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PII: S0378-1135(11)00146-5
DOI: doi:10.1016/j.vetmic.2011.03.008
Reference: VETMIC 5231
Please cite this article as: Ntafis, V., Mari, V., Decaro, N., Papanastassopoulou,
M., Papaioannou, N., Mpatziou, R., Buonavoglia, C., Xylouri, E., Isolation, Tissue
Distribution and Molecular Characterization of Two Recombinant Canine Coronavirus
Strains, Veterinary Microbiology (2010), doi:10.1016/j.vetmic.2011.03.008
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1 Isolation, Tissue Distribution and Molecular Characterization of Two
4 Ntafis V.1*, Mari V.2, Decaro N.2, Papanastassopoulou M.3, Papaioannou N.4,
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5 Mpatziou R. 1, Buonavoglia C.2, Xylouri E.1
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7 Department of Anatomy and Physiology of Farm Animals, Faculty of Animal
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8 Science and Aquaculture, Agricultural University of Athens, Iera Odos 75, 118 55,
9 Athens, Greece.
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10 Department of Animal Health and Well-being, Faculty of Veterinary Medicine of
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14 Department of Pathology, School of Veterinary Medicine, Aristotle University of
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22 *Corresponding author. Tel.: +30 2105294399; fax: +30 2105294388; E-mail address:
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26 Abstract
28 gastrointestinal infection in dogs. To date, two different CCoV genotypes have been
29 recognized, CCoV type I and CCoV type II. Recently, CCoV type II strains of
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30 potential recombinant origin with transmissible gastroenteritis virus (TGEV) were
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31 detected and characterized as a new subtype (CCoV-IIb) of canine coronavirus, in
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32 order to be differentiated from the “classical” CCoV type II strains (CCoV-IIa). In the
33 present study, two CCoV-IIb strains were detected in the faeces and internal organs of
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34 two puppies, which died after presenting gastrointestinal symptoms. Mixed infection
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35 of both subtypes (CCoV-IIa/IIb) was detected in the faeces, while only CCoV-IIb was
36 detected in the organs. Puppies were also infected by canine parvovirus type 2 (CPV-
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37 2). Both CCoV-IIb strains were isolated on cell cultures and subjected to sequence
38 analysis and phylogeny. By means of RT-PCR and real time RT-PCR assays, tissue
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39 distribution and quantitation of viral loads took place. These cases represent the first
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41 organs. The detection of CCoV-IIa strains, which is restricted to the faeces, suggests
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42 that CCoV-IIb strains may have an advantage in disseminating throughout a dog with
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51 Introduction
53 large, enveloped, single stranded, RNA virus responsible for enteritis in dogs (Decaro
54 and Buonavoglia, 2008). Recently, due to changes in virus classification, the virus
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55 was classified as a member of the genus Alphacoronavirus, species
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56 Alphacoronavirus-1, together with transmissible gastroenteritis virus of swine
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57 (TGEV) and feline coronavirus (FCoV) (Carstens, 2010). The genome, 27 kb in
58 length, contains two large overlapping open reading frames (ORFs), ORF1a and
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59 ORF1b which encompass the 5΄ two thirds of the genomic RNA and encode
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60 polyproteins leading to the replicase complex. The ORFs, encoding for the structural
61 spike (S), envelope (E), membrane (M) and nucleocapsid (N) proteins and the non-
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62 structural proteins (3a, 3b, 3c, 7a and 7b), are located downstream of the replicase
65 To date, two different CCoV types have been recognized, CCoV type I (CCoV-I) and
66 CCoV type II (CCoV-II), that share significant genetic similarity with FCoV type I
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67 (FCoV-I) and FCoV type II (FCoV-II), respectively (Decaro and Buonavoglia, 2008).
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69 identified and characterized as a new CCoV subtype (CCoV-IIb) (Decaro et al., 2009;
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72 morbidity and low mortality. Clinical signs include anorexia, lethargy, vomiting, mild
73 to severe diarrhoea (usually lasting 1-2 weeks) and occasionally death, mainly in
74 puppies. The disease is more severe in young animals (Carmichael and Binn, 1981).
