Abstract
Background: Injecting drugs substantially increases the risk of hepatitis C virus (HCV) infection and is common in vulnerable population groups, such as the homeless and prisoners. Capturing accurate data on relative genotype distribution within these groups is essential to inform strategies to reduce HCV transmission. The aim of this study was to utilise a next-generation whole-genome sequencing method recently validated by Public Health England, in order to produce near complete HCV genomes. Methods: In total, 98 HCV positive patients were recruited from homeless hostels and drug treatment services through the National Health Services (NHS) Find and Treat (F&T) Service between May 2011 and June 2013 in London, UK. Samples were sequenced by Next-generation sequencing, with 88 complete HCV genomes constructed by a de novo assembly pipeline. They were analysed phylogenetically for an estimate of their genetic distance. Results: Of the 88 complete HCV genomes, 50/88 (56.8%) were genotype 1; 32/88 (36.4%) genotype 3; 4/88 (4.5%) genotype 2; and 1/88 (1.1%) for genotypes 4 and 6 each. Subtype 1a had the highest number of samples (51.1%), followed by subtype 3a (35.2%), 1b (5.7%), and 2b (3.4%). Samples collected from drug treatment services had the highest number of genotype 1 (69%); genotypes 4 and 6 were only found from samples collected in homeless shelters. Small clusters of highly related genomic sequences were observed both across and within the vulnerable groups sampled. Conclusions: Subsequent phylogenetic analysis provides a first indication that there are related HCV sequences amongst the three vulnerable population groups, reflecting their overlapping social behaviours. This study is the first presentation of whole genome HCV sequences from such vulnerable groups in London and paves the way for similar research in the future.
Highlights
Hepatitis C virus (HCV) infection is recognised as the worldwide leading cause of chronic liver disease
Subsequent phylogenetic analysis provides a first indication that there are related hepatitis C virus (HCV) sequences amongst the three vulnerable population groups, reflecting their overlapping social behaviours
This study is the first presentation of whole genome HCV sequences from such vulnerable groups in London and paves the way for similar research in the future
Summary
Hepatitis C virus (HCV) infection is recognised as the worldwide leading cause of chronic liver disease. People who are homeless are known to have high levels of exposure to injecting drug use and are exposed to higher risk of blood borne infections, including by HCV10; they tend to have higher rates of morbidity and mortality related or unrelated to disease[11]. A third related patrisk population group is that of prisoners, who report high risk of HCV infection. Injecting drugs substantially increases the risk of hepatitis C virus (HCV) infection and is common in vulnerable population groups, such as the homeless and prisoners. Samples were sequenced by Nextgeneration sequencing, with 88 complete HCV genomes constructed by a de novo assembly pipeline. They were analysed phylogenetically for an estimate of their genetic distance. Small clusters of highly related genomic sequences were observed both across and within the vulnerable groups sampled
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