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 spatio-temporal 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 determined
that PDCoV originated in Asia—most likely in Southeast Asia—through
inference of migration rate and transmission routes. 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.