Elsevier

Virology

Volume 539, 2 January 2020, Pages 69-79
Virology

Human pegivirus 2 exhibits minimal geographic and temporal genetic diversity

https://doi.org/10.1016/j.virol.2019.10.012Get rights and content
Under a Creative Commons license
open access

Highlights

  • Human pegivirus 2 continues to be linked to HCV and HCV/HIV coinfection.

  • Metagenomic NGS coupled to target enrichment enables HPgV-2 genome characterization.

  • HPgV-2 sequences are highly conserved globally and stable in infected individuals.

  • Low genetic diversity indicates sporadic infections originating from a common source.

Abstract

We applied an NGS based target capture approach to amplify HPgV-2 sequences from metagenomic libraries and enable full genome characterization. Despite expanded geographical sampling, sequence variability remains low, with diversity concentrated in approximately 3.3% of all amino acids. Serial samples from one HPgV-2 positive individual co-infected with comparable titers of HIV, HCV, and GBV-C showed that HPgV-2 remains highly stable over several weeks compared to other RNA viruses, despite a similarly error-prone polymerase. The consistent epidemiological association with and structural similarities to HCV, and the weak positive correlation of HCV and HPgV-2 titers shown here, suggests it may benefit from co-infection. While minimal selective pressure on HPgV-2 to evolve could suggest fitness, the rarity of HPgV-2 and the tight phylogenetic clustering of global strains likely indicates origination from a common source and a virus that is ill-suited to its host. Sporadic infections may explain the limited genetic diversity observed worldwide.

Keywords

Next-generation sequencing
Pegivirus
Hepatitis C virus
Viral diversity
xGen target enrichment

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