Supplementary Figure S1. Numbers of bat samples, the provinces of origin of these samples, and the 136 sequenced viruses of the 11 families. The number
of bat samples in each province was marked in the map. Viruses confirmed by sequencing in each province were counted by pie chart around the map; viruses of
different families were differentiated by different colors.
Supplementary Figure S2. Phylogenetic tree based on diverse sequences of partial amino acid of the polymerases of BtAdVs.
Supplementary Figure S3. Phylogenetic trees based on the complete E, M, and N proteins of lineage C beta-CoVs.
Supplementary Figure S4. Genomic organization differences between Bat Hp-betacoronavirus/Zhejiang2013 and lineage B CoVs.
Supplementary Figure S5. (A) Phylogenetic tree based on diverse S proteins of BtVs-BetaCoV/SC2013. (B) Phylogenetic tree based on diverse ORF8s of
BtRs-betaCoV/YN2013.
Supplementary Figure S6. Phylogenetic analysis of lineage B beta-CoVs. (A) Phylogenetic tree based on the concatenated unique structural ORF sequences. (B)
Phylogenetic analysis based on concatenated ORF1ab, E, M, N, ORF6, ORF7a, ORF7b, and ORF8. (C) Phylogenetic analysis based on S proteins.
Supplementary Figure S7. Pairwise alignment of ORF8s between different lineage B betaCoVs. The alignment of ORF8s of these CoVs was conducted by
Clustal W under the MegAlign program (Lasergene).
Supplementary Figure S8. Recombination analysis of five genomes.The bat M. fuliginosus genomesBtMf-AlphaCoV/GD2012 (GD),BtMf-AlphaCoV/HuB2013
(HB), BtMf-AlphaCoV/FJ2012 (FJ), and BtMf-AlphaCoV/HeN2013 (HN), were compared to the M. pusillus genome,BtCoV HKU8. Similarity plot (top) and
Bootscan analyses (bottom) were conducted with Simplot, version 3.5.1 (Kimura model; window size, 1,000 nt; step, 300 nt) on a gapless nucleotide alignment
generated with MUSCLE; the genomic sequence of BtCoV HKU8 was the query sequence.
Supplementary Figure S9. Comparison of genomic organization of BtMf-ParaV/AH2011 and BtMl-ParaV/QH2013 (blue) to typical Jeilongvirus (bright red).
Supplementary Figure S10. Genome organization differences between CoVs of each lineage of beta-CoVs and alpha-CoVs. The unique structural ORFs of
lineage B beta-CoVs are labeled in orange.