Bootscanning plot and phylogenetic analysis of the clone sequence 08mLDTD003-1 and 09mLDTD011-23/25 based on
segment. A) the bootscan plot (left panel) and phylogenetic trees of three sub-segments (right panel) of 08mLDTD003-1 based on pol region. B) and C) the bootscan plots and sub-region trees for clone 09mLDTD011-23 and 09mLDTD011-25, respectively. 08mLDTD003-1 and all other clone sequences from 08mLDTD003 were highlighted by red and blue closed circle. 09mLDTD011-23, 09mLDTD011-25 and all other clone sequences from 09mLDTD011 were highlighted by red, green and purple closed circles, respectively. The subtype references for bootscan were selected as follows: A (92UG037), B’ (RL42), C (95IN21068), CRF01_AE (90CM240). The phylogenetic trees for each sub-segments were constructed by MEGA 5.0 using the neighbor-joining method, and with the clones’ sequence obtained from the same driver as well. The stability of the nodes was assessed by bootstrap analysis with 1000 replications, and only bootstrap values of >75% were shown.