Contributors:Z. Ahmed, P.C.Y. Woo, S.K.P. Lau, M. Mahbub Alam, S. Shakeel Ahmed, A.K.L. Tsang, P.-C. Wong, K.-Y. Yuen
Phylogenetic tree constructed from complete genomes of BufCoV and other members of Betacoronavirus lineage A (top). Tree was constructed by maximum likelihood method using general-time-reversible model including proportion of invariable sites with gamma-distributed substitution rates and bootstrap values calculated from 100 trees. Betacoronavirus 1 indicated at right. Boldface type indicates 2 strains of BufCoV with complete genomes sequenced in this study. SACoV, sable antelope coronavirus (EF424621); GiCoV, giraffe coronavirus (EF424623); ACoV, alpaca coronavirus (DQ915164); WtDCoV, white-tailed deer coronavirus (FJ425187); SDCoV, sambar deer coronavirus (FJ425189); WbCoV, waterbuck coronavirus (FJ425186); BCoV, bovine coronavirus (DQ811784); BufCoV, buffalo coronavirus; DcCoV, dromedary camel coronavirus (KF906249); CRCoV, canine respiratory coronavirus (JX860640); HCoV OC43, human coronavirus OC43 (AY391777); PHEV, porcine haemagglutinating encephalomyelitis virus (DQ011855); ECoV, equine coronavirus (EF446615); RbCoV HKU14, rabbit coronavirus HKU14 (JN874559); ChRCoV, China Rattus coronavirus HKU24 (KM349742); HCoV HKU1, human coronavirus HKU1 (AY597011); MHV, murine hepatitis virus (FJ647223); RCoV, rat coronavirus (FJ938068). Genome organization of BufCoV (bottom). Position of transcriptional regulatory sequences of each gene is indicated. ORFs between spike (S) and envelope (E) gene are magnified to show differences between two BufCoVs. ORF1ab are represented by green boxes. Haemagglutinin-esterase (HE), S, E, membrane (M) and nucleocapsid (N) are represented by red boxes. Putative accessory proteins are represented by blue boxes.
Contributors:Crista Toomey, Harriet W Brooks, Joe Brownlie, Kerstin Erles
Primers designed from an alignment of the spike genes of bovine coronavirus (GenBank Accession No. AF058942) and human coronavirus, OC43 (GenBank Accession No. L14643)
... RT–PCR using consensus primers directed to the hemagglutinin/esterase gene of bovine and human coronavirus (strain OC43). The agarose gel electrophoresis shows PCR products of the expected size of 497 bp for the positive control (BCV) and four tracheal samples (T90–T105). BCV, bovine coronavirus positive control sample; A72, coronavirus-negative A72 cells; H2O, PCR mix without DNA; T90–T105, tracheal samples of study dogs; 1 kb, molecular size standard (Promega).
... Consensus tree for cDNA sequences from a 251-nucleotide region of the polymerase gene of 12 coronaviruses. The sequence obtained from the canine respiratory coronavirus is designated T101. The numbers indicate bootstrap values obtained by analysis of 100 data sets. BCV, bovine coronavirus; CCV, canine coronavirus; FIPV, feline infectious peritonitis virus; HEV, hemagglutinating encephalomyelitis virus; IBV, infectious bronchitis virus; MHV, mouse hepatitis virus; OC43, human coronavirus strain OC43; SDAV, sialodacryoadenitis virus; TCV, turkey coronavirus; TGEV, transmissible gastroenteritis virus; 229E, human coronavirus strain 229E; T101, canine respiratory coronavirus (PCR product from tracheal sample T101).
... Coronavirus... Comparison of the prevalence of respiratory disease in two groups of dogs: Dogs in group 1 were positive for serum antibodies to respiratory coronavirus on the day of entry into the kennel; dogs in group 2 were negative. The graph shows the percentage of dogs developing respiratory disease in group 1 compared to group 2 (P < 0.001). N is the total number of dogs in each group.
Sequence comparisons of ACoV with selected Group 2 coronaviruses
... A phylogenetic tree of selected Group 2 spike proteins and hemagglutinin-esterase amino acid sequences. (A) The S proteins from the selected strains were analyzed by the neighbor-joining method. (B) The hemagglutinin-esterase protein of the alpaca strain was compared to other selected Group 2 coronavirus hemagglutinin-esterase proteins. For information on the viruses analyzed, see legend to Fig. 2.
... Bovine coronavirus... Coronavirus... A maximum-likelihood phylogenetic tree of selected coronavirus genomes. ACoV (GenBank accession no. DQ915164) was compared to other Group 2 Coronaviruses including porcine hemagglutinating encephalomyelitis virus (PHEV VW572, GenBank accession no. YP_459958); human coronavirus OC43 (HCoV-OC43, AY391777); bovine coronavirus Mebus strain (BCoV-Meb, U00735); bovine coronavirus Quebec strain (BCoV-Q, D00662); bovine coronavirus DB2 strain (BCoV-DB2, DQ811784); bovine coronavirus ENT strain (BCoV-ENT, Q91A22); bovine coronavirus LUN strain (BCoV-LUN, AF391542). The scale bar represents the genetic distance (nucleotide substitution per site).
