This is really irritating me as this is version 3 of the same story. It is not even a particularly interesting story except it is if you think deeply about it.
What I want to show is that H5N8 in the US is a subtype that has been produced by multiple events where an H5 containing virus reassorts with an N8 containing virus. To do this I constructed a tree for ALL the H5 sequences in the database and ALL the N8 sequences in the database.
If I am wrong then the H5N8 sequences from the US would cluster in one group and not be spread across the tree in many distinct clades. They would at least be close neighbours. Am I wrong? Nope they are spread all over both trees. In the H5 tree there are lots of neighbouring H5 sequences that have been sampled but they are from other subtypes. In the N8 tree they are also widely spread with sequences from many other subtypes in between.
So here is the referees comment https://f1000research.com/articles/5-2463/v1#referee-response-18901
I am completely incredulous about how this is a possible argument for rejection.
If the referees are right int their arguments then you CAN have clades in a tree that are polyphyletic for subtype without reassortment being the cause. I can simply get from H5N2 to H5N8 by spontaneous mutation of the N2 to the N8 form. I can make hundreds of base changes and insertions and deletions and this is more likely than a simple reassortment event.
Now let me imagine this is not their argument and that they will admit that reassortment does exist in the clades but that they are not convinced about the specific H5N8 reassortment events. They are suggesting that these occur in both the N8 and H5 tree which are two independent samples in the same pattern by chance and that there is a need for the internal gene trees to corroborate these events. I say in the paper very clearly that I cannot KNOW what the origins of the H5 and N8 are and I can just make suppositions about them, but I know that a reassortment event has definitely occurred. Otherwise what are the chances that the H5 and N8 genes both undergo substantial mutational changes between samplings of H5N8 and that the neighbours include large numbers of sequences from many other subtypes? If this is true then H5N8 sampling must have been carried out appallingly or in a very biased manner while we detect all the other subtypes with ease.
To be honest I have the internal gene trees as I just finished them for another paper about a different subject and oddly enough they show exactly what I said in the paper. I was 100% right. These two referees are 100% WRONG. In fact their arguments are so illogical and unsupported by evidence that I was surprised that they were brave enough to put their names to them.
So let me ignore the sneering way the review is written, because everyone has a time in their life when they thing they know it all and recent graduates tend to fall into this trap more often than not. I know that I was the same 20 years ago when I started my career.
Let me consider how they use rhetoric in order to create a straw-man to knock down by suggesting that the paper is about discovering reassortment - it is not. The title is very clear it says reassortment in H5N8 and then only part of the H5N8 tree - the US part is actually the main focus of the study. It is a paper about a specific example and the dangers of collecting data by subtype as this gives an incomplete picture of sequence evolution in a segmented virus that can undergo reassortment.
This is the point. If the segments can reassort then they can pass between multiple subtypes in their evolutionary pathway. This is not rocket science this is just suggesting it is better to consider this possibility in trees and sampling and not just carry out phylogenetic analysis by subtype.
This gives me with two options:
1) The referees are idiots.
2) The referees forgot to declare the conflict of interest in that they have a skewed view-point in order to protect their existing work. This paper starts to undermine the idea of monophyletic clades for subtype which underpins the WHO nomenclature system for H5 which Justin Bahl helps to manage.
I do not think the referees are idiots, but I do think the second point is true and that there are good reasons why Dr Bahl should have declared a real and prejudicial interest and NOT taken up the review. Nobody is objective about seeing their work undermined, ever. I also think this is a good reason for me to ban Dr Bahl and Joseph Hicks from EVER reviewing any of my papers and for editors to consider any review that they provide with suspicion.