Virus and Animals

The YN strain was isolated in 2005 from 30-day-old broilers that had been inoculated oculonasally with H120 vaccines of IBV on days 1, 7, and 21, respectively. The sick birds had respiratory signs, severe renal disease, and a death rate of 30%. The virus was propagated in 10-day-old specific-pathogen–free (SPF) embryonated chicken eggs at 37°C for 40 h. Allantoic fluid was recovered from infected eggs and stored at −80°C. All animal research was approved by the Beijing Administration Committee of Laboratory Animals under the leadership of the Beijing Association for Science and Technology (approval ID is SYXK [Beijing] 2007–0023).

Viral RNA Extraction, Reverse Transcription PCR, and DNA Sequencing

On the basis of IBV nucleotide sequences (M41, A2, BJ, ZJ971, and SC021202; GenBank accession nos. DQ834384, AY043312, AY319651, AF352313, and AY237817, respectively), 22 pairs of specific primers (Table 1) were designed to amplify the complete genome (excluding the 5′- and 3′-terminal segments) of the YN strain. Viral RNA was extracted from virus-infected allantoic fluid by using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. Reverse transcription (RT) was performed at 37°C for 1 h by using 3 μg total RNA, 1 μL random primers (500 μg/mL, random hexadeoxynucleotides; Promega, Madison, WI, USA) and 0.5 μL M-MLV RT (200 U/μL) (Promega). For PCR, 1 U Taq DNA Polymerase (Promega) and 10 pmol of each primer were added to 100 ng cDNA as template in a total of 20 μL reaction volume. PCR was performed at 95°C for 5 min, followed by 35 cycles of denaturation (95°C, 45 s), annealing (53°C or 55°C, 45 s), and polymerization (72°C, 2 min), and the postpolymerization step was performed at 72°C for 10 min. Amplified sequences were analyzed by 1.2% agarose gel electrophoresis.

The amplified DNA products were purified by using an AxyPrep DNA Gel Extraction Kit (AxyGEN, Union City, CA, USA), and the purified products were ligated to the pMD18-T Easy Vector system (Promega). Recombinant plasmids were extracted from positive clones by using the E.Z.N.A.R. Plasmid Miniprep Kit (Omega, Norcross, GA, USA) and identified by EcoRI restriction digestion (Promega). Nucleotide sequencing reactions were performed by Sunbio Biotech (Bejjing, China).

Sequence and Phylogenetic Analysis

Complete genome or S1 gene sequences of IBV were obtained from GenBank, and these IBV sequences and the complete coding sequence of the IBV YN isolate were aligned and analyzed by using the ClustalW multiple alignment algorithm in the MegAlign program of the DNASTAR software suite (version 3.1; DNAstar, Madison, WI, USA).

The phylogenetic tree of S1 gene or complete genomic sequences was constructed by using MEGA4.0 software (www.megasoftware.net) by the neighbor-joining method (1,000 bootstrap replicates). Evolutionary distances were computed by the pairwise distance method using the maximum composite likelihood model (19).

Clinicopathologic Assessment in Chickens

Forty 30-day-old SPF white leghorn chickens were randomly divided into 2 groups of 20 birds each. All birds in 1 group were challenged intranasally with at least 10⁵ 50% egg infectious dose per 0.2 mL of IBV YN strain. Birds in another group were inoculated with 0.2 mL phosphate-buffered saline (PBS) as noninfected controls. Birds were housed in isolators and provided feed and water ad libitum.

All birds were observed daily for signs of disease (e.g., disheveled feathers, depression, respiratory signs, or diarrhea) and death for 21 days. Gross pathologic changes were observed, and tissues (trachea, lung, kidney, bursa, liver, and brain) were collected for RT-PCR from 10 randomly selected chickens that died within 4–10 days after inoculation, virus isolation, and histopathologic and IHC analyses. Serum samples collected from birds that survived were tested for IBV antibodies by a commercial ELISA kit (IDEXX Laboratories, Westbrook, ME, USA). The endpoint titers were calculated according to the manufacturer’s instructions, and titers >396 were considered positive for IBV antibody.

RT-PCR of Tissue Samples

Tissue samples from deceased birds were collected and used for RT-PCR to determine tissue distribution of the virus. Total RNA was obtained by using Trizol Reagent (Invitrogen) as recommended for tissue samples. RT-PCR was performed as described above by using a pair of primers (forward: 5′-TTTTGGTGATGACAAGATGAA-3′; reverse: 5′- CGCATTGTTCCTCTCCTC-3′), which amplify and detect a 403-bp fragment of the S1 gene of IBV. PCR products were analyzed on 1.5% agarose gels.

