Transmission patterns of HIV and hepatitis C virus among networks of people who inject drugs. PLoS One. 2011;6:e22245. [PMID: 21799802 PMCID: PMC3140499 DOI: 10.1371/journal.pone.0022245]

Study of drug resistance-associated genetic mutations, and phylo-genetic analysis of HCV in the Province of Sindh, Pakistan

Current management of HCV infection is based on Direct-Acting Antiviral Drugs (DAAs). However, resistance-associated mutations, especially in the NS3 and NS5B regions are gradually decreasing the efficacy of DAAs. The aim of the current study was to identify such mutations in the NS3, and NS5B genes in DAAs treatment-naïve Pakistani chronic HCV 3a patients. Peripheral blood samples were collected from 233 chronic HCV 3a patients at different tertiary care hospitals in Karachi, Pakistan, between August 2020 to September 2021. PCR-amplified target regions of the NS3/NS5B gene were subjected to Sanger sequencing to identify resistance-associated mutations. Phylogenetic analysis of the identified amino acid sequences was performed using HCV3a sequences of the global population in the virus pathogen resource (VIPR) database. Sequence analysis identified five amino acid mutations, Leu36Pro, Gln41His, Gln80Lys/Arg, Ala156Tyr, and Gln168Arg in the NS3 region, and two mutations Leu159Phe and Cys316Arg in the NS5B region. Phylogenetic analysis revealed a high genetic diversity in the studied isolates. Overall, the prevalence of resistance-associated substitutions was almost similar to other geographic regions worldwide. This data could be helpful in selecting the most effective treatment regimen for HCV chronically infected people in Pakistan.

Patterns and correlates of hepatitis C virus phylogenetic clustering among people living with HIV in Australia in the direct-acting antiviral era: A molecular epidemiology study among participants in the CEASE cohort

Background and Aims

In moving towards the elimination of hepatitis C virus (HCV) infection among people living with HIV, understanding HCV transmission patterns may provide insights to guide and evaluate interventions. In this study, we evaluated patterns of, and factors associated with HCV phylogenetic clustering among people living with HIV/HCV co-infection in Australia in the direct-acting antiviral era.

Methods

HCV RNA was extracted from dried blood spot (DBS) samples collected between 2014 and 2018 in the CEASE cohort study. The HCV Core-E2 region was amplified by a polymerase chain reaction and Sanger sequenced. Maximum likelihood phylogenetic trees (1000 bootstrap replicates) were used to identify patterns of clustering (3% genetic distance threshold). Mixed-effects logistic regression was used to determine correlates of phylogenetic clustering. Factors assessed were sexual risk behavior, education, injecting drug use, housing, employment, HIV viral load, age, sex, and sexuality.

Results

Phylogenetic trees were reconstructed for HCV subtype 1a (n = 139) and 3a (n = 63) sequences, with 29% (58/202) in a pair or cluster. Overall (n = 202), phylogenetic clustering was positively associated with younger age (under 40; adjusted odds ratio [aOR] 2.52, 95% confidence interval [CI] 1.20-5.29), and among gay and bisexual men (n = 168), was positively associated with younger age (aOR 2.61, 95% CI 1.10-6.19), higher education (aOR 2.58, 95% CI 1.09-6.13), and reporting high-risk sexual behavior (aOR 3.94, 95% CI 1.31-11.84). During follow-up, five reinfections were observed, but none were in phylogenetic clusters.

Conclusion

This study found a high proportion of phylogenetic relatedness, predominantly among younger people and gay and bisexual men reporting high-risk sexual behavior. Despite this, few reinfections were observed, and reinfections demonstrated little relationship with known clusters. These findings highlight the importance of rapid HCV treatment initiation, together with monitoring of the phylogeny.

Characterisation of a Hepatitis C Virus Subtype 2a Cluster in Scottish PWID with a Suboptimal Response to Glecaprevir/Pibrentasvir Treatment

Direct-acting antivirals (DAAs) have revolutionised the treatment of Hepatitis C virus (HCV), allowing the World Health Organisation (WHO) to set a target of eliminating HCV by 2030. In this study we aimed to investigate glecaprevir and pibrentasvir (GP) treatment outcomes in a cohort of patients with genotype 2a infection.

METHODS

Clinical data and plasma samples were collected in NHS Greater Glasgow & Clyde. Next generation whole genome sequencing and replicon assays were carried out at the MRC-University of Glasgow Centre for Virus Research.

RESULTS

132 cases infected with genotype 2a HCV were identified. The SVR rate for this group was 91% (112/123) following treatment with GP. An NS5A polymorphism, L31M, was detected in all cases of g2a infection, and L31M+R353K in individuals that failed treatment. The results showed that R353K was present in 90% of individuals in the Glasgow genotype 2a phylogenetic cluster but in less than 5% of all HCV subtype 2a published sequences. In vitro efficacy of pibrentasvir against sub-genomic replicon constructs containing these mutations showed a 2-fold increase in IC₅₀ compared to wildtype.

CONCLUSION

This study describes a cluster of HCV genotype 2a infection associated with a lower-than-expected SVR rate following GP treatment in association with the NS5A mutations L31M+R353K.

HIV Response Interventions that Integrate HIV Molecular Cluster and Social Network Analysis: A Systematic Review

Due to improved efficiency and reduced cost of viral sequencing, molecular cluster analysis can be feasibly utilized alongside existing human immunodeficiency virus (HIV) prevention strategies. The goal of this paper is to elucidate how HIV molecular cluster and social network analyses are being integrated to implement HIV response interventions. We searched PubMed, Scopus, PsycINFO, and Cochrane Library databases for studies incorporating both HIV molecular cluster and social network data. We identified 32 articles that combined analyses of HIV molecular sequences and social or sexual networks. All studies were descriptive. Six studies described network interventions informed by molecular and social data but did not fully evaluate their efficacy. There is no current standard for incorporating molecular and social network analyses to inform interventions or data demonstrating its utility. More research must be conducted to delineate benefits and best practices for leveraging molecular data for network-based interventions.

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

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.

Phylogenetic and Phylodynamic Analyses of HCV Strains Circulating among Patients Using Injectable Drugs in Central Italy

Approximately 71 million people worldwide are infected with the hepatitis C virus (HCV). Injectable drug use represents the most common route of transmission in Europe and other developed countries. We studied the molecular characteristics of the HCV infection among mono-infected people who used drugs (PWUD) in Italy. Among 208 PWUD with anti-HCV antibodies, 101 (48.6%) were HCV RNA-positive, the majority (47%) were infected with the HCV genotype (Gt)1a, followed by Gt3a (34.9%), Gt4 (9.1%), Gt1b (4.5%), and Gt2 (4.5%). Bayesian phylogenetic analyses of clustered HCV NS5B sequences from 66 HCV-positive PWUDs with available plasma samples indicated age and neighborhood proximity as the most common characteristics between closely related HCV strains. Population dynamics, as measured by a coalescent Bayesian skyline analysis, revealed an increase in HCV Gt1a infections from the mid-1980s to mid-1990s. While HCV Gt3a infections were first detected in the 1980s, patient numbers with this genotype subtype remained relatively constant. For both Gt1a and Gt3a, Birth–Death Bayesian Skyline analyses produced higher reproduction numbers post 2014. For earlier time intervals, slow growths were observed for both Gt1a and Gt3a with reproduction numbers (Re) of approximately 1. The evolutionary rates for Gt1a and Gt3a were estimated as 2.23 × 10⁻⁴ and 3.85 × 10⁻⁴, respectively.

Late Relapse and Reinfection in HCV Patients Treated with Direct-Acting Antiviral (DAA) Drugs

The risk of hepatitis C virus (HCV) recurrence after direct-acting antiviral (DAA) treatment is <0.5%. However, the distinction between HCV RNA late relapse and reinfection still represents a challenge in virological diagnostics. The aim of this study was to employ next-generation sequencing (NGS) to investigate HCV RNA recurrence in patients achieving a sustained virologic response (SVR) at least six months post-treatment. NGS was performed on plasma samples from six HCV-positive patients (Pt1–6) treated with DAA. NGS of HCV NS5B was analyzed before treatment (T0), after HCV RNA rebound (T1), and, for Pt3, after a second rebound (T2). Reinfection was confirmed for Pt5, and for the first rebound observed in Pt3. Conversely, viral relapse was observed when comparing T0 and T1 for Pt6 and T1 and T2 for Pt3. Z-scores were calculated and used to predict whether HCV-positive patient samples at different time points belonged to the same quasispecies population. A low Z-score of <2.58 confirmed that viral quasispecies detected at T0 and T1 were closely related for both Pt1 and Pt2, while the Z-score for Pt4 was suggestive of possible reinfection. NGS data analyses indicate that the Z-score may be a useful parameter for distinguishing late relapse from reinfection.

