samples. DoT was predicted incorrectly for 4 pairs (15%) by using SC or early index samples. In the bootstrap analysis, DoT was predicted correctly for 18 pairs (55%) by using SC samples and for 24 pairs (73%) by using early index samples. DoT was predicted incorrectly for 7 pairs (21%) by using SC samples and for 4 pairs (13%) by using early index samples.

CONCLUSIONS

Phylogenetic methods based solely on the tree topology of HIV env sequences, particularly without consideration of phylogenetic uncertainty, may be insufficient for determining DoT.

Role of HCV Viremia in Corroborated HCV Transmission Events Within Young Adult Injecting Partnerships

Background

Hepatitis C virus (HCV), a major cause of morbidity and mortality, is common and rising among young persons who inject drugs (PWID). Reducing the level of viremia may be an intervention, yet the impact of viremia on HCV transmission is unknown.

Methods

We conducted a prospective study of injecting partnerships (Partner Study) of young adult (age < 30 years) PWID within the UFO Study, which enrolled those at risk for HCV or with seronegative viremic infection and up to 3 HCV RNA-positive regular injecting partners. We examined the level of HCV viremia and stage of infection in the HCV-positive partner in regression analyses of HCV transmission events that were corroborated via HCV phylogenetic linkage analyses.

Results

We enrolled 69 at-risk/acutely infected PWID. There were 25 new HCV infections (incidence rate, 35.9 per 100 person-years; 95% confidence interval [CI], 24.3-53.2 per 100 person-years); 12/25 (48%) were phylogenetically linked to at least 1 partner. We found no association between the infected partner's quantitative level of HCV viremia and likely transmission in multivariate analyses (adjusted odds ratio [AOR], 0.90; 95% confidence interval [CI], 0.55-1.46); however, seronegative viremic infection in the infected partner was associated with increased transmission (AOR, 28.02; 95% CI, 5.61-139.95).

Conclusions

The HCV viremia level was not associated with increased odds of transmission, yet acute HCV infection (seronegative viremic) was. Explanations include high-risk behavior during acute infection or missed fluctuations in viremia during acute infection. Both point to the need for frequent testing to detect new infection and attempt to prevent onward transmission.

Opioid agonist treatment and the process of injection drug use initiation

BACKGROUND

Opioid agonist treatment (OAT) is an effective biomedical intervention to manage opioid use disorder among persons who inject drugs (PWID). Preliminary evidence suggests that OAT may also disrupt the social communicability of injection drug use (IDU) practices by established PWID. We therefore aim to investigate the association between OAT enrollment and initiating others into IDU among PWID in Vancouver, Canada.

METHODS

Preventing Injecting by Modifying Existing Responses (PRIMER; NIDA DP2-DA040256-01) is a prospective multi-cohort study seeking to identify structural interventions that reduce the risk that PWID initiate others into IDU. The present analysis was conducted using data from a participating cohort of PWID in Vancouver, Canada, between December 2014 and May 2017. Multivariable logistic regression models were built to assess the association between reporting active (i.e., within the past six months) OAT enrollment and assisting others in injection initiation. A final model was determined using a manual stepwise approach whereby covariates were excluded if their removal altered the coefficient of interest by <5%.

RESULTS

Participants (n = 1740) were predominantly male (62.3%); 35.1% reported daily injecting (n = 611); 860 (49.4%) reported active OAT enrollment, and 80 (4.6%) reported recently providing injection initiation assistance. In a multivariable model, participants who reported active OAT enrollment had significantly lower odds of recently providing injection initiation assistance (Adjusted Odds Ratio = 0.52, 95% Confidence Interval: 0.31-0.87, P = 0.01).

CONCLUSION

Results suggest a protective association between OAT and the expansion of IDU practices among vulnerable populations, suggesting its potential use as 'addiction treatment as prevention.'

