Genetic Analysis of Hepatitis C Virus Detected among Low-Risk Populations of Voluntary Blood Donors in Kenya Using Partial NSB5 Gene

Hepatitis C Virus (HCV) infection remains a significant threat to public health globally. For instance, in sub-Saharan Africa alone, about 10 million people are chronically infected. The virus is genetically diverse and classified into genotypes/sub-genotypes, with varied distribution patterns across the globe. Knowledge of HCV genotype distribution in a given geographic area, as well as virus resistance-associated substitutions, is essential to patient management. Unfortunately, data on the genetic characteristics and diversity of HCV genotypes circulating among low-risk blood donor populations in Kenya are scarce. In this study, we screened for HCV RNA among 450 anti-HCV-positive serum samples collected from voluntary blood donors in Kenya between April 2019 and March 2024 using a real-time RT-qPCR assay. A portion of the virus NSB5 gene was subsequently amplified from three samples that were HCV RNA positive using a hemi-nested PCR and sequenced. Phylogenetic analysis revealed that two of the HCV strains belonged to sub-genotype 1a, while the other belonged to sub-genotype 4v. Mutational analysis indicated that antiviral therapy using sofosbuvir could be effective against these strains. Overall, our results demonstrate the co-circulation of HCV genotypes 1a and 4v among voluntary blood donors in Kenya during the study period. This is the second study to describe the genetic characteristics of HCV among low-risk populations of voluntary blood donors in Kenya. Large-scale prospective genomic surveillance studies on HCV are needed to provide comprehensive insights into virus genotype distribution and resistance-associated substitutions that may impact the efficacy of direct-acting antiviral therapy in infected HCV patients in Kenya.