Phylogenetic analyses confirm the high prevalence of hepatitis C virus (HCV) type 4 in the Seine-Saint-Denis district (France) and indicate seven different HCV-4 subtypes linked to two different epidemiological patterns

Morice, Yoann; Roulot, Dominique; Grando, Véronique; Stirnemann, Jérôme; Gault, Elyanne; Jeantils, Vincent; Bentata, Michelle; Jarrousse, B; Lortholary, Olivier; Pallier, C.; Dény, Paul

doi:10.1099/0022-1317-82-5-1001

Cited by 94 publications

(108 citation statements)

References 47 publications

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“…HDV phylogeography. Due to historical geopolitical factors, and similar to hepatitis C virus (HCV) (26) and HBV, the delta viruses characterized in Paris (France) showed a wide African distribution (Table 1). For example, the six full-length viral RNA sequences were obtained from five patients from Western or Central sub-Saharan African countries (Cameroon, Guinea, Ivory Coast, Mali, and Republic of Congo) and from an adult Polish woman who had lived in Cameroon for 3 years.…”

Section: Phylogenetic Analyses Of Hdv Genomesmentioning

confidence: 99%

Molecular Phylogenetic Analyses Indicate a Wide and Ancient Radiation of African Hepatitis Delta Virus, Suggesting a Deltavirus Genus of at Least Seven Major Clades

Radjef

Gordien

Ivaniushina

et al. 2004

J Virol

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210

214

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Hepatitis D virus (HDV) is a satellite of hepatitis B virus (HBV) for transmission and propagation andinfects nearly 20 million people worldwide. The HDV genome is a compact circular single-stranded RNA genome with extensive intramolecular complementarity. Despite its different epidemiological and pathological patterns, the variability and geographical distribution of HDV are limited to three genotypes and two subtypes that have been characterized to date. Phylogenetic reconstructions based on the delta antigen gene and full-length genome sequence data show an extensive and probably ancient radiation of African lineages, suggesting that the genetic variability of HDV is much more complex than was previously thought, with evidence of additional clades. These results relate the geographic distribution of HDV more closely to the genetic variability of its helper HBV.Hepatitis D virus (HDV) is a transmissible agent discovered 26 years ago (30) that requires helper functions from the hepatitis B virus (HBV) for virion assembly and propagation (37). Thus, HDV infection is necessarily associated with HBV infection because HDV ribonucleoprotein buds through the hepatitis B surface antigen (HBsAg) excretory pathway. The HDV genome is a circular single-stranded RNA genome of approximately 1,680 bases with extensive intramolecular complementarity (41). Part of the HDV genome might have historical homology to viroids or plant virus satellite RNA sequences (10, 15), and a rolling-circle model has been developed for viral RNA replication (reviewed in reference 39). However, in contrast to viroids, which do not code for any protein, the HDV antigenome contains an open reading frame that was probably acquired by HDV from a cellular ancestor transcript, leading to the expression of the delta protein (1,20). Indeed, HDV mRNA is translated to sHD and LHD proteins, corresponding respectively to the "small-p24" and the "large-p27" hepatitis Delta proteins. The LHD amino acid sequence is identical to sHD with the addition of a carboxy-terminal extension of 19 to 20 amino acids following the editing of the sHD stop codon during the viral RNA replication cycle (23,43). sHD is required for viral replication and might promote RNA polymerase II elongation of nascent HDV RNA (45), while LHD is essential for HDV particle assembly (5).

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Section: Phylogenetic Analyses Of Hdv Genomesmentioning

confidence: 99%

Molecular Phylogenetic Analyses Indicate a Wide and Ancient Radiation of African Hepatitis Delta Virus, Suggesting a Deltavirus Genus of at Least Seven Major Clades

Radjef

Gordien

Ivaniushina

et al. 2004

J Virol

Self Cite

210

214

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“…For resolution of discrepant results, sequencing of the HCV NS5B region was done as described earlier [5]. Plasma samples (1000 μL) were extracted on the MagNA Pure LC 2.0 (Roche Diagnostics, Penzberg, Germany) using the MagNA Pure LC total NA Isolation Kit LV (Roche) according to the manufacturer's instructions.…”

Section: Molecular Assaysmentioning

confidence: 99%

Evaluation of the new cobas® HCV genotyping test based on real-time PCRs of three different HCV genome regions

Stelzl

Appel

Mehta

et al. 2017

Clinical Chemistry and Laboratory Medicine (CCLM)

