Structurally informed evolutionary models improve phylogenetic reconstruction for emerging, seasonal, and pandemic influenza viruses

Xueting Qiu; Justin Bahl

The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/228692 doi: bioRxiv preprint 6 HKY and HKY with protein structure partitioning model (HKY model and P model in Fig. 1c) . 108 Compared to SRD06 codon model (C model in Fig. 1c The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/228692 doi: bioRxiv preprint 7 Comparing the overall substitution rates for each influenza subtype, we observed that the 131 pandemic H1N1pdm09 had the highest substitution rate (~7.5 ï‚´ 10-3 substitution/site/year). 132 HPAI H7N9 and H5Nx had the substitution rates around 4.0 -4.8 ï‚´ 10-3 substitution/site/year. 133 Seasonal influenza viruses had the range as 2.0 -3.5 ï‚´ 10-3 substitution/site/year, where the two 134 type B lineages had lower rates than the two A subtypes. 135 Furthermore, we compared the separate substitution rates for stalk and head domains Table 2 .2, the range of dC1+2/dC3 was 0.10 -0.32 for stalk domain and 150 0.25 -0.87 for head domain from all subtypes of influenza viruses included in the study. The 151 overall dC1+2/dC3 for the whole HA protein calculated from the c model was lower than head 152 domain but higher than stalk domain for each influenza subtype. We also observed that the stalk 153 All rights reserved. No reuse allowed without permission.