Abstract
Infectious bronchitis virus (IBV) is one of the major diseases affecting the poultry industry worldwide. The high mutation rates of viral genome pose serious challenges to the prevention and control of IB. Based on our previous studies on IBV isolates in southern China during 2009-2017, we continued to carry out the genetic evolution analyses of S1 gene from IBV isolates during 2018-2023. Furthermore, we investigated the temporal and geographical origin of 245 IBV strains from southern China during 1985-2023, and reconstructed their transmission dynamics. Our findings revealed that GI-19 (LX4-type) was still the most dominant genotype, with the coexistence of multiple genotypes. Notably, the GI-19 strains were further classified into three subgroups, one of which was a new GI-19 subtype with nucleotide sequence similarities less than 90 % compared to the vaccine strain QXL87, along with five and eight consecutive amino acid substitutions, respectively. GI-28 (LDT3-A-type) strains re-emerged in 2019 and remained predominant thereafter. In addition, there was an increasing isolation rate of GI-7 (Taiwan-I-type). The purification pressure was detected in the S1 protein IBV isolates during 2018-2023, but eight positive selection sites with high entropy values were identified. Five isolates were confirmed to be recombinants, and GI-22 strains involved in all five recombinants as major or minor parents. The estimated times for the most recent common ancestors based on the S1 gene was the years of 1905. Bayesian skyline analysis indicated a rapid increase in genetic diversity of the S1 gene in IBV strains since late 2015. Bayesian geographical analysis demonstrated that the southern China IBVs originated from Nanning and identified four principal transmission pathways. In conclusion, our findings revealed the emergence of a new GI-19 subtype of IBV, the re-emergence of GI-28, and multiple transmission routes in southern China during 2018-2023, underscoring the importance of real-time and continuous surveillance of circulating strains and the urgency of developing safe, effective, and broad-spectrum new vaccines against emerging and re-emerging IBVs.