Fig. 4

Evolutionary dynamics of the first 10 dominant quansispecies of U3 fragment in different infectious ecosystems. a The first 10 dominant quasispecies haplotype (in the order according ranks) and their percentages of total valid reads in DF1 cell cultures (combined two passages, the left part). CC1001 = the quasispecies ranked the first in segment C from chicken 1; O0 = the original liver inoculum; C2 = chicken 2; P1 = passage1; P5 = passage 5 in cell culture. The last 3 numbers represents their ranks in the quasispecies population in each sample. b Base sequence alignment of the first 10 dominant quasispecies of U3 detected in each different infectious ecosystems. The reference sequence is the most dominant quasispecies in the original inoculum (CO0001, 60.45%), corresponding to bases #122–225 of LTR of ALV-J prototype strain HPRS-103. The dots indicate identical residues, while the letters indicate amino acid substitutions. The motifs as transcription regulatory elements were labeled on the top