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.

Three amino acid substitutions, A454V, E461K, and K525Q, occurred in the glycoprotein HN and were detected either at the consensus sequence or minority variant level in a majority of the BAL samples. The respective underlying nt changes were C8053T, G8073A, and A8265C. Although all three substitutions already existed at the minority level in the seed stock, their frequencies were far higher in the mice P10 samples (all diet groups) and the guinea pigs. Notably, the frequency of these three amino acid substitutions was highly correlated across the samples (Fig. 5A-C) , prompting us to carry out a closer examination of the linkage relationship at the three positions based on the sequencing reads. Indeed, the linkage association between the alleles at these three positions was highly significant. For residues 454 and 461, linkage between the seed stock WT alleles A454 and E461 and the linkage between mutant alleles V454 and K461 were significant at P-value <10 À300 for all samples sequenced (Fisher's exact test, Supplementary Table S3 ). At residues 461 and 525, the E461-K525 seed stock WT alleles linkage and the K461-Q525 mutant alleles linkage were significant at P-values < 10 À28 (Supplementary Table S3 ) for all samples sequenced.