GB virus C (GBV-C) evolutionary patterns revealed by analyses of reference genomes, E2 and NS5B sequences amplified from viral strains circulating in the Lisbon area (Portugal)

Parreira, Ricardo; Branco, Cristina de; Piedade, João; Esteves, Aida

doi:10.1016/j.meegid.2011.10.011

Cited by 7 publications

(15 citation statements)

References 35 publications

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“…To compare our newly described sequences to published HPgV sequences, we reconstructed a Bayesian phylogenetic tree that included our sequences as well as publicly available full-length HPgV sequences. Our Bayesian phylogeny is largely consistent with recently published HPgV phylogenies (Feng et al, 2011;Parreira et al, 2012), showing 100 % posterior clade support for proposed genotypes 1-5 ( Fig. 1).…”

Section: Resultssupporting

confidence: 88%

“…Of the 46 full-length coding genomes now available in public databases, the majority are genotypes 2 and 3, likely representing focused sampling from the geographical areas corresponding to these genotypes. Only two full coding genomes exist from genotype 1, despite evidence from partial-genome sequencing suggesting that genotype 1 may be the most genetically diverse genotype (Parreira et al , 2012). Full coding genomes from the African continent include two from west Africa (Leary et al , 1996; Saito et al , 1999), one from east Africa (Erker et al , 1996), and one from South Africa (Muerhoff et al , 2005).…”

Section: Introductionmentioning

confidence: 99%

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Deep sequencing identifies two genotypes and high viral genetic diversity of human pegivirus (GB virus C) in rural Ugandan patients

Ghai

Sibley

Lauck

et al. 2013

Journal of General Virology

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Human pegivirus (HPgV), formerly 'GB virus C' or 'hepatitis G virus', is a member of the genus Flavivirus (Flaviviridae) that has garnered significant attention due to its inhibition of HIV, including slowing disease progression and prolonging survival in HIV-infected patients. Currently, there are six proposed HPgV genotypes that have roughly distinct geographical distributions. Genotypes 2 and 3 are the most comprehensively characterized, whereas those genotypes occurring on the African continent, where HPgV prevalence is highest, are less well studied. Using deep sequencing methods, we identified complete coding HPgV sequences in four of 28 patients (14.3 %) in rural Uganda, east Africa. One of these sequences corresponds to genotype 1 and is the first complete genome of this genotype from east Africa. The remaining three sequences correspond to genotype 5, a genotype that was previously considered exclusively South African. All four positive samples were collected within a geographical area of less than 25 km 2 , showing that multiple HPgV genotypes co-circulate in this area. Analysis of intra-host viral genetic diversity revealed that total single-nucleotide polymorphism frequency was approximately tenfold lower in HPgV than in hepatitis C virus. Finally, one patient was co-infected with HPgV and HIV, which, in combination with the high prevalence of HIV, suggests that this region would be a useful locale to study the interactions and co-evolution of these viruses. The nucleotide sequences reported in this study were deposited in GenBank with accession numbers KC618398-KC618401.

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Section: Resultssupporting

confidence: 88%

Section: Introductionmentioning

confidence: 99%

Deep sequencing identifies two genotypes and high viral genetic diversity of human pegivirus (GB virus C) in rural Ugandan patients

Ghai

Sibley

Lauck

et al. 2013

Journal of General Virology

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“…Although HPgV E1-E2 glycoprotein genomic region is constrained by purifying selection [13] and also the viral genome is characterized by the presence of abundant RNA secondary structure motifs [34, 35], recombination can potentially acquire genetic diversity by generating combinations of preexisting nucleotide polymorphisms, and recombination could also act to shuffle the partial or entire RNA secondary structure region to accelerate the process. Consistent with the results of the present study, previous studies have reported that genetic recombination is the likely cause for the observation of the phylogenetic incongruence among the subgenomic regions of HPgV [36, 37], thus suggesting that genetic recombination has a profound influence on the genomic architecture of HPgV.…”

Section: Discussionsupporting

confidence: 92%

Evidence for Within-Host Genetic Recombination among the Human Pegiviral Strains in HIV Infected Subjects

