1 INTRODUCTION
Coronaviruses (CoVs) belong to Nidovirales , familyCoronaviridae, Orthocoronavirinae , which are divided into four
genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus andDeltacoronavirus (King et al., 2012), and can infect many animals
including humans (Cheng et al.,2017; Guan et al., 2003; Rota et al.,
2003;Woo et al., 2006; Woo et al., 2009; Marra et al., 2003). Among
them, Alphacoronavirus mainly infects humans and pigs, dogs,
cats, bats, etc. Betacoronavirus mainly infects humans, cattle,
horses, pigs, mice, bats and other mammals. Gammacoronavirusmainly infects domestic poultry, and Deltacoronavirus mainly
infects wild birds and pigs. CoVs that can infect birds are mainly
originated from the Gammacoronavirus and Deltacoronavirusof Coronaviridae (King et al., 2011; Jordan et al., 2015). CoVs isolated
from domestic poultry such as avian infectious bronchitis virus (IBV)
are belonged to Gammacoronavirus (King et al., 2012). In the
avian CoVs, IBV is more harmful to the poultry industry and were listed
as notifiable disease by World Organization for Animal Health (OIE). In
addition, duck coronavirus (DuCoV), goose coronavirus and pigeon
coronavirus (PiCoV) were also detected and showed highly genetic
differences compared with IBVs (Chen et al., 2013; Jonassen et al.,
2005; Zhuang et al., 2020).
In December, 2019, an outbreak of unknown pneumonia occurred in Wuhan,
China (Zhou et al., 2020). The pathogen was soon identified to be an new
emerging coronavirus, named as severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) by International Committee on Taxonomy of
Viruses (ICTV), and the disease was designated coronavirus disease 2019
(COVID-19) by World Health Organization (WHO) (Zhou et al., 2020; Chen
et al., 2020). The clinical symptoms of COVID-19 mainly include
asymptomatic infection, mild-to-severe respiratory tract illness, and
even death (Huang et al., 2020). Compared with severe acute respiratory
syndrome coronavirus (SARS-CoV), SARS-CoV-2 has the higher basic
reproduction number, representing more transmissibility (Liu et al.,
2020). Within a very short period of time, COVID-19 has quickly become a
very serious threat to human health, travel and commerce in the
worldwide (Stoecklin et al., 2020; Ghinai et al., 2020; Tuite et al.,
2020).
The viruses have been successfully isolated, but the pathogenesis
mechanisms and effective vaccines are undergoing extensively study.
SARS-CoV-2 belongs to the Betacoronavirus , in which SARS-CoV and
middle east respiratory syndrome coronavirus (MERS-CoV) are also
included in the same group. The natural host of highly pathogenic SARS
and MERS coronaviruses was confirmed as bats, and bats are also thought
to be the natural hosts for SARS-CoV-2 based upon genomic sequence
analysis (Wang et al., 2020). The transmission of SARS-CoV-2 from bats
to humans was suspected to via the direct contact between humans and
intermediate host animals (Guo et al., 2020). However, it remains
unclear which animals were the intermediate host of SARS-CoV-2. Previous
report demonstrated that SARS-CoV can infect ferrets and cats (Martina
et al., 2003), implying that these host might be also susceptible to
SARS-CoV-2. Since poultry have very close contact with humans, it is
very important to identify the possible source of SARS-CoV-2 from avian,
especially in the outbreak areas.
In this study, traceable surveillance was conducted to identify the
possibility of SRAS-CoV-2 originated from poultry. Tracheal and cloacal
swabs collected for routine surveillance of avian diseases in 2019 were
tested by real-time reverse transcription-polymerase chain reaction
(RT-PCR)recommended by Chinese Center for Disease Control and Prevention
(CDC) to detect the SARS-CoV-2 and universal RT-PCR developed by our
laboratory to analysis the molecular characterization of coronaviruses
detected from poultry by sequencing respectively. Our study indicated
the genetic diversities of avian CoVs and no infection of SARS-CoV-2 in
poultry of China in 2019.