The contrasting phylodynamics of human influenza B viruses

Thank you for sending your work entitled “The contrasting phylodynamics of human influenza B viruses” for consideration at eLife. Your article has been favorably evaluated by Diethard Tautz (Senior editor) and 2 reviewers, one of whom is a member of our Board of Reviewing Editors.

The Reviewing editor and the other reviewer discussed their comments before we reached this decision, and the Reviewing editor has assembled the following comments to help you prepare a revised submission.

We agreed that your paper provides the first comprehensive portrait of influenza B phylodynamics and epidemiology and that the comparisons of the Yam and Vic lineages with each other and with the dominant seasonal influenza A lineages greatly advance our understanding of influenza dynamics in general. We did, however, have a number of concerns regarding some of the presented analysis and the presentation of some of the results.

1) Reassortment analysis: we were not convinced that the comparison of reassortment between different seasonal influenza strains via multidimensional scaling is appropriate. The analysis of A/H3N2 (Rambaut et al., 2008) uses a different distance measure and it is not clear whether the results are comparable. It is also not clear how sensitive and robust MDS based on the proposed distance measure is. It may be hard to conclude quantitative differences from this analysis as the dispersion in the plot will not only reflect the number of reassortment events, but also whether those events shuffle closely or distantly related lineages. In terms of inter-lineage reassortment, the MDS in Figure 10 does not add much to Figure 9 (which shows each probable reassortment event) and meaningful quantification of intra-lineage reassortment would require going beyond the MDS. We suggest cutting the MDS. Also, results by Dudas, Bedford, Lycett, Rambaut, MBE, 2014 should be discussed; the preprint has been available since March.

2) More direct measures of genetic diversity: Figure 3 and Figure 8 are labeled as “relative genetic diversity” (relative to what?). We would like to see a more direct measure of diversity such as the average pairwise distance in windows of a few months. We would also like to ask you to offer a clearer interpretation of the GMRF results. The GMRF method gives smoothed estimate of the rate of coalescence and is based on a neutral coalescent model. This measure is not the same as genetic diversity and the meaning of estimates based on a neutral coalescent is not clear.

The take home message from these plots seems to be that Vic has a “burstier” and shallower phylogeny than Yam, with fewer lineages carrying over from one season to another. This would show up as spikes and troughs in the rate of coalescence and is consistent with the higher R0 and the smaller number of introductions for Vic. If this is the desired interpretation, please discuss as such.

3) Phylodynamic analysis: how were the reported years chosen? (please double check the color code in Figure 2. 2011 seems to be fully dominated by Yam, but you report Vic estimates in Figure 4-5). The discussion of the implications of higher R0 for Vic needs clarification. Prevalence within one season depends on the start of the exponential growth phase, R0, and the number of independent introductions (i.e., the number of lineages at the beginning if the growth phase). The two strains differ in the latter two of these characteristics in ways that affect prevalence in opposite ways. This needs more careful discussion: the assertion that “these results are consistent with the more frequent detection of Victoria lineage viruses during our sampling period (see Source data in Dryad), indicating that Victoria viruses infected a higher proportion of the population” (in the Results and discussion section) is a tautology (more frequent detection corresponding to higher prevalence…). Would it be possible to explicitly show that exponential growth of Vic and Yam differs between years? The >5000 samples used for the age distribution should be sufficient to directly show differences in dynamics if date information beyond year is available. If this is not possible, Figure 6 should be presented on a log scale and real incidence data should be included.

4) Age distribution and glycosylation: Figure 16C shows odds ratios of for an association between glycosylation at 212 and infections in age group 0-5. In Figure 16B, however, it would be much more useful to show that the fraction without 212 glycosylation correlates with the fraction of in age group 0-5. Otherwise, the correlation is confounded by the total number of strain. When discussing the structural implications of the observed sequences changes, more care should be taken to distinguish hard evidence from previously solved structures (give PDB IDs and references in figure or caption!), modeling, and hypothesis. Figure 15 could be absorbed as a supplement to Figure 14. The “three major clusters” in Figure 14C are not as clear as the text suggests. Elaborate or tone down.

5) Presentation and shortening: the manuscript is long with 16 figures in the main text and its length dilutes the most important points. Also, please make every effort to include parameters of programs used, scripts, and input files (such as BEAST xmls).