Increasing importance of European lineages in seeding the hepatitis C virus subtype 1a epidemic in Spain

BackgroundReducing the burden of the hepatitis C virus (HCV) requires large-scale deployment of intervention programmes, which can be informed by the dynamic pattern of HCV spread. In Spain, ongoing transmission of HCV is mostly fuelled by people who inject drugs (PWID) infected with subtype 1a (HCV1a).AimOur aim was to map how infections spread within and between populations, which could help formulate more effective intervention programmes to halt the HCV1a epidemic in Spain.MethodsEpidemiological links between HCV1a viruses from a convenience sample of 283 patients in Spain, mostly PWID, collected between 2014 and 2016, and 1,317, 1,291 and 1,009 samples collected abroad between 1989 and 2016 were reconstructed using sequences covering the NS3, NS5A and NS5B genes. To efficiently do so, fast maximum likelihood-based tree estimation was coupled to a flexible Bayesian discrete phylogeographic inference method.ResultsThe transmission network structure of the Spanish HCV1a epidemic was shaped by continuous seeding of HCV1a into Spain, almost exclusively from North America and European countries. The latter became increasingly relevant and have dominated in recent times. Export from Spain to other countries in Europe was also strongly supported, although Spain was a net sink for European HCV1a lineages. Spatial reconstructions showed that the epidemic in Spain is diffuse, without large, dominant within-country networks.ConclusionTo boost the effectiveness of local intervention efforts, concerted supra-national strategies to control HCV1a transmission are needed, with a strong focus on the most important drivers of ongoing transmission, i.e. PWID and other high-risk populations.

Hepatitis C virus reinfection after successful treatment with direct-acting antiviral therapy in a large population-based cohort

BACKGROUND & AIMS

Direct-acting antiviral therapies (DAA) are an important tool for hepatitis C virus (HCV) elimination. However, reinfection among people who inject drugs (PWID) may hamper elimination targets. Therefore, we estimated HCV reinfection rates among DAA-treated individuals, including PWID.

METHODS

We analyzed data from the British Columbia Hepatitis Testers Cohort which included ∼1.7 million individuals screened for HCV in British Columbia, Canada. We followed HCV-infected individuals treated with DAAs who achieved a sustained virologic response (SVR) and had ≥1 subsequent HCV RNA measurement to April 22nd, 2018. Reinfection was defined as a positive RNA measurement after SVR. PWID were identified using a validated algorithm and classified based on recent (<3 years) or former (≥3 years before SVR) use. Crude reinfection rates per 100 person-years (PYs) were calculated. Poisson regression was used to model adjusted incidence rate ratios (IRRs) and 95% CIs.

RESULTS

Of 4,114 individuals who met the inclusion criteria, most were male (n = 2,692, 65%), born before 1965 (n = 3,411, 83%) and were either recent (n = 875, 21%) or former PWID (n = 1,793, 44%). Opioid-agonist therapy (OAT) was received by 19% of PWID. We identified 40 reinfections during 2,767 PYs. Reinfection rates were higher among recent (3.1/100 PYs; IRR 6.7; 95% CI 1.9-23.5) and former PWID (1.4/100 PYs; IRR 3.7; 95% CI 1.1-12.9) than non-PWID (0.3/100 PYs). Among recent PWID, reinfection rates were higher among individuals born after 1975 (10.2/100 PYs) and those co-infected with HIV (5.7/100 PYs). Only one PWID receiving daily OAT developed reinfection.

CONCLUSIONS

Population-level reinfection rates remain elevated after DAA therapy among PWID because of ongoing exposure risk. Engagement of PWID in harm-reduction and support services is needed to prevent reinfections.

LAY SUMMARY

Direct-acting antivirals are an effective tool for the treatment of hepatitis C virus, enabling the elimination of the virus. However, some patients who have been successfully treated with direct-acting antivirals are at risk of reinfection. Our findings showed that the risk of reinfection was highest among people with recent injection drug use. Among people who inject drugs, daily use of opioid-agonist therapy was associated with a lower risk of reinfection.

Relapse or reinfection after failing hepatitis C direct acting antiviral treatment: Unravelled by phylogenetic analysis

