HCV Phylogeography of the General Population and High-Risk Groups in Cyprus Identifies the Island as a Global Sink for and Source of Infection

Abstract

Hepatitis C virus (HCV) genotype and subtype distribution differs according to geographic origin and transmission risk category. Previous molecular epidemiology studies suggest the presence of multiple subtypes among Cypriot subjects. To investigate HCV genotype- and subtype-specific dissemination patterns, origins, and transmission in Cyprus, we analyzed HCV sequences encoding partial Core-E1 and NS5B regions. Analyzed populations comprised the general population and high-risk cohorts in Cyprus and a globally sampled dataset. Maximum-likelihood phylogeny reconstruction with bootstrap evaluation, character reconstruction using parsimony, and bootstrap trees estimated by ML were performed to identify the geographic origin of HCV subtypes and statistically significant dispersal pathways among geographic regions. Phylogeographic analyses traced the origin of subtypes in the general population and among PWID in Cyprus to unique and overlapping globally distributed regions. Phylogenetic analysis in Core-E1 revealed that most sequences from incarcerated populations in Cyprus clustered with the general population and PWID. We estimate that HCV infections in Cyprus originate from multiple global sources while most HCV transmissions among incarcerated individuals occur locally. This analysis is one of a few studies tracing HCV dispersal patterns using global datasets, and these practices and findings should inform how HCV epidemics are targeted by future prevention policies.

Simultaneous Hepatitis C Virus Genotyping and Variant Detection in Patients with Thalassemia: A Single-Center Phylogenetic Study

“…Moreover, both core/E1 and NS5B regions could be used for phylogenetic analysis. 17 Whole-genome sequencing or complete genome sequencing is another high-throughput method for HCV subtype determination. There are a few studies focused on phylogenetic analysis of HCV subtypes in Iran.…”

Simultaneous determination of HCV genotype and NS5B resistance associated substitutions using dried serum spots from São Paulo state, Brazil

“…Sequences were trimmed to 288 bases in length corresponding to 8311–8598 of H77 reference, accession NC_004102. The curated NS5B sequences were uploaded to seven different online HCV subtyping tools to compare outcomes: [ 1 ] Los Alamos database (LANL) [ 47 ]; [ 2 ] Virus Pathogen Database and Analysis (VIRP) [ 48 ]; [ 3 ] Oxford HCV automated subtyping tool (version 2.0) [ 49 ]; [ 4 ] NCBI genotyping tool [ 50 ]; [ 5 ] Geno2Pheno HCV Subtyping tool [ 51 ]; [ 6 ] HCV Comet [ 52 ]; and [ 7 ] HCV Glue Subtyping tool [ 53 ]. Further characterization of the sequences was performed by phylogenetic analysis using each confirmed HCV genotypes/subtypes for easy visualization/visibility from reference datasets in the International Committee on Taxonomy of Viruses (ICTV) to determine HCV subtype [ 15 ].…”

“…Hepatitis C virus (HCV) is a major cause of chronic hepatitis and hepatocellular carcinoma globally [1]. This pathogen has infected nearly 180 million people worldwide [2,3], and about 80 % of infections are reported in Low and Middle-income countries (LMICs) [4,5]. Despite this high prevalence rate, data on molecular epidemiology of HCV seem relatively scarce in LMICs, which can be associated with a lack of adequate throughput facilities to study the virus [6,7].…”

Hepatitis C virus subtype diversity and transmission clusters characteristics among drug users in Zhuhai, South China

“…Hepatitis C virus (HCV) infection can cause both acute and chronic hepatitis and is considered to be the leading cause of liver cirrhosis, hepatocellular carcinoma, and liver-related death, representing a significant public health issue globally [ 1 ]. The primary transmission routes of HCV include sharing contaminated needles and syringes for injecting drugs, transfusion of contaminated blood or blood products, engaging in unsafe sexual practices, and so forth [ 2 , 3 ].…”