75 Systemic infections are not usual; however, during the past few years, there have been
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76 reports of fatal disease, with CCoV strains detected in the enteric tract, as well as in
79 analysis took place for the first time in Greece, regarding common enteric CCoV-II
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80 strains detected in a severe outbreak of diarrhoea in a kennel (Ntafis et al., 2010). In
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81 the current study we report the quantitation and molecular characterization of two
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82 TGEV-like CCoV strains, detected in the organs of two puppies displaying fatal
83 enteritis.
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85 Materials and Methods
86 Clinical Case
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87 During summer of 2009, two dead dogs were submitted for laboratory
88 investigation. The dogs were coming from two different pet shops of Thessaloniki, a
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89 city of northern Greece. Both dogs, a 6-weeks-old Yorkshire Terrier (66/09) and a 16-
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91 haemorrhagic diarrhea and vomiting leading to death, 2 days after the onset of the
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92 symptoms. The first puppy was vaccinated with a single dose of a polyvalent vaccine
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93 against all major infectious diseases (canine distemper, infectious hepatitis, parvoviral
94 enteritis, parainfluenza and leptospirosis) 2 weeks before the symptoms, while the
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98 fluid was observed in the abdominal cavity of the Pomeranian. Lungs of both puppies
99 were congested with multiple areas of emphysema. No lesions were observed at the
100 heart. Liver of both puppies appeared enlarged, friable and yellow-brown in color
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101 with multifocal discolorated spots. Congested vessels in the dura mater of the brain
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105 Samples from the faeces and the parenchymatous organs were subjected to
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106 virological investigations, using methods previously described, regarding common
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107 canine viral pathogens e.g., canine parvovirus type 2 (CPV-2) (PCR and real time
108 PCR) (Decaro et al., 2005a, Decaro et al., 2006a, Decaro et al., 2006b), canine
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109 distemper virus (CDV) (RT-PCR) (Frisk et al., 1999), canine adenovirus type 1 and
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110 type 2 (CAV-1 and CAV-2) (PCR) (Hu et al., 2001) and CCoV (RT-PCR) (Pratelli et
114 For virus isolation, A-72 cell line (canine fibrosarcoma) was used. The cells
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116 10% foetal bovine serum (FBS). Faecal and tissue samples were homogenized (10%
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117 w/v) in D-MEM and centrifuged at 8,000 x g for 10 min. Supernatants were treated
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118 with antibiotics (1,000 IU/ml penicillin and 100 μg/ml streptomycin) for 30 min,
119 inoculated on partially confluent A72 cell cultures and then, they were incubated at 37
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120 ºC in a 5% CO2 incubator. After an adsorption period of 30 min, D-MEM was added.
121 Cells were daily observed for cytopathic effect (cpe) of CCoV for 5 days. An
122 immunofluorescence (IF) assay was used for the detection of CCoV at the infected
123 cells. For the IF assay a 1:100 dilution of cat polyclonal serum specific for
124 Alphacoronavirus-1 and a 1:100 dilution of goat anti-cat IgG conjugated with
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125 fluorescein isothiocyanate (Sigma Aldrich, USA). Each sample was considered
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129 RNA was extracted from faecal and organ samples of both dogs using the
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130 QIAamp Viral RNA Mini Kit and the RNeasy Mini Kit (Qiagen GmbH, Hilden,
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131 Germany), respectively. For CCoV type I and II detection and quantitation in faecal
132 and organ samples, two real time RT-PCR assays with the same sensitivity were used
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133 (Decaro et al., 2005b). Reverse transcription was performed using GeneAmp® RNA
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134 PCR (Applied Biosystems, Italy) according to the manufacturer’s instructions.