1) Reassortment analysis: we were not convinced that the comparison of reassortment between different seasonal influenza strains via multidimensional scaling is appropriate. The analysis of A/H3N2 (Rambaut et al., 2008) uses a different distance measure and it is not clear whether the results are comparable. It is also not clear how sensitive and robust MDS based on the proposed distance measure is. It may be hard to conclude quantitative differences from this analysis as the dispersion in the plot will not only reflect the number of reassortment events, but also whether those events shuffle closely or distantly related lineages. In terms of inter-lineage reassortment, the MDS in Figure 10 does not add much to Figure 9 (which shows each probable reassortment event) and meaningful quantification of intra-lineage reassortment would require going beyond the MDS. We suggest cutting the MDS. Also, results by Dudas, Bedford, Lycett, Rambaut, MBE, 2014 should be discussed; the preprint has been available since March.

We agree that the MDS may not accurately quantify the degree of reassortment. As suggested, we have therefore removed MDS from our manuscript (including the figure), and now directly use the phylogenetic trees of each gene segment to discuss our findings. In addition, we have also included a discussion of the Dudas et al. paper. Their observation that the PB2, PB1 and HA were genetically linked since the divergence of Victoria and Yamagata lineages is consistent with our results. The new text in the Results and discussion section is copied below:

“Phylogenies also suggest that the PB2 and PB1 gene trees (Figure 8B, C) exhibit deep divergence, similar to the HA gene where cocirculating viruses contain distinct Victoria and Yamagata genes. In contrast, the other gene segments exhibit relatively recent divergence indicating that the prevailing diversity of these genes originate from a single lineage. These results are consistent with a detailed investigation of long term reassortment patterns of influenza B virus lineages that revealed genetic linkage between the PB2, PB1 and HA protein genes. Specifically, we observe that the PB2, PB1 and HA genes were consistently derived from a single lineage, except for the short-lived subpopulation in 2004.”

2) More direct measures of genetic diversity: Figure 3 and Figure 8 are labeled as “relative genetic diversity” (relative to what?). We would like to see a more direct measure of diversity such as the average pairwise distance in windows of a few months. We would also like to ask you to offer a clearer interpretation of the GMRF results. The GMRF method gives smoothed estimate of the rate of coalescence and is based on a neutral coalescent model. This measure is not the same as genetic diversity and the meaning of estimates based on a neutral coalescent is not clear.

The take home message from these plots seems to be that Vic has a “burstier” and shallower phylogeny than Yam, with fewer lineages carrying over from one season to another. This would show up as spikes and troughs in the rate of coalescence and is consistent with the higher R0 and the smaller number of introductions for Vic. If this is the desired interpretation, please discuss as such.

The term ‘relative genetic diversity’ (relative to itself through time) is technically correct, appropriate, and has been used in many prior publications. We used it in the place of ‘effective population size’ or ‘diversity’ because of the likely action of natural selection in shaping the genetic structure of influenza virus, and to be consistent with prior publications (e.g. Rambaut et al., 2008, Nature, 453: 615-9). We have elaborated on our usage of this term in the Materials and methods section as follows:

“In the absence of natural selection (i.e. under a strictly neutral evolutionary process) the genetic diversity measure obtained reflects the change in effective number of infections over time (N_et, where t is the average generation time). However, because natural selection can play a major role in the evolution of influenza HA, these are interpreted as ‘relative genetic diversity’, and which is consistent with previous studies of influenza A virus (Rambaut et al., 2008, Nature, 453: 615-9).”

We agree with the astute interpretation of the GMRF plots, that the coalescent represents the shape of the phylogeny. Accordingly, we have made extensive revisions to the text in the Results and discussion section. Specifically, the increase and decrease in ‘relative genetic diversity’ for Victoria signifies the genetic bottleneck that occurs between seasonal epidemics, whereas for Yamagata diversity is maintained between seasonal peaks and troughs, and which results in a gradual increase of genealogical diversity through time. To make a better connection between the coalescent analysis and the phylogeny, we have moved the description of the dated tree (including Figure 4 of the revised manuscript), to just below the GMRF description, within the section ‘Population dynamics of influenza B virus’.

Furthermore, as suggested by the reviewers, we now provide an explicit measure of changes in genetic diversity; the genealogical diversity (in years) (Figure 4 of the revised manuscript). The genealogical diversity was measured by averaging the pairwise distance as time units on the tree between random contemporaneous sample pairs. This measure is related to the pairwise genetic diversity as measured on an accurate molecular clock-based phylogenetic tree (Bedford et al., 2011, BMC Evol Biol 11: 220; Zinder et al., 2013, PLoS Pathog 9: e1003104), and we believe is preferable to the pairwise methods proposed by the reviewers, which do not account for phylogenetic structure and hence include extensive pseudoreplication.