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Background: Determination of the hepatitis C virus (HCV) genotype and discrimination between HCV subtypes 1a and 1b is still mandatory prior to anti-HCV treatment initiation. The aim of this study was to evaluate the performance of the recently introduced cobas ® HCV GT assay (Roche) and to compare it to two comparator assays. Methods: The cobas ® HCV GT assay is based on primerspecific real-time polymerase chain reaction (PCR). For comparison, the TRUGENE ® HCV 5′NC Genotyping Kit (Siemens) and the VERSANT ® HCV Genotype 2.0 Assay (Siemens) were employed. Accuracy of the new assay was determined using proficiency panels. For clinical evaluation, 183 residual clinical samples obtained from patients with chronic hepatitis C infection were included. Results: When accuracy was tested, panel members containing HCV subtypes 1a, 1b, and 3a were identified as expected; however, the new assay failed to identify low titer panel members containing HCV subtype 5a correctly. Of 183 clinical samples, 160 gave concordant results. For seven samples, an indeterminate result was reported with the cobas ® HCV GT assay and the remaining 16 samples were found discordant with one of the comparator assays. When time-to-results of the assays were compared, the

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“…Full-length sequences of 13 HCV-4 subtypes (Gabon, Cameroon, Congo, Central Africa, Democratic Republic of the Congo, Rwanda, Burundi and Uganda) and the Middle East (Yemen, Saudi Arabia and Egypt) (Bukh et al, 1992;Morice et al, 2001;Njouom et al, 2003Njouom et al, , 2005Pasquier et al, 2005;Ray et al, 2000;Stuyver et al, 1994;Tokita et al, 1998). Recently, they were also detected in Europe (France, Belgium, Spain and the UK) (van Doorn et al, 1994;Nicot et al, 2005;Franco et al, 2007) and North America (USA and Canada) (Murphy et al, 2007;Timm et al, 2007;Kuntzen et al, 2008), frequently among intravenous drug users (IDUs) and immigrants.…”

Section: Full-length Sequences Of 13 Hcv-4 Subtypesmentioning

confidence: 99%

Complete genomic sequences for hepatitis C virus subtypes 4b, 4c, 4d, 4g, 4k, 4l, 4m, 4n, 4o, 4p, 4q, 4r and 4t

Lü

Wú

et al. 2009

Journal of General Virology

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Short CommunicationComplete genomic sequences for hepatitis C virus subtypes 4b, 4c, 4d, 4g, 4k, 4l, 4m, 4n, 4o, 4p, 4q, 4r and 4t In this study, we characterized the full-length genomic sequences of 13 distinct hepatitis C virus (HCV) genotype 4 isolates/subtypes: QC264/4b, QC381/4c, QC382/4d, QC193/4g, QC383/ 4k, QC274/4l, QC249/4m, QC97/4n, QC93/4o, QC139/4p, QC262/4q, QC384/4r and QC155/4t. These were amplified, using RT-PCR, from the sera of patients now residing in Canada, 11 of which were African immigrants. The resulting genomes varied between 9421 and 9475 nt in length and each contains a single ORF of 9018-9069 nt. The sequences showed nucleotide similarities of 77.3-84.3 % in comparison with subtypes 4a (GenBank accession no. Y11604) and 4f (EF589160) and 70.6-72.8 % in comparison with genotype 1 (M62321/1a, M58335/1b, D14853/1c, and 1?/AJ851228) reference sequences. These similarities were often higher than those currently defined by HCV classification criteria for subtype (75.0-80.0 %) and genotype (67.0-70.0 %) division, respectively. Further analyses of the complete and partial E1 and partial NS5B sequences confirmed these 13 'provisionally assigned subtypes'.

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Phylogenetic analyses confirm the high prevalence of hepatitis C virus (HCV) type 4 in the Seine-Saint-Denis district (France) and indicate seven different HCV-4 subtypes linked to two different epidemiological patterns

Abstract: Hepatitis C virus (HCV) has been classified into six clades as

Cited by 94 publications

References 47 publications

Molecular Phylogenetic Analyses Indicate a Wide and Ancient Radiation of African Hepatitis Delta Virus, Suggesting a Deltavirus Genus of at Least Seven Major Clades

Molecular Phylogenetic Analyses Indicate a Wide and Ancient Radiation of African Hepatitis Delta Virus, Suggesting a Deltavirus Genus of at Least Seven Major Clades

Evaluation of the new cobas® HCV genotyping test based on real-time PCRs of three different HCV genome regions

Complete genomic sequences for hepatitis C virus subtypes 4b, 4c, 4d, 4g, 4k, 4l, 4m, 4n, 4o, 4p, 4q, 4r and 4t

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