Phylogeography and evolutionary dynamics analysis of porcine delta‐coronavirus with host expansion to humans

Abstract

From 2003 onwards, three pandemics have been caused by coronaviruses: severe acute respiratory syndrome coronavirus (SARS‐CoV); middle east respiratory syndrome coronavirus (MERS‐CoV); and, most recently, SARS‐CoV‐2. Notably, all three were transmitted from animals to humans. This would suggest that animals are potential sources of epidemics for humans. The emerging porcine delta‐coronavirus was reported to infect children. This is a red flag that marks the ability of PDCoV to break barriers of cross‐species transmission to humans. Therefore, we conducted molecular genetic analysis of global clade PDCoV to characterize spatiotemporal patterns of viral diffusion and genetic diversity. PDCoV was classified into three major lineages, according to distribution and phylogenetic analysis of PDCoV. It can be inferred based on the analysis results of the currently known PDCoV strains that PDCoV might originate in Asia. We also selected six special spike amino acid sequences to align and analyze to find seven significant mutation sites. The accumulation of these mutations may enhance dynamic movements, accelerating spike protein membrane fusion events and transmission. Altogether, our study offers a novel insight into the diversification, evolution, and interspecies transmission and origin of PDCoV and emphasizes the need to study the zoonotic potential of the PDCoV and comprehensive surveillance and enhanced biosecurity precautions for PDCoV.

Comprehensive analysis of codon usage patterns of porcine deltacoronavirus and its host adaptability

“…Li et al (2022) suggested that the accumulated mutations in the S gene may enhance dynamics movements and transmission of PDCoV. The recent PDCoV isolates are more adaptable to humans than the early PDCoV strains, indicating that PDCoV gradually adapted to humans by the evolution processes, but further biological assays are needed to confirm this conclusion.…”

Nanoparticle vaccines based on the receptor binding domain of porcine deltacoronavirus elicit robust protective immune responses in mice

“…It is reported that frequent recombination between different lineages may result in the emergence of PDCoV strains with divergent pathogenicity and host tropism ( 1 , 32 ). PDCoV as a novel coronavirus has been reported to infect humans, suggesting that PDCoV has potential to proceed interspecies transmission or evolute as a new human strain ( 10 ).…”

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

“…An increasing number of studies have demonstrated the ability of CoVs to spread across species and become zoonotic viruses [ 36 , 37 , 38 ]. As an economically important animal for humans, pigs may serve as a container for SeCoVs and other CoVs and thus spread them to other organisms [ 21 , 39 ]. Therefore, increased surveillance and research on pigs are needed to prevent future pandemics of CoVs.…”