FIG 6.

Recombination analysis of LYRa11 and other SARS-like CoVs. Similarity plots (A) and bootscan analyses (B) were conducted with LYRa11 as the query and bat SARS-like CoVs, including Rs3367, Yunnan2011, and Rf1, as potential parental sequences. (C) A gene map of LYRa11 is used to position breakpoints. Four breakpoints at nt 20968, 23443, 24643, and 26143 in the LYRa11 genome were detected, generating three recombinant fragments, 1, 2, and 3. Phylogenetic trees were constructed based on the three fragments (D to F, corresponding to fragments 1 to 3) by the maximum likelihood method. LYRa11 (bold italic), Rs3367, Yunnan2011, and Rf1 used in SimPlot are shaded. Leading capitals: H, human SARS CoV; C, civet SARS CoV; B, bat SARS-like CoV.