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

• Published in: Journal of medical virology Vol. 91; no. 1; pp. 38 - 44
• Main Authors: Jordier, François, Deligny, Marie‐Laurence, Barré, Romain, Robert, Catherine, Galicher, Vital, Uch, Rathviro, Fournier, Pierre‐Edouard, Raoult, Didier, Biagini, Philippe
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 01.01.2019; Wiley-Blackwell
• Subjects: Amino acids; Blood; Blood & organ donations; Blood Donors; Coupling (molecular); deep sequencing; Divergence; Exploration; Flaviviridae Infections - virology; Flavivirus - classification; Flavivirus - genetics; Flavivirus - isolation & purification; France; GBV‐C; Gene sequencing; Genetic diversity; Genetic Variation; Genomes; Genotype; Genotype & phenotype; Genotypes; Hepatitis; Hepatitis C; Hepatitis C - complications; High-Throughput Nucleotide Sequencing; HIV; HIV Infections - complications; HPgV; Human immunodeficiency virus; human pegivirus; Humans; Life Sciences; Phylogeny; Ribonucleic acid; RNA; RNA viruses; RNA, Viral - genetics; Virology; Viruses; France; human pegivirus; France; deep sequencing; blood; GBV-C; HPgV; Human pegivirus
• ISSN: 0146-6615; 1096-9071
• DOI: 10.1002/jmv.25290

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. Highlights‐Sixteen French human pegivirus (HPgV) isolates obtained from HCV‐ and HIV‐RNA positive blood donations were investigated.‐Deep sequencing and coupled molecular protocols were used.‐Partial and nearly complete HPgV sequences were characterized and analysed phylogenetically.‐Genotype 1 and 2 isolates were identified, with complete polyprotein coding sequences exhibiting up to 13% genetic diversity.‐Deletions located on NS4B and 5′‐UTR were identified in some sequences characterized.