Ultradeep Pyrosequencing of Hepatitis C Virus Hypervariable Region 1 in Quasispecies Analysis
Joint Authors
Caraballo Cortés, Kamila
Zagordi, Osvaldo
Płoski, Rafał
Pawełczyk, Agnieszka
Berak, Hanna
Radkowski, Marek
Laskus, Tomasz
Bukowska-Ośko, Iwona
Source
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-10, 10 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-04-28
Country of Publication
Egypt
No. of Pages
10
Main Subjects
Abstract EN
Genetic variability of hepatitis C virus (HCV) determines pathogenesis of infection, including viral persistence and resistance to treatment.
The aim of the present study was to characterize HCV genetic heterogeneity within a hypervariable region 1 (HVR1) of a chronically infected patient by ultradeep 454 sequencing strategy.
Three independent sequencing error correction methods were applied.
First correction method (Method I) implemented cut-off for genetic variants present in less than 1%.
In the second method (Method II), a condition to call a variant was bidirectional coverage of sequencing reads.
Third method (Method III) used Short Read Assembly into Haplotypes (ShoRAH) program.
After the application of these three different algorithms, HVR1 population consisted of 8, 40, and 186 genetic haplotypes.
The most sensitive method was ShoRAH, allowing to reconstruct haplotypes constituting as little as 0.013% of the population.
The most abundant genetic variant constituted only 10.5%.
Seventeen haplotypes were present in a frequency above 1%, and there was wide dispersion of the population into very sparse haplotypes.
Our results indicate that HCV HVR1 heterogeneity and quasispecies population structure may be reconstructed by ultradeep sequencing.
However, credible analysis requires proper reconstruction methods, which would distinguish sequencing error from real variability in vivo.
American Psychological Association (APA)
Caraballo Cortés, Kamila& Zagordi, Osvaldo& Laskus, Tomasz& Płoski, Rafał& Bukowska-Ośko, Iwona& Pawełczyk, Agnieszka…[et al.]. 2013. Ultradeep Pyrosequencing of Hepatitis C Virus Hypervariable Region 1 in Quasispecies Analysis. BioMed Research International،Vol. 2013, no. 2013, pp.1-10.
https://search.emarefa.net/detail/BIM-1030730
Modern Language Association (MLA)
Caraballo Cortés, Kamila…[et al.]. Ultradeep Pyrosequencing of Hepatitis C Virus Hypervariable Region 1 in Quasispecies Analysis. BioMed Research International No. 2013 (2013), pp.1-10.
https://search.emarefa.net/detail/BIM-1030730
American Medical Association (AMA)
Caraballo Cortés, Kamila& Zagordi, Osvaldo& Laskus, Tomasz& Płoski, Rafał& Bukowska-Ośko, Iwona& Pawełczyk, Agnieszka…[et al.]. Ultradeep Pyrosequencing of Hepatitis C Virus Hypervariable Region 1 in Quasispecies Analysis. BioMed Research International. 2013. Vol. 2013, no. 2013, pp.1-10.
https://search.emarefa.net/detail/BIM-1030730
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1030730