"He's under oath": Privacy and Confidentiality Views Among People Who Inject Drugs Enrolled in a Study of Social Networks and Human Immunodeficiency Virus/Hepatitis C Virus Risk

Despite the promise of social network research, this method raises important ethical questions regarding privacy and confidentiality. Although researchers and bioethicists have considered research obligations in relation to marginal or vulnerable populations, the views of people who inject drugs (PWIDs) have not been sufficiently considered. To elicit participants' views of research obligations, we conducted in-depth interviews with a subset (n = 40) of active PWIDs enrolled in a large social network study. Findings suggest participants have an expectation of confidentiality but believe this obligation need not be absolute and can be waived if a participant violates community norms or place others at risk. Ethics boards should recognize that marginalized populations are able to articulate complex moral views about privacy and confidentiality. Engaging participants in dialogue about the responsible conduct of research presents an opportunity to correct under- or overestimations of research vulnerabilities when such decisions are restricted to the perspectives of investigators or Institutional Review Board members.

Combining viral genetic and animal mobility network data to unravel peste des petits ruminants transmission dynamics in West Africa

Peste des petits ruminants (PPR) is a deadly viral disease that mainly affects small domestic ruminants. This disease threaten global food security and rural economy but its control is complicated notably because of extensive, poorly monitored animal movements in infected regions. Here we combined the largest PPR virus genetic and animal mobility network data ever collected in a single region to improve our understanding of PPR endemic transmission dynamics in West African countries. Phylogenetic analyses identified the presence of multiple PPRV genetic clades that may be considered as part of different transmission networks evolving in parallel in West Africa. A strong correlation was found between virus genetic distance and network-related distances. Viruses sampled within the same mobility communities are significantly more likely to belong to the same genetic clade. These results provide evidence for the importance of animal mobility in PPR transmission in the region. Some nodes of the network were associated with PPRV sequences belonging to different clades, representing potential "hotspots" for PPR circulation. Our results suggest that combining genetic and mobility network data could help identifying sites that are key for virus entrance and spread in specific areas. Such information could enhance our capacity to develop locally adapted control and surveillance strategies, using among other risk factors, information on animal mobility.

A Phylogenetic Analysis of Hepatitis C Virus Transmission, Relapse, and Reinfection Among People Who Inject Drugs Receiving Opioid Agonist Therapy

BACKGROUND

Understanding hepatitis C virus (HCV) transmission among people who inject drugs (PWID) is essential for HCV elimination. We aimed to differentiate reinfections from treatment failures and to identify transmission linkages and associated factors in a cohort of PWID receiving opioid agonist therapy (OAT).

METHODS

We analyzed baseline and follow-up specimens from 150 PWID from 3 OAT clinics in the Bronx, New York. Next-generation sequencing data from the hypervariable region 1 of HCV were analyzed using Global Hepatitis Outbreak and Surveillance Technology.

RESULTS

There were 3 transmission linkages between study participants. Sustained virologic response (SVR) was not achieved in 9 participants: 7 had follow-up specimens with similar sequences to baseline, and 2 died. In 4 additional participants, SVR was achieved but the participants were viremic at later follow-up: 2 were reinfected with different strains, 1 had a late treatment failure, and 1 was transiently viremic 17 months after treatment. All transmission linkages were from the same OAT clinic and involved spousal or common-law partnerships.

CONCLUSION

This study highlights the use of next-generation sequencing as an important tool for identifying viral transmission and to help distinguish relapse and reinfection among PWID. Results reinforce the need for harm reduction interventions among couples and those who report ongoing risk factors after SVR.

Factors associated with phylogenetic clustering of hepatitis C among people who inject drugs in Baltimore

Background

The availability of effective, oral direct acting antivirals (DAAs) for hepatitis C virus (HCV) treatment has put elimination of HCV as a public health challenge within reach. However, little is known about the characteristics of transmission networks of people who inject drugs (PWID).

Methods

Sequencing of a segment of the HCV genome was performed on samples collected from a community-based cohort of PWID between August 2005 and December 2016. Phylogenetic trees were inferred, and clusters were identified (70% bootstrap threshold; 0.04 maximum genetic distance threshold). We describe sex, race, age difference, and HIV infection status of potential transmission partners. Logistic regression was used to assess factors associated with being in an HCV cluster.

Results

Of 508 HCV genotype 1 viremic PWID, 8% (n = 41) were grouped into 20 clusters, consisting of 19 pairs and 1 triad. In adjusted analyses, female sex (odds ratio [OR] 2.3 [95% confidence interval (CI) 1.2–4.5]) and HIV infection (OR 5.7 [CI 2.7–11.9]) remained independently associated with being in an HCV infection cluster.

Conclusions

Molecular epidemiological analysis reveals that, in this cohort of PWID in Baltimore, HIV infection and female sex were associated with HCV clustering. Combination HCV prevention interventions targeting HIV infected PWID and addressing HCV infection prevention needs of women have potential to advance HCV elimination efforts.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-020-05546-x.

Global prevalence of HCV and/or HBV coinfections among people who inject drugs and female sex workers who live with HIV/AIDS: a systematic review and meta-analysis

Coinfections of hepatitis C virus (HCV) and/or hepatitis B virus (HBV) with human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) are associated with high morbidity and mortality and poor prognosis. The main objective of this study was to evaluate the prevalence of HCV and/or HBV coinfections among people who inject drugs (PWID) and female sex workers (FSWs) who live with HIV/AIDS worldwide. Data sources were searched from January 2008 to October 2018 in different databases, including PubMed, Scopus, Web of Science, Embase, and Ovid. Data were analyzed in Stata 14 software using the Metaprop command. The results showed that the prevalence of HCV among PWID and FSWs with HIV/AIDS was 72% (95% CI: 59%-83%) and 40% (95% CI: 0%-94%), respectively. The prevalence of HBV among PWID and FSWs with HIV/AIDS was 8% (95% CI: 5%-13%) and 2% (95% CI: 0%-7%), respectively, and the prevalence of HCV/HBV in PWID with HIV/AIDS was 11% (95% CI: 7%-15%). The highest prevalence of HCV was observed in PWID in the Eastern Mediterranean and Europe regions, and the lowest was observed in the Africa region. The South-East Asia region had the highest prevalence of HBV among PWID, and the Africa region had the lowest prevalence. The high prevalence of HCV coinfection among PWID and FSWs with HIV/AIDS was an alarming health problem and requires appropriate interventions. Therefore, considering that these populations are key populations for HCV elimination, it is recommended to screen them regularly for HCV. In addition, harm reduction and HBV vaccination should be carefully considered.

Systematic Review and Meta-Analysis of Global Prevalence of HBsAg and HIV and HCV Antibodies among People Who Inject Drugs and Female Sex Workers

The main objective of this study was to evaluate the prevalence of human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS), hepatitis C virus (HCV) and hepatitis B virus (HBV) and their co-infections among people who inject drugs (PWID) and female sex workers (FSWs). Data sources were searched from January 2008 to October 2018 in different databases. Data were analyzed in Stata 16 software using the Metaprop command. The results showed that the prevalence of HIV, HCV and HBV among PWID was 15%, 60% and 6%, respectively. The prevalence of HIV, HCV and HBV among FSWs was 5%, 1% and 3%, respectively. The prevalence of HIV/HCV, HIV/HBV, HCV/HBV and HIV/HCV/HBV co-infections among PWID was 13%, 2%, 3% and 2%, respectively. The prevalence of HIV/HCV and HIV/HBV co-infections among FSWs was 3% and 1%, respectively. The results show that the prevalence of HCV and HIV infections in PWID and the prevalence of HIV in FSWs is higher than their prevalence in the general population. Interventions for the prevention of HIV and HCV in PWID appear to be poor, and may not be sufficient to effectively prevent HIV and HCV transmission.