Despite high response rates associated to hepatitis C virus (HCV) treatment, no protective immunity is acquired, allowing for reinfection and continued infectiousness. Distinguishing between relapse and reinfection is crucial for patient counselling and to choose the most appropriate retreatment. Here, refined phylogenetic analysis using multiple genes served to assess genotype and reinfection for 53 patients for whom the virus was sampled before start of therapy and at time of sustained virological response evaluation at week 12. At baseline, genotypes were determined as HCV1a (41.5%), HCV1b (24.5%), HCV4 (18.9%) and HCV3a (15.1%), while six cases revealed to be discordantly assigned by phylogeny and commercial assays. Overall, 60.4% was co-infected with HIV. The large majority was classified as people who inject drugs (78.6%), often co-infected with HIV. Transmission was sexual in seven cases, of which five in HIV-positive men-who-have-sex-with-men. Overall, relapse was defined for 44 patients, while no conclusion was drawn for four patients. Five patients were reinfected with a different HCV strain, of which three with a different genotype, showing that phylogeny is needed not only to determine the genotype, but also to distinguish between relapse and intra-subtype reinfection. Of note, phylogenies are more reliable when longer fragments of the viral genome are being sequenced.

Drug use and phylogenetic clustering of hepatitis C virus infection among people who use drugs in Vancouver, Canada: A latent class analysis approach

This study estimated latent classes (ie, unobserved subgroups in a population) of people who use drugs in Vancouver, Canada, and examined how these classes relate to phylogenetic clustering of hepatitis C virus (HCV) infection. HCV antibody-positive people who use drugs from two cohorts in Vancouver, Canada (1996-2012), with a Core-E2 sequence were included. Time-stamped phylogenetic trees were inferred, and phylogenetic clustering was determined by time to most common recent ancestor. Latent classes were estimated, and the association with the phylogenetic clustering outcome was assessed using an inclusive classify/analyse approach. Among 699 HCV RNA-positive participants (26% female, 24% HIV+), recent drug use included injecting cocaine (80%), injecting heroin (70%), injecting cocaine/heroin (ie, speedball, 38%) and crack cocaine smoking (28%). Latent class analysis identified four distinct subgroups of drug use typologies: (i) cocaine injecting, (ii) opioid and cocaine injecting, (iii) crack cocaine smoking and (iv) heroin injecting and currently receiving opioid substitution therapy. After adjusting for age and HIV infection, compared to the group defined by heroin injecting and currently receiving opioid substitution therapy, the odds of phylogenetic cluster membership was greater in the cocaine injecting group (adjusted OR [aOR]: 3.06; 95% CI: 1.73, 5.42) and lower in the crack cocaine smoking group (aOR: 0.06; 95% CI: 0.01, 0.48). Combining latent class and phylogenetic clustering analyses provides novel insights into the complex dynamics of HCV transmission. Incorporating differing risk profiles associated with drug use may provide opportunities to further optimize and target HCV treatment and prevention strategies.

Complex patterns of Hepatitis-C virus longitudinal clustering in a high-risk population

We investigated longitudinal viral clustering among and within subjects in a highly networked cohort of people who inject drugs (PWID). All subjects had estimated dates of infection and two or more E1 sequences (bp 943-1288 relative to H77) with 1 to 14years of follow up. Two methods (HIV-TRACE and PhyloPart) were used to determine clusters. Genetic distance thresholds were determined by comparing intra-and inter-host distances. Additional phylogenetic analysis was performed on subjects with complicated viral histories. At the optimal threshold of 3.9%, HIV-TRACE found 77 clusters and PhyloPart found 63 clusters, of which 27 and 32 contained multiple subjects, respectively. Furthermore, 1/3 of the subjects had sequences in different clusters over the course of the study, including some cases in which a later-sampled sequence matched a cluster detected much earlier in the infection, despite being separated by RNA-negative lab visit and detection of sequences in different clusters. A detailed phylogenetic analysis of four subjects with such patterns showed that in all four cases, the earlier and later variants grouped closely on the tree, and did not group with concurrent sequences from any other subject. These observations suggest that subjects are either experiencing rapid and recurring infection-clearance-reinfection cycles from the same source, or a single transmission event produces a chronic infection that may go undetected and/or co-circulate with different viruses from separate transmission events. Furthermore, our results show the utility of using longitudinal sampling to obtain a more comprehensive view of the viral linkages in high-risk populations.

