Reviewer's report
Title:Subgenotype reclassification of genotype B hepatitis B virus
Version: 1Date:13 August 2012
Reviewer: Samad Amini-Bavil-Olyaee
Reviewer's report:
Shi and coworkers evolutionary reanalyzed all complete HBV genome sequence
genotype B to reconstruct and introduce a novel classification of HBV
subgenotypes B phylogenetically. Their finding is relevant since nine HBV
subgenotypes B had been reported worldwide without a conclusive analysis.
They showed that HBV subgenotypes B5, B6’, B3, B7, B9, B8 and Bx do not
meet subgenotypes definitions according to Pourkarim et al’s HBV
subgenotyping roles. They then classified those isolates as
quasi-subgenotype-B3. I have only some concerns that should be addressed to
improve their work:
1- Tables 1 and 2 should be mixed together (as Table 1) and also all mean
nucleotides distance should be presented as “percentage ± SD” that it makes all
variables constant within the manuscript. Therefore, SD from upper part of each
table should be removed and is brought up in front of each variable.
2- The authors should add a new table (Table 3) to present the comparison of
mean nucleotide divergence (percentage ± SD) of B1, B2, QSB3, B4 and B5
(previous B6).
3- Please edit “quasi-genotype B3” to “quasi-subgenotype B3” in the entire
manuscript.
4- Table 3 should be renamed to Table 2 and all data should be presented as
mean percentage ± SD, and all SD should be removed.
5- Please define a cut-off value for the bootstrap numbers in the trees. I would
recommend 45% as cut-off and vanish all values below 45% in trees.
6- If the authors really want to follow Pourkarim at al (Ref 25) roles, then they
should remove all recombinant strains from all analysis. I would suggest that. Of
course the authors mentioned that all B2 are recombinant, I am wondering that
all 655 isolates are recombinant or not. If few of them are recombinant, so they
can be excluded from analyses.
7- Please check that whether isolates EU660226 and GQ377595 and Bx isolates
are recombinant or not (using BootScan analysis); if so, please remove them
form trees and analysis.
8- Please add scale bar for trees.
9- Please add this references to the manuscript. Pourkarim et al. HBV
subgenotype misclassification expands quasi-subgenotype A3, CMI;17(6):947-9.
Note to AE: I would suggest “Minor Revision”.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests.
Reviewer's report
Title:Subgenotype reclassification of genotype B hepatitis B virus
Version: 1Date:13 August 2012
Reviewer: Samad Amini-Bavil-Olyaee
Reviewer's report:
Shi and coworkers evolutionary reanalyzed all complete HBV genome sequence
genotype B to reconstruct and introduce a novel classification of HBV
subgenotypes B phylogenetically. Their finding is relevant since nine HBV
subgenotypes B had been reported worldwide without a conclusive analysis.
They showed that HBV subgenotypes B5, B6’, B3, B7, B9, B8 and Bx do not
meet subgenotypes definitions according to Pourkarim et al’s HBV
subgenotyping roles. They then classified those isolates as
quasi-subgenotype-B3. I have only some concerns that should be addressed to
improve their work:
1- Tables 1 and 2 should be mixed together (as Table 1) and also all mean
nucleotides distance should be presented as “percentage ± SD” that it makes all
variables constant within the manuscript. Therefore, SD from upper part of each
table should be removed and is brought up in front of each variable.
2- The authors should add a new table (Table 3) to present the comparison of
mean nucleotide divergence (percentage ± SD) of B1, B2, QSB3, B4 and B5
(previous B6).
3- Please edit “quasi-genotype B3” to “quasi-subgenotype B3” in the entire
manuscript.
4- Table 3 should be renamed to Table 2 and all data should be presented as
mean percentage ± SD, and all SD should be removed.
5- Please define a cut-off value for the bootstrap numbers in the trees. I would
recommend 45% as cut-off and vanish all values below 45% in trees.
6- If the authors really want to follow Pourkarim at al (Ref 25) roles, then they
should remove all recombinant strains from all analysis. I would suggest that. Of
course the authors mentioned that all B2 are recombinant, I am wondering that
all 655 isolates are recombinant or not. If few of them are recombinant, so they
can be excluded from analyses.
7- Please check that whether isolates EU660226 and GQ377595 and Bx isolates
are recombinant or not (using BootScan analysis); if so, please remove them
form trees and analysis.
8- Please add scale bar for trees.
9- Please add this references to the manuscript. Pourkarim et al. HBV
subgenotype misclassification expands quasi-subgenotype A3, CMI;17(6):947-9.
Note to AE: I would suggest “Minor Revision”.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests.
Please review this paper.
user
Reviewer's report
Title:Subgenotype reclassification of genotype B hepatitis B virus
Version: 1Date:13 August 2012
Reviewer: Samad Amini-Bavil-Olyaee
Reviewer's report:
Shi and coworkers evolutionary reanalyzed all complete HBV genome sequence
genotype B to reconstruct and introduce a novel classification of HBV
subgenotypes B phylogenetically. Their finding is relevant since nine HBV
subgenotypes B had been reported worldwide without a conclusive analysis.
They showed that HBV subgenotypes B5, B6’, B3, B7, B9, B8 and Bx do not
meet subgenotypes definitions according to Pourkarim et al’s HBV
subgenotyping roles. They then classified those isolates as
quasi-subgenotype-B3. I have only some concerns that should be addressed to
improve their work:
1- Tables 1 and 2 should be mixed together (as Table 1) and also all mean
nucleotides distance should be presented as “percentage ± SD” that it makes all
variables constant within the manuscript. Therefore, SD from upper part of each
table should be removed and is brought up in front of each variable.
2- The authors should add a new table (Table 3) to present the comparison of
mean nucleotide divergence (percentage ± SD) of B1, B2, QSB3, B4 and B5
(previous B6).
3- Please edit “quasi-genotype B3” to “quasi-subgenotype B3” in the entire
manuscript.
4- Table 3 should be renamed to Table 2 and all data should be presented as
mean percentage ± SD, and all SD should be removed.
5- Please define a cut-off value for the bootstrap numbers in the trees. I would
recommend 45% as cut-off and vanish all values below 45% in trees.
6- If the authors really want to follow Pourkarim at al (Ref 25) roles, then they
should remove all recombinant strains from all analysis. I would suggest that. Of
course the authors mentioned that all B2 are recombinant, I am wondering that
all 655 isolates are recombinant or not. If few of them are recombinant, so they
can be excluded from analyses.
7- Please check that whether isolates EU660226 and GQ377595 and Bx isolates
are recombinant or not (using BootScan analysis); if so, please remove them
form trees and analysis.
8- Please add scale bar for trees.
9- Please add this references to the manuscript. Pourkarim et al. HBV
subgenotype misclassification expands quasi-subgenotype A3, CMI;17(6):947-9.
Note to AE: I would suggest “Minor Revision”.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests.
assistant