Article Figures & Data
Figures
- FIG 1
(A) Geo-distribution of bat CoVs in China (gray provinces); (B) locations of bat alphacoronaviruses (open circles) and SARS-like CoVs identified in our study (solid circle) and in Ge et al.'s study (open triangle) (29). α, alphacoronavirus; β, betacoronavirus; S, SARS-like CoV.
- FIG 2
Taxonomic summary of viral reads with BLASTn (E < 10−5) results exhibited in MEGAN 4. The number of reads in each taxonomic level is shown after the level name.
- FIG 3
Phylogenetic analysis of RdRp amplicons obtained in this study and representatives of species in genera Alphacoronavirus and Betacoronavirus based on the maximum likelihood method. All sequences were classified into two groups: group Alphacoronavirus comprising 17 clades, and group Betacoronavirus comprising 10 clades. Clades containing approved species are in italics; clades containing unapproved novel species are marked with an asterisk. All amplicons in this study are marked as filled triangles, with previously reported bat CoVs as open triangles. Middle letters identify the viral host: H, human; C, civet; B, bat; Bo, bovine; M, murine; Ca, canine; F, feline.
- FIG 4
Characterization of S1 domains of SARS and SARS-like CoVs. (A) Phylogenetic analysis of entire S1 amino acid sequences based on the maximum likelihood method; (B) phylogenetic analysis of RBD amino acid sequences based on the maximum likelihood method; (C) sequence comparison of entire RBMs of SARS CoVs, LYRa11 (boxed), and other closely related bat SARS-like CoVs. The sequences of SARS-like CoVs in this study are marked as filled triangles, with other bat SARS-like CoVs as open triangles. Middle letters: H, human SARS CoV; C, civet SARS CoV; B, bat SARS-like CoV. Amino acid (aa) positions refer to SARS CoV Tor2 (AY274119). Critical residues that play key roles in receptor binding are indicated with asterisks.
- FIG 5
(A) Expression of EGFP-S1 fusion proteins in BHK-21 cells; (B) Western blot of expressed EGFP-S1 fusion proteins using rabbit anti-EGFP antibody (left) and SARS-convalescent human serum (right). The molecular masses are given on the right. BJ, LY, Rp3, and E, respectively, represent EGFP-S1 proteins of SARS CoV BJ01, bat SARS-like CoVs LYRa11 and Rp3, and EGFP control.
- 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.
- FIG 7
CoV-like particle considered to be LYRa11.
Tables
- TABLE 1
Details of rectal swabs from bats and positive number of bats detected by nested RT-PCR
Organism Xiangyun Bingchuan Jinghong Baoshan Total No. No. (%) positivea Cladeb No. No. (%) positivea Cladeb No. No. (%) positivea Cladeb No. No. (%) positivea Cladeb No. No. (%) positivea Cladeb Rhinolophus ferrumequinum 15 0 32 2 (9) αC 30 1 (3) αC 77 3 (4) αC Rhinolophus affinis 11 2 (18) β 11 2 (18) β Rhinolophus hipposideros 4 4 1 (25) αC 3 11 1 (9) αC Myotis daubentonii 22 2 (9) αA/E 64 5 (8) αA/D/E 86 7 (8) αA/D/E Myotis davidii 83 11 (13) αA/B/D/E 83 11 (13) αA/B/D/E Total 120 13 (11) αA/B/D/E 100 7 (7) αA/C/D/E 34 2 (6) αC 14 2 (14) β 268 24 (9) αA/B/C/D/E/β - TABLE 2
Comparison of full genomic lengths and ORF amino acid identities of SARS and SARS-like CoVsa
- TABLE 3
Bat CoV distribution in China
a α, alphacoronavirus; β, betacoronavirus. S in parentheses means only positive for SARS-like CoV.