135 For the discrimination of classical (subtype IIa) and TGEV-like (subtype IIb)
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136 CCoVs, two RT-PCR assays with comparable levels of sensitivity were performed, as
137 previously described (Decaro et al., 2010). RT-PCRs with primers 20179/INS-R
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139 Step RT-PCR for Long Templates (Invitrogen S.R.L.). In order to verify the absence
140 of TGEV strains in the samples that were positive by CCoV-IIb specific assay, an RT-
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141 PCR, able to discriminate CCoV and TGEV according to the amplicon size was used
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143
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145 The 3΄ end of the genome of the CCoV-IIb strains was amplified as previously
146 described, using viral RNA extracted from the lungs, SuperScript One-Step RT-PCR
147 for Long Templates (Invitrogen S.R.L.) and six pairs of primers, specific for
148 overlapping fragments, encompassing ORFs 2, 3a, 3b, 3c, 4, 5, 6, 7a and 7b (Decaro
149 et al., 2007). The nucleotide sequences were determined in both directions by a
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150 commercial facility (Beckman Coulter Genomics, United Kingdom). Sequence
151 assembling and analysis were carried out using the BioEdit software package (Hall,
152 1999) and the National Center for Biotechnology Information (NCBI;
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154 http://www.ebi.ac.uk) analysis tools. Phylogenetic analysis was conducted using
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155 MEGA4 program (Tamura et al., 2007). Phylogenetic trees, based on the amino acid
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156 sequences of S, E, M and N proteins, were elaborated using neighbor-joining method,
157 supplying a statistical support with bootstrapping over 1,000 replicates. SimPlot was
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158 used for nucleotide sequence comparison of the two strains to Alphacoronavirus-1
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159 reference strains (Lole et al., 1999). The sequences of strains 66/09 and 68/09 were
160 registered in GenBank under the accession numbers HQ450376 and HQ450377,
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161 respectively.
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163 Results
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165 By means of nested PCR assay for CCoV, viral RNA was detected in faeces,
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166 lungs, spleen, kidneys, pancreas, heart, and liver of both puppies. In addition, the
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167 brain of the Pomeranian (68/09) was tested positive, while the brain of the Yorkshire
168 Terrier (66/09) was tested negative. By genotype specific real time RT-PCR assays,
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169 only CCoV-II was detected in all positive samples. CCoV-II RNA copies/μl of
171 In the faecal samples of the two puppies, both CCoV-II subtypes were
172 detected, whilst in the organs which tested positive, only CCoV which was
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175 The CCoV-IIb strains (66/09 and 68/09) were isolated from the lung
176 homogenates of both puppies. A-72 cells developed a cytopathic effect that consisted
177 of cell rounding and lysis of the monolayer. In addition, cells were tested positive by
178 the immunofluorescence assay. Viral titres on cell cultures were 104.25 (66/09) and 104
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179 TCID50/50 μl (68/09) at the 3rd passage.
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180
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181 Detection of other viral pathogens
182 Both puppies were tested positive for CPV-2a field strains and negative for
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183 CDV, CAV-1 and CAV-2.
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187 68/09, respectively, encompassing ORFs 2 (S protein), 3a, 3b, 3c, 4 (E protein), 5 (M
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188 protein), 6 (N protein), 7a and 7b. Alignment of the sequences with TGEV, CCoV and
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189 FCoV reference strains available in GenBank showed the highest identity to CCoV-
190 IIb reference strain 119/08 (EU924791) (98.2% and 98.9% for 66/09 and 68/09
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192 The spike protein gene of both strains was 4,374 nucleotides long, encoding a
193 protein of 1,457 amino acids. When compared to four TGEV-like reference strains
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194 (430/07, 119/08, 174/06 and 341/05), no insertions or deletions were observed. The
195 two strains shared 97.6% aa identity to each other, while they showed the highest aa
196 identity to CCoV-IIb reference strain 119/08 (98.3%). By Simplot analysis, the two
197 strains displayed higher nucleotide conservation with the TGEV strain Purdue than
198 with the pantropic CCoV-IIa strain CB/05, at the 5΄-end of the S gene (Figure 1).
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199 Phylogenetic analysis revealed that the two Greek strains were more closely related to
200 the four CCoV-IIb reference strains detected in dogs’ organs (Figure 2a).
