4 Discussion
The outbreak of COVID-19 has raised great concern all over the world and
poses serious threat to global public health. Therefore, Covs gained
increasing attention. When researchers examined blood samples from Ayiti
children in early 2021, three samples were found to be infected with
PDCoV (Lednicky et al., 2021). Of note, PDCoV has repeatedly crossed the
host barrier to chicken (Boley et al., 2020; Liang et al., 2019). This
phenomenon exhibits the same cross-species transmission as SARS-COV-2,
which suggested that the emerging porcine delta-coronavirus may be a
potential threat to human health. Here, we adopted a phylogeographic
approach to examine the time of origin, evolutionary rate,
diversification patterns and potential transmission routes of PDCoV and
selected six special spike amino acid sequences to align and analyze.
PDCoV is an emerging coronavirus causing severe enteritis, diarrhea, and
vomiting in piglets. PDCoV was first discovered in Hong Kong, China in
2012, but began to spread in the United States in 2014. Now many
countries in the world have reported that pigs were infected with PDCoV.
We attained 42 positive samples for PDCoV from eight intensive pig
farms, located in Guangdong Province, China and sequenced two PDCoV
completed genomes. Moreover, a strain of PDCoV, which could be stably
passaged on the LLC-PK cell line was successfully isolated. According to
phylogenetic analysis of PDCoV, our findings indicated that PDCoV would
be classified into three major lineages: China lineage; USA lineage; and
Southeast Asia lineage. There were three PDCoV in Ayiti that can infect
children, two of which were highly similar to KY065120 in Tianjin, China
(99.8%), and the rest were highly similar to KR150443 in Arkansas, USA
(98.9%). However, after suffering from African swine fever in Ayiti,
pigs were reintroduced mainly from American populations. The worldwide
spatial dispersal networks of PDCoV also indicated the US lineage was
one of the origins to Ayiti. Therefore, PDCoV infected in Ayiti was most
likely from America (Alexander, 1992; Lednicky et al., 2021).
The MCC tree showed that PDCoV originated in Asia, between China and
southeast Asia, and more likely in Southeast Asia in 1989. In addition,
according to Bayesian Skyline Plot analysis, effective population size
of PDCoV tended to level off and stabilize at around 70. We observed the
association between geographic distance and migration rate to clarify
space dynamics. However, we observed a strong signal of viral
dissemination (migration rate = 3.55) from US to Japan and South Korea,
with a long distance (about 11200 km). This showed there was no certain
connection between geographic distance and migration rate. Moreover, the
scatter plot of distance and migration rate also did not display a
certain trend (Supplementary Tables S6, Fig S2). It may be due to the
swine trade between countries and artificial or feed contamination that
affects the rate of natural transmission.
To analyse the effect of amino acid mutation on cross-species
transmission, we found six PDCoV sequences that can spread across
species, and align the amino acids of their spike protein. By analyzing
the amino acid sequence of spike protein, seven significant mutation
sites were defined. The accumulation of these mutations may enhance
dynamic movements, accelerating virus membrane fusion events and
transmission.
Frankly, this study has several limitations. First, sampling bias, no
same number of samples in different regions, may have affected the
Bayesian phylogenic reconstruction and inference of the transmission
networks (Alexander, 1992; Lednicky et al., 2021). Second, the
information from sequences contains the most regions infected with PDCoV
but does not cover all regions, because there are some places infected
with PDCoV, but no sequence uploaded in GenBank.
In summary, our findings offer
novel insights into the diversification, evolution, and interspecies
transmission and origin of PDCoV. We also briefly analyzed why humans
are infected with PDCoV. Increasing evidence strongly implicates that
CoVs have a high capacity for cross-species transmission. Given that
pigs are in frequent contact with humans and wild animals, the lower
interspecies hurdles in pigs would make them a potential mixing vessel
for CoVs (Ye et al., 2020). Therefore,
comprehensive surveillance and
enhanced biosecurity precautions for PDCoV should be taken to prevent
further pandemic such as COVID-19.