Porcine deltacoronavirus (PDCoV) is a recently discovered RNA virus that belongs to the family Coronaviridae and genus Deltacoronavirus. This virus causes enteric disease in piglets that is characterized by enteritis and diarrhoea. In our present investigation, 189 diarrhoeic samples were collected between July 2016 and May 2017 from Tibetan pigs inhabiting in three different provinces surrounding the Qinghai-Tibet Plateau of China. We then applied the molecular-based method of reverse transcription polymerase chain reactions (RT-PCRs) to detect the presence of PDCoV in collected samples, and RT-PCR indicated that the prevalence of PDCoV was 3.70% (7/189) in Tibetan pigs. Four of 7 PDCoV-positive pigs were monoinfections of PDCoV, three samples were co-infections of PDCoV with porcine epidemic diarrhoea virus (PEDV), and 52 (27.51%) samples were positive for PEDV. Four strains with different full-length genomes were identified (CHN/GS/2016/1, CHN/GS/2016/2, CHN/GS-/2017/1 and CHN/QH/2017/1), and their genomes were used to analyse the characteristics of PDCoV currently prevalent in Tibetan pigs. We found a 3-nt insertion in the spike gene in four strains in Tibetan pigs. Phylogenetic analysis of the complete genome and spike and nucleocapsid gene sequences revealed that these strains shared ancestors with the strain CHN-AH-2004, which was found in pigs from the Anhui province of China mainland. However, PDCoV strains from Tibetan pigs formed different branches within the same cluster, implying continuous evolution in the field. Our present findings highlight the importance of epidemiologic surveillance to limit the spread of PDCoV in livestock at high altitudes in China.
- MeSH
- Coronavirus genetika izolace a purifikace MeSH
- feces virologie MeSH
- fylogeneze MeSH
- genom virový genetika MeSH
- koronavirové infekce diagnóza epidemiologie veterinární virologie MeSH
- kvantitativní polymerázová řetězová reakce veterinární MeSH
- nemoci prasat diagnóza epidemiologie virologie MeSH
- prasata virologie MeSH
- prevalence MeSH
- průjem veterinární virologie MeSH
- sekvenční analýza DNA MeSH
- virové proteiny genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Tibet epidemiologie MeSH
During a severe outbreak of diarrhoea and vomiting in a pig herd in Central Eastern Europe, faecal samples were tested positive for porcine epidemic diarrhoea virus (PEDV) and negative for transmissible gastroenteritis virus (TGEV) using a commercial RT-qPCR assay that can detect both of these coronaviruses. However, further analyses, using other TGEV- and PEDV-specific RT-qPCR assays, provided results inconsistent with infection by either of these viruses. Sequencing of an amplicon (ca. 1.6 kb), generated by an RT-PCR specific for the PEDV S-gene, indicated a very close similarity (ca. 99% identity) to recently described chimeric viruses termed swine enteric coronaviruses (SeCoVs). These viruses (with an RNA genome of ca. 28 kb) were first identified in Italy in samples from 2009 but have not been detected there since 2012. A closely related virus was detected in archived samples in Germany from 2012, but has not been detected subsequently. Building on the initial sequence data, further amplicons were generated and over 9 kb of sequence corresponding to the 3'-terminus of the new SeCoV genome was determined. Sequence comparisons showed that the three known SeCoVs are ≥98% identical across this region and contain the S-gene and 3a sequences from PEDV within a backbone of TGEV, but the viruses are clearly distinct from each other. It is demonstrated, for the first time, that pigs from within the SeCoV-infected herd seroconverted against PEDV but tested negative in a TGEV-specific ELISA that detects antibodies against the S protein. These results indicate that SeCoV is continuing to circulate in Europe and suggest it can cause a disease that is very similar to PED. Specific detection of the chimeric SeCoVs either requires development of a new diagnostic RT-qPCR assay or the combined use of assays targeting the PEDV S-gene and another part of the TGEV genome.
- MeSH
- ELISA MeSH
- feces virologie MeSH
- koronavirové infekce veterinární MeSH
- kvantitativní polymerázová řetězová reakce MeSH
- molekulární sekvence - údaje MeSH
- nemoci prasat virologie MeSH
- prasata MeSH
- přenosná gastroenteritida prasat diagnóza virologie MeSH
- Sus scrofa MeSH
- virus epidemického průjmu prasat genetika izolace a purifikace MeSH
- virus přenosné gastroenteritidy prasat genetika izolace a purifikace MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Evropa MeSH
- Itálie MeSH
- Německo MeSH
- východní Evropa MeSH
- MeSH
- elektroforéza v polyakrylamidovém gelu MeSH
- koronavirové infekce diagnóza veterinární MeSH
- monoklonální protilátky imunologie MeSH
- nemoci prasat virologie MeSH
- protilátky blokující imunologie MeSH
- průjem veterinární virologie MeSH
- respirační koronavirus prasat izolace a purifikace patogenita MeSH
- skot MeSH
- zvířata MeSH
- Check Tag
- skot MeSH
- zvířata MeSH
- Publikační typ
- srovnávací studie MeSH
