Human pegivirus isolates characterized by deep sequencing from hepatitis C virus‐RNA and human immunodeficiency virus‐RNA–positive blood donations, France

Abstract

Human pegivirus (HPgV, formerly GBV-C) is a member of the genus Pegivirus, family Flaviviridae. Despite its identification more than 20 years ago, both natural history and distribution of this viral group in human hosts remain under exploration. Analysis of HPgV genomes characterized up to now points out the scarcity of French pegivirus sequences in databases. To bring new data regarding HPgV genomic diversity, we investigated 16 French isolates obtained from hepatitis C virus-RNA and human immunodeficiency virus-RNA-positive blood donations following deep sequencing and coupled molecular protocols. Initial phylogenetic analysis of 5'-untranslated region (5'-UTR)/E2 partial sequences permitted to assign HPgV isolates to genotypes 2 (n = 15) and 1 (n = 1), with up to 16% genetic diversity observed for both regions considered. Seven nearly full-length representative genomes were characterized subsequently, with complete polyprotein coding sequences exhibiting up to 13% genetic diversity; closest nucleotide (nt) divergence with available HPgV sequences was in the range 7% to 11%. A 36 nts deletion located on the NS4B coding region (N-terminal part, 12 amino acids) of the genotype 1 HPgV genome characterized was identified, along with single nucleotide deletions in two genotype 2, 5'-UTR sequences.

Exploring the Diversity of the Human Blood Virome

“…The relatively low number of HPgV full-length coding sequences available in public databases shows a clear predominance of genotypes 2 and 3, probably as a result of increased sampling in geographical regions where these genotypes are more abundant. The predominance of genotype 2 isolates in our data is consistent with studies from other European countries [57,61]. This bias can confound certain analyses, such as the higher genetic diversity reported for genotype 1 [62].…”

Exploring the Diversity of the Human Blood Virome

“…The relatively low number of HPgV full-length coding sequences available in public databases shows a clear predominance of genotypes 2 and 3, probably as a result of increased sampling in geographical regions where these genotypes are more abundant. The predominance of genotype 2 isolates in our data is consistent with studies from other European countries 49,53 . This bias can confound certain analyses, such as the higher genetic diversity reported for genotype 1 54 .…”

Semi‐quantitative duplex RT ‐ PCR reveals the low occurrence of Porcine Pegivirus and Atypical Porcine Pestivirus in diagnostic samples from the United States

“…The pathogenicity and role of pegiviruses as causative agents of diseases are host species dependent. Human pegivirus is prevalent in 5% of the world's population and was reported as co‐infections with other viruses, such as hepatitis C virus and HIV infected individuals (Berg et al., ; Jordier et al., ; N'Guessan et al., ; Schwarze‐Zander, Blackard, & Rockstroh, ; Wang et al., ). In addition, human pegivirus strains can be associated with febrile illness, haemophilia, acute mycocarditis and lymphoma (Bijvand et al., ; Fama et al., ; Takeuchi et al., ; Williams et al., ).…”