Factors influencing HIV-1 phylogenetic clustering

PURPOSE OF REVIEW

A major goal of public health in relation to HIV/AIDS is to prevent new transmissions in communities. Phylogenetic techniques have improved our understanding of the structure and dynamics of HIV transmissions. However, there is still no consensus about phylogenetic methodology, sampling coverage, gene target and/or minimum fragment size.

RECENT FINDINGS

Several studies use a combined methodology, which includes both a genetic or patristic distance cut-off and a branching support threshold to identify phylogenetic clusters. However, the choice about these thresholds remains an inherently subjective process, which affects the results of these studies. There is still a lack of consensus about the genomic region and the size of fragments that should be used, although there seems to be emerging a consensus that using longer segments, allied with the use of a realistic model of evolution and a codon alignment, increases the likelihood of inferring true transmission clusters. The pol gene is still the most used genomic region, but recent studies have suggested that whole genomes and/or sequences from nef and gp41 are also good targets for cluster reconstruction.

SUMMARY

The development and application of standard methodologies for phylogenetic clustering analysis will advance our understanding of factors associated with HIV transmission. This will lead to the design of more precise public health interventions.

Natural selection favoring more transmissible HIV detected in United States molecular transmission network

HIV molecular epidemiology can identify clusters of individuals with elevated rates of HIV transmission. These variable transmission rates are primarily driven by host risk behavior; however, the effect of viral traits on variable transmission rates is poorly understood. Viral load, the concentration of HIV in blood, is a heritable viral trait that influences HIV infectiousness and disease progression. Here, we reconstruct HIV genetic transmission clusters using data from the United States National HIV Surveillance System and report that viruses in clusters, inferred to be frequently transmitted, have higher viral loads at diagnosis. Further, viral load is higher in people in larger clusters and with increased network connectivity, suggesting that HIV in the United States is experiencing natural selection to be more infectious and virulent. We also observe a concurrent increase in viral load at diagnosis over the last decade. This evolutionary trajectory may be slowed by prevention strategies prioritized toward rapidly growing transmission clusters.

Network Evolution of a Large Online MSM Dating Community: 2005-2018

Due to multiple sexual partners and low rates of condom use, the HIV infection rate among MSM (men who have sex with men) is much higher than that of the general population. In order to analyze the characteristics of online activities of MSM, and to understand the evolution of their social networks, in this study we collect a comprehensive dataset, covering the period from January 2005 to June 2018, from the largest Chinese online community, Baidu Tieba. We build an online dating network for MSM-related individuals in the gay-bar community, and analyze the network from static and dynamic aspects. It is found that there is a strong homophily regarding the cities where users reside when developing interactions with others, and that most network measurements tend to be stable at the later stages of evolution, while the size of the largest community fluctuates. This is an indication that the network is formed of rapidly flexible interactions which changes quickly. In comparison with studies on heterosexual networks, we find that the MSM dating network shows differences in many aspects, such as the positive degree-degree correlation and high clustering coefficient, suggesting different thinking and measures should be taken in the policy making of public health management towards the MSM population.

Correlates of hepatitis C viral clustering among people who inject drugs in Baltimore

This study examines correlates of hepatitis C virus (HCV) genetic clustering among community-recruited people who inject drugs enrolled in the AIDS Linked to the IntraVenous Experience cohort in Baltimore between 1988 and 1989. HCV RNA was extracted and the core/envelope-1 region was sequenced. Clusters were identified from maximum likelihood trees with 1000 bootstrap replicates using a 70% aLRT and a 4% genetic-distance threshold in Cluster Picker. Overall, 46% of participants were in a cluster, including 122 genotype-1a and 36 genotype-1b clusters with an average of 2-3 genetically linked HCV infections. The largest cluster consists of 9 participants. In univariable analysis, black race (PR = 1.66 [95% CI: 1.12-2.45]), age <35 years (PR = 1.18 [95% CI: 1.02-1.37]), and injection drug use of cocaine alone (PR = 1.30 [95% CI: 1.02-1.65]) were significantly associated with being in a cluster. Conversely, a history of medication-associated treatment (MAT) was negatively associated with being in a cluster (PR = 0.82 [95% CI: 0.71-0.95]). In multivariable analysis, black race (APR = 1.62 [95% CI: 1.11-2.38]) remained independently associated being in a cluster while MAT (APR = 0.85 [95% CI: 0.74-0.99]) remained negatively associated with clustering. Our findings suggest strong locally-propagated transmission networks during the early epidemic that was driven by younger PWID. In light of the current opioid epidemic in the US, these findings suggest an urgent need for preventive interventions to mitigate the growth of large HCV transmission networks.

Inconsistent temporal patterns of genetic variation of HCV among high-risk subjects may impact inference of transmission networks

Hepatitis-C Virus (HCV) sequences are often used to establish networks of people who inject drugs (PWID). However, the degree to which within-host evolutionary dynamics affect those inferences has not been carefully studied. Here, we analyzed 702 longitudinally-sampled HCV E1 sequences from 88 HCV+ people who inject drugs (PWID) in the Baltimore Before and After Acute Study of Hepatitis (BBAASH) cohort. Individuals were tested for HCV RNA over multiple visits to the clinic, and the HCV E1 gene was sequenced for HCV+ samples. Genetic clustering was performed on the full set of sequences using a 3% genetic distance threshold to define epidemiological linkage. Maximum-likelihood (ML) phylogenies were inferred to assess evolutionary relationships. We found 22 clusters containing sequences sampled over five or more years (long-term clusters, LTC), of which 17 had >1 subject. In six of the multi-subject LTC, one subject had a sequence sampled >3 years earlier or later than the next-closest subject in the cluster (time-gap LTC). ML trees showed that, in three of the time-gap LTC, two subjects had identical sequences despite 7-10 years separating the sampling times. In four of the time-gap LTC for whom additional data were available, the subject with the later detected shared variant had both different variants and visits with no detectable HCV RNA (RNA-) prior to the appearance of the shared variant. In the subject with the earlier detection of the shared variant, different variants and RNA- visits were also detected in multiple cases subsequent to appearance of the shared variant. Complex patterns of shared viral variation among PWID reflect on-going re-infection, multiple transmission partners, and/or inconsistent detection of viral variants. Our results suggest that transmission events are currently underestimated by analysis of sequences at a single point in time.

Clinical and virological properties of hepatitis C virus genotype 4 infection in patients treated with different direct-acting antiviral agents

Background

The efficacy of direct-acting antivirals (DAAs) depends on the hepatitis C virus (HCV) genotype 4 (GT4) subtype which are used in the treatment of HCV. We aimed to retrospectively investigate the baseline prevalence of HCV NS5A and NS5B polymorphisms and their impact on virological outcome in GT4-infected patients treated with various DAA regimens.

Patients and methods

Available plasma samples from HCV GT4-infected patients treated with different DAA regimens were analyzed at baseline and after treatment failure, where applicable. Sanger sequencing of patient-derived NS5A and NS5B regions was performed on all available samples, while ultradeep pyrosequencing (UDPS) of NS5A and NS5B regions was performed only on samples from treatment failures at different time points.

Results

Sustained virological response (SVR) was achieved by 96% (48/50) of patients. Of 16 patients with baseline NS5A sequence, polymorphisms at amino acid positions associated with drug resistance were detected only at position 58: P58 (69.2%) and T58 (30.8%). Of 21 patients with baseline NS5B sequence, N142S was detected only in the two treatment failures, both with GT4d were treated with sofosbuvir (SOF)-based regimens, suggesting a potential involvement in SOF efficacy. Two patients (patient 1 [Pt1] and patient 2 [Pt2]) relapsed. In Pt1, NS5A-T56I and NS5A-Y93H/S emerged. In Pt2, NS5A-L28F emerged and a novel NS5B resistance-associated substitution (RAS), L204F, representing 1.5% of the viral population at baseline, enriched to 71% and 91.6% during and after treatment failure, respectively. UDPS of NS5B from Pt2 indicated a mixed infection of approximately 1:5, GT1a:GT4d, at baseline and GT4d during failure. Phylogenetic analysis of NS5A sequences indicated no clustering of HCV strains from patients achieving SVR vs patients who relapsed. The mean genetic distance in NS5A sequences was 5.8%, while a lower genetic distance (3.1%) was observed in NS5B sequences.