201 The envelope protein was found to be 82 amino acids in length, like in most
202 canine coronavirus strains and in three TGEV-like reference strains, 119/08, 174/06
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203 and 341/05, with the exception of 430/07, which is 7 amino acids shorter. The Greek
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204 strains had high amino acid identity to each other (98.7%). E protein of strains 66/09
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205 and 68/09 had the highest amino acid identity (100% and 98.7%, respectively) to the
206 CCoV-IIb strains 341/05, 119/08, and to CCoV-IIa CB/05. In the E protein,
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207 phylogenetic analysis revealed that the two strains were closely related to CCoV type
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208 II strains (Figure 2b).
209 The membrane protein (M protein) of strains 66/09 and 68/09 was found to be
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210 260 and 262 amino acids long, respectively. Two amino acids were missing from the
211 N-terminal end of the M protein of strain 66/09 in positions 24 and 36, as it has been
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212 also observed in reference CCoV-IIb strains 174/06 and 341/05. The two strains
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213 shared high amino acid similarity (94.6%). M protein of strains 66/09 and 68/09 had
214 the highest amino acid identity to the CCoV-IIb reference strains detected in the
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215 organs (97.3% and 100%, respectively). Phylogenetic analysis of the M protein
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216 showed that the two strains were closely related to CCoV-IIa and CCoV-IIb strains
219 coding for a polypeptide of 382 amino acids. The two proteins were 98.1% similar.
220 The amino acid sequences had the highest identity with CCoV-IIb 119/08 (98.6% and
221 99.4%, for 66/09 and 68/09, respectively). Phylogenetic analysis revealed that the two
222 Greek strains were more closely related to CCoV-II reference strains (Figure 2d).
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224 Discussion
226 genetic evolution and diversity, regarding coronaviruses (Woo et al., 2009). Under
227 field conditions, mixed infections are required to give rise to recombination events. So
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228 far, experimental infections of piglets (Woods and Wesley, 1992) and dogs (Larson et
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229 al., 1979) with CCoV and TGEV strains, respectively, and the fact that feline
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230 aminopeptidase N serves as a functional receptor for both CCoV and TGEV (Tresnan
231 et al., 1996), strongly suggest that the two viruses can be found growing at the same
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232 “environment” in nature, although the exact host of recombination still remains
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233 unknown.
236 TGEV-like strains were reported, circulating in dogs in different countries of Europe
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237 (Decaro et al., 2010). The strains were detected in faecal samples of dogs with
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238 gastroenteritis, they were classified as the new subtype CCoV-IIb and it was
239 suggested that they were a result of recombination events, occurring at different times
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240 of these, regarding the old strain UCD-1 (Decaro et al., 2010). In the present study,
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241 sequence and phylogenetic analysis takes place for the first time in CCoV-IIb strains
243 Moreover, our findings suggest that TGEV-like CCoV strains spreading to the
244 internal organs are circulating in dogs, since so far, there has been only one report in
245 Italy (Decaro et al., 2009). By means of real time RT-PCR, tissue distribution and
246 quantitation of both strains was assessed for the first time, revealing the spreading of
247 the virus to the internal organs. The CPV-2 coinfection may contribute to the
248 spreading of TGEV-like CCoV strains, since so far, they have been only detected in
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249 organs of dogs infected also with CPV-2 (Decaro et al., 2009). However, the detection
250 of CCoV-IIa strains strictly in the faeces, in both cases, suggests that CCoV-IIb may
251 have an advantage in disseminating through the dog. In the first report of TGEV-like
252 strains detected in the organs, CCoV-I was also detected strictly in the intestinal
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253 content in two cases (Decaro et al., 2009). These cases strongly suggest a difference in
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254 pathobiology of CCoV-IIb with respect to CCoV-I/IIa.
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255 By sequence and phylogenetic analysis, it was shown that both strains
256 segregate constantly with the CCoV-IIb reference strains detected in the organs of
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257 dogs. Accordingly, the strains were highly similar to TGEV in the 5΄ end of the S
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258 gene, whereas they clustered with the pantropic CCoV variant CB/05 (subtype CCoV-
259 IIa) in the E, M and N proteins. In a previous study, CCoV-IIb strains detected in the
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260 organs were found to share higher amino acid identity with CB/05 than with CCoV
261 common enteric strains, at the level of the same proteins (Decaro et al., 2009).