... Map of the alpaca coronavirus genome (GenBank accession no. DQ915164) and ORFs of the viral coding sequence. NS1, non-structural protein gene 1; HE, hemagglutinin-esterase gene; S, spike gene; NS2, non-structural protein gene 2; E, envelope protein gene; M, membrane protein gene; N, nucleocapsid gene; I, internal ORF. The numbers above and below each ORF correspond to the nt coordinates of each gene.
... Alpaca coronavirus
Contributors:Kwok-Yung Yuen, Honglin Chen, Kenneth S.M. Li, Vincent C.C. Cheng, Kelvin K.W. To, Jasper F.W. Chan
(A) and (B) Lesser bamboo bat (Tylonycteris pachypus), often found dwelling in hollows of bamboo plants in South East Asia, from which bat coronavirus HKU4 was first discovered. (C) and (D) Japanese Pipistrelle (Pipistrelle abramus), often found at ceilings and roof tops of residential houses in South East Asia, from which bat coronavirus HKU5 was first discovered.
... (A) Phylogenetic tree of the novel human betacoronavirus 2c EMC/2012 (HCoV-EMC) and other coronaviruses. The tree was constructed by the neighbour-joining method using clustalX 2.0.12. The scale bar indicates the estimated number of substitutions per 20 nucleotides. ALCCoV, Asian leopard cat coronavirus (EF584908); AntelopeCoV, sable antelope coronavirus (EF424621); BCoV, bovine coronavirus (NC_003045); BuCoV HKU11, bulbul coronavirus HKU11 (FJ376619); BWCoV-SW1, beluga whale coronavirus SW1 (NC_010646); CCoV, canine coronavirus (GQ477367); CMCoV HKU21, common moorhen coronavirus HKU21 (NC_016996); ECoV, equine coronavirus (NC_010327); FIPV, feline infectious peritonitis virus (AY994055); GiCoV, giraffe coronavirus (EF424622); HCoV-EMC, human betacoronavirus 2c EMC/2012; HCoV-229E, human coronavirus 229E (NC_002645); HCoV-HKU1, human coronavirus HKU1 (NC_006577); HCoV-NL63, human coronavirus NL63 (NC_005831); HCoV-OC43, human coronavirus OC43 (NC_005147); Hi-BatCoV HKU10, Hipposideros bat coronavirus HKU10 (JQ989269); IBV, infectious bronchitis virus (NC_001451); IBV-partridge, partridge coronavirus (AY646283); IBV-peafowl, peafowl coronavirus (AY641576); MHV, murine hepatitis virus (NC_001846); Mi-BatCoV 1A, Miniopterus bat coronavirus 1A (NC_010437); Mi-BatCoV 1B, Miniopterus bat coronavirus 1B (NC_010436); Mi-BatCoV HKU8, Miniopterus bat coronavirus HKU8 (NC_010438); MRCoV HKU18, magpie robin coronavirus HKU18 (NC_016993); MunCoV HKU13, munia coronavirus HKU13 (FJ376622); NHCoV HKU19, night heron coronavirus HKU19 (NC_016994); PEDV, porcine epidemic diarrhoea virus (NC_003436); PHEV, porcine haemagglutinating encephalomyelitis virus (NC_007732); Pi-BatCoV-HKU5, Pipistrellus bat coronavirus HKU5 (NC_009020); PorCoV HKU15, porcine coronavirus HKU15 (NC_016990); PRCV, porcine respiratory coronavirus (DQ811787); RbCoV HKU14, rabbit coronavirus HKU14 (NC_017083); RCoV, rat coronavirus (NC_012936); Rh-BatCoV HKU2, Rhinolophus bat coronavirus HKU2 (EF203064); Ro-BatCoV-HKU9, Rousettus bat coronavirus HKU9 (NC_009021); Ro-BatCoV HKU10, Rousettus bat coronavirus HKU10 (JQ989270); SARS CoV, SARS-related human coronavirus (NC_004718); SARSr-CiCoV, SARS-related palm civet coronavirus (AY304488); SARSr CoV CFB, SARS-related Chinese ferret badger coronavirus (AY545919); SARSr-Rh-BatCoV HKU3, SARS-related Rhinolophus bat coronavirus HKU3 (DQ022305); Sc-BatCoV 512, Scotophilus bat coronavirus 512 (NC_009657); SpCoV HKU17, sparrow coronavirus HKU17 (NC_016992); TCoV, turkey coronavirus (NC_010800); TGEV, transmissible gastroenteritis virus (NC_002306); ThCoV HKU12, thrush coronavirus HKU12 (FJ376621); Ty-BatCoV-HKU4, Tylonycteris bat coronavirus HKU4 (NC_009019); WECoV HKU16, white-eye coronavirus HKU16 (NC_016991); WiCoV HKU20, wigeon coronavirus HKU20 (NC_016995). (B) Genome organizations of members of group B and group C betacoronaviruses showing that the novel HCoV-EMC has similar genome arrangements to other group C betacoronaviruses but different from other group B betacoronaviruses. PL, papain-like protease; 3CL, chymotrypsin-like protease; RdRp, RNA-dependent RNA polymerase; Hel, helicase; S, spike; E, envelope; M, membrane; N, nucleocapsid.