Conclusion

Results from these analyses confirm the importance of UDPS in the analysis of viral quasispecies variability and the identification of novel RASs potentially associated with DAA treatment failure in HCV GT4-infected patients.

Injection Partners, HCV, and HIV Status among Rural Persons Who Inject Drugs in Puerto Rico

BACKGROUND

The prevalence of hepatitis C (HCV) and HIV among persons who inject drugs (PWID) and the ability of these diseases to spread through injection networks are well documented in urban areas. However, less is known about injection behaviors in rural areas.

OBJECTIVES

This study focuses on the association between the number of self-reported injection partners with the PWID's self-reported HCV and HIV status. Injection networks provide paths for infection and information to flow, and are important to consider when developing prevention and intervention strategies.

METHODS

Respondent driven sampling was used to conduct 315 interviews with PWID in rural Puerto Rico during 2015. Negative binomial regression was used to test for associations between the number of self-reported injection partners and self-reported HCV and HIV statuses. Multinomial logistic regression was used to test for associations with the participant's self-reported HCV and HIV statuses.

RESULTS

Self-reported HCV status is significantly associated with injection risk network size. Injection partner networks of self-reported HCV- respondents are half what is reported by those with a positive or unknown status. Self-reported HIV statuses are not associated with different numbers of injection partners.

CONCLUSIONS

Smaller injection networks among those who self-report a HCV- status suggests that those who believe their status to be negative may take protective action by reducing their injection network compared to those have a self-reported HCV+ or an unknown status. Although the cross-sectional design of the study makes it difficult verify, such behavior has implications for prevention programs attempting to prevent HCV transmission.

Network Viral Load: A Critical Metric for HIV Elimination

BACKGROUND

Associations have been observed between an aggregate viral load measure, the community viral load, and new HIV diagnoses. The community viral load aggregates viral loads within chosen geographic areas, restricting inferences about HIV acquisition risk to these areas. We develop a more precise metric, the network viral load (NVL), to measure the composite viral load within a risk network of a HIV-negative individual.

METHODS

We examined the relationship between NVL and HIV infection among young men who have sex with men in Chicago, United States. Networks were generated using respondent-driven sampling. NVL was defined as the prevalence of viremic individuals in one's risk network, characterized as those with a viral load ≥20 k copies per milliliter. Permutation tests were conducted to account for dependency.

RESULTS

After controlling for total connections, age, substance use during sex, syphilis diagnosis (previous 12 months), and frequency of condomless anal sex (previous 6 months), we found a positive association between NVL and HIV infection. Compared with a network with all HIV-seronegative members, the odds of HIV infection with an NVL of <10% viremia were 1.85 (95% confidence interval: 1.18 to 2.92) times higher and those with an NVL of ≥10% viremia were 2.73 (95% confidence interval: 1.54 to 4.85) times higher.

CONCLUSIONS

We found a positive association between NVL and HIV seroprevalence. Although limited in its ability to infer causality, NVL could have substantial public health implications for persons most at risk for HIV infection, given that this novel metric avoids overreliance on individual level behavior or broad community indices.

Analyzing hidden populations online: topic, emotion, and social network of HIV-related users in the largest Chinese online community

BACKGROUND

Traditional survey methods are limited in the study of hidden populations due to the hard to access properties, including lack of a sampling frame, sensitivity issue, reporting error, small sample size, etc. The rapid increase of online communities, of which members interact with others via the Internet, have generated large amounts of data, offering new opportunities for understanding hidden populations with unprecedented sample sizes and richness of information. In this study, we try to understand the multidimensional characteristics of a hidden population by analyzing the massive data generated in the online community.

METHODS

By elaborately designing crawlers, we retrieved a complete dataset from the "HIV bar," the largest bar related to HIV on the Baidu Tieba platform, for all records from January 2005 to August 2016. Through natural language processing and social network analysis, we explored the psychology, behavior and demand of online HIV population and examined the network community structure.

RESULTS

In HIV communities, the average topic similarity among members is positively correlated to network efficiency (r = 0.70, p < 0.001), indicating that the closer the social distance between members of the community, the more similar their topics. The proportion of negative users in each community is around 60%, weakly correlated with community size (r = 0.25, p = 0.002). It is found that users suspecting initial HIV infection or first in contact with high-risk behaviors tend to seek help and advice on the social networking platform, rather than immediately going to a hospital for blood tests.

CONCLUSIONS

Online communities have generated copious amounts of data offering new opportunities for understanding hidden populations with unprecedented sample sizes and richness of information. It is recommended that support through online services for HIV/AIDS consultation and diagnosis be improved to avoid privacy concerns and social discrimination in China.

Characterization of Naturally Occurring NS5A and NS5B Polymorphisms in Patients Infected with HCV Genotype 3a Treated with Direct-Acting Antiviral Agents

Hepatitis C virus (HCV) genotype (GT)3 is associated with increased risk of steatosis, development of cirrhosis and hepatocellular carcinoma. Limited data are available regarding genetic variability and use of direct-acting antiviral agents in these patients. non-structural protein 5A (NS5A) and non-structural protein 5B (NS5B) sequencing was performed on 45 HCV GT3-infected Italian patients subsequently treated with sofosbuvir ± daclatasvir (SOF ± DCV). Novel GT3a polymorphisms were observed by Sanger sequencing in three NS5A (T79S, T107K, and T107S) and three NS5B (G166R, Q180K, and C274W) baseline sequences in patients who achieved sustained virological response (SVR). Baseline NS5A resistance-associated substitutions (RASs) A30K and Y93H were detected in 9.5% of patients; one patient with A30K did not achieve SVR. Phylogenetic analyses of sequences showed no distinct clustering. Genetic heterogeneity of NS5A and NS5B was evaluated using ultra-deep pyrosequencing (UDPS) in samples longitudinally collected in patients not achieving SVR. Some novel NS5A and NS5B polymorphisms detected at baseline may not impact treatment outcome, as they were not enriched in post-failure samples. In contrast, the clinically novel GT3 NS5A-L31F RAS emerged in one treatment failure, and I184T, G188D and N310S, located on the same NS5B haplotype, became predominant after failure. These findings suggest a potential impact of these novel substitutions on the treatment outcome; however, their significance requires further investigation.

NEW SURVEY QUESTIONS AND ESTIMATORS FOR NETWORK CLUSTERING WITH RESPONDENT-DRIVEN SAMPLING DATA

Respondent-driven sampling (RDS) is a popular method for sampling hard-to-survey populations that leverages social network connections through peer recruitment. While RDS is most frequently applied to estimate the prevalence of infections and risk behaviors of interest to public health, such as HIV/AIDS or condom use, it is rarely used to draw inferences about the structural properties of social networks among such populations because it does not typically collect the necessary data. Drawing on recent advances in computer science, we introduce a set of data collection instruments and RDS estimators for network clustering, an important topological property that has been linked to a network's potential for diffusion of information, disease, and health behaviors. We use simulations to explore how these estimators, originally developed for random walk samples of computer networks, perform when applied to RDS samples with characteristics encountered in realistic field settings that depart from random walks. In particular, we explore the effects of multiple seeds, without replacement versus with replacement, branching chains, imperfect response rates, preferential recruitment, and misreporting of ties. We find that clustering coefficient estimators retain desirable properties in RDS samples. This paper takes an important step toward calculating network characteristics using nontraditional sampling methods, and it expands the potential of RDS to tell researchers more about hidden populations and the social factors driving disease prevalence.

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.

A comparison of network sampling designs for a hidden population of drug users: Random walk vs. respondent-driven sampling

Both random walk and respondent-driven sampling (RDS) exploit social networks and may reduce biases introduced by earlier methods for sampling from hidden populations. Although RDS has become much more widely used by social researchers than random walk (RW), there has been little discussion of the tradeoffs in choosing RDS over RW. This paper compares experiences of implementing RW and RDS to recruit drug users to a network-based study in Houston, Texas. Both recruitment methods were implemented over comparable periods of time, with the same population, by the same research staff. RDS methods recruited more participants with less strain on staff. However, participants recruited through RW were more forthcoming than RDS participants in helping to recruit members of their social networks. Findings indicate that, dependent upon study goals, researchers' choice of design may influence participant recruitment, participant commitment, and impact on staff, factors that may in turn affect overall study success.

