Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus

Abstract

<jats:title>Abstract</jats:title> <jats:p>The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown once again that coronavirus (CoV) in animals are potential sources for epidemics in humans. Porcine deltacoronavirus (PDCoV) is an emerging enteropathogen of swine with a worldwide distribution. Here, we implemented and described an approach to analyze the epidemiology of PDCoV following its emergence in the pig population. We performed an integrated analysis of full genome sequence data from 21 newly sequenced viruses, along with comprehensive epidemiological surveillance data collected globally over the last 15 years. We found four distinct phylogenetic lineages of PDCoV, which differ in their geographic circulation patterns. Interestingly, we identified more frequent intra- and interlineage recombination and higher virus genetic diversity in the Chinese lineages compared with the USA lineage where pigs are raised in different farming systems and ecological environments. Most recombination breakpoints are located in the ORF1ab gene rather than in genes encoding structural proteins. We also identified five amino acids under positive selection in the spike protein suggesting a role for adaptive evolution. According to structural mapping, three positively selected sites are located in the N-terminal domain of the S1 subunit, which is the most likely involved in binding to a carbohydrate receptor, whereas the other two are located in or near the fusion peptide of the S2 subunit and thus might affect membrane fusion. Finally, our phylogeographic investigations highlighted notable South-North transmission as well as frequent long-distance dispersal events in China that could implicate human-mediated transmission. Our findings provide new insights into the evolution and dispersal of PDCoV that contribute to our understanding of the critical factors involved in CoVs emergence.</jats:p>

Deltacoronavirus Evolution and Transmission: Current Scenario and Evolutionary Perspectives

“…Recent serological data confirm the presence of swine PDCoV IgG antibodies as early as 2010 ( 32 ). The fact that the diversity of PDCoV in US swine is restricted (≥99.7% nucleotide identity) ( 31 , 33 , 34 ) is also consistent with the relatively recent introduction of the virus. While the exact route of emergence of PDCoV in the US is unknown, Asia is considered to be the area of PDCoV origin, where no association of this pathogen with significant clinical disease was reported ( 28 ).…”

“…He et al have recently demonstrated the presence of at least four distinct phylogenetic lineages of PDCoV that differ in their geographic circulation patterns ( 34 ). Of interest, more frequent intra- and inter-lineage recombination events (resulting in higher virus genetic diversity) were observed among PDCoV strains of the Chinese lineage than among those of the US lineage.…”

Development of a TaqMan-probe-based multiplex real-time PCR for the simultaneous detection of emerging and reemerging swine coronaviruses

“…This suggests possible periodic outbreaks of SADS-CoV could be observed in years to come. PDCoV, a δ-coronavirus, was first detected in 2012 and caused PEDV-like signs in pigs [19][20][21]22]. Birds can be considered as the natural hosts of δ-coronaviruses.…”

Involvement of Spike Protein, Furin, and ACE2 in SARS-CoV-2-Related Cardiovascular Complications

“…Coronavirus S protein is a granule-shaped structural protein with a length of about 1200 aa, which helps the virus to bind to cell receptors and participate in mediating viral infection and pathogenesis [11,12]. During viral infection, the host cell PCs cleave the S1/S2 cleavage site of the trimer S protein dividing it into an N-terminal S1 extracellular domain that recognizes the relevant cell surface receptor and a C terminal S2 membrane anchor protein that is involved in translocation of the virus into the cells [13,14]. SARS-Cov-S2 and SARS-CoV-S1 proteins contain a conserved receptor-binding domain (RBD), which can recognize ACE2 [15].…”