On 2016 Dec 13, Stuart RAY commented:

This finding is intriguing, but the reported findings seem inconclusive, for the following reasons: (1) figure 2a - the tree of sequences from Core/E1 region - has weak clustering with no significant bootstrap value to show confident clustering with subtype 3a, and no significant bootstrap value in genotype 1 to exclude the query sequence; (2) the nearly full-length sequence was cobbled together from 12 overlapping PCR amplifications, raising the possibility that this was a mixed infection with different regions amplified from different variants in the blood, rather than a single recombinant genome; and (3) the title says "not uncommon" but it appears that detailed study was only done for one specimen. It would be more convincing if a single longer amplicon, with phylogenetically-informative sequences on both sides of the breakpoint and showing a reproducible breakpoint, were recovered from separate blood aliquots (i.e. fully independent amplifications). Submission of the resulting sequence(s) to GenBank is a reasonable and important expectation of such studies. In addition, the title of the paper should not say "not uncommon" unless the prevalence can be estimated with some modicum of confidence.

On 2016 Dec 13, Stuart RAY commented:

This finding is intriguing, but the reported findings seem inconclusive, for the following reasons: (1) figure 2a - the tree of sequences from Core/E1 region - has weak clustering with no significant bootstrap value to show confident clustering with subtype 3a, and no significant bootstrap value in genotype 1 to exclude the query sequence; (2) the nearly full-length sequence was cobbled together from 12 overlapping PCR amplifications, raising the possibility that this was a mixed infection with different regions amplified from different variants in the blood, rather than a single recombinant genome; and (3) the title says "not uncommon" but it appears that detailed study was only done for one specimen. It would be more convincing if a single longer amplicon, with phylogenetically-informative sequences on both sides of the breakpoint and showing a reproducible breakpoint, were recovered from separate blood aliquots (i.e. fully independent amplifications). Submission of the resulting sequence(s) to GenBank is a reasonable and important expectation of such studies. In addition, the title of the paper should not say "not uncommon" unless the prevalence can be estimated with some modicum of confidence.