Retrospective detection and phylogenetic analysis of swine acute diarrhoea syndrome coronavirus in pigs in southern China

Transbound Emerg Dis. 2019 Mar;66(2):687-695. doi: 10.1111/tbed.13008. Epub 2019 Jan 9.


Swine acute diarrhoea syndrome coronavirus (SADS-CoV), a novel coronavirus, was first discovered in southern China in January 2017 and caused a large scale outbreak of fatal diarrheal disease in piglets. Here, we conducted a retrospective investigation of 236 samples from 45 swine farms with a clinical history of diarrheal disease to evaluate the emergence and the distribution of SADS-CoV in pigs in China. Our results suggest that SADS-CoV has emerged in China at least since August 2016. Meanwhile, we detected a prevalence of SADS-CoV (43.53%), porcine deltacoronavirus (8.83%), porcine epidemic diarrhoea virus (PEDV) (78.25%), rotavirus (21.77%), and transmissible gastroenteritis virus (0%), and we also found the co-infection of SADS-CoV and PEDV occurred most frequently with the rate of 17.65%. We screened and obtained two new complete genomes, five N and five S genes of SADS-CoV. Phylogenetic analysis based on these sequences revealed that all SADS-CoV sequences in this study clustered with previously reported SADS-CoV strains to form a well defined branch that grouped with the bat coronavirus HKU2 strains. This study is the first retrospective investigation for SADS-CoV and provides the epidemiological information of this new virus in China, which highlights the urgency to develop effective measures to control SADS-CoV.

Keywords: Swine Acute Diarrhoea Syndrome Coronavirus; phylogenetic analysis; prevalence; retrospective detection.

MeSH terms

  • Alphacoronavirus / classification
  • Alphacoronavirus / genetics*
  • Alphacoronavirus / isolation & purification*
  • Animals
  • China / epidemiology
  • Coronavirus Infections / epidemiology
  • Coronavirus Infections / veterinary*
  • Coronavirus Infections / virology
  • Coronavirus Nucleocapsid Proteins
  • Feces / virology
  • Female
  • Genome, Viral*
  • Nucleocapsid Proteins / analysis
  • Phylogeny
  • Polymerase Chain Reaction / veterinary
  • Prevalence
  • Retrospective Studies
  • Spike Glycoprotein, Coronavirus / analysis
  • Swine
  • Swine Diseases / epidemiology*
  • Swine Diseases / virology


  • Coronavirus Nucleocapsid Proteins
  • Nucleocapsid Proteins
  • Spike Glycoprotein, Coronavirus

Supplementary concepts

  • Swine acute diarrhea syndrome coronavirus

Associated data

  • GENBANK/MF094681
  • GENBANK/MF094684
  • GENBANK/MG605090
  • GENBANK/MG605091
  • GENBANK/MG605087
  • GENBANK/MG605088
  • GENBANK/MG605089
  • GENBANK/MG775251
  • GENBANK/MG775253
  • GENBANK/MG605084
  • GENBANK/MG605085
  • GENBANK/MG605086
  • GENBANK/MG775250
  • GENBANK/MG775252
  • GENBANK/MF167434
  • GENBANK/MF370205