Evaluation of Viremia Frequencies of a Novel Human Pegivirus by Using Bioinformatic Screening and PCR

Abstract

Next-generation sequencing has critical applications in virus discovery, diagnostics, and environmental surveillance. We used metagenomic sequence libraries for retrospective screening of plasma samples for the recently discovered human hepegivirus 1 (HHpgV-1). From a cohort of 150 hepatitis C virus (HCV)-positive case-patients, we identified 2 persons with HHpgV-1 viremia and a high frequency of human pegivirus (HPgV) viremia (14%). Detection of HHpgV-1 and HPgV was concordant with parallel PCR-based screening using conserved primers matching groups 1 (HPgV) and 2 (HHPgV-1) nonstructural 3 region sequences. PCR identified 1 HHPgV-1-positive person with viremia from a group of 195 persons with hemophilia who had been exposed to nonvirally inactivated factor VII/IX; 18 (9%) were HPgV-positive. Relative to HCV and HPgV, active infections with HHpgV-1 were infrequently detected in blood, even in groups that had substantial parenteral exposure. Our findings are consistent with lower transmissibility or higher rates of virus clearance for HHpgV-1 than for other bloodborne human flaviviruses.

Keywords: Flaviviridae; HCV; HHpgV-1; Hepacivirus; Hepegivirus; Pegivirus; bloodborne pathogens; hemophilia; parenteral; persons who inject drugs; sexually transmitted disease; transfusion; virus persistence; viruses.

Figure 1

Maximum-likelihood phylogenetic analysis of complete genome sequences of human pegivirus assembled in this study (black circles) compared with available human hepegivirus (HPgV) sequences of genotypes 1–6 published in GenBank (accession numbers shown). The tree was constructed by using the maximum-likelihood algorithm implemented in the MEGA6 software package (16). For this dataset, the optimum maximum model was general time reversible model (18) with a gamma distribution (5 rates) and invariant sites. Phylogenetic analysis of each dataset used 100 bootstrap resamplings to infer the robustness of groupings. Genotypes previously assigned to HPgV sequences are shown on the right with the exception of sequence AB013501 (from the United Kingdom, shown with genotype “?”). Scale bar indicates nucleotide substitutions per site.

Figure 2

Maximum-likelihood (ML) phylogenetic analysis of human pegivirus sequences. NS3 region sequences (positions 4609–4880 as numbered in the AK-790 reference sequence, denoted here as tt790) were selected to overlap with sequences from PCR-derived amplicons generated in this study (black circles) and partial NS3 region sequences reported previously (6). The tree was constructed by using the maximum likelihood algorithm implemented in the MEGA6 software package (16). The optimum ML model (lowest Bayesian information criterion score and typically greatest ML value) was Kimura 2 parameter and invariant sites. Phylogenetic analysis of each dataset used 100 bootstrap re-samplings to infer the robustness of groupings. The tree was rooted with a rat pegivirus sequence (GenBank accession no. KC815311, not shown). IDU, injection drug use; NS, nonstructural. Scale bar indicates nucleotide substitutions per site.