Complete genome of a European hepatitis C virus subtype 1g isolate: phylogenetic and genetic analyses

Abstract

Background: Hepatitis C virus isolates have been classified into six main genotypes and a variable number of subtypes within each genotype, mainly based on phylogenetic analysis. Analyses of the genetic relationship among genotypes and subtypes are more reliable when complete genome sequences (or at least the full coding region) are used; however, so far 31 of 80 confirmed or proposed subtypes have at least one complete genome available. Of these, 20 correspond to confirmed subtypes of epidemic interest.

Results: We present and analyse the first complete genome sequence of a HCV subtype 1g isolate. Phylogenetic and genetic distance analyses reveal that HCV-1g is the most divergent subtype among the HCV-1 confirmed subtypes. Potential genomic recombination events between genotypes or subtype 1 genomes were ruled out. We demonstrate phylogenetic congruence of previously deposited partial sequences of HCV-1g with respect to our sequence.

Conclusion: In light of this, we propose changing the current status of its subtype-specific designation from provisional to confirmed.

Figure 1

Maximum likelihood phylogenetic tree of complete genome sequences. Phylogenetic tree was obtained with PHYML using GTR+G+I for the new sequence and 29 complete genomes (coding region) representative of all 6 HCV genotypes. Genotype and subtype labels (in bold) are next to accession numbers. The sequence obtained in this study is underlined. Bar represents 0.1 substitutions per nucleotide position. Support value of nodes was estimated by bootstrap (1000 replicates using neighbour-joining with the maximum likelihood distance). Only values >75% are shown.

Figure 2

Maximum likelihood phylogenetic trees including partial HCV-1g sequences. Four regions were studied (a) 5'UTR, (b) core, (c) E1 and (d) NS5B. Only genotype 1 clade is shown. Support value of nodes was estimated by bootstrap (1000 replicates using neighbour joining with maximum likelihood distance). Only values >75% are shown. Bar represents in each case number of substitutions per nucleotide position. Patient code label (in parenthesis), genotype and subtype labels (in bold) are next to accession numbers. The sequence obtained in this study is underlined. Country names are CA, Canada; EG, Egypt; ES, Spain; LB, Lebanon and SD, Sudan.