Article Figures & Data
Figures
- FIG. 1.
Map of China showing 15 provinces where coronavirus surveillance in bats was conducted. Numbers indicate number of sites positive over the total number of sites sampled in each province.
- FIG. 2.
Phylogenetic relationships of 64 coronaviruses isolated from bats in China. The tree was generated based on 440 nucleotides of the RNA-dependent RNA polymerase region by the neighbor-joining method in the MEGA program. Numbers above branches indicate neighbor-joining bootstrap values (percent) calculated from 1,000 bootstrap replicates. Terminal nodes containing bat coronaviruses isolated in this study are collapsed and represented by a blue triangle with the number of viruses indicated within. The tree was rooted to Breda virus (AY427798). Scale bar, 0.05 substitution per site. Red text indicates provinces from where viruses were isolated. Abbreviations: AH, Anhui; FJ, Fujian; GD, Guangdong; GX, Guangxi; HA, Hainan; HB, Hubei; HE, Henan; JX, Jiangxi; SC, Sichuan; SD, Shandong; YN, Yunnan.
- FIG. 3.
Linear representation of the ORFs of the bat coronaviruses and representative known coronaviruses from each group. Conserved functional domains in ORF1a and ORF1b are indicated by yellow boxes. The following predicted domains are shown: pepain-like proteases 1 and 2 (PL1 and PL2), 3C-like protease (3CL), RdRp, metal ion-binding domain (MB), and helicase (Hel). Putative ORFs are indicated by blue boxes and numbered according to their order in the genome: BtCoV/R. ferrumequinum/Hubei/273/04 (BtCoV/273/04), BtCoV/R. macrotis/Hubei/279/04 (BtCoV/279/04), BtCoV/T. pachypus/Guangdong/133/05 (BtCoV/133/05), BtCoV/S. kuhlii/Hainan/512/05 (BtCoV/512/05), SARS-CoV, PEDV, avian IBV, and human coronavirus OC43 (HCoV-OC43).
- FIG. 4.
Similarity histogram of RdRp (A) and spike (B) genes based on alignments from the program TransAlign.
- FIG. 5.
Phylogenetic relationships of the helicase (A) and spike (B) genes of representative coronaviruses isolated from bats in China. Trees were generated by the neighbor-joining method in the PAUP program. Numbers above branches indicate neighbor-joining bootstrap values (percent) calculated from 1,000 bootstrap replicates. Analyses were based on 1,833 nucleotides for the helicase gene and 3,510 nucleotides for the spike gene. The trees were rooted to Breda virus (AY427798). Scale bar, 0.1 substitution per site.
Tables
- TABLE 1.
Coronavirus distribution in different bat species and locations
Family and species of bat Common name No. sampled (no. positive) Group(s) Sites Bats Rhinolophidae Rhinolophus pusillus Least horseshoe bat 27 101 Rhinolophus malayanus Malayan horseshoe bat 2 15 Rhinolophus affinis Intermediate horseshoe bat 9 60 Rhinolophus ferrumequinum Greater horseshoe bat 11 (3) 41 (4) 1, 4, and 5 Rhinolophus thomasi Thomas's horseshoe bat 5 12 Rhinolophus sinicus Chinese horseshoe bat 16 (1) 66 (1) 4 Rhinolophus pearsoni Pearson's horseshoe bat 10 (1) 48 (1) 1 Rhinolophus macrotis Big-eared horseshoe bat 11 (1) 38 (1) 4 Rhinolophus rex King horseshoe bat 2 2 Rhinolophus luctus Woolly horseshoe bat 4 4 Rhinolophus osgoodi Osgood's horseshoe bat 1 1 Hipposideros armiger Great leaf-nosed bat 13 58 Hipposideros larvatus Intermediate leaf-nosed bat 1 3 Hipposideros pratti Pratt's leaf-nosed bat 2 9 Hipposideros pomona Pomona leaf-nosed bat 1 1 Coelops frithi East Asian tailless leaf-nosed bat 2 6 Aselliscus stoliczkanus Stoliczka's Asian trident bat 1 7 Vespertilionidae Pipistrellus pipistrellus Common pipistrelle 4 (1) 27 (6) 5 Pipstrellus abramus Japanese pipistrelle 8 (3) 41 (14) 5 Scotophilus kuhlii Lesser Asiatic yellow house bat 2 (1) 43 (5) 1 Myotis daubentonii Daubenton's bat 4 41 Myotis mystacinus Whiskered bat 1 1 Myotis ricketti Rickett's big-footed bat 8 (4) 53 (13) 1 Myotis chinensis Large Myotis 2 3 Myotis sp.a 9 80 Nyctalus aviator Birdlike noctule 2 6 Nyctalus noctula Noctule bat 3 17 Scotomanes ornatus Harlequin bat 1 1 Barbastella leucomelas Eastern barbastelle 1 1 Tylonycteris pachypus Lesser bamboo bat 1 (1) 14 (2) 5 Ia io Great evening bat 1 8 Murina leucogaster Greater tube-nosed bat 1 5 Miniopterus schreibersi Schreiber's long-fingered bat 15 (3) 135 (17) 1 Pteropodidae Cynopterus sphinx Greater short-nosed fruit bat 2 6 Rousettus leschenaulti Leschenault's Rousette 1 31 Total 35 82 (19) 985 (64) ↵ a Identification of many Myotis specimens was possible only to generic level.
