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.
Highlights
Hepatitis C virus infection is a global public health problem
Due to the heterogenous distribution of a clinically important NS5A Resistance associated substitutions (RASs), Y93H, in GT1b population, we investigated its presence by nest-generation sequencing in a validation set of direct-acting antiviral agents (DAAs) treatmentnaïve patients
Through comparing NS5A sequences determined by both methods side-by-side, we found that the Y93H prevalence is 20.5% by Sanger sequencing (20% cut off) or 19.5% by Next Generation Sequencing (NGS) sequencing (15% cut off), which is comparable to Kingmed result
Summary
Hepatitis C virus infection is a global public health problem. HCV chronically infects about 3% of the world’s population, many of whom will develop liver cirrhosis and hepatocellular carcinoma (Mohd Hanafiah et al, 2013).Hepatitis C virus has a high degree of genetic heterogeneity. Hepatitis C virus infection is a global public health problem. HCV chronically infects about 3% of the world’s population, many of whom will develop liver cirrhosis and hepatocellular carcinoma (Mohd Hanafiah et al, 2013). Hepatitis C virus has a high degree of genetic heterogeneity. It can be classified into seven GTs and numerous subtypes (Simmonds et al, 2005). HCV NS5A RASs Prevalence in China than 50% of total HCV infections (Chen Y. et al, 2017). GT3 is the most prevalent globally and has increased dramatically in China (Messina et al, 2015; Lu et al, 2017). HCV exists in host as quasispecies, which is defined as genetically distinct, but closely related viral populations (Martell et al, 1992). Quasispecies may play a role in disease progression and treatment response (Perales, 2018)
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