Sendai virus intra-host population dynamics and host immunocompetence influence viral virulence during in vivo passage

Peña, José; Chen-Harris, Haiyin; Allen, Jonathan E.; Hwang, Mona; Elsheikh, Maher; Mabery, Shalini; Bielefeldt-Ohmann, Helle; Zemla, Adam T.; Bowen, Richard A.; Borucki, Monica K.

Our analysis of the potential impact to HN protein structure indicates that none of the mutations observed at residues 454, 461, or 525 should interfere with receptor binding. Based on structural modeling we conclude the following characteristics of identified mutation positions: (1) they are located on the surface, but should not interfere with critical functional regions such as the sialic acid-binding site, interfaces of HN tetramer formations, and interfaces within F-HN complex (Fig. 8). (2) These positions are in regions of high sequence variability among strains, serotypes or other related viruses. (3) Position 525 is located in the structurally variable region, while the two other positions, 454 and 461, can be considered as structurally conserved on the backbone level among number of closely related viruses. (4) Observations suggest that these positions are not involved in some critical function of the protein where conservation in both structure and sequence would be expected but they may play an important role to help virus adjustment to particular conditions or escape immune response. For example, Figure 7 . Results from the structure conservation analysis. Homology model of HN protein from SeV is structurally compared with HN proteins from HPIV3, Sv5, NDV, Bat Paramyxovirus (GH-M74a), Nipah and Hendra viruses. Regions identified as structurally conserved are colored from green when Calpha-Calpha deviations in corresponding residues are <2 Å to red (>6 Å ), with gray indicating no match. Pairwise structural superposition between homology model of HN protein from SeV and PDB structure (2 Â 9 m_B) of HN protein from Hendra virus is shown in Figure 7A structurally conserved between paramyxovirus species (colored in green), and the position 525 is located in the structurally variable region (colored in yellow). Calculated structural alignments show strong conformational similarities (structure similarity measured by LGA_S is above 61%) even for proteins with sequence identity (Seq_Id) as low as 21%. results from the antigenic sites predictions on HN proteins characterize the region 451-464 (overlapping with two of our mutation positions) as an epitope with good scores 0.6 and 0.4 by BepiPred and BEOracle prediction algorithms, respectively (Larsen, Lund, and Nielsen 2006; Wang et al. 2011) .