Identification and molecular characterization of a novel serotype infectious bronchitis virus (GI-28) in China

Abstract

Avian infectious bronchitis coronavirus (IBV) is a major poultry pathogen. A characteristic feature of IBV is the occurrence of many different strains belonging to different serotypes, which renders complete control of the disease by vaccination a challenging task due to the poor cross-protection between different serotypes. In this study, based on the results of S1 sequence analysis and virus cross-neutralization tests, IBV strain ck/CH/LGX/111119 was found to be genetically and antigenically different from other known IBV types, representing not only a novel genotype, but also a novel serotype (designated as GI-28). Viruses belonging to this novel serotype have been isolated from several regions in China in recent years, suggesting endemic circulation of the serotype in various geographic locations in China. Further studies by complete genomic analysis showed that strain ck/CH/LGX/111119 may have originated from recombination events involving LX4 genotype IBVs and an as-yet-unidentified IBV donating a S1 gene, or from the result of accumulation of mutations and selections, especially in the S1 gene, from a LX4 genotype virus. ck/CH/LGX/111119 is a nephropathogenic strain, although it had broader tissue tropism (respiratory, digestive, urinary, and reproductive tracts) among chickens challenged at one day old. Infection of the oviducts with ck/CH/LGX/111119 found in this study may have severe implications because the virus will likely induce the occurrence of false layers.

Keywords: Cystic oviduct; GI-28 genotype; Infectious bronchitis coronavirus; Nephropathogenicity; Serotype; Tissue tropism.

Fig. 1

Phylogenetic trees constructed with the nucleotide sequence alignments of the S1 glycoprotein genes using the nearest neighbor-joining method with 1000 bootstrap calculations (Valastro et al., 2016). The GenBank accession numbers of the IBV strains are shown in parentheses. The strain ck/CH/LGX/111119 is indicated by a ★. All the IBV strains were clustered into 6 genotypes (GI–GVI) and a number of inter-lineage recombinants. Ninety-three IBV reference strains in GI were further grouped into 27 distinct viral lineages (GI-1–GI-27) (Valastro et al., 2016). Our ck/CH/LGX/111119 strain was clustered into a novel lineage in GI with other 6 IBV reference strains and designated as GI-28.

Fig. 2

SimPlot analysis of the complete genomic sequences of strains ck/CH/LGX/111119 and ck/CH/LDL/091022. Analysis was performed using SimPlot software version 3.5.1 to identify potential recombination breakpoints (Chen et al., 2015). A 1000-bp window with a 100-bp step was used. Strain H120 was used as the query strain.

Fig. 3

Renal lesions of the kidney (A) and cystic dilution of the oviduct (B) in SPF chickens caused by inoculation with the GI-28 type ck/CH/LGX/111119 strain. Kidneys are swollen, tubules and ureters are distended, and uric acid crystals are present.

Fig. 4

Detection of IBV antigen by immunohistochemical analysis in the bronchi (A and B), enterocytes of the cecal tonsils (C and D), and kidneys (E and F) of dead chickens infected with the IBV GI-28 type ck/CH/LGX/111119 strain.

Fig. 5

The grey regions of the map show seven Chinese provinces, where the 48 GI-28 type viruses were isolated. The difference in gray color is related to the numbers of viruses (showed on the right).