Social and Genetic Networks of HIV-1 Transmission in New York City

Background

Sexually transmitted infections spread across contact networks. Partner elicitation and notification are commonly used public health tools to identify, notify, and offer testing to persons linked in these contact networks. For HIV-1, a rapidly evolving pathogen with low per-contact transmission rates, viral genetic sequences are an additional source of data that can be used to infer or refine transmission networks.

Methods and Findings

The New York City Department of Health and Mental Hygiene interviews individuals newly diagnosed with HIV and elicits names of sexual and injection drug using partners. By law, the Department of Health also receives HIV sequences when these individuals enter healthcare and their physicians order resistance testing. Our study used both HIV sequence and partner naming data from 1342 HIV-infected persons in New York City between 2006 and 2012 to infer and compare sexual/drug-use named partner and genetic transmission networks. Using these networks, we determined a range of genetic distance thresholds suitable for identifying potential transmission partners. In 48% of cases, named partners were infected with genetically closely related viruses, compatible with but not necessarily representing or implying, direct transmission. Partner pairs linked through the genetic similarity of their HIV sequences were also linked by naming in 53% of cases. Persons who reported high-risk heterosexual contact were more likely to name at least one partner with a genetically similar virus than those reporting their risk as injection drug use or men who have sex with men.

Conclusions

We analyzed an unprecedentedly large and detailed partner tracing and HIV sequence dataset and determined an empirically justified range of genetic distance thresholds for identifying potential transmission partners. We conclude that genetic linkage provides more reliable evidence for identifying potential transmission partners than partner naming, highlighting the importance and complementarity of both epidemiological and molecular genetic surveillance for characterizing regional HIV-1 epidemics.

Understanding the path over which viruses such as HIV have been transmitted may be crucial for directing public health resources and guiding policy decisions. Contact tracing of named sexual and injection drug-use partners of people recently diagnosed with HIV is an indispensible tool for reconstructing this transmission network. Viral genetic sequence data—routinely collected by public health agencies—can also be used to infer the dynamics of HIV transmission. We analyzed partner naming and viral genetic sequence data in 1342 people living with HIV in New York City reported to the New York City Department of Health and Mental Hygiene between 2006 and 2012. Genetically linked partners were more likely to be named partners than named partners were to be genetically linked. This finding indicates that genetic sequence data are better than partner naming data for reconstructing this viral transmission network. Importantly, the success rate in naming a genetically linked partner varied by transmission risk category (e.g., men who have sex with men, heterosexuals, and injection drug users). This study validates the use viral genetic sequences in reconstructing these viral transmission networks in a public health surveillance setting.

Impacts and shortcomings of genetic clustering methods for infectious disease outbreaks

For infectious diseases, a genetic cluster is a group of closely related infections that is usually interpreted as representing a recent outbreak of transmission. Genetic clustering methods are becoming increasingly popular for molecular epidemiology, especially in the context of HIV where there is now considerable interest in applying these methods to prioritize groups for public health resources such as pre-exposure prophylaxis. To date, genetic clustering has generally been performed with ad hoc algorithms, only some of which have since been encoded and distributed as free software. These algorithms have seldom been validated on simulated data where clusters are known, and their interpretation and similarities are not transparent to users outside of the field. Here, I provide a brief overview on the development and inter-relationships of genetic clustering methods, and an evaluation of six methods on data simulated under an epidemic model in a risk-structured population. The simulation analysis demonstrates that the majority of clustering methods are systematically biased to detect variation in sampling rates among subpopulations, not variation in transmission rates. I discuss these results in the context of previous work and the implications for public health applications of genetic clustering.

HCV dispersal patterns among intravenous drug users (IDUs) in Athens metropolitan area

BACKGROUND

Most of the HCV transmission the recent years in Greece was among IDUs. Our aim was to estimate the prevalence of HCV genotypes and to investigate the patterns of HCV dispersal among IDUs in Athens using current state of the art molecular epidemiology methods.

METHODS

HCV sequences were determined from 238 HIV-negative IDUs collected on the basis of the "ARISTOTLE" prevention program carried out in Athens between 2012 and 2013. Phylogenetic trees were inferred on HCV sequences isolated from IDUs in Athens for the most prevalent HCV clades (subtypes 1a and 3a). Phylogenetic analysis was performed by Neighbor-Joining and Bayesian methods using GTR+G as nucleotide substitution model. HCV dispersal patterns were estimated using as references, all globally available HCV sequences for subtypes 1a and 3a.

RESULTS

The prevalence of HCV subtypes was: 3a (59.2%), 1a (21.9%), 4 (13.0%), 1b (5.4%) and 2 (0.5%). Phylogenetic analyses revealed that most sequences (63.5%) οf subtypes 1a and 3a fell within IDU-specific monophyletic groups. The proportion of sequences in monophyletic clades was similar for subtype 3a (62.9%) and 1a (65.3%). For the latter group, monophyletic clades were smaller in size. Multivariable logistic regression analyses showed that monophyletic clustering was marginally associated recent onset of injecting ([AOR]=1.44; 95% CI (0.97-2.13), p=0.068).

CONCLUSIONS

The high proportions of HCV sequences within IDU-specific monophyletic clusters suggest that transmissions occurred locally among IDUs in Greece. The numerous clusters for both 1a and 3a provide evidence that both sub-epidemics were the result of multiple introductions among the IDUs. Higher regional clustering was probably associated with a more recent onset of drug use.

Triangulating Syndemic Services and Drug Treatment Policy: Improving Drug Treatment Portal Locations in Baltimore City

THE PROBLEM

The prevalence of injection drug use (IDU) and incidence of human immunodeficiency virus (HIV) remain high in Baltimore, where IDU is a primary HIV risk factor. Substance use disorders and HIV are related syndemically--their causes and consequences interact synergistically. Baltimore is increasingly considering the syndemic relationship of substance use disorders, IDU, and HIV in making decisions about drug treatment funding and location.

PURPOSE OF ARTICLE

Our goal was to empirically identify the optimal location of new drug treatment programs through the development and application of a novel, practical tool.

KEY POINTS

Syndemic triangles were constructed to measure and visualize unmet need for drug treatment services. These data were used to determine priority zones for new treatment centers.

CONCLUSIONS

The application of this tool helped inform strategies for locating drug treatment services in Baltimore, and its successful use suggests its potential value in other metropolitan areas.

Integrating molecular epidemiology and social network analysis to study infectious diseases: Towards a socio-molecular era for public health

The number of public health applications for molecular epidemiology and social network analysis has increased rapidly since the improvement in computational capacities and the development of new sequencing techniques. Currently, molecular epidemiology methods are used in a variety of settings: from infectious disease surveillance systems to the description of disease transmission pathways. The latter are of great epidemiological importance as they let us describe how a virus spreads in a community, make predictions for the further epidemic developments, and plan preventive interventions. Social network methods are used to understand how infections spread through communities and what the risk factors for this are, as well as in improved contact tracing and message-dissemination interventions. Research is needed on how to combine molecular and social network data as both include essential, but not fully sufficient information on infection transmission pathways. The main differences between the two data sources are that, firstly, social network data include uninfected individuals unlike the molecular data sampled only from infected network members. Thus, social network data include more detailed picture of a network and can improve inferences made from molecular data. Secondly, network data refer to the current state and interactions within the social network, while molecular data refer to the time points when transmissions happened, which might have happened years before the sampling date. As of today, there have been attempts to combine and compare the data obtained from the two sources. Even though there is no consensus on whether and how social and genetic data complement each other, this research might significantly improve our understanding of how viruses spread through communities.

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We summarise and analyse the roles of molecular evolution studies in molecular epidemiology of infectious diseases.

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We review how social network and molecular sequence data have been integrated in the past.

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We show how integrating social network and molecular evolution approaches may change the study of infectious diseases.

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

BACKGROUND & AIMS

Understanding HCV transmission among people who inject drugs (PWID) is important for designing prevention strategies. This study investigated whether HCV infection among younger injectors occurs from few or many transmission events from older injectors to younger injectors among PWID in Vancouver, Canada.

METHODS

HCV antibody positive participants at enrolment or follow-up (1996-2012) were tested for HCV RNA and sequenced (Core-E2). Time-stamped phylogenetic trees were inferred using Bayesian Evolutionary Analysis Sampling Trees (BEAST). Association of age with phylogeny was tested using statistics implemented in the software Bayesian Tip Significance (BaTS) testing. Factors associated with clustering (maximum cluster age: five years) were identified using logistic regression.