Virus Re-isolation from Infected Tissue Samples

Tissue samples collected after challenge were used for virus isolation. Briefly, at least 6 SPF embryos were inoculated through the allantoic cavity, with each sample, containing 10,000 U/mL penicillin and 10,000 µg/mL streptomycin (0.2 mL/egg). The eggs were candled daily, and allantoic fluids from 3 inoculated embryos were collected 48 h after inoculation for RT-PCR amplification. The remaining embryos were examined 6 days after inoculation for characteristic IBV lesions, such as dwarfing, stunting, or curling of embryos.

Histopathology

Tissues (trachea, lung, kidney, bursa, liver, and brain) were collected and fixed by immersion in 10% neutral formalin at room temperature for 48 h. Tissue was then routinely processed, embedded in paraffin wax, and cut into 5-μm sections. The sections were stained with hematoxylin and eosin and examined by light microscopy for lesions resulting from IBV infection.

Immunohistochemistry

All sampled tissues were examined by IHC analysis to detect viral antigen. Briefly, 5-μm tissue sections were subjected to antigen retrieval (20) and were then incubated in 10% normal goat serum in PBS for 30 min to block nonspecific binding sites. Slides were further incubated with chicken anti-IBV hyperimmune serum at 1:500 dilution in PBS for 2 h, followed by incubation with a horseradish peroxidase–conjugated rabbit chicken IgG for 1 h. The reaction was visualized by the addition of 3,3-diaminobenzidine (DAB; Sigma, St. Louis, MO, USA) for 15 min. After IHC staining, sections were counterstained with hematoxylin, air dried, and examined by light microscopy.

Genome Sequencing

The complete genome sequence (excluding the 5′- and 3′-terminal segments) of YN strain was obtained by assembling 22 overlapping sequences that ranged from 856 bp to 1,686 bp by the DNAstar software. The nucleotide sequences were submitted to GenBank under accession no. JF893452. The complete genomic sequences (excluding the 5′- and 3′-terminal segments) of YN isolate comprised 27,635 nt, which putatively contains 6 different genes, each containing single or multiple open reading frames.

Phylogenetic Analysis

Figure 1

Figure 1. . Phylogenetic tree of avian infectious bronchitis virus based on the nucleotide sequences of the complete genome (A), S1 gene (B), S2 gene (C), E gene (D), M gene (E), and...

Phylogenetic trees for the genome and each gene of IBV reinforced the viral nucleotide sequencing results, suggesting that the YN isolate shares an immediate ancestor with the SC021202 strain (Figure 1). To elucidate the phylogenetic relationships of China IBV strains, we further analyzed S1 genes of 70 IBVs, including 51 China isolates and 19 standard strains or vaccine strains (Figure 1, panel B). The data indicated that China isolates could be differentiated into 3 distinct genetic groups or genotypes. Group I included 41 of the 51 field isolates, which were tentatively named A2-like viruses. Four China field isolates were included in group II, which were tentatively named LSD-like viruses. China group III comprised 6 isolates, which were grouped with the Massachusetts serotype. These results showed that at least 3 distinct groups existed in chicken flocks in China, and A2-like and M41-like viruses were mainly responsible for the IB panzootic, consistent with findngs of our previous studies (5,16).

Sequence Comparisons

Ten virus sequences were selected for pairwise comparisons with the YN strain according to the phylogenetic analysis for S1 (Figure 1, panel B), which included 2 common vaccine strains in China (M41 and H120) and 8 China isolates from 3 different gene clusters (DY07, LX4, A2, and SC021202 from cluster I; CK/CH/LSD/05I and CK/CH/LHB/100801 from cluster II; CK/CH/LHLJ/07VII and CK/CH/LDL/101212 from cluster III) (Table 2). Overall, the complete genomic sequences (excluding the 5′- and 3′-terminal segments) were 87.1%–98.0% identical among the isolates, and the YN strain had the highest nucleotide identity (98.0%) to the SC021202 strain isolated in southern China (GenBank accession no. EU714029). For each gene, the identity hanged from 93.7% to 100% between YN and SC021202 strains (Table 2).

Figure 2

Figure 2. . Amino acid sequence alignment for the S1 gene (A, B) and S2 gene (C) of 14 strains of avian infectious bronchitis virus. Strains YN, SC021202, A2, and SAIBK have a...

The S glycoprotein is the major functional protein for IBV; thus, the putative differences between the YN strain and other IBVs were investigated. Analyses showed that a single amino acid insertion was present at position 22 (Figure 2, panel A) in addition to a 7-aa insertion at positions 74–81 (Figure 2, panel B) in the S1 gene of the YN isolate, in which a putative N-glycosylation site was found. Among available sequences in GenBank, strains A2, BJ, CQ04–1, SC021202, and SAIBK had the same insertion in the S1 gene. Compared with other available strains, 9-aa deletions were located at the N terminal of the S2 gene (Figure 2, panel C) from a base transition (G→T) at position 1,849 nt, resulting in premature stop codon in the open reading frame.

Clinicopathologic Assessment in Chickens

Figure 3

