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.

Detecting BCoV seqeuences in the mixture would mean a variant detection sensitivity of 1 in 10,000 copies (0.01%). However, amplification efficiency was affected by slight differences in plasmid insert size between the controls (SeV 877 bp, RABV 1138 bp, and BCoV 1003 bp) causing the insert sequence from the smaller inserts to have slightly more coverage as compared with the larger insert (i.e. RABV). In the resulting sequencing data, the SeV plasmid insert had $1,000Â more coverage as compared with the RABV insert, about 10Â more than expected ratio of 100Â. However the ratio of RABV to BCoV insert was about 88.5Â, much closer to the expected value of 100Â. These data indicate that very rare sequences (BCoV insert was present at 0.01% in the mixture) are readily detectable using this ultradeep sequencing (UDS) methodology.