Sunday, 4 October 2015

Telling the story properly. The original rejection letter.

To put my irate posts in context you need to have the full story. Here is the original rejection letter and referees comments.

Thank you for your submission to Journal B. I am writing to inform you that your manuscript, "The multiple origins of the H5N8 avian influenza sub-type" (#2015:07:5858:0:0:REVIEW), has been rejected for publication.The comments supplied by the reviewers on this revision are pasted below. My comments are as follows:Editor's commentsYour paper has now been reviewed by two experts in the field. They both found the general topic of avian influenza of interest, but both also agree that your study seems to provide little advance with respect to previous research. The study adds no new data and apparently no new interpretation of results. Both reviewers found your method descriptions lacking in detail as well as the discussion of your results. As reviewer 2 points out, it would be impossible to reproduce your results given the lack of detail in the manuscript on the methods employed. Likewise, reviewer 1 identified discussions of methods (e.g., bootstrapping) for which there were no available results. Given these significant concerns with the manuscript and the lack of clear articulation of the novel contribution your analysis makes beyond other studies of avian influenza, I am forced to recommend rejection of your paper.Editor 1

Reviewer CommentsReviewer 1 Basic reportingNo CommentsExperimental designNo CommentsValidity of the findingsNo CommentsComments for the authorMajor strengths and weaknesses:This study is a successful attempt in using the datasets from website to analysis the multiple orgins of the H5N8 avian influenza subtype. The study has further phylogenetic analyses of all of the H5 hemagglutinin and N8 neuraminidase sequences to show that each of the H5N8 outbreaks has resulted from a different reassortment event and that there have been at least 7 distinct origins of the viral sub-type since it was first characterised in a turkey in Ireland in 1983.
However, I also feel the phylogenetic results and discussion contained mostly results from the analyses, but very little discussion. Given that almost all of the data for these analyses came from published studies, it was not clear if there were differences between these results and those studies –and if so, was this due to using different datasets or different analyses from those studies? From your MS, you used MEGA v6.06 to construct the ML tree, could you use other phylogenetic software to build ML tree or BI tree, to verify each other? I suggested that you could mark the clades in figure 1 in order to make the relationship more distinct. In addition, from figure 3 to figure 10, I couldn’t find the bootstrap values in your trees, so please add the values into tree figures., and you can also add some description in this section. The classification of H5, maybe you can refer to recent research (e.g. Donis et al, 2015).
Minor issues:- Line 36: change to “shown”- L100: should be “turkeys”Reviewer 2 Basic reportingThe article is written in English using clear and unambiguous text. I think the article introduction and background fit into the broader field of knowledge. I think the figures need some work regarding clarity. For instance, phylogenetic trees show clades that are too busy and could be collapsed for more clarity without losing information.Experimental designI am not sure whether this manuscript conforms to "original primary research". While the manuscript aims to provide an epidemiological analysis of highly pathogenic avian influenza (HPAI) from a recent outbreak in Korea, it does not add much in comparison to other published articles.The two main objectives of this manuscript are 1) to test whether there's phylogenetic evidence for reassortment, and 2) whether there are multiple origins to the Korean outbreak. A cursory review of literature shows that both aspects have already been studied. Some examples are PMID: 24856098; PMID: 25625281; PMID: 25192767. Also, while I am not opposed to manuscripts that use data from GenBank only (that's why it's there to begin with), I think that in this case this has a negative impact since the data are not novel and the analysis provide little new information.In my opinion, the author should re organize the article to focus on something more original. Some examples come to mind: using molecular clocks to uncover temporal patterns in this outbreak, looking at past population dynamics to infer whether this serotype is becoming more or less diverse over time, or perform a phytogeographic analysis to provide insights into its origin and spread.Validity of the findingsMethods
I think this manuscript uses a very rich dataset but the analysis seem precipitous, exploratory and "out-of-the-box". My overall impression is that there is little exploration of the parameter space.
In Methods, line 52, what was the criterion by which the nucleotide substitution model was selected? Was it Akaike Information Criterion, Bayesian Information Criterion or else?
I think the methods section needs more detail. Statements such as “The sequences were aligned using MAFFT” are insufficient to allow full reproducibility. What parameter values were used and why? What version is the program? Did you fit a codon model to the coding sequences? Did you check for intra-gene recombination? Also, how many sequences were used? It says “all” but how many? Was the alignment done on the coding sequences or in the nucleotides? What parameter values were used? Finally, the phylogenetic reconstruction step is not clear as to how it was performed. Are the trees rooted? Were outgroups used? What is a “condensed phylogenetic tree”? Is it some type of consensus? If so, is it a majority rule consensus?
Results and Discussion
The description of the results is very qualitative, e.g., “the current outbreak shows some structure”. It would be more objective to quantify the degree of structure by using distance metrics or population genetic estimators of structure.Comments for the author
no comments
An important point is that Referee 2 is the PhD student of Editor 1

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