Comprehensive cloning of patient-derived 9022-bp amplicons of hepatitis C virus.

•Instability of recombinant clones harboring large or full-length viral genomes is a common but difficult issue in virological research.•Exhaustive experimentation that estimated nearly all available options to enhance the cloning stability.•The first report to reveal remarkable difference with regard to cloning instability among phylogenetic clades of hepatitis C virus genotype 1a.