3) Phylodynamic analysis: how were the reported years chosen? (please double check the color code in Figure 2. 2011 seems to be fully dominated by Yam, but you report Vic estimates in Figure 4-5). The discussion of the implications of higher R0 for Vic needs clarification. Prevalence within one season depends on the start of the exponential growth phase, R0, and the number of independent introductions (i.e., the number of lineages at the beginning if the growth phase). The two strains differ in the latter two of these characteristics in ways that affect prevalence in opposite ways. This needs more careful discussion: the assertion that “these results are consistent with the more frequent detection of Victoria lineage viruses during our sampling period (see Source data in Dryad), indicating that Victoria viruses infected a higher proportion of the population” (in the Results and discussion section) is a tautology (more frequent detection corresponding to higher prevalence…). Would it be possible to explicitly show that exponential growth of Vic and Yam differs between years? The >5000 samples used for the age distribution should be sufficient to directly show differences in dynamics if date information beyond year is available. If this is not possible, Figure 6 should be presented on a log scale and real incidence data should be included.

We apologize for the error in the color legend, where the names of Victoria and Yamagata were swapped. We thank the reviewers for pointing this out. We have rectified this in Figure 2 (of our revised manuscript) and improved the colors to be consistent (red and black) with the rest of the manuscript.

We have also revised the section on phylodynamics extensively, creating a new section entitled ‘Transmission dynamics of influenza B virus’ (in the Results and discussion section). As suggested, we have also included a cumulative case plot (in semi-log scale) (Figure 5C of the revised manuscript), using all positive cases for the same years that we estimated R_e (see Results and disscussion for the results of this analysis).

4) Age distribution and glycosylation: Figure 16C shows odds ratios of for an association between glycosylation at 212 and infections in age group 0-5. In Figure 16B, however, it would be much more useful to show that the fraction without 212 glycosylation correlates with the fraction of in age group 0-5. Otherwise, the correlation is confounded by the total number of strain. When discussing the structural implications of the observed sequences changes, more care should be taken to distinguish hard evidence from previously solved structures (give PDB IDs and references in figure or caption!), modeling, and hypothesis. Figure 15 could be absorbed as a supplement to Figure 14. The “three major clusters” in Figure 14C are not as clear as the text suggests. Elaborate or tone down.

This is a good question. We agree with the reviewers and therefore have switched to fractions rather than absolute numbers (Figure 12 in the manuscript), although the confounding effect is the same for the other age groups and the relative difference of the correlations could be compared. The correlation with the youngest age group is still apparent, although weaker than before; however, the difference to the other age groups remain as strong as before. Moreover, as years with zero or one strain translate into extreme fractions (0 or 1) dominating the correlation, we only show correlations for years with 10 or more Vic strains. The figure legend has been adjusted accordingly.

We appreciate the comment on using previously resolved structures and their implications to our findings and have taken great care when discussing them. In particular, we have cleaned up our language to use strong wording only when we refer to the backbone differences as observed in solved crystal structures for both lineages independently. For visualization and comparison of general residue positions, such as for mutation mapping (Figure 9 and Figure 11–figure supplement 1 of the revised manuscript), we necessarily used homology models to account for the changes in the respective sequences of each strain to be compared. However, these models are expected to be structurally very close to the crystal structure templates simply due to the high percentage identity (>90%) and lack of insertion/deletion changes. Importantly, interpretation is made only at the level of rough structural residue positions (rather than detailed side-chain conformations), which are expected to be reasonably accurate. Furthermore, when adding ligands by superposition (Figure 11D, E in the manuscript), we computationally energy-minimized the side-chains near the ligand to avoid any clashes following a successfully benchmarked protocol (Krieger et al., 2009, Proteins 77 Suppl 9: 114-22). Finally, we have also added the PBD IDs to all figures, and specified their exact use.

We have also toned down our description of the three major clusters in the legend of Figure 11.

5) Presentation and shortening: the manuscript is long with 16 figures in the main text and its length dilutes the most important points. Also, please make every effort to include parameters of programs used, scripts, and input files (such as BEAST xmls).

We have made several changes to reduce the length of the manuscript (major changes listed below), and also uploaded BEAST xml files to Dryad:

(a) The figure panel along with text that compares the phylodynamics between Australia and New Zealand during 2002 was removed (Figure 6B in the original submission).

(b) We have combined multiple panels in Figure 5 (of the revised manuscript), including R_e estimates, comparison of incidence/prevalence in 2008 (previously presented as a panel with (a)), and a new panel showing cumulative cases as suggested in comment 3.

(c) We have considerably reduced the length of the section on reassortment by removing any reference to MDS (and the figure) as suggested.

(d) We have removed the figure showing HA-NA site selection as suggested (Figure 11 in the original submission).

(e) We have moved a figure on structure to the figure supplement (Figure 11–figure supplement 1 in the revised manuscript), as suggested.