scholarly journals Near-Full Genome Characterisation of Two Natural Intergenotypic 2k/1b Recombinant Hepatitis C Virus Isolates

2011 ◽  
Vol 2011 ◽  
pp. 1-7 ◽  
Author(s):  
Victoria L. Demetriou ◽  
Eftychia Kyriakou ◽  
Leondios G. Kostrikis
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Pcr Amplification ◽  
Intravenous Drug Use ◽  
Rt Pcr ◽  
Recombination Point ◽  
Full Length Genome ◽  
Virus Isolates

Few natural intergenotypic hepatitis C virus (HCV) recombinants have been characterised, and only RF1_2k/1b has demonstrated widespread transmission. The near-full length genome sequences for two cases of 2k/1b recombinants (CYHCV037 and CYHCV093) sampled in Cyprus were obtained using strain-specific RT-PCR amplification and sequencing protocols. Sequence analysis confirmed their similarity with the original RF1_2k/1b strain from St. Petersburg, N687. These two isolates significantly contribute to the sequence data available on this recombinant and confirm its increasing spread among individuals from Eastern Europe, and its association with transmission through intravenous drug use. Phylogenetic analyses reveal clustering of the sequence 3′ to the recombination point, not seen in the topology of the 5′ sequences, implying a more complicated evolutionary history than that held to date. The increasing cases of HCV recombinant strains underline the requirement of their contribution to the standardised rules of HCV classification and nomenclature, molecular epidemiology, diagnosis, and treatment.

scholarly journals Dynamics of hepatitis C virus NS5A quasispecies during interferon and ribavirin therapy in responder and non-responder patients with genotype 1b chronic hepatitis C

2005 ◽  
Vol 86 (4) ◽  
pp. 1067-1075 ◽  
Author(s):  
Francesc Puig-Basagoiti ◽  
Xavier Forns ◽  
Ivana Furčić ◽  
Sergi Ampurdanés ◽  
Mireia Giménez-Barcons ◽  
...  
Keyword(s):  
Chronic Hepatitis ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Amino Acid ◽  
Genetic Distance ◽  
Antiviral Agents ◽  
Pcr Amplification ◽  
Rt Pcr ◽  
Sequence Analyses ◽  
Synonymous Substitutions

The quasispecies nature of hepatitis C virus (HCV) may have important implications concerning resistance to antiviral agents. To determine whether HCV NS5A quasispecies composition and dynamics are related to responsiveness to combined interferon (IFN) and ribavirin therapy, extensive sequence analyses of cloned RT-PCR amplification products of HCV-1b NS5A quasispecies of sequential isolates from 15 treated (nine sustained responders and six non-responders) and three untreated patients were performed. Accumulation of mutations in NS5A during therapy was relatively frequent in the V3 domain, but unusual elsewhere. Amino acid changes were the result of the imposition of minor variants that were already present before treatment and always occurred within the first week of therapy. Before treatment, the complexity and diversity of quasispecies were lower in isolates from responders than in those from non-responders, particularly in the V3 domain, where differences in nucleotide entropy (0·35 vs 0·64, P=0·003), genetic distance (0·0145 vs 0·0302, P=0·05) and non-synonymous substitutions (0·0102 vs 0·0203, P=0·036) were statistically significant. These differences became more apparent during treatment, because complexity and diversity remained stable or tended to increase in non-responders, whereas they tended to decrease in responders. These observations suggest that the composition and dynamics of HCV NS5A quasispecies, particularly in the V3 domain, may play a role in the response to combined IFN/ribavirin therapy.

scholarly journals Full-length genome sequences of five hepatitis C virus isolates representing subtypes 3g, 3h, 3i and 3k, and a unique genotype 3 variant