RESULTS

Among 699 participants with HCV subtype 1a, 1b, 2b and 3a infection (26% female, 24% HIV+): 21% were younger (<27years), and 10% had recent HCV seroconversion. When inferred cluster age was limited to <5years, 15% (n=108) were in clusters/pairs. Although a moderate degree of segregation was observed between younger and older participants, there was also transmission between age groups. Younger age (<27 vs. >40, AOR: 3.14; 95% CI: 1.54, 6.39), HIV (AOR: 1.97; 95% CI: 1.22, 3.18) and subtype 3a (AOR: 2.12; 95% CI: 1.33, 3.38) were independently associated with clustering.

CONCLUSIONS

In this population of PWID from Vancouver, HCV among young injectors was seeded from many transmission events between HCV-infected older and younger injectors. Phylogenetic clustering was associated with younger age and HIV. These data suggest that HCV transmission among PWID is complex, with transmission occurring between and among older and younger PWID.

On-site bundled rapid HIV/HCV testing in substance use disorder treatment programs: study protocol for a hybrid design randomized controlled trial

BACKGROUND

More than 1.2 million people in the United States are living with human immunodeficiency virus (HIV), and 3.2 million are living with hepatitis C virus (HCV). An estimated 25 % of persons living with HIV also have HCV. It is therefore of great public health importance to ensure the prompt diagnosis of both HIV and HCV in populations that have the highest prevalence of both infections, including individuals with substance use disorders (SUD).

METHODS/DESIGN

In this theory-driven, efficacy-effectiveness-implementation hybrid study, we will develop and test an on-site bundled rapid HIV/HCV testing intervention for SUD treatment programs. Its aim is to increase the receipt of HIV and HCV test results among SUD treatment patients. Using a rigorous process involving patients, providers, and program managers, we will incorporate rapid HCV testing into evidence-based HIV testing and linkage to care interventions. We will then test, in a randomized controlled trial, the extent to which this bundled rapid HIV/HCV testing approach increases receipt of HIV and HCV test results. Lastly, we will conduct formative research to understand the barriers to, and facilitators of, the adoption, implementation, and sustainability of the bundled rapid testing strategy in SUD treatment programs.

DISCUSSION

Novel approaches that effectively integrate on-site rapid HIV and rapid HCV testing are needed to address both the HIV and HCV epidemics. If feasible and efficacious, bundled rapid HIV/HCV testing may offer a scalable, potentially cost-effective approach to testing high-risk populations, such as patients of SUD treatment programs. It may ultimately lead to improved linkage to care and progress through the HIV and HCV care and treatment cascades.

TRIAL REGISTRATION

ClinicalTrials.gov: NCT02355080 . (30 January 2015).

Transmission of Hepatitis C Virus among Prisoners, Australia, 2005-2012

Ongoing transmission is associated with drug injection.

Hepatitis C virus (HCV) is predominantly transmitted between persons who inject drugs. For this population, global prevalence of HCV infection is high and incarceration is common and an independent risk factor for HCV acquisition. To explore HCV transmission dynamics in incarcerated populations, we integrated virus sequences with risk behavior and spatiotemporal data and analyzed transmission clusters among prisoners in Australia. We detected 3 clusters of recent HCV transmission consisting of 4 likely in-custody transmission events involving source/recipient pairs located in the same prison at the same time. Of these 4 events, 3 were associated with drug injecting and equipment sharing. Despite a large population of prisoners with chronic HCV, recent transmission events were identified in the prison setting. This ongoing HCV transmission among high-risk prisoners argues for expansion of prevention programs to reduce HCV transmission in prisons.

Self-Reported HIV and HCV Screening Rates and Serostatus Among Substance Abuse Treatment Patients

Substance users are at increased risk for HIV and HCV infection. Still, many substance use treatment programs (SUTP) fail to offer HIV/HCV testing. The present secondary analysis of screening data from a multi-site randomized trial of rapid HIV testing examines self-reported HIV/HCV testing patterns and serostatus of 2473 SUTP patients in 12 community-based sites that had not previously offered on-site testing. Results indicate that most respondents screened for the randomized trial tested more than a year prior to intake for HIV (52 %) and HCV (38 %). Prevalence rates were 3.6 and 30 % for HIV and HCV, respectively. The majority of participants that were HIV (52.2 %) and HCV-positive (40.5 %) reported having been diagnosed within the last 1-5 years. Multivariable logistic regression showed that members of high-risk groups were more likely to have tested. Bundled HIV/HCV testing and linkage to care issues are recommended for expanding testing in community-based SUTP settings.

Risk environments facing potential users of a supervised injection site in Ottawa, Canada

Background

Supervised injection sites (SISs) have been effective in reducing health risks among people who inject drugs (PWID), including those who face issues of homelessness, mental health illness, interactions with local policing practices, and HIV infection. We investigate the risk behaviours and risk environments currently faced by potential users of an SIS in Ottawa to establish the need for such a service and to contribute to the design of an SIS that can address current health risks and reduce harm.

Methods

The PROUD cohort is a community-based participatory research (CBPR) project that examines the HIV risk environment among people who use drugs in Ottawa. From March to October 2013, 593 people who reported using injection drugs or smoking crack cocaine were enrolled through street-based recruitment in the ByWard Market neighbourhood, an area of the city with a high concentration of public drug use and homelessness. Participants completed a demographic, behavioural, and risk environment questionnaire and were offered HIV point-of-care testing. We undertook descriptive and univariate analyses to estimate potential use of an SIS by PWID in Ottawa and to explore risk behaviours and features of the risk environment faced by potential users of the service.

Results

Of those participants who reported injecting drugs in the previous 12 months (n = 270), 75.2 % (203) reported a willingness to use an SIS in Ottawa. Among potential SIS users, 24.6 % had recently injected with a used needle, 19.0 % had trouble accessing new needles, 60.6 % were unstably housed, 49.8 % had been redzoned by the police, and 12.8 % were HIV positive. Participants willing to use an SIS more frequently injected in public (OR = 1.98, 95 % CI = 1.06–3.70), required assistance to inject (OR = 1.84, 95 % CI = 1.00–3.38), were hepatitis C positive (OR = 2.13, 95 % CI = 1.16–3.91), had overdosed in the previous year (OR = 2.00, 95 % CI = 1.02–3.92), and identified as LGBTQ (OR = 5.61, 95 % CI = 1.30–24.19).

Conclusion

An SIS in Ottawa would be well-positioned to reach its target group of highly marginalized PWID and reduce drug-related harms. The application of CBPR methods to a large-scale quantitative survey supported the mobilization of communities of PWID to identify and advocate for their own service needs, creating an enabling environment for harm reduction action.

Injecting drug use: A vector for the introduction of new hepatitis C virus genotypes

Hepatitis C virus (HCV) genotypes’ monitoring allows real-time insight into the dynamic changes that occur in the global epidemiological picture of HCV infection. Intravenous drug use is currently the primary driver for HCV transmission in developed and developing countries. The distribution of HCV genotypes/subtypes differs significantly between people who inject drugs (PWID) and the general population. HCV genotypes that previously exhibited a limited geographical distribution (3a, 4) are becoming more prevalent in this high-risk group. Immigration from HCV-endemic countries and the evolving networks of HCV transmission in PWID influence HCV genotypes distribution in Europe. Social vulnerabilities (e.g., unemployment, homelessness, and limited access to social and healthcare insurances systems) are important triggers for illicit drug use, which increases the associated risks of HCV infection and the frequent emergence of less prevalent genotypes. Genotype/subtype determination bears important clinical consequences in the progression of liver disease, susceptibility to antiviral therapies and the emergence of resistance-associated variants. An estimated half of the chronically HCV-infected PWID are unaware of their infection, and only one in ten of those diagnosed enter treatment. Nevertheless, PWID exhibit high response rates to new antiviral regimens, and the level of HCV reinfection is unexpectedly low. The focus of the healthcare system must be on the early detection and treatment of infection, to avoid late presentations that are associated with high levels of viremia and liver fibrosis, which may diminish the therapeutic success rate.

Correlates of HIV testing and receipt of test results in addiction health services in Los Angeles County

Background

HIV testing and receipt of HIV test results among individuals with substance use disorders is less than optimal. We examined rates and correlates of HIV testing and receipt of test results in one of the largest public addiction health services systems in the United States.

