Molecular epidemiology of newly acquired hepatitis C infections in England 2008-2011: genotype, phylogeny and mutation analysis

A latent class approach to identify multi-risk profiles associated with phylogenetic clustering of recent hepatitis C virus infection in Australia and New Zealand from 2004 to 2015

INTRODUCTION

Over the last two decades, the incidence of hepatitis C virus (HCV) co-infection among men who have sex with men (MSM) living with HIV began increasing in post-industrialized countries. Little is known about transmission of acute or recent HCV, in particular among MSM living with HIV co-infection, which creates uncertainty about potential for reinfection after HCV treatment. Using phylogenetic methods, clinical, epidemiological and molecular data can be combined to better understand transmission patterns. These insights may help identify strategies to reduce reinfection risk, enhancing effectiveness of HCV treatment as prevention strategies. The aim of this study was to identify multi-risk profiles and factors associated with phylogenetic pairs and clusters among people with recent HCV infection.

METHODS

Data and specimens from five studies of recent HCV in Australia and New Zealand (2004 to 2015) were used. HCV Core-E2 sequences were used to infer maximum likelihood trees. Clusters were identified using 90% bootstrap and 5% genetic distance threshold. Multivariate logistic regression and latent class analyses were performed.

RESULTS

Among 237 participants with Core-E2 sequences, 47% were in a pair/cluster. Among HIV/HCV co-infected participants, 60% (74/123) were in a pair/cluster, compared to 30% (34/114) with HCV mono-infection (p < 0.001). HIV/HCV co-infection (vs. HCV mono-infection; adjusted odds ratio (AOR), 2.37, 95% confidence interval (CI), 1.45, 5.15) was independently associated with phylogenetic clustering. Latent class analysis identified three distinct risk profiles: (1) people who inject drugs, (2) HIV-positive gay and bisexual men (GBM) with low probability of injecting drug use (IDU) and (3) GBM with IDU & sexual risk behaviour. Class 2 (vs. Class 1, AOR 3.40; 95% CI, 1.52, 7.60), was independently associated with phylogenetic clustering. Many clusters displayed homogeneous characteristics, such as containing individuals exclusively from one city, individuals all with HIV/HCV co-infection or individuals sharing the same route of acquisition of HCV.

CONCLUSIONS

Clusters containing individuals with specific characteristics suggest that HCV transmission occurs through discrete networks, particularly among HIV/HCV co-infected individuals. The greater proportion of clustering found among HIV/HCV co-infected participants highlights the need to provide broad direct-acting antiviral access encouraging rapid uptake in this population and ongoing monitoring of the phylogeny.

Dissecting the decline of hepatitis C in first-time donors in England and Wales

BACKGROUND AND OBJECTIVES

The rate of confirmed hepatitis C virus (HCV) cases, in first-time donors, is much lower in 2015 than 20 years ago. We investigate reasons for the decline.

MATERIALS AND METHODS

HCV rates were analysed by gender and birth cohort for 1996 to 2015 and ethnic group for 2006 to 2015. Variables for confirmed positive cases were compared for two ten-year periods (1996 to 2005 and 2006 to 2015) including genotyping data for 2006 to 2015.

RESULTS

There were 2007 confirmed HCV cases identified between 1996 and 2015. The rate per 100 000 donations fell from 78·6 in 1996 to 26·9 by 2015. By birth cohort, HCV rates were highest in donors born in the 1950s and 1960s who contributed a decreasing proportion of first-time donors. Between 2006 and 2015, there was no significant decline in HCV rate. The HCV-positive donor profile has changed in the last 10 years with increased proportions of younger donors, donors born abroad and decreased reported injecting drug use. Genotype 1a remains predominate, but genotype 1b has increased associated with this change in birth cohort and ethnicity.

CONCLUSION

The decline in number and rate of confirmed HCV-positive first-time donors is mainly due to a decrease in first-time donors born before 1970, with the highest rate of HCV. However, the decline has slowed and the profile of HCV-positive first-time donors is changing. A better understanding of behaviour and sources of HCV in younger and ethnic minority donors are needed.

Exposure to hepatitis C virus in homeless men in Central Brazil: a cross-sectional study

Background

Homeless men are highly vulnerable to acquisition of the hepatitis C virus (HCV) compared to the general population. In Brazil, a country of continental dimensions, the extent of HCV infection in this population remains unknown. The objective of this study is to investigate the epidemiological profile of exposure to HCV in homeless men in Central Brazil.

Methods

A Cross-sectional study was conducted in 481 men aged over 18 years attending therapeutic communities specialized in the recovery and reintegration of homeless people. Participants were tested for anti-HCV markers using rapid tests. Poisson regression analysis was used to verify the risk factors associated with exposure to HCV.

Results

The prevalence of HCV exposure was 2.5% (95.0% CI: 1.4 to 4.3%) and was associated with age, absence of family life, injection drug use, number of sexual partners, and history of sexually transmitted infections (STI). Participants reported multiple risk behaviors, such as alcohol (78.9%), cocaine (37.1%) and/or crack use (53.1%), and inconsistent condom use (82.6%). Injection drug use was reported by 8.7% of participants.

Conclusions

The prevalence of HCV infection among homeless men was relatively high. Several risk behaviors were commonly reported, which shows the high vulnerability of this population. These findings emphasize the need for the development of specific strategies to reduce the risk of HCV among homeless men.

