A Highly Divergent Hepacivirus Identified in Domestic Ducks Further Reveals the Genetic Diversity of Hepaciviruses

Abstract

Hepaciviruses represent a group of viruses that pose a significant threat to the health of humans and animals. During the last decade, new members of the genus Hepacivirus have been identified in various host species worldwide, indicating the widespread distribution of genetically diversified hepaciviruses among animals. By applying unbiased high-throughput sequencing, a novel hepacivirus, provisionally designated Hepacivirus Q, was discovered in duck liver samples collected in Guangdong province of China. Genetic analysis revealed that the complete polyprotein of Hepacivirus Q shares 23.9-46.6% amino acid identity with other representatives of the genus Hepacivirus. Considering the species demarcation criteria for hepaciviruses, Hepacivirus Q should be regarded as a novel hepacivirus species of the genus Hepacivirus within the family Flaviviridae. Phylogenetic analyses also indicate the large genetic distance between Hepacivirus Q and other known hepaciviruses. Molecular detection of this novel hepacivirus showed an overall prevalence of 15.9% in duck populations in partial areas of Guangdong province. These results expand knowledge about the genetic diversity and evolution of hepaciviruses and indicate that genetically divergent hepaciviruses are circulating in duck populations in China.

Keywords: China; domestic duck; genetic diversity; novel hepacivirus.

Figure 1

Geographic maps showing the location of sampling sites where the duck liver samples in this study were collected. This map was plotted with a combination of Surfer software version 4 (Golden Software, Golden, CO, USA) and Adobe illustrator version CC2017 (Adobe, San Jose, CA, USA).

Figure 2

Mapped read count plot of the Hepacivirus Q genome. The histograms show the coverage depth per base of the Hepacivirus Q genome, and the mean sequencing depth was 8.5×.

Figure 3

Genomic characterization and phylogenetic analysis based on the complete polyprotein of Hepacivirus Q and other reference hepaciviruses. (A) Genome organization of Hepacivirus Q identified in this study. Red arrows indicate N-linked glycosylation sites. (B) Phylogenetic analysis based on the amino acid sequence of the complete polyprotein of Hepacivirus Q. The trees were constructed based on the maximum likelihood method implemented in PhyML v3.0 and mid-point rooted for clarity; the scale bar represents the number of nucleotide substitutions per site. Bootstrap values were calculated with 100 replicates of the alignment, and only bootstrap values > 70% are shown at relevant nodes.

Figure 4

Phylogenetic analysis based on amino acid sequence of NS3 and NS5B proteins of hepaciviruses. The trees were constructed based on the maximum likelihood method implemented in PhyML v3.0 and mid-point rooted for clarity; the scale bar represents the number of nucleotide substitutions per site. Bootstrap values were calculated with 100 replicates of the alignment, and only bootstrap values >70% are shown at relevant nodes.