1 Introduction
Coronaviruses (CoVs) are
positive-stranded and single-stranded RNA viruses with an envelope,
which belong to members of the order Nidomiformes , familycoronaviridae and have the largest genomes, from 25kb to 32kb,
among known RNA viruses (Weiss & Navas-Martin, 2005). CoVs were the
first to isolate in 1937 from the chicken and had the ability of
cross-species transmission. It can infect birds and mammals, including
humans, and mainly cause respiratory and digestive tract symptoms (Weiss
& Navas-Martin, 2005). Since the outbreak of SARS in 2003, new
coronaviruses continue to be discovered. MERS-CoV has been reported in
recent years. SARS-CoV-2 is still sweeping the globe now (Gates, 2020;
Lancet, 2013; Li, Niu, Fan, Chen, & He, 2021; Stadler et al., 2003). As
of 13 August 2021, there have been 205,338,159 confirmed cases of
COVID-19, including 4,333,094 deaths, reported to the WHO
(https://covid19.who.int/). Current research suggests that SARS-CoV-2
may have originated from bats or pangolins (Xiao et al., 2020; Zhou et
al., 2020).
The emerging porcine
delta-coronavirus was first identified in swine specimens collected from
2011 to 2012 in Hong Kong (Woo et al., 2012). In 2014, a severe diarrhea
outbreak occurred on a US pig farm, suspected of PEDV infection.
However, PDCoV was detected in the feces of pigs instead of PEDV.
Subsequently, PDCoV was detected in Korea, Canada, India, Thailand, and
mainland China (Ajayi et al., 2018; Hu et al., 2015; Lee et al., 2016;
Lorsirigool et al., 2017), posing a significant threat to the swine
industry.
In 2017, Woo found PDCoV may be able to cause respiratory infections in
pigs and that in addition to fecal-oral transmission, the virus could
possibly spread through the respiratory route (Woo et al., 2017). In
2019, specific pathogen-free (SPF) chickens were inoculated with PDCoV
and showed mild diarrhea symptoms and low fecal viral RNA shedding
(Liang et al., 2019). From May 2014 to December 2015, Lednicky collected
a total of 369 samples from children presenting to the school clinic
with acute undifferentiated febrile illness in Ayiti and found three of
them were infected with coronavirus strains, which clustered with PDCoV
(Lednicky et al., 2021). Therefore, PDCoV represented significant
potential in cross-species transmission and spread in new host
populations, implying their
potential threat to human health.
To dig into the origin, evolution and transmission of PDCoV, phylogenic
analysis was used to analyze full genome and S gene sequences of PDCoV
to examine source population, time of origin, evolutionary rate, amino
acid sites and potential dissemination routes. The data in the study
will help to formulate countermeasures to deal with the possible future
risk of zoonotic transmission of PDCoV to humans.