Limits...
Recombination in hepatitis C virus: identification of four novel naturally occurring inter-subtype recombinants.

Shi W, Freitas IT, Zhu C, Zheng W, Hall WW, Higgins DG - PLoS ONE (2012)

Bottom Line: This confirms the rarity of inter-genotype HCV recombinants.While the locations of the breakpoints identified by RDP were not identical, they are very close.Our study suggests that while recombination in HCV is rare, this warrants further investigation.

View Article: PubMed Central - PubMed

Affiliation: The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland. wfshi.tsmc@gmail.com

ABSTRACT
Recombination in Hepatitis C virus (HCV) is considered to be rare. In this study, we performed a phylogenetic analysis of 1278 full-length HCV genome sequences to identify potential recombination events. Nine inter-genotype recombinants were identified, all of which have been previously reported. This confirms the rarity of inter-genotype HCV recombinants. The analysis also identified five inter-subtype recombinants, four of which are documented for the first time (EU246930, EU246931, EU246932, and EU246937). Specifically, the latter represent four different novel recombination types (6a/6o, 6e/6o, 6e/6h, and 6n/6o), and this was well supported by seven independent methods embedded in RDP. The breakpoints of the four novel HCV recombinants are located within the NS5B coding region and were different from all previously reported breakpoints. While the locations of the breakpoints identified by RDP were not identical, they are very close. Our study suggests that while recombination in HCV is rare, this warrants further investigation.

Show MeSH

Related in: MedlinePlus

The genotype 6 part of the phylogenetic tree constructed using the last 827 bp of the alignment.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3404033&req=5

pone-0041997-g002: The genotype 6 part of the phylogenetic tree constructed using the last 827 bp of the alignment.

Mentions: Figures 1 and 2 demonstrate how potential recombination events are identified from the trees. Figures 1 and 2 present the genotype 6 lineages of the phylogenetic trees constructed using the first fragment (600 bp in length) and the last fragment (827 bp in length) in the first sub-division strategy. In Figure 1, EU246930 (6a) is clustered within a lineage of 6a sequences and the bootstrap support value for this lineage is 84%. EU246931 and EU246932 (6e) fall within a cluster of 6e, with a bootstrap value of 92%, while EU246937 belongs to subtype 6n with a bootstrap value of 91%. However, in Figure 2, different phylogenetic relationships are found. EU246930 (6a), EU246932 (6e) and EU246937 (6n) are clustered with a lineage of subtype 6o sequences and the bootstrap support is 98%, while EU246931 (6e) forms a separate lineage with D84265 (6h) with 100% bootstrap support. Employing this approach, we analyzed all the trees and summarized the discordant phylogenetic signals suggesting evidence of recombination.


Recombination in hepatitis C virus: identification of four novel naturally occurring inter-subtype recombinants.

Shi W, Freitas IT, Zhu C, Zheng W, Hall WW, Higgins DG - PLoS ONE (2012)

The genotype 6 part of the phylogenetic tree constructed using the last 827 bp of the alignment.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3404033&req=5

pone-0041997-g002: The genotype 6 part of the phylogenetic tree constructed using the last 827 bp of the alignment.
Mentions: Figures 1 and 2 demonstrate how potential recombination events are identified from the trees. Figures 1 and 2 present the genotype 6 lineages of the phylogenetic trees constructed using the first fragment (600 bp in length) and the last fragment (827 bp in length) in the first sub-division strategy. In Figure 1, EU246930 (6a) is clustered within a lineage of 6a sequences and the bootstrap support value for this lineage is 84%. EU246931 and EU246932 (6e) fall within a cluster of 6e, with a bootstrap value of 92%, while EU246937 belongs to subtype 6n with a bootstrap value of 91%. However, in Figure 2, different phylogenetic relationships are found. EU246930 (6a), EU246932 (6e) and EU246937 (6n) are clustered with a lineage of subtype 6o sequences and the bootstrap support is 98%, while EU246931 (6e) forms a separate lineage with D84265 (6h) with 100% bootstrap support. Employing this approach, we analyzed all the trees and summarized the discordant phylogenetic signals suggesting evidence of recombination.

Bottom Line: This confirms the rarity of inter-genotype HCV recombinants.While the locations of the breakpoints identified by RDP were not identical, they are very close.Our study suggests that while recombination in HCV is rare, this warrants further investigation.

View Article: PubMed Central - PubMed

Affiliation: The Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland. wfshi.tsmc@gmail.com

ABSTRACT
Recombination in Hepatitis C virus (HCV) is considered to be rare. In this study, we performed a phylogenetic analysis of 1278 full-length HCV genome sequences to identify potential recombination events. Nine inter-genotype recombinants were identified, all of which have been previously reported. This confirms the rarity of inter-genotype HCV recombinants. The analysis also identified five inter-subtype recombinants, four of which are documented for the first time (EU246930, EU246931, EU246932, and EU246937). Specifically, the latter represent four different novel recombination types (6a/6o, 6e/6o, 6e/6h, and 6n/6o), and this was well supported by seven independent methods embedded in RDP. The breakpoints of the four novel HCV recombinants are located within the NS5B coding region and were different from all previously reported breakpoints. While the locations of the breakpoints identified by RDP were not identical, they are very close. Our study suggests that while recombination in HCV is rare, this warrants further investigation.

Show MeSH
Related in: MedlinePlus