Subtype-Specific Prevalence of Hepatitis C Virus NS5A Resistance Associated Substitutions in Mainland China

Abstract

Resistance associated substitutions (RASs) can reduce the efficacy of direct-acting antiviral agents (DAAs) targeting hepatitis C virus (HCV) and lead to treatment failure. Clinical data of HCV NS5A RASs prevalence are limited in China and need to be investigated. A total of 878 unique patient samples with different genotypes (GT) (1b: n = 489, 2a: n = 203, 3a: n = 60, 3b: n = 78, 6a: n = 48) were collected from around mainland China by KingMed Laboratory and analyzed for NS5A RASs distribution by Sanger sequencing. Phylogeographic analyses based on NS5A domain 1 sequences indicated circulation of both locally and nationally epidemic strains. Relatively high frequency of Y93H (14.1%) was only detected in GT1b but not in other subtypes. High frequency of L31M was found in both GT2a (95.6%) and GT3b (98.7%) sequences. Due to the overlapping incidence of A30K, 96% of GT3b isolates had NS5A RASs combination A30K + L31M, which confers high levels of resistance to most NS5A inhibitors. No RASs were detected in GT6a strains. Meanwhile, baseline NS5A RASs fingerprints were also evaluated in 185 DAA treatment-naive GT1b patients with next generation sequencing method. Patients presenting with Y93H had statistically higher entropy of HCV NS5A sequences. Taken together, subtype-specific distribution patterns of NS5A RASs were observed. GT1b patients with higher HCV complexity tend to have a greater chance of Y93H presence, while GT3b patients are naturally resistant to current NS5A inhibitors and their treatment may pose a challenge to real-world DAA application.

DAA failures in African patients with “unusual” HCV subtypes: Hey! Didn’t you know there was another world?

“…Genotype 3, subtype 3b is prevalent in South-East Asia, accounting for 9.7% of cases in a recent study from Thailand 9 and 8.9% in a report from mainland China including 27 provinces or municipalities across the country. 10 In a Chinese single-arm, open-label, phase III trial, 89% of patients infected with subtype 3b without cirrhosis (25/28) and only 50% of those with cirrhosis (7/14 patients) achieved SVR after 12 weeks of sofosbuvir/velpatasvir. 11 Resistance analysis indicated that subtype 3b is inherently resistant to NS5A inhibitors, due to the presence at baseline of the A30K + L31M RAS combination that confers high-level resistance to daclatasvir, elbasvir and velpatasvir and intermediate-level resistance to pibrentasvir.…”

Factors Influencing the Prevalence of Resistance-Associated Substitutions in NS5A Protein in Treatment-Naive Patients with Chronic Hepatitis C

“…The proportion of these variants in the treatment-naïve Russian patients infected with the HCV genotypes 1b and 3a (predominant in Russia [12]) was < 5.5%, except for A30S clinical significance of which is limited. Low prevalence of these RASs in the Russian sequence set mirrored their occurrence in treatment naïve patients in the North America, Europe and China [9,31,32]. Thus, while prevalence of RAS in some positions varies geographically [22,31,32], prevalence of polymorphisms in positions 30, 31, and 93 is not subjected to significant geographical variations.…”

“…Low prevalence of these RASs in the Russian sequence set mirrored their occurrence in treatment naïve patients in the North America, Europe and China [9,31,32]. Thus, while prevalence of RAS in some positions varies geographically [22,31,32], prevalence of polymorphisms in positions 30, 31, and 93 is not subjected to significant geographical variations. At the same time, the M28V polymorphism in the Russian strains of HCV genotype 1a was found to be unexpectedly frequent (57.9%).…”

“…HCV NS5A is composed of three domains (DI, DII, and DIII) separated by two linker regions [40]. The majority of the known RAS-associated residues of NS5A protein are located within the linker between amphipathic α-helix and domain I (residues [26][27][28][29][30][31][32] or inside domain I (residues 33-213) not involved in the protein-protein interactions or protein phosphorylation [14]. DI domain, and full-length NS5A were shown to form dimers [41,42] suggested to serve as a scaffold for viral replication [43].…”

“…Alignment of the nucleotide and predicted amino acid sequences of HCV were performed using MEGA 7.0.18. The frequency of clinically significant polymorphisms in NS5A amino acid positions 28,30,31,54,58,62,92, and 93 was calculated using Microsoft Office Excel. The data were analyzed using Graphpad.com.…”