Methods

The study included 139,516 adult clients in treatment between 2006 and 2011. We used logistic regression models to examine associations between predisposing, enabling, and need factors and two dependent variables, HIV testing rates and receipt of test results. Associations were considered statistically significance at p < .01.

Results

We found that 64 % of clients reported being tested for HIV, of whom 85 % reported receiving their test results. Likelihood of being tested was positively associated with being female, a minority, homeless, employed, having prior treatment episodes, comorbidities, injection drug use, or a history of mental illness. It was negatively associated with alcohol or marijuana as primary drug. Receipt of test results was more likely among clients on medication (methadone or buprenorphine) or whose method of drug use was smoking, inhalation, or injecting; it was less likely among older clients and those with more outpatient psychiatric visits.

Conclusions

Findings from this study may inform strategies and targeting of population groups to improve HIV testing practices and ultimately increase awareness of infection status among clients of addiction health services.

Hepatitis C virus infection and pain sensitivity in patients on methadone or buprenorphine maintenance therapy for opioid use disorders

BACKGROUND

Patients with opioid use disorders on opioid agonist therapy (OAT) have lower pain tolerance compared to controls. While chronic viral infections such as HCV and HIV have been associated with chronic pain in this population, no studies have examined their impact on pain sensitivity.

METHODS

We recruited 106 adults (41 uninfected controls; 40 HCV mono-infected; and 25 HCV/HIV co-infected) on buprenorphine or methadone to assess whether HCV infection (with or without HIV) was associated with increased experimental pain sensitivity and self-reported pain. The primary outcome was cold pain tolerance assessed by cold-pressor test. Secondary outcomes were cold pain thresholds, wind-up ratios to repetitive mechanical stimulation (i.e., temporal summation) and acute and chronic pain. Multivariable regression models evaluated associations between viral infection status and outcomes, adjusting for other factors.

RESULTS

No significant differences were detected across groups for primary or secondary outcomes. Adjusted mean cold pain tolerance was 25.7 (uninfected controls) vs. 26.8 (HCV mono-infection) vs. 25.3 (HCV/HIV co-infection) seconds (global p-value=0.93). Current pain appeared more prevalent among HCV mono-infected (93%) compared to HCV/HIV co-infected participants (76%) and uninfected controls (80%), as did chronic pain (77% vs. 64% vs. 61%, respectively). However, differences were not statistically significant in multivariable models.

CONCLUSION

This study did not detect an association between HCV infection and increased sensitivity to pain among adults with and without HIV who were treated with buprenorphine or methadone for opioid use disorders. Results reinforce that pain and hyperalgesia are common problems in this population.

Methamphetamine injecting is associated with phylogenetic clustering of hepatitis C virus infection among street-involved youth in Vancouver, Canada

BACKGROUND

Among prospective cohorts of people who inject drugs (PWID), phylogenetic clustering of HCV infection has been observed. However, the majority of studies have included older PWID, representing distant transmission events. The aim of this study was to investigate phylogenetic clustering of HCV infection among a cohort of street-involved youth.

METHODS

Data were derived from a prospective cohort of street-involved youth aged 14-26 recruited between 2005 and 2012 in Vancouver, Canada (At Risk Youth Study, ARYS). HCV RNA testing and sequencing (Core-E2) were performed on HCV positive participants. Phylogenetic trees were inferred using maximum likelihood methods and clusters were identified using ClusterPicker (Core-E2 without HVR1, 90% bootstrap threshold, 0.05 genetic distance threshold).

RESULTS

Among 945 individuals enrolled in ARYS, 16% (n=149, 100% recent injectors) were HCV antibody positive at baseline interview (n=86) or seroconverted during follow-up (n=63). Among HCV antibody positive participants with available samples (n=131), 75% (n=98) had detectable HCV RNA and 66% (n=65, mean age 23, 58% with recent methamphetamine injection, 31% female, 3% HIV+) had available Core-E2 sequences. Of those with Core-E2 sequence, 14% (n=9) were in a cluster (one cluster of three) or pair (two pairs), with all reporting recent methamphetamine injection. Recent methamphetamine injection was associated with membership in a cluster or pair (P=0.009).

CONCLUSION

In this study of street-involved youth with HCV infection and recent injecting, 14% demonstrated phylogenetic clustering. Phylogenetic clustering was associated with recent methamphetamine injection, suggesting that methamphetamine drug injection may play an important role in networks of HCV transmission.

Next generation sequencing of the hepatitis C virus NS5B gene reveals potential novel S282 drug resistance mutations

Identifying HCV drug resistance mutations (DRMs) is increasingly important as new direct acting antiviral therapies (DAA) become available. Tagged pooled pyrosequencing (TPP) was originally developed as cost-effective approach for detecting low abundance HIV DRMs. Using 127 HCV-positive samples from a Canadian injection drug user cohort, we demonstrated the suitability and efficiency of TPP for evaluating DRMs in HCV NS5B gene. At a mutation identification threshold of 1%, no nucleoside inhibitor DRMs were detected among these DAA naïve subjects. Clinical NS5B resistance to non-nucleoside inhibitors and interferon/ribavirin was predicted to be low within this cohort. S282T mutation, the primary mutation selected by sofosbuvir in vitro, was not identified while S282G/C/R variants were detected in 9 subjects. Further characterization on these new S282 variants using in silico molecular modeling implied their potential association with resistance. Combining TPP with in silico analysis detects NS5B polymorphisms that may explain differences in treatment outcomes.

Phylogenetic clustering of hepatitis C virus among people who inject drugs in Vancouver, Canada

Little is known about factors associated with hepatitis C virus (HCV) transmission among people who inject drugs (PWID). Phylogenetic clustering and associated factors were evaluated among PWID in Vancouver, Canada. Data were derived from the Vancouver Injection Drug Users Study. Participants who were HCV antibody-positive at enrolment and those with HCV antibody seroconversion during follow-up (1996 to 2012) were tested for HCV RNA and sequenced (Core-E2 region). Phylogenetic trees were inferred using maximum likelihood analysis and clusters were identified using ClusterPicker (90% bootstrap threshold, 0.05 genetic distance threshold). Factors associated with clustering were assessed using logistic regression. Among 655 eligible participants, HCV genotype prevalence was: G1a: 48% (n=313), G1b: 6% (n=41), G2a: 3% (n=20), G2b: 7% (n=46), G3a: 33% (n=213), G4a: <1% (n=4), G6a: 1% (n=8), G6e: <1% (n=1), and unclassifiable: 1% (n=9). The mean age was 36 years, 162 (25%) were female, and 164 (25%) were HIV+. Among 501 participants with HCV G1a and G3a, 31% (n=156) were in a pair/cluster. Factors independently associated with phylogenetic clustering included: age <40 (versus age≥40, adjusted odds ratio [AOR]=1.64; 95% confidence interval [CI] 1.03, 2.63), human immunodeficiency virus (HIV) infection (AOR=1.82; 95% CI 1.18, 2.81), HCV seroconversion (AOR=3.05; 95% CI 1.40, 6.66), and recent syringe borrowing (AOR 1.59; 95% CI 1.07, 2.36).

CONCLUSION

In this sample of PWID, one-third demonstrated phylogenetic clustering. Factors independently associated with phylogenetic clustering included younger age, recent HCV seroconversion, prevalent HIV infection, and recent syringe borrowing. Strategies to enhance the delivery of prevention and/or treatment strategies to those with HIV and recent HCV seroconversion should be explored, given an increased likelihood of HCV transmission in these subpopulations.

A cost-benefit/cost-effectiveness analysis of proposed supervised injection facilities in Ottawa, Canada

BACKGROUND

Supervised injection facilities (SIFs) are venues where people who inject drugs (PWID) have access to a clean and medically supervised environment in which they can safely inject their own illicit drugs. There is currently only one legal SIF in North America: Insite in Vancouver, British Columbia, Canada. The responses and feedback generated by the evaluations of Insite in Vancouver have been overwhelmingly positive. This study assesses whether the above mentioned facility in the Downtown Eastside of Vancouver needs to be expanded to other locations, more specifically that of Canada's capital city, Ottawa.