Padhi

et al. 2016

PLoS ONE

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The non-pathogenic Human Pegivirus (HPgV, formerly GBV-C/HGV), the most prevalent RNA virus worldwide, is known to be associated with reduced morbidity and mortality in HIV-infected individuals. Although previous studies documented its ubiquity and important role in HIV-infected individuals, little is known about the underlying genetic mechanisms that maintain high genetic diversity of HPgV within the HIV-infected individuals. To assess the within-host genetic diversity of HPgV and forces that maintain such diversity within the co-infected hosts, we performed phylogenetic analyses taking into account 229 HPgV partial E1-E2 clonal sequences representing 15 male and 8 female co-infected HIV patients from Hubei province of central China. Our results revealed the presence of eleven strongly supported clades. While nine clades belonged to genotype 3, two clades belonged to genotype 2. Additionally, four clades that belonged to genotype 3 exhibited inter-clade recombination events. The presence of clonal sequences representing multiple clades within the HIV-infected individual provided the evidence of co-circulation of HPgV strains across the region. Of the 23 patients, six patients (i.e., five males and one female) were detected to have HPgV recombinant sequences. Our results also revealed that while male patients shared the viral strains with other patients, viral strains from the female patients had restricted dispersal. Taken together, the present study revealed that multiple infections with divergent HPgV viral strains may have caused within-host genetic recombination, predominantly in male patients, and therefore, could be the major driver in shaping genetic diversity of HPgV.

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“…Interestingly, within individual SPgV samples – SPgV krc in particular – the distribution of nonsynonymous substitutions was similarly biased, with their prevalence in E2, P7, NS2 and NS5A suggesting greater tolerance and/or greater functional significance of nonsynonymous mutations in these genes. Similarly, across NS3, the absence of nonsynonymous substitutions within individual samples combined with low and steady dN/dS ratios for each of the Kibale SPgVs signify the impacts purifying selection on this functionally important and constrained gene [82]. For NS5B we also observed low dN/dS ratios.…”

Section: Discussionsupporting

confidence: 53%

Discovery and Characterization of Distinct Simian Pegiviruses in Three Wild African Old World Monkey Species

et al. 2014

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Within the Flaviviridae, the recently designated genus Pegivirus has expanded greatly due to new discoveries in bats, horses, and rodents. Here we report the discovery and characterization of three simian pegiviruses (SPgV) that resemble human pegivirus (HPgV) and infect red colobus monkeys (Procolobus tephrosceles), red-tailed guenons (Cercopithecus ascanius) and an olive baboon (Papio anubis). We have designated these viruses SPgVkrc, SPgVkrtg and SPgVkbab, reflecting their host species’ common names, which include reference to their location of origin in Kibale National Park, Uganda. SPgVkrc and SPgVkrtg were detected in 47% (28/60) of red colobus and 42% (5/12) red-tailed guenons, respectively, while SPgVkbab infection was observed in 1 of 23 olive baboons tested. Infections were not associated with any apparent disease, despite the generally high viral loads observed for each variant. These viruses were monophyletic and equally divergent from HPgV and pegiviruses previously identified in chimpanzees (SPgVcpz). Overall, the high degree of conservation of genetic features among the novel SPgVs, HPgV and SPgVcpz suggests conservation of function among these closely related viruses. Our study describes the first primate pegiviruses detected in Old World monkeys, expanding the known genetic diversity and host range of pegiviruses and providing insight into the natural history of this genus.

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GB virus C (GBV-C) evolutionary patterns revealed by analyses of reference genomes, E2 and NS5B sequences amplified from viral strains circulating in the Lisbon area (Portugal)

Cited by 7 publications

References 35 publications

Deep sequencing identifies two genotypes and high viral genetic diversity of human pegivirus (GB virus C) in rural Ugandan patients

Deep sequencing identifies two genotypes and high viral genetic diversity of human pegivirus (GB virus C) in rural Ugandan patients

Evidence for Within-Host Genetic Recombination among the Human Pegiviral Strains in HIV Infected Subjects

Discovery and Characterization of Distinct Simian Pegiviruses in Three Wild African Old World Monkey Species

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