Phylogenetic Transmission Clusters of Hepatitis C Virus Among People Who Use Drugs Who Access Harm Reduction Services in Three South African Cities, 2016 – 2017

Author: Nkosenhle Ndlovu Nishi Prabdial-Sing

Theme: Epidemiology & Public Health Research Year: 2022

People who inject drugs (PWID) including men who have sex with men who use drugs (MSM/UD),
are disproportionately infected with HCV in SA. Samples were collected from PWID and MSM/UD
with HCV viraemia in three South African cities (Pretoria, Durban, and Cape Town) as part of a larger
study. 99% of infections were HCV genotypes 1 or 3. Infection transmission dynamics can be
inferred using phylogenetic clustering, which can inform prevention interventions. We aimed to use
genetic sequence and demographic data to investigate factors associated with HCV phylogenetic
clustering among PWID and MSM/UD in SA.
RNA Sanger sequencing of the Core-E2 was performed for genotypes 1 and 3. Descriptive analysis
of the demographic data was conducted on sequenced samples. Phylogenetic trees were inferred
using maximum likelihood implemented in RAxML (Cipres Gateway). Clusters were determined on
Clusterpicker using a 90% bootstrap threshold and a genetic cut-off of 0.035. Factors associated with
clustering were assessed using logistic regression (STATA 17).
The Core-E2 was amplified on 232 samples and successfully sequenced for 130 participants.
Phylogenetic clustering was found with 55% of participants (n = 71), with 44 having genotype 1a and
27 with genotype 3a. Ten clusters were identified, ranging from 3 to 15 participants. Clustering
among the mixed ancestry group in Cape Town was noted with ages 18 – 55 years. Factors
independently associated with phylogenetic clustering included sharing a needle (aOR 4.87, 95% CI
1.20 – 19.79, p 0.027), age ≥29 (aOR 3.02, 95% CI 1.12 – 8.16, p 0.029), and mixed ancestry race (aOR
5.90, 95% CI 1.44 – 24.23, p 0.014).
High clustering suggests transmission especially among the mixed ancestry group in Cape Town.
There is a need to reduce transmission through providing safe injecting equipment and tailored
education for preventing HCV transmission between older experienced drug users with young
Disclosure of Interest Statement:
No conflicts of interest exist.

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