METHODS

The current study is aimed at contributing to the existing literature on health policy by conducting cost-benefit and cost-effective analyses for the opening of SIFs in Ottawa, Ontario. In particular, the costs of operating numerous SIFs in Ottawa was compared to the savings incurred; this was done after accounting for the prevention of new HIV and Hepatitis C (HCV) infections. To ensure accuracy, two distinct mathematical models and a sensitivity analysis were employed.

RESULTS

The sensitivity analyses conducted with the models reveals the potential for SIFs in Ottawa to be a fiscally responsible harm reduction strategy for the prevention of HCV cases--when considered independently. With a baseline sharing rate of 19%, the cumulative annual cost model supported the establishment of two SIFs and the marginal annual cost model supported the establishment of a single SIF. More often, the prevention of HIV or HCV alone were not sufficient to justify the establishment cost-effectiveness; rather, only when both HIV and HCV are considered does sufficient economic support became apparent.

CONCLUSIONS

Funded supervised injection facilities in Ottawa appear to be an efficient and effective use of financial resources in the public health domain.

Community-level income inequality and HIV prevalence among persons who inject drugs in Thai Nguyen, Vietnam

Socioeconomic status has a robust positive relationship with several health outcomes at the individual and population levels, but in the case of HIV prevalence, income inequality may be a better predictor than absolute level of income. Most studies showing a relationship between income inequality and HIV have used entire countries as the unit of analysis. In this study, we examine the association between income inequality at the community level and HIV prevalence in a sample of persons who inject drugs (PWID) in a concentrated epidemic setting. We recruited PWID and non-PWID community participants in Thai Nguyen, Vietnam, and administered a cross-sectional questionnaire; PWID were tested for HIV. We used ecologic regression to model HIV burden in our PWID study population on GINI indices of inequality calculated from total reported incomes of non-PWID community members in each commune. We also modeled HIV burden on interaction terms between GINI index and median commune income, and finally used a multi-level model to control for community level inequality and individual level income. HIV burden among PWID was significantly correlated with the commune GINI coefficient (r = 0.53, p = 0.002). HIV burden was also associated with GINI coefficient (β = 0.082, p = 0.008) and with median commune income (β = −0.018, p = 0.023) in ecological regression. In the multi-level model, higher GINI coefficient at the community level was associated with higher odds of individual HIV infection in PWID (OR = 1.46 per 0.01, p = 0.003) while higher personal income was associated with reduced odds of infection (OR = 0.98 per $10, p = 0.022). This study demonstrates a context where income inequality is associated with HIV prevalence at the community level in a concentrated epidemic. It further suggests that community level socioeconomic factors, both contextual and compositional, could be indirect determinants of HIV infection in PWID.

Social network structure and HIV infection among injecting drug users in Lithuania: gatekeepers as bridges of infection

The aim of the study was to assess-while controlling for individual risk characteristics-how certain social network structural characteristics (degree, eigenvector, and betweenness centrality) are related to HIV infections. Injecting drug users (N = 299) in Vilnius, Lithuania were recruited using incentivized chain referral sampling for a cross-sectional study. Sociometric social links were established between participants, and UCINET was used to calculate network measures. HIV prevalence was 10 %, and all except two knew they were infected. Of the five variables that remained significant in the final multivariate model, one showed temporal cumulative infection risk (more years since first drug injecting), three reflected informed altruism (always using condoms, less distributive syringe sharing and having not more than one sex partner), and one pointed to the importance of social network structure (betweenness centrality, indicating bridge populations). Loess regression indicates that betweenness may have the highest impact on HIV prevalence (about 60 vs. 20 % estimated HIV prevalence for the highest betweenness centrality values vs. highest age values). This analysis contributes to existing evidence showing both potential informed altruism (or maybe social desirability bias) in connection with HIV infection, and a link between HIV infection risk and the role of bridges within the social network of injecting drug user populations. These findings suggest the importance of harm reduction activities, including confidential testing and counseling, and of social network interventions.

Automated analysis of phylogenetic clusters

BACKGROUND

As sequence data sets used for the investigation of pathogen transmission patterns increase in size, automated tools and standardized methods for cluster analysis have become necessary. We have developed an automated Cluster Picker which identifies monophyletic clades meeting user-input criteria for bootstrap support and maximum genetic distance within large phylogenetic trees. A second tool, the Cluster Matcher, automates the process of linking genetic data to epidemiological or clinical data, and matches clusters between runs of the Cluster Picker.

RESULTS

We explore the effect of different bootstrap and genetic distance thresholds on clusters identified in a data set of publicly available HIV sequences, and compare these results to those of a previously published tool for cluster identification. To demonstrate their utility, we then use the Cluster Picker and Cluster Matcher together to investigate how clusters in the data set changed over time. We find that clusters containing sequences from more than one UK location at the first time point (multiple origin) were significantly more likely to grow than those representing only a single location.

CONCLUSIONS

The Cluster Picker and Cluster Matcher can rapidly process phylogenetic trees containing tens of thousands of sequences. Together these tools will facilitate comparisons of pathogen transmission dynamics between studies and countries.

Decreased injecting is associated with increased alcohol consumption among injecting drug users in northern Vietnam

BACKGROUND

Reducing injecting frequency may reduce the risk of HIV infection and improve health outcomes among injection drug users (IDUs). However, the reduction of one risk behavior may be associated with an increase in other risk behaviors, including the use of other risk-associated substances. Our objective was to determine if an association exists between a reduction in injecting and level of alcohol use among IDU.

METHODS

We conducted a longitudinal analysis of data collected for a randomized controlled trial examining the efficacy of a peer education intervention in reducing HIV risk among IDU and their network members in Thai Nguyen, Vietnam. Our analysis included active male injectors (n = 629) who were study participants and attended both baseline and 3-month visits. Frequency of alcohol consumption was assessed as the number of alcoholic drinks in the past 30 days. Change in risk and outcome behaviors was calculated as the difference in frequencies of behaviors between baseline and 3-month follow-up visits. The outcome of interest was concurrent decreased drug injection and increased alcohol consumption.

RESULTS

The mean difference between baseline and 3-month follow-up of alcohol consumption and injection frequency in the past 30 days was 19.03 drinks (93.68 SD) and 20.22 injections (35.66 SD), respectively. Participants who reported reduced injection frequency were almost three times as likely to report increased alcohol consumption (OR 2.8; 95% CI, 2.0, 4.0). The proportion that both decreased injecting and increased alcohol by any amount in the past 30 days was 35.6%. In multivariate analysis higher education was significantly associated with an increase in alcohol and decrease in injecting of any amount.

CONCLUSION

Male IDU may be at risk for increasing alcohol consumption when they reduce injection frequency. Interventions with male IDU that encourage reduction of injection may need to review specific strategies to limit alcohol consumption.

Social network-based recruitment successfully reveals HIV-1 transmission networks among high-risk individuals in El Salvador

OBJECTIVE

HIV in Central America is concentrated among certain groups such as men who have sex with men (MSM) and female sex workers (FSWs). We compared social recruitment chains and HIV transmission clusters from 699 MSM and 787 FSWs to better understand factors contributing to ongoing HIV transmission in El Salvador.

METHODS

Phylogenies were reconstructed using pol sequences from 119 HIV-positive individuals recruited by respondent-driven sampling (RDS) and compared with RDS chains in 3 cities in El Salvador. Transmission clusters with a mean pairwise genetic distance ≤ 0.015 and Bayesian posterior probabilities =1 were identified. Factors associated with cluster membership were evaluated among MSM.

RESULTS

Sequences from 34 (43%) MSM and 4 (10%) FSW grouped in 14 transmission clusters. Clusters were defined by risk group (12 MSM clusters) and geographic residence (only 1 spanned separate cities). In 4 MSM clusters (all n = 2), individuals were also members of the same RDS chain, but only 2 had members directly linked through recruitment. All large clusters (n ≥ 3) spanned >1 RDS chain. Among MSM, factors independently associated with cluster membership included recent infection by BED assay (P = 0.02), sex with stable male partners (P = 0.02), and sex with ≥ 3 male partners in the past year (P = 0.04).

CONCLUSIONS

We found few HIV transmissions corresponding directly with the social recruitment. However, we identified clustering in nearly one-half of MSM suggesting that RDS recruitment was indirectly but successfully uncovering transmission networks, particularly among recent infections. Interrogating RDS chains with phylogenetic analyses may help refine methods for identifying transmission clusters.