title: Occurrence and sequence analysis of porcine deltacoronaviruses in southern China.
abstract: Following the initial isolation of porcine deltacoronavirus (PDCoV) from pigs with diarrheal disease in the United States in 2014, the virus has been detected on swine farms in some provinces of China. To date, little is known about the molecular epidemiology of PDCoV in southern China where major swine production is operated.
  
  
  
  To investigate the prevalence of PDCoV in this region and compare its activity to other enteric disease of swine caused by porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis coronavirus (TGEV), and porcine rotavirus group C (Rota C), 390 fecal samples were collected from swine of various ages from 15 swine farms with reported diarrhea. Fecal samples were tested by reverse transcription-PCR (RT-PCR) that targeted PDCoV, PEDV, TGEV, and Rota C, respectively. PDCoV was detected exclusively from nursing piglets with an overall prevalence of approximate 1.28 % (5/390), not in suckling and fattening piglets. Interestingly, all of PDCoV-positive samples were from 2015 rather than 2012-2014. Despite a low detection rate, PDCoV emerged in each province/region of southern China. In addition, compared to TGEV (1.54 %, 5/390) or Rota C (1.28 %, 6/390), there were highly detection rates of PEDV (22.6 %, 88/390) in those samples. Notably, all five PDCoV-positive piglets were co-infected by PEDV. Furthermore, phylogenetic analysis of spike (S) and nucleocapsid (N) gene sequences of PDCoVs revealed that currently circulating PDCoVs in southern China were more closely related to other Chinese strains of PDCoVs than to those reported in United States, South Korea and Thailand.
  
  
  
  This study demonstrated that PDCoV was present in southern China despite the low prevalence, and supported an evolutionary theory of geographical clustering of PDCoVs.
authors: Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Animal Disease Prevention, Guangdong Open Laboratory of Veterinary Public Health, Guangzhou, 510640, China.
authors: Shao-Lun
authors: SL
authors: Zhai
authors: Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Animal Disease Prevention, Guangdong Open Laboratory of Veterinary Public Health, Guangzhou, 510640, China.
authors: Wen-Kang
authors: WK
authors: Wei
authors: Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Animal Disease Prevention, Guangdong Open Laboratory of Veterinary Public Health, Guangzhou, 510640, China.
authors: Xiao-Peng
authors: XP
authors: Li
authors: Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Animal Disease Prevention, Guangdong Open Laboratory of Veterinary Public Health, Guangzhou, 510640, China.
authors: Xiao-Hui
authors: XH
authors: Wen
authors: Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Animal Disease Prevention, Guangdong Open Laboratory of Veterinary Public Health, Guangzhou, 510640, China.
authors: Xia
authors: X
authors: Zhou
authors: Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Animal Disease Prevention, Guangdong Open Laboratory of Veterinary Public Health, Guangzhou, 510640, China.
authors: He
authors: H
authors: Zhang
authors: Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of Animal Disease Prevention, Guangdong Open Laboratory of Veterinary Public Health, Guangzhou, 510640, China. gdred@163.com.
authors: Dian-Hong
authors: DH
authors: Lv
authors: Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA.|Department of Veterinary and Biomedical Science, South Dakota State University, Brookings, SD, 57007, USA.
authors: Feng
authors: F
authors: Li
authors: Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA. dan.wang@sdstate.edu.
authors: Dan
authors: D
authors: Wang
mesh_terms: D000818:Animals; D002681:China / Q000453:epidemiology; D003332:Coronaviridae / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D003333:Coronaviridae Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D005243:Feces / Q000821:virology*; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013552:Swine; D013553:Swine Diseases / Q000821:virology*; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins
keywords: Nucleocapsid gene; Occurrence; Porcine deltacoronavirus; Sequence analysis; Southern China; Spike gene