title: HIV infection and hepatitis C virus genotype 1a are associated with phylogenetic clustering among people with recently acquired hepatitis C virus infection.
abstract: The aim of this study was to identify factors associated with phylogenetic clustering among people with recently acquired hepatitis C virus (HCV) infection. Participants with available sample at time of HCV detection were selected from three studies; the Australian Trial in Acute Hepatitis C, the Hepatitis C Incidence and Transmission Study - Prison and Community. HCV RNA was extracted and Core to E2 region of HCV sequenced. Clusters were identified from maximum likelihood trees with 1000 bootstrap replicates using 90% bootstrap and 5% genetic distance threshold. Among 225 participants with available Core-E2 sequence (ATAHC, n=113; HITS-p, n=90; and HITS-c, n=22), HCV genotype prevalence was: G1a: 38% (n=86), G1b: 5% (n=12), G2a: 1% (n=2), G2b: 5% (n=11), G3a: 48% (n=109), G6a: 1% (n=2) and G6l 1% (n=3). Of participants included in phylogenetic trees, 22% of participants were in a pair/cluster (G1a-35%, 30/85, mean maximum genetic distance=0.031; G3a-11%, 12/106, mean maximum genetic distance=0.021; other genotypes-21%, 6/28, mean maximum genetic distance=0.023). Among HCV/HIV co-infected participants, 50% (18/36) were in a pair/cluster, compared to 16% (30/183) with HCV mono-infection (P=<0.001). Factors independently associated with phylogenetic clustering were HIV co-infection [vs. HCV mono-infection; adjusted odds ratio (AOR) 4.24; 95%CI 1.91, 9.39], and HCV G1a infection (vs. other HCV genotypes; AOR 3.33, 95%CI 0.14, 0.61).HCV treatment and prevention strategies, including enhanced antiviral therapy, should be optimised. The impact of targeting of HCV treatment as prevention to populations with higher phylogenetic clustering, such as those with HIV co-infection, could be explored through mathematical modelling.
authors.affiliation: Kirby Institute, UNSW Australia, Sydney, Australia. Electronic address: sbartlett@kirby.unsw.edu.au.
authors.forename: Sofia R
authors.initials: SR
authors.lastname: Bartlett
authors.affiliation: Kirby Institute, UNSW Australia, Sydney, Australia.
authors.forename: Brendan
authors.initials: B
authors.lastname: Jacka
authors.affiliation: Inflammation and Infection Research Centre (IIRC), UNSW Australia, Sydney, Australia.
authors.forename: Rowena A
authors.initials: RA
authors.lastname: Bull
authors.affiliation: Inflammation and Infection Research Centre (IIRC), UNSW Australia, Sydney, Australia.
authors.forename: Fabio
authors.initials: F
authors.lastname: Luciani
authors.affiliation: Kirby Institute, UNSW Australia, Sydney, Australia.
authors.forename: Gail V
authors.initials: GV
authors.lastname: Matthews
authors.affiliation: Kirby Institute, UNSW Australia, Sydney, Australia.
authors.forename: Francois M J
authors.initials: FM
authors.lastname: Lamoury
authors.affiliation: Burnet Institute, Melbourne, Australia.
authors.forename: Margaret E
authors.initials: ME
authors.lastname: Hellard
authors.affiliation: Kirby Institute, UNSW Australia, Sydney, Australia.
authors.forename: Behzad
authors.initials: B
authors.lastname: Hajarizadeh
authors.affiliation: Inflammation and Infection Research Centre (IIRC), UNSW Australia, Sydney, Australia.
authors.forename: Suzy
authors.initials: S
authors.lastname: Teutsch
authors.affiliation: Kirby Institute, UNSW Australia, Sydney, Australia.
authors.forename: Bethany
authors.initials: B
authors.lastname: White
authors.affiliation: Kirby Institute, UNSW Australia, Sydney, Australia.
authors.forename: Lisa
authors.initials: L
authors.lastname: Maher
authors.affiliation: Kirby Institute, UNSW Australia, Sydney, Australia.
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Dore
authors.affiliation: Inflammation and Infection Research Centre (IIRC), UNSW Australia, Sydney, Australia.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Lloyd
authors.affiliation: Kirby Institute, UNSW Australia, Sydney, Australia.
authors.forename: Jason
authors.initials: J
authors.lastname: Grebely
authors.affiliation: Kirby Institute, UNSW Australia, Sydney, Australia.
authors.forename: Tanya L
authors.initials: TL
authors.lastname: Applegate
mesh_terms: D000328:Adult; D001315:Australia; D016000:Cluster Analysis; D060085:Coinfection / Q000821:virology; D005260:Female; D005838:Genotype; D006678:HIV / Q000235:genetics*; D015658:HIV Infections / Q000821:virology*; D016174:Hepacivirus / Q000145:classification / Q000235:genetics*; D006526:Hepatitis C / Q000821:virology*; D006801:Humans; D016013:Likelihood Functions; D008297:Male; D010802:Phylogeny; D012367:RNA, Viral / Q000032:analysis; D017423:Sequence Analysis, RNA; D055815:Young Adult
chemical_list: D012367:RNA, Viral
keywords: Gay and bisexual men; Hepatitis C virus; Human immunodeficiency virus; Molecular epidemiology; People who inject drugs; Prison