3.4 Phylogenetic and diversity analysis of CoVs circulating in poultry
Phylogenetic analysis revealed that the 593 CoVs detected from poultry could be classified into three lineages corresponding to IBV (n=485), DuCoV (n=72), and PiCoV (n=36), respectively (Figure 2 ). The emerging SARS-CoV-2 belongs to the Betacoronavirus ofCoronaviridae , and the detected 593 avian CoVs in this study belongs to the Gammacoronavirus . SARS-CoV-2 showed higher genetic distance compared with avian CoV.
The positive rates of IBVs, DuCoVs, and PiCoVs were 15.35%, 2.28% and 1.14%, respectively (Table1). Besides, these data suggested that IBVs mainly circulate in chickens, DuCoVs mainly circulate in ducks, and PiCoVs mainly circulate in pigeons. The number of samples and positive rate of three lineages of CoVs in each province were shown inTable 2. The results showed that IBV was detected in all provinces investigated in this study, with DuCoV and PiCoV were detected in most provinces. The province with the highest positive rate of CoVs was Hubei (36.20%), with the lowest was Yunnan (5.95%).
The numbers of due-species infections and cross-species infections in the samples collected from living poultry markets (LPMs) were shown inTable 3. The results showed that cross-species infections of the CoVs, namely that infections of IBVs in birds other than chickens, infections of DuCoVs in birds other than ducks, and infections of PiCoVs in birds other than pigeons were identified in 23 of the 3160 samples from four sites (6 with IBVs, 9 with DuCoVs and 8 with PiCoVs).