Historical Evolutionary Dynamics and Phylogeography Analysis of Transmissible Gastroenteritis Virus and Porcine Deltacoronavirus: Findings from 59 Suspected Swine Viral Samples from China.

Since the beginning of the 21st century, humans have experienced three coronavirus pandemics, all of which were transmitted to humans via animals. Recent studies have found that porcine deltacoronavirus (PDCoV) can infect humans, so swine enteric coronavirus (SeCoV) may cause harm through cross-species transmission. Transmissible gastroenteritis virus (TGEV) and PDCoV have caused tremendous damage and loss to the pig industry around the world. Therefore, we analyzed the genome sequence data of these two SeCoVs by evolutionary dynamics and phylogeography, revealing the genetic diversity and spatiotemporal distribution characteristics. Maximum likelihood and Bayesian inference analysis showed that TGEV could be divided into two different genotypes, and PDCoV could be divided into four main lineages. Based on the analysis results inferred by phylogeography, we inferred that TGEV might originate from America, PDCoV might originate from Asia, and different migration events had different migration rates. In addition, we also identified positive selection sites of spike protein in TGEV and PDCoV, indicating that the above sites play an essential role in promoting membrane fusion to achieve adaptive evolution. In a word, TGEV and PDCoV are the past and future of SeCoV, and the relatively smooth transmission rate of TGEV and the increasing transmission events of PDCoV are their respective transmission characteristics. Our results provide new insights into the evolutionary characteristics and transmission diversity of these SeCoVs, highlighting the potential for cross-species transmission of SeCoV and the importance of enhanced surveillance and biosecurity measures for SeCoV in the context of the COVID-19 epidemic.

Swine Enteric Coronavirus: Diverse Pathogen-Host Interactions.

Swine enteric coronavirus (SeCoV) causes acute gastroenteritis and high mortality in newborn piglets. Since the last century, porcine transmissible gastroenteritis virus (TGEV) and porcine epidemic diarrhea virus (PEDV) have swept farms all over the world and caused substantial economic losses. In recent years, porcine delta coronavirus (PDCoV) and swine acute diarrhea syndrome coronavirus (SADS-CoV) have been emerging SeCoVs. Some of them even spread across species, which made the epidemic situation of SeCoV more complex and changeable. Recent studies have begun to reveal the complex SeCoV-host interaction mechanism in detail. This review summarizes the current advances in autophagy, apoptosis, and innate immunity induced by SeCoV infection. These complex interactions may be directly involved in viral replication or the alteration of some signal pathways.

Isolation and characterization of a porcine epidemic diarrhea virus strain Jiaozuo1012/2019

In order to determine the causative agent of diarrhea of suckling piglets in a pig farm in Jiaozuo city in 2019, RTPCR was used to detect the related viral pathogens from five clinical samples. The results showed that all five samples were positive for PEDV, but negative for TGEV and PoRV. A PEDV strain named as Jiaozuo1012/2019 was isolated from the positive samples by using Vero cells through detecting the fifth passaged virus by RT-PCR. The S gene and ORF3 gene of the isolated PEDV were amplified by RT-PCR, and the homology and phylogenetic tree of these two genes were analyzed by compared with PEDV reference strain in GenBank. Based on the homology analysis of S gene and ORF3 gene, S gene of this isolated PEDV had the highest homology (99.3%) with PEDV CH/HNLH/2015 strain isolated in Henan province. The homology of S gene of PEDV Jiaozuo1012/2019 strain with other strains isolated in Henan province was 96.4%-99.0%. The homology of S gene of this isolated virus with the classic PEDV CV777 strain was 93.4%, and there are 4 insertions (59QGVN62) and 3 deletions (140N and 163NI164) in S protein of this isolated virus. The ORF3 gene shared 99.7% homology with PEDV JSCZ1601 strain isolated in Jiangsu province, among 96.4%-99.0% homology with other strains isolated in Henan province, and 96.6% homology with classical PEDV CV777 strain. The phylogenetic tree analysis of S gene and ORF3 gene showed that the isolated virus had the closest genetic relationship with the current domestically epidemic strains. This study provides reference data for further studying the variation of PEDV in Henan province.