Use of genome sequencing to identify hepatitis C virus transmission in a renal healthcare setting

BACKGROUND

Hepatitis C virus (HCV) infection is a major health burden worldwide. A patient with no history of HCV infection while on a renal unit was found to seroconvert to HCV.

AIM

To report the use of sequencing to postulate how transmission of HCV occurred in a healthcare setting, and how this guided our outbreak investigation.

FINDINGS

Based on infection control inspections the transmission event was surmised to be due to ward environmental contamination with blood and subsequent inoculation from intravenous interventions on the patient acquiring HCV. We discuss the interventions put in place in response to the outbreak investigation findings.

CONCLUSION

Sequencing of healthcare-acquired HCV infections should be undertaken as routine practice in outbreak investigations.

Limited naturally occurring escape in broadly neutralizing antibody epitopes in hepatitis C glycoprotein E2 and constrained sequence usage in acute infection

Broadly neutralizing antibodies have been associated with spontaneous clearance of the hepatitis C infection as well as viral persistence by immune escape. Further study of neutralizing antibody epitopes is needed to unravel pathways of resistance to virus neutralization, and to identify conserved regions for vaccine design. All reported broadly neutralizing antibody (BNAb) epitopes in the HCV Envelope (E2) glycoprotein were identified. The critical contact residues of these epitopes were mapped onto the linear E2 sequence. All publicly available E2 sequences were then downloaded and the contact residues within the BNAb epitopes were assessed for the level of conservation, as well as the frequency of occurrence of experimentally-proven resistance mutations. Epitopes were also compared between two sequence datasets obtained from samples collected at well-defined time points from acute (<180days) and chronic (>180days) infections, to identify any significant differences in residue usage. The contact residues for all BNAbs were contained within 3 linear regions of the E2 protein sequence. An analysis of 1749 full length E2 sequences from public databases showed that only 10 out of 29 experimentally-proven resistance mutations were present at a frequency >5%. Comparison of subtype 1a viral sequences obtained from samples collected during acute or chronic infection revealed significant differences at positions 610 and 655 with changes in residue (p<0.05), and at position 422 (p<0.001) with a significant difference in variability (entropy). The majority of experimentally-described escape variants do not occur frequently in nature. The observed differences between acute and chronically isolated sequences suggest constraints on residue usage early in infection.

Hepatitis C virus (HCV) genotypes distribution: an epidemiological up-date in Europe

Hepatitis C virus (HCV) infection is a major public health burden in Europe, causing an increasing level of liver-related morbidity and mortality, characterized by several regional variations in the genotypes distribution.

A comprehensive review of the literature from 2000 to 2015 was used to gather country-specific data on prevalence and genotype distribution of HCV infection in 33 European countries (about 80 % of the European population), grouped in three geographical areas (Western, Eastern and Central Europe), as defined by the Global Burden of Diseases project (GBD).

The estimated prevalence of HCV in Europe is 1.7 % showing a decrease than previously reported (− 0.6 %) and accounting over 13 million of estimated cases. The lowest prevalence (0.9 %) is reported from Western Europe (except for some rural areas of Southern Italy and Greece) and the highest (3.1 %) from Central Europe, especially Romania and Russia. The average HCV viraemic rate is 72.4 %, with a population of almost 10 million of HCV RNA positive patients.

Genotype distribution does not show high variability among the three macro-areas studied, ranging between 70.0 % (Central Europe), 68.1 % (Eastern Europe) and 55.1 % (Western Europe) for genotype 1, 29.0 % (Western Europe), 26.6 % (Eastern Europe) and 21.0 % (Central Europe) for genotype 3. Genotype 2 seems, instead, to have a major prevalence in the Western Europe (8.9 %), if compared to Eastern (4.3 %) or Central (3.2 %), whereas genotype 4 is present especially in Central and Western area (4.9 % and 5.8 %, respectively).

Despite the eradication of transmission by blood products, HCV infection continues to be one of the leading blood-borne infections in Europe. The aim of this review is, therefore, to provide an update on the epidemiology of HCV infection across Europe, and to foster the discussion about eventual potential strategies to eradicate it.

Adaptive immunity in the liver

The anatomical architecture of the human liver and the diversity of its immune components endow the liver with its physiological function of immune competence. Adaptive immunity is a major arm of the immune system that is organized in a highly specialized and systematic manner, thus providing long-lasting protection with immunological memory. Adaptive immunity consists of humoral immunity and cellular immunity. Cellular immunity is known to have a crucial role in controlling infection, cancer and autoimmune disorders in the liver. In this article, we will focus on hepatic virus infections, hepatocellular carcinoma and autoimmune disorders as examples to illustrate the current understanding of the contribution of T cells to cellular immunity in these maladies. Cellular immune suppression is primarily responsible for chronic viral infections and cancer. However, an uncontrolled auto-reactive immune response accounts for autoimmunity. Consequently, these immune abnormalities are ascribed to the quantitative and functional changes in adaptive immune cells and their subsets, innate immunocytes, chemokines, cytokines and various surface receptors on immune cells. A greater understanding of the complex orchestration of the hepatic adaptive immune regulators during homeostasis and immune competence are much needed to identify relevant targets for clinical intervention to treat immunological disorders in the liver.