Through gene-specific phylogenetic analyses, we also identified phylogenetic incongruence for 2019-nCoV compared with other bat-SL-CoVs at different genes, suggesting potential recombination event. Specifically, 2019-nCoV was closely related to strains bat-SL-CoVZXC21 and bat-SL-CoVZC45 at ORF1a, S, and N genes, but not at ORF1b gene. At ORF1b gene, bat-SL-CoVZXC21 and bat-SL-CoVZC45 were related to strains Longquan-140 and HKU3-10 (Figure 2C). Simplot analyses based on genome alignment of 2019-nCoV, bat-SL-CoVZC45, Longquan-140, and SARS-CoV suggest that the recombinant strain was not likely to be 2019-nCoV, but bat-SL-CoVZC45 (Figure 3B). And it also revealed at least four recombination breakpoints at positions 11,754, 20,664, 22,321, and 24,134 nt of the genome alignment, respectively (Figure 3B).