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

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

Ling Zhou  1   2 , Yuan Sun  1   2 , Tian Lan  1 , Ruiting Wu  1   2 , Junwei Chen  3 , Zixian Wu  3 , Qingmei Xie  1   2 , Xiangbin Zhang  1   2   3 , Jingyun Ma  1   2
Affiliations

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

Ling Zhou et al. Transbound Emerg Dis. 2019 Mar.

Abstract

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.

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Conflict of interest statement

The authors declare no conflict of interests with any organization.

Figures

Figure 1
Figure 1
Locations of positive farms for study of SADS‐CoV in Guangdong Province, China [Colour figure can be viewed at http://www.wileyonlinelibrary.com]
Figure 2
Figure 2
Phylogenetic analysis of the complete genomes of SADS‐CoV and reference coronavirus species. The tree was constructed using MEGA 7.0 software with neighbour‐joining methods and 1,000 replicate sets on bootstrap analysis. Two new complete genomes studied in this work were indicated with “black solid circles”
Figure 3
Figure 3
Phylogenetic analysis of the N genes of SADS‐CoV and reference coronavirus species. The tree was constructed as per Figure 2 above. Five new sequences of N genes studied in this work were indicated with “black solid circles”
Figure 4
Figure 4
Phylogenetic analysis of the S genes of SADS‐CoV and reference coronavirus species. The tree was constructed as per Figure 2 above. Five new sequences of S genes studied in this work were indicated with “black solid circles”
See this image and copyright information in PMC

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