Defining HIV-1 transmission clusters based on sequence data

Understanding HIV-1 transmission dynamics is relevant to both screening and intervention strategies of HIV-1 infection. Commonly, HIV-1 transmission chains are determined based on sequence similarity assessed either directly from a sequence alignment or by inferring a phylogenetic tree. This review is aimed at both nonexperts interested in understanding and interpreting studies of HIV-1 transmission, and experts interested in finding the most appropriate cluster definition for a specific dataset and research question. We start by introducing the concepts and methodologies of how HIV-1 transmission clusters usually have been defined. We then present the results of a systematic review of 105 HIV-1 molecular epidemiology studies summarizing the most common methods and definitions in the literature. Finally, we offer our perspectives on how HIV-1 transmission clusters can be defined and provide some guidance based on examples from real life datasets.

"Getting out of downtown": a longitudinal study of how street-entrenched youth attempt to exit an inner city drug scene

BACKGROUND

Urban drug "scenes" have been identified as important risk environments that shape the health of street-entrenched youth. New knowledge is needed to inform policy and programing interventions to help reduce youths' drug scene involvement and related health risks. The aim of this study was to identify how young people envisioned exiting a local, inner-city drug scene in Vancouver, Canada, as well as the individual, social and structural factors that shaped their experiences.

METHODS

Between 2008 and 2016, we draw on 150 semi-structured interviews with 75 street-entrenched youth. We also draw on data generated through ethnographic fieldwork conducted with a subgroup of 25 of these youth between.

RESULTS

Youth described that, in order to successfully exit Vancouver's inner city drug scene, they would need to: (a) secure legitimate employment and/or obtain education or occupational training; (b) distance themselves - both physically and socially - from the urban drug scene; and (c) reduce their drug consumption. As youth attempted to leave the scene, most experienced substantial social and structural barriers (e.g., cycling in and out of jail, the need to access services that are centralized within a place that they are trying to avoid), in addition to managing complex individual health issues (e.g., substance dependence). Factors that increased youth's capacity to successfully exit the drug scene included access to various forms of social and cultural capital operating outside of the scene, including supportive networks of friends and/or family, as well as engagement with addiction treatment services (e.g., low-threshold access to methadone) to support cessation or reduction of harmful forms of drug consumption.

CONCLUSIONS

Policies and programming interventions that can facilitate young people's efforts to reduce engagement with Vancouver's inner-city drug scene are critically needed, including meaningful educational and/or occupational training opportunities, 'low threshold' addiction treatment services, as well as access to supportive housing outside of the scene.

The epidemic dynamics of hepatitis C virus subtypes 4a and 4d in Saudi Arabia

The relatedness between viral variants sampled at different locations through time can provide information pertinent to public health that cannot readily be obtained through standard surveillance methods. Here, we use virus genetic data to identify the transmission dynamics that drive the hepatitis C virus subtypes 4a (HCV4a) and 4d (HCV4d) epidemics in Saudi Arabia. We use a comprehensive dataset of newly generated and publicly available sequence data to infer the HCV4a and HCV4d evolutionary histories in a Bayesian statistical framework. We also introduce a novel analytical method for an objective assessment of the migration intensity between locations. We find that international host mobility patterns dominate over within country spread in shaping the Saudi Arabia HCV4a epidemic, while this may be different for the HCV4d epidemic. This indicates that the subtypes 4a and 4d burden can be most effectively reduced by combining the prioritized screening and treatment of Egyptian immigrants with domestic prevention campaigns. Our results highlight that the joint investigation of evolutionary and epidemiological processes can provide valuable public health information, even in the absence of extensive metadata information.

Implications of hepatitis C virus subtype 1a migration patterns for virus genetic sequencing policies in Italy

Background

In-depth phylogeographic analysis can reveal migration patterns relevant for public health planning. Here, as a model, we focused on the provenance, in the current Italian HCV subtype 1a epidemic, of the NS3 resistance-associated variant (RAV) Q80K, known to interfere with the action of NS3/4A protease inhibitor simeprevir. HCV1a migration patterns were analysed using Bayesian phylodynamic tools, capitalising on newly generated and publicly available time and geo-referenced NS3 encoding virus genetic sequence data.

Results

Our results showed that both immigration and local circulation fuel the current Italian HCV1a epidemic. The United States and European continental lineages dominate import into Italy, with the latter taking the lead from the 1970s onwards. Since similar migration patterns were found for Q80K and other lineages, no clear differentiation of the risk for failing simeprevir can be made between patients based on their migration and travel history. Importantly, since HCV only occasionally recombines, these results are readily transferable to the genetic sequencing policy concerning NS5A RAVs.

