Occurrence and sequence analysis of porcine deltacoronaviruses in southern China

Abstract

Background: 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. Results: 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. Conclusions: This study demonstrated that PDCoV was present in southern China despite the low prevalence, and supported an evolutionary theory of geographical clustering of PDCoVs.

The detection and phylogenetic analysis of porcine deltacoronavirus from Guangdong Province in Southern China

“…For example, strain 05 was most closely to KNU14‐04 (S. Korea), OH11846 and Minnesota292 (0.993) (USA). The other strains were most closely to CH/SXD1/2015, Sichuan/S27 and CHN/GX01/2015 (Chen, Gauger et al., ; Chen, Zhu et al., ; Wang, Yue, Fang, & Huang, ; Zhai et al., ) originating in different regions in China (Table S3). The phylogenetic tree of the N gene indicated that strain 05 was located at the US branch, while other positive samples from this work were all clustered in a group within the Chinese branch (Figure ).…”

“…The whole S gene (3,483 nt) of published porcine deltacoronavirus isolates was analysed by pairwise alignments. Most of the Chinese strains (HKU15‐155, HB/2014, JS/2014, HN/2014, SXD1, CHJXIN2, GD01/2015, GD02/2015, HN01/2015 and GX01/2015) contained a 3‐nt (AAT) deletion (Chen, Gauger et al., ; Chen, Zhu et al., ; Dong et al., ; Song et al., ; Wang et al., ; Zhai et al., ). In strain CHN/AH/2004 (Dong et al., ), a 3‐nt (TAA) deletion existed in its 3′‐UTR.…”

“…As all reported PDCoV isolates from China are clustered into a single Chinese group, this is the first case of a US and Korean strain detected in diarrhoeal samples from pigs in China. Strain 03 is more related on a genomic scale to the Thai strains and had the lowest nucleotide identity with CHN/GD02/2015 and CHN/GX01/2015 (95.8%, Table S2) (Zhai et al., ), which were collected from Guangdong and nearby Guangxi provinces. However, the N gene of this strain revealed a completely reverse conclusion; that it belongs to the Chinese group with a low nt identity (96.7%) with the Thai strains S5011 and 5015L (Janetanakit et al., ) (Fig.…”

“…RT‐PCR detection methods have provided data for the prevalence of PDCoV in China (Dong et al., ; Song et al., ; Zhai et al., ). A previous study (Zhai et al., ) reported that the current prevalence in Southern China was 1.54% (5/390), and three of the five detected strains were from Guangdong Province, revealing that the information regarding the molecular epidemiology of PDCoVs in Guangdong was still limited. The current study further investigates the prevalence, epidemiology and genomic properties of PDCoV in Guangdong.…”

A novel porcine kobuvirus emerged in piglets with severe diarrhoea in China

“…To confirm the cause of the diarrhoea, eight commercial kits were used to test the presence of porcine common diarrhoea‐associated pathogens (including porcine circovirus type 2, pseudorabies virus, classical swine fever virus, porcine epidemic diarrhoea virus, porcine transmissible gastroenteritis virus, porcine rotavirus, pathogenic Escherichia coli and Salmonella ). In addition, four novel porcine diarrhoea‐related viruses (including PKV, porcine astrovirus, porcine deltacoronavirus and porcine bocavirus) were further tested according to previously published PCR protocols (Zhai et al., ; Zheng et al., ; Zhou et al., ).…”