2013 ◽  
Vol 94 (3) ◽  
pp. 543-548 ◽  
Author(s):  
Ling Lu ◽  
Chunhua Li ◽  
Jie Yuan ◽  
Teng Lu ◽  
Hiroaki Okamoto ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Full Length ◽  
Genotype 3 ◽  
Genome Sequences ◽  
Asian Origin ◽  
Novel Variant ◽  
Full Length Genome ◽  
Virus Isolates ◽  
Unique Genotype

We characterized the full-length genomes of five distinct hepatitis C virus (HCV)-3 isolates. These represent the first complete genomes for subtypes 3g and 3h, the second such genomes for 3k and 3i, and of one novel variant presently not assigned to a subtype. Each genome was determined from 18–25 overlapping fragments. They had lengths of 9579–9660 nt and each contained a single ORF encoding 3020–3025 aa. They were isolated from five patients residing in Canada; four were of Asian origin and one was of Somali origin. Phylogenetic analysis using 64 partial NS5B sequences differentiated 10 assigned subtypes, 3a–3i and 3k, and two additional lineages within genotype 3. From the data of this study, HCV-3 full-length sequences are now available for six of the assigned subtypes and one unassigned. Our findings should add insights to HCV evolutionary studies and clinical applications.

Comparative evaluation of five rapid methods for identifying subtype 1b and 2c hepatitis C virus isolates

1997 ◽  
Vol 66 (2) ◽  
pp. 187-194 ◽  
Author(s):  
Marialinda Vatteroni ◽  
Fabrizio Maggi ◽  
Antonietta Morrica ◽  
Claudia Fornai ◽  
Massimo Giorgi ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Comparative Evaluation ◽  
Rapid Methods ◽  
Subtype 1B ◽  
Virus Isolates

Strategy for the maximization of clinically relevant information from hepatitis C virus, RT-PCR quantification

2001 ◽  
Vol 20 (3) ◽  
pp. 163-171 ◽  
Author(s):  
John Levis ◽  
Elizabeth Kenny-Walsh ◽  
Kathleen O'Sullivan ◽  
Mary Horgan ◽  
Michael Whelton ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Relevant Information ◽  
Rt Pcr

scholarly journals Detection and Localization by In Situ Molecular Biology Techniques and Immunohistochemistry of Hepatitis C Virus in Livers of Chronically Infected Patients

1998 ◽  
Vol 46 (5) ◽  
pp. 653-660 ◽  
Author(s):  
Francine M. Walker ◽  
Marie-Christine Dazza ◽  
Marie-Christine Dauge ◽  
Olivier Boucher ◽  
Christophe Bedel ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Interferon Α ◽  
Rt Pcr ◽  
Biopsy Specimens ◽  
Bile Ductule ◽  
Liver Biopsies ◽  
Cytoplasmic Signals ◽  
Detection And Localization

Hepatitis C virus (HCV) detection in the livers of chronically infected patients remains a debatable issue. We used immunohistochemistry, in situ hybridization (ISH) alone or after microwave heating with FITC-labeled probes, RT-PCR with unlabeled primers followed by ISH (RT-PCR-ISH), and in situ RT-PCR with FITC-labeled primers (in situ RT-PCRd) to localize the virus in 38 liver biopsy specimens from 21 chronically infected HCV patients treated with interferon-α (IFN-α). Biopsies were taken at the beginning and end of IFN-α treatment and 1 year later. Results were compared with that of HCV-PCR in serum. RT-PCR-ISH and in situ RT-PCRd showed HCV signal in all liver biopsies even in responders with seronegative HCV PCR. This signal was intranuclear, diffuse, or peripheral, in hepatocytes, bile ductule cells, and lymphocytes. Cytoplasmic signals were occasionally observed. Whereas the percentage of labeled hepatocytes remained constant, the number of labeled lymphoid follicles decreased after INF-α therapy. Immunohistochemistry resulted in the same pattern of positivity but it was weaker and inconstant. This study indicates the persistency of HCV latency in IFN-α responders 1 year after IFN-α treatment cessation, a finding that certainly deserves confirmation.

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