Contributors:Tao Ren, Gui-hong Zhang, Jia-dong Fu, Wen-jun Liu, Lei Sun, Wei-sheng Cao, Chao-an Xin, Ming Liao, Jing-wei Jiang
Genome size comparison among KQ6 and other coronavirus isolates
... Coronavirus... Radialized phylogenetic tree for coronaviruses. The nucleotide sequences were analyzed with MEGA program (version 3.1) by using neighbor-joining analysis. The full-length genome sequences were used for the phylogenetic analysis. Scale bar: 1000 nucleotide changes. BCoV: bovine coronavirus; HCoV-229E: human coronavirus 229E; IBV: infectious bronchitis virus M41; MHV: murine hepatitis virus strain A59; PEDV: porcine epidemic diarrhea virus; TGEV: transmissible gastroenteritis virus; SARS-CoV: severe acute respiratory syndrome.
Contributors:Heribert Hofer, Karin Moestl, Christian Pitra, Oliver P Höner, Bettina Wachter, Marion L East, Viviane Benetka
RT-PCRs for the differentiation between feline coronavirus (FCoV) type I and FCoV type II/canine coronavirus (CCV)
... Comparison of coronavirus serum antibody titers determined by an indirect immunofluorescence assay for 28 adult hyenas (≥24 months of age) and 7 cubs (≤12 months of age) (Mann–Whitney U-test, U = 139.5, P = 0.08). The central line marks the median titer, each box shows the range of 50% of the values around the median, and the vertical lines indicate the total range of values.
... Phylogenetic relationship between coronavirus isolates from a spotted hyena (HYENA) in the Serengeti National Park, feline enteric coronavirus (X80799), feline infectious peritonitis virus (X06170), canine coronavirus (AF116247, AB017789, AF116245), and the canine coronavirus vaccine strain CCVInSAVC-1 (A22884). The unrooted maximum-likelihood tree (−lnL = 1581.61) based on the 429bp segment of the 5′ region of the S gene (Posch et al., 2001) was recovered under the best-fit model (HKY + G) selected by hLRTs in Modeltest Version 3.06 (Posada and Crandall, 1998). Base frequencies: A = 0.3042, C = 0.1875, G = 0.1908, T = 0.3175; transition/transversion ratio: 1.6559; gamma distribution shape parameter: 0.2864. Numbers at nodes represent the percentage of 100 bootstrap replicates.
... Coronavirus... Percentages of homology between three amplification products of a positive hyena fecal sample and feline and canine coronavirus reference strains
Contributors:S Bellmann, A Kipar, K Köhler, M Reinacher, J Kremendahl
Granuloma with area of necrosis in omentum. (a.) Coronavirus antigen in macrophages (granular reaction; arrow) within a granuloma with area of necrosis. Coronavirus-specific antibodies in plasma-cells close to the same granuloma (homogeneous reaction; arrowhead). Bar=40μm. (b.) Macrophages expressing the myeloid/histiocyte antigen in a granuloma. Bar=40μm.
... Diffuse alteration at the serosal surface of the liver. Layers of exudate on serosal surface with focal infiltration by macrophages positive for coronavirus antigen (arrow). Bar=70μm.
... Diffuse alteration at the serosal surface of the spleen. Activation of mesothelial cells and infiltration by macrophages expressing coronavirus antigen (arrows). Bar=40μm.
... Omentum. (a.) Infiltration of the omentum by CD45R antigen-positive B-cells and plasma-cells. Bar=40μm. (b.) Single plasma cells positive for coronavirus-specific antibodies (arrows) are found in a perivascular infiltrate consisting of B- and plasma-cells. Bar=40μm.
... Coronavirus antigen... Brain. (a.) Few plasma-cells positive for coronavirus-specific antibodies (arrow) are found in a mononuclear perivascular infiltrate in the neuropil close to the leptomeninx. Bar=80μm. (b.) Granulomatous vasculitis. Part of the macrophages strongly express coronavirus antigen. Bar=40μm.
... Coronavirus-specific antibodies