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.