Conclusions

The patient migration and travel history cannot be used to target only part of the HCV1a infected population for drug resistance testing before start of antiviral therapy. Consequently, it may be cost-effective to expand genotyping efforts to all HCV1a infected patients eligible for simeprevir-based therapies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0913-3) contains supplementary material, which is available to authorized users.

Ledipasvir plus sofosbuvir fixed-dose combination for 6 weeks in patients with acute hepatitis C virus genotype 1 monoinfection (HepNet Acute HCV IV): an open-label, single-arm, phase 2 study

BACKGROUND

Early treatment of acute hepatitis C virus (HCV) infection with interferon alfa is highly effective, but can be associated with frequent side-effects. We investigated the safety and efficacy of an interferon-free regimen for treatment of acute HCV infection.

METHODS

In this prospective, open-label, multicentre, single-arm pilot study, we enrolled adults (≥18 years) with acute HCV genotype 1 monoinfection from ten centres in Germany. Patients were given ledipasvir (90 mg) plus sofosbuvir (400 mg) as a fixed-dose combination tablet once daily for 6 weeks. The primary efficacy outcome was the proportion of patients with sustained virological response (defined as undetectable HCV RNA 12 weeks after the end of treatment; other primary outcomes were safety and tolerability of ledipasvir plus sofosbuvir. The primary analysis population consisted of all patients who received at least one dose of study drug. Safety was also assessed in all patients who received at least one dose of the study drug. This trial is registered with ClinicalTrials.gov, number NCT02309918.

FINDINGS

Between Nov 19, 2014, and Nov 10, 2015, we enrolled 20 patients. Median HCV RNA viral load at baseline was 4·04 log₁₀ IU/mL (1·71-7·20); 11 patients were infected with HCV genotype 1a and nine patients with genotype 1b. All patients achieved a sustained virological response 12 weeks after the end of treatment (20 [100%] of 20 patients). Treatment was well tolerated; there were no drug-related serious adverse events. Up to 12 weeks after treatment, 22 possible or probable drug-related adverse events were reported. There was one serious adverse event, which was judged unrelated to the study drug; one patient was admitted to hospital for surgery of a ruptured cruciate ligament.

INTERPRETATION

Treatment for 6 weeks with ledipasvir plus sofosbuvir was well tolerated and highly effective in patients with acute HCV genotype 1 monoinfection. Short-duration treatment of acute hepatitis C might prevent the spread of HCV in high-risk populations.

FUNDING

Gilead Sciences, HepNet Study-House/German Liver Foundation, and German Centre for Infection Research (DZIF).

Deep sequencing increases hepatitis C virus phylogenetic cluster detection compared to Sanger sequencing

Effective surveillance and treatment strategies are required to control the hepatitis C virus (HCV) epidemic. Phylogenetic analyses are powerful tools for reconstructing the evolutionary history of viral outbreaks and identifying transmission clusters. These studies often rely on Sanger sequencing which typically generates a single consensus sequence for each infected individual. For rapidly mutating viruses such as HCV, consensus sequencing underestimates the complexity of the viral quasispecies population and could therefore generate different phylogenetic tree topologies. Although deep sequencing provides a more detailed quasispecies characterization, in-depth phylogenetic analyses are challenging due to dataset complexity and computational limitations. Here, we apply deep sequencing to a characterized population to assess its ability to identify phylogenetic clusters compared with consensus Sanger sequencing. For deep sequencing, a sample specific threshold determined by the 50th percentile of the patristic distance distribution for all variants within each individual was used to identify clusters. Among seven patristic distance thresholds tested for the Sanger sequence phylogeny ranging from 0.005-0.06, a threshold of 0.03 was found to provide the maximum balance between positive agreement (samples in a cluster) and negative agreement (samples not in a cluster) relative to the deep sequencing dataset. From 77 HCV seroconverters, 10 individuals were identified in phylogenetic clusters using both methods. Deep sequencing analysis identified an additional 4 individuals and excluded 8 other individuals relative to Sanger sequencing. The application of this deep sequencing approach could be a more effective tool to understand onward HCV transmission dynamics compared with Sanger sequencing, since the incorporation of minority sequence variants improves the discrimination of phylogenetically linked clusters.