Publications & Reports

Genomic characterization of hepatitis C virus transmitted founder variants with deep sequencing.

Abayasingam A, Leung P, Eltahla A, Bull RA, Luciani F, Grebely J, Dore GJ, Applegate T, Page K, Bruneau J, Cox AL, Kim AY, Schinkel J, Shoukry NH, Lauer GM, Maher L, Hellard M, Prins M, Lloyd A, Rodrigo C
School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, NSW, Australia.


Transfer of hepatitis C virus (HCV) infection from a donor to a new recipient is associated with a bottleneck of genetic diversity in the transmitted viral variants. Existing data suggests that one, or very few, variants emerge from this bottleneck to establish the infection (transmitted founder [T/F] variants). In HCV, very few T/F variants have been characterized due to the challenges of obtaining early infection samples and of high throughput viral genome sequencing. This study used a large, acute HCV, deep-sequenced dataset from first viremia samples collected in nine prospective cohorts across four countries, to estimate the prevalence of single T/F viruses, and to identify host and virus-related factors associated with infections initiated by a single T/F variant. The short reads generated by Illumina sequencing were used to reconstruct viral haplotypes with two haplotype reconstruction algorithms. The haplotypes were examined for random mutations (Poisson distribution) and a star-like phylogeny to identify T/F viruses. The findings were cross-validated by haplotype reconstructions across three regions of the genome (Core-E2, NS3, NS5A) to minimize the possibility of spurious overestimation of single T/F variants. Of 190 acute infection samples examined, 54 were very early acute infections (HCV antibody negative, RNA positive), and single transmitted founders were identified in 14 (26%, 95% CI: 16-39%) after cross validation across multiple regions of the genome with two haplotype reconstruction algorithms. The presence of a single T/F virus was not associated with any host or virus-related factors, notably viral genotype or spontaneous clearance. In conclusion, approximately one in four new HCV infections originates from a single T/F virus. Resolution of genomic sequences of single T/F variants is the first step in exploring unique properties of these variants in the infection of host hepatocytes.

Link to publisher’s web site


  • Journal: Infection, Genetics and Evolution
  • Published: 01/07/2019
  • Volume: 71
  • Pagination: 36-41