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262 Whether the ability of CCoV-IIb strains to spread to the organs is related to the
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263 recently recognized recombinant protein S or to the CB/05-like proteins (E, M and N)
264 needs further research. However, the S-protein “scenario” seems to be more possible,
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265 since in coronaviruses S protein mediates receptor attachment, and tissue tropism shift
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266 has been associated with mutations in the S gene (Masters, 2006).
267 In the last decade, new genotypes and subtypes of canine coronavirus have
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268 been recognized. Furthermore, a pantropic variant with the ability to cause fatal
269 systemic infection was detected (Buonavoglia et al., 2006). Previous studies revealed
270 that there are antigenic differences between CCoV-I and II (Pratelli et al., 2004). In
271 addition, antigenic differences were observed between the two subtypes, CCoV-IIa
272 and CCoV-IIb (TGEV-like CCoVs) (Decaro et al., 2009). Whether the currently
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273 circulating vaccines can protect against the TGEV-like recombinant isolates or not has
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276 Conclusion
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277 In conclusion, this was the first report of CCoV-IIb tissue distribution. Up to
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278 now, there has been only one report of TGEV-like strains detected in internal organs
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279 of puppies in Italy. Based on sequence and phylogenetic analysis of the structural
280 proteins, the two Greek isolates were found to be related to the Italian prototype
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281 CCoV-IIb strains. In addition, in all cases a mixed infection with CPV-2 was reported.
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282 However, the detection of CCoV-IIa strains, strictly at the faeces, suggests that
283 CCoV-IIb strains may have an advantage in disseminating throughout a dog with
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284 CPV-2 coinfection, in contrast to common enteric CCoV-IIa strains.
285
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286 Acknowledgements
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289
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290 References
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292 Castagnaro, M., Tempesta, M., 2006. Canine coronavirus highly pathogenic for
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350 Pratelli, A., Tempesta, M., Greco, G., Martella, V., Buonavoglia, C., 1999.
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351 Development of a nested PCR assay for the detection of canine coronavirus. J.
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352 Virol. Methods 80: 11–15.
353 Pratelli, A., Elia, G., Decaro, N., Tola, S., Tinelli, A., Martella, V., Rocca, S.,
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359 Tresnan, D.B., Levis, R., Holmes, K.V., 1996. Feline Aminopeptidase N Serves as a
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360 Receptor for Feline, Canine, Porcine, and Human Coronaviruses in Serogroup I.
362 Wesley, R.D., 1999. The S gene of canine coronavirus, strain UCD-1, is more closely
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363 related to the S gene of transmissible gastroenteritis virus than to that of feline
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366 phylogeny and interspecies jumping. Exp. Biol. Med. 234, 1117-27.
367 Woods, R.D., Wesley, R.D., 1992. Seroconversion of pigs in contact with dogs
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371 Figure captions
372 Figure 1. S gene sequences analysis with Simplot. The S gene of CCoV-IIb strain
373 68/09, TGEV strain Purdue and CCoV-IIa pantropic strain CB/05 were plotted against
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375 Figure 2. Neighbor-joining trees of the Greek strains, based on the S (a), E (b), M (c)
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376 and N (d) protein. The trees are rooted on the group 2 canine respiratory coronavirus
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377 (CRCoV). The numbers represent the percentage of replicate trees based on 1,000
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Table 1
Tables
Table 1. CCoV-II RNA copies/μl of template in the samples of the two puppies, tested
66/09 68/09
Sample
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(Yorkshire Terrier) (Pomeranian)
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Faeces 3.59 x 103 7.22 x 105
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Liver 4.64 x 104 3.21 x 105
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Spleen 5.20 x 105 1.55 x 107
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Figure 1
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Figure 2a
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Figure 2b
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Figure 2c
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Figure 2d
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