Spatiotemporal Phylodynamics of Hepatitis C Among People Who Inject Drugs in India

Abstract

BaCKgRoUND aND aIMS: Implementing effective interventions for HCV requires a detailed understanding of local transmission dynamics and geospatial spread. Little is known about HCV phylodynamics, particularly among high-burden populations, such as people who inject drugs (PWID).

Molecular Epidemiology and Baseline Resistance of Hepatitis C Virus to Direct Acting Antivirals in Croatia

“…Sequence analysis of fast evolving viruses such as HCV was shown to be efficient method for viral transmission tracing [ 16 , 17 , 49 , 51 ]. Phylogenetic analysis demonstrated that 27 (9.0%) of Croatian HCV sequences had a presumed epidemiological link with another sequence and classified into 13 transmission pairs or clusters which were the most common in GT3a, while IDU was shown to be a risk factor statistically associated with clustering.…”

“…Hackman et al (2020) found that 46% of 820 community recruited IDU in Baltimore had genetically linked HCV infections with an average cluster size of 2–3 patients [ 49 ]. Clipman et al (2021) analysed 483 HCV sequences from IDU in India and found transmission cluster prevalence of 28.8% with a median cluster size of three individuals [ 16 ]. Cluster analysis showed that younger age (<35 years) was significantly associated with being in a cluster, similarly to our study [ 16 , 50 ].…”

“…Clipman et al (2021) analysed 483 HCV sequences from IDU in India and found transmission cluster prevalence of 28.8% with a median cluster size of three individuals [16]. Cluster analysis showed that younger age (<35 years) was significantly associated with being in a cluster, similarly to our study [16,50]. A study by Parczewski et al (2018) showed that sequences obtained from patients with F3-F4 liver fibrosis less commonly formed clusters and pairs (22.2% vs. 43.7%, p < 0.001) and that NS5A RAS were less frequent among clustered sequences (5.2% vs. 11.2%, p = 0.039) [55].…”

“…In Croatia, blood transfusion and haemodialysis before 1992 were strongly associated with an infection with HCV GT1, especially subtype 1b (GT1b) [ 11 , 14 ]. Today, intravenous drug use represents the major route of HCV transmission in developed countries, with a prevalence of 2–80% among intravenous drug users (IDU) [ 15 , 16 , 17 ]. Estimated population size of IDU in Croatia is around 15,000, and the most common HCV subtypes in this population are subtype 3a (GT3a) (61%) and subtype 1a (GT1a) (24%) [ 11 , 18 ].…”

Plasma Virome Reveals Blooms and Transmission of Anellovirus in Intravenous Drug Users with HIV-1, HCV, and/or HBV Infections

“…Phylogenetic trees based on nucleotide sequences were generated using the bootstrap method (1,000 times) under a GTR+G model. According to previous studies of HIV-1 and HCV ( 72 ), we used a stringent threshold of 1% genetic distance for the detection of transmission clusters (TC) of pegiviruses.…”