Genetic diversity of hepatitis D virus genotype-1 in Europe allows classification into subtypes.

Hepatitis delta virus (HDV) is an RNA virus which leads to both acute and chronic forms of hepatitis. At present, HDV isolates have been classified into eight major genotypes distributed over different geographical regions. Recent increase in HDV sequences in Europe and worldwide has enabled us to revisit the taxonomic classification of HDV. A total of 116 large hepatitis delta antigen (L-HDAg) nucleotide sequences and 13 full-length HDV genome sequences belonging to genotype-1 from our European cohort, as well as 621 L-HDAg nucleotide sequences belonging to genotype-1 to genotype-8 retrieved from the GenBank NCBI were included in this study. All 116 isolates of our cohort and 341 of 621 isolates (60%) account for genotype-1, while the remaining 40% of isolates were unevenly distributed across genotype-2 to genotype-8. Phylogenetic analysis of 98 L-HDAg sequences selected after elimination of redundant sequences of all 737 isolates was performed to identify plausible subtypes within HDV genotype-1. Pairwise genetic distances for L-HDAg sequences were calculated to estimate the inter-genotype and inter-subtype differences. The HDV genotype-1 isolates phylogenetically formed five distinct clusters (genotype 1a-1e), each of them corresponding to a distinct geographic region. Two distinct subtypes for HDV genotype-2 and -4 (ie -2a and -2b; -4a and -4b, respectively) could be identified based on isolate sequences from GenBank. The previously defined genotype-1 to genotype-8 have an inter-genotypic difference of ≥10%, while the newly defined subtypes of genotype-1, -2 and -4 show an inter-subtype difference of ≥3% to <10% from the average diversity. In addition, we identified unique amino acid residues, known as specificity-determining positions, amongst the proposed subtypes.