Fig. 1

Evolutionary dynamics of gp85-B dominant quasispecies of ALV-J under different infectious ecosystems. a Percentages of the first 10 dominant quasispecies of gp85-B in the ori and their equals in cell culture supernatants of 5th passage (B-C5). Ori = black bars; chickens #1 (B1) and #2 (B2) plasmas = red bars. X-axis represents the first 10 dominant quasispecies of gp85-B in the original inoculum ordered based their ranks. Y-axis represents their percentages from total valid reads in each samples collected under different replication ecosystem. b Percentages of the first 10 dominant quasispecies of gp85-B in cell culture supernatants of 5th passage (B-C5) and their equals in the Ori. chickens #1 (B1) and #2 (B2) plasmas = red bars; Ori = black bars. c Haplotypes’ rank and their percentages of the first 10 dominant quasispecies of gp85-B in cell culture supernatants of 5th passage, plasma samples, and in the Ori. P5 = the cell culture supernatant samples of 5th passages; chicken 1 = plasma of #1 infected chicken; chicken 2 = plasma of #2 infected chicken, Ori = original liver inoculum. d The gp85-B amino acid alignment of the first 10 dominant quasispecies for viral samples collected in different replication ecosystyms. The dots indicate identical residues; the letter indicate amino acid substitutions; the dashes indicate gaps produced in the alignment; the blue square indicates two known variable regions (vr3 and hr2) and a new possible variable region X. The most dominant quasispecies (BO0001,32.85%) in the original inoculum (Ori) is used as the reference sequence on the top line corresponding to the amino acids sites #163-264 of gp85 in ALV-J prototype HPRS-103 [Genbank:Z46390]