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. 2016 Nov 17;198:9–16. doi: 10.1016/j.vetmic.2016.11.014

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© 2016 Elsevier B.V. All rights reserved.

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Fig. 5 — Recombination analysis of the IBV strains ck/CH/LHLJ/130744 (A and B) and ck/CH/LJL/140734 (C and D). SimPlot using H120 as the query sequence. The dotted lines show the deduced recombination breakpoints (A and C). The hollow arrows show the different fragments similar to those of the parental viruses. Multiple sequence alignments of the predicted breakpoints and flanking sequences among 4/91, ck/CH/LHLJ/130822 and ck/CH/LHLJ/130744 (B), and H120, ck/CH/LHLJ/130822 and ck/CH/LJL/140734 (D). The numbers on the right of each alignment show the nucleotide positions in the genome of each virus. The sequences of ck/CH/LHLJ/130744 (B) and ck/CH/LJL/140734 (D) are listed, respectively, and only the nucleotides differing from those of these two strains are depicted. The regions where the template switches (breakpoint) have taken place are in bold.