Evolutionary sites drive avian influenza virus adaptation

The DMS library was serially passaged ten times in both MDCK cells and 10-day-old SPF chicken eggs. For in vitro passages, MDCK cells were infected at an MOI of 0.01 for each passage. For in ovo passages, 10000 pfu of virus in a 100 uL volume was inoculated into each egg. Cell culture supernatants and allantoic fluids from the 5th and 10th passages were subjected to deep sequencing to evaluate changes in library size and diversity.