- TABLE 2.
Comparison of coronavirus genome structuresa
Feature BtCoV/273/04 (29,704b) BtCoV/279/04 (29,741) SARS-CoV (29,751) IBV (27,608) BtCoV/133/05 (30,307) HCoV-OC43 (30,738) BtCoV/512/05 (28,204) PEDV (28,033) Start (bp) End (bp) No. of aa Start (bp) End (bp) No. of aa Start (bp) End (bp) No. of aa Start (bp) End (bp) No. of aa Start (bp) End (bp) No. of aa Start (bp) End (bp) No. of aa Start (bp) End (bp) No. of aa Start (bp) End (bp) No. of aa ORF1a 261 13,382 4,373 897 13,415 4,173 265 13,398 4,378 529 12,354 3,942 260 13,564 4,435 211 13,341 4,377 294 12,650 4,119 297 12,620 4,108 nsp1 261 797 179 897 1,157 87 265 801 179 529 753 75 260 2,800 847 211 948 246 294 1,514 407 297 626 110 nsp2 798 2,717 640 1,158 2,717 520 802 2,718 639 754 2,547 598 2,801 4,420 540 949 2,763 605 1,515 2,984 490 627 2,918 764 nsp3 (PL pro) 2,718 8,468 1,917 2,718 8,501 1,928 2,719 8,484 1,922 2,548 7,323 1,592 4,421 8,632 1,404 2,764 8,460 1,899 2,985 7,886 1,634 2,982 7,847 1,622 nsp5 (3CL) 9,969 10,886 306 10,002 10,919 306 9,985 10,902 306 8,866 9,786 307 10,154 11,071 306 9,949 10,857 303 9,330 10,235 302 9,288 10,193 302 ORF1b 13,382 21,469 2,695 13,415 21,502 2,695 13,398 21,485 2,695 12,354 20,417 2,687 13,564 21,639 2,691 13,341 21,497 2,718 12,650 20,674 2,674 12,620 20,641 2,673 nsp12 (RdRp) 13,356 16,150 932 13,389 16,183 932 13,372 16,166 932 12,313 15,131 940 13,541 16,341 934 13,318 16,100 928 12,627 15,406 927 12,597 15,376 927 nsp13 (HEL) 16,151 17,953 601 16,184 17,986 601 16,167 17,969 601 15,132 16,931 600 16,342 18,135 598 16,101 17,909 603 15,407 17,197 597 15,377 17,167 597 Ns2 21,507 22,343 279 HE 22,355 23,629 425 S 21,476 25,201 1,241 21,509 25,234 1,241 21,492 25,259 1,255 20,368 23,856 1,162 21,584 25,636 1,350 23,644 27,729 1,361 20,671 24,786 1,371 20,638 24,789 1,383 ORF3/3a 25,211 26,035 274 25,244 26,068 274 25,268 26,092 274 23,856 24,029 57 25,663 25,938 91 27,817 28,146 109 24,786 25,460 224 24,789 25,463 224 ORF3b 24,029 24,223 64 26,119 26,976 285 ORF3c 26,992 27,675 227 E 26,060 26,290 76 26,093 26,323 76 26,117 26,347 76 24,207 24,533 108 27,745 27,993 82 28,133 28,387 84 25,441 25,671 76 25,444 25,674 76 M 26,337 27,002 221 26,374 27,039 221 26,398 27,063 221 24,505 25,182 225 28,008 28,667 219 28,402 29,094 230 25,678 26,361 227 25,682 26,362 226 ORF6 27,013 27,204 63 27,050 27,241 63 27,074 27,265 63 25,488 25,685 65 ORF7 27,212 27,580 122 27,249 27,617 122 27,273 27,641 122 25,682 25,930 82 ORF8 27,718 28,086 122 27,755 28,120 122 27,864 28,118 84 N 28,088 29,353 421 28,135 29,397 420 28,120 29,388 422 25,873 27,102 409 28,705 29,979 424 29,104 30,450 448 26,372 27,556 394 26,374 27,699 441 ORF10 27,571 27,960 129 s2m 29,555 29,586 29,599 29,630 29,590 29,621 27,477 27,508
