Newly emerged porcine enteric alphacoronavirus in southern China: Identification, origin and evolutionary history analysis

Abstract

Coronaviruses have a wide host range and can cause a variety of diseases with varying severity in different animals. Several enteric coronaviruses have been identified that are associated with diarrhea in swine and that have caused substantial economic losses. In this study, a newly emerged porcine enteric alphacoronavirus (PEAV), PEAV-GD-CH/2017, was identified from suckling piglets with diarrhea in southern China, and a full-length genome sequence of PEAV was obtained for systematic analysis. The novel PEAV sequence was most identical to that of bat-HKU2, and the differences between them were comprehensively compared, especially the uniform features of the S protein, which was shown to have a close relationship with betacoronaviruses and to perhaps represent unrecognized betacoronaviruses. In addition, Bayesian analysis was conducted to address the origin of PEAV, and the divergence time between PEAV and bat-HKU2 was estimated at 1926, which indicates that PEAV is not newly emerged and may have circulated in swine herds for several decades since the interspecies transmission of this coronavirus from bat to swine. The evolutionary rate of coronaviruses was estimated to be 1.93 × 10 substitutions per site per year for the RdRp gene in our analysis. For the origin of PEAV, we suspect that it is the result of the interspecies transmission of bat-HKU2 from bat to swine. Our results provide valuable information about the uniform features, origin and evolution of the novel PEAV, which will facilitate further investigations of this newly emerged pathogen.

Point‐of‐care diagnostic assay for rapid detection of porcine deltacoronavirus using the recombinase polymerase amplification method

“…Porcine deltacoronavirus (PDCoV), a new member of Deltacoronavirus , was firstly detected in pig faeces in the molecular investigation of CoV in Hong Kong in 2012 (Woo et al., ). Up to now, PDCoV has been detected/isolated in pigs across the world, including USA, Mexico, Canada, South Korea, China and Thailand (Dong et al., ; Fu et al., ; Janetanakit et al., ; Jang et al., ; Jung, Hu, & Saif, ; Lee & Lee, ; Mai et al., ; Song et al., ; Wang, Byrum, & Zhang, ; Xu et al., ). PDCoV has become a reportable disease in the United States by United States Department of Agriculture, and an infection case is published weekly at http://www.aphis.usda.gov.…”

Development of a SYBR green-based real-time RT-PCR assay for rapid detection of the emerging swine acute diarrhea syndrome coronavirus

“…When these samples were tested by probe-based RT-qPCR, the detection result was consistent with result by SYBR RT-qPCR. The detection results were summarized in Table 2. SADS-CoV is a recently discovered virus that has resulted in serious outbreaks and huge financial losses to pig farming industry in south China (Fu et al, 2018;Gong et al, 2017;Pan et al, 2017;Zhou et al, 2018b). Most of these studies applied the conventional RT-PCR to detection of SADS-CoV.…”

Significant inhibition of re-emerged and emerging swine enteric coronavirus in vitro using the multiple shRNA expression vector

“…Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a novel coronavirus which was first reported in southern China in 2017. It also can cause severe diarrhea disease in newborn piglets (Fu et al, 2018;Pan et al, 2017;Wang et al, 2018aWang et al, , 2018bXu et al, 2018;Zhou et al, 2018aZhou et al, , 2018b. Similar to other SECoVs, such as transmissible gastroenteritis virus (TGEV), these re-emerged and emerging SECoV diseases are age-dependent with high morbidity and mortality in neonatal pigs.…”

“…Traditional inactivated and attenuated PEDV vaccines failed to provide robust protection against PEDV variants infection Li et al, , 2018bPark and Shin, 2018). Meanwhile, SADS-CoV and PDCoV have no commercial vaccines yet (Fu et al, 2018;Hu et al, 2015;Ma et al, 2015). Therefore, given complexity of mixed viral infection and issues associated with novel antigenic variants, novel antiviral strategies may provide means of effectively addressing issues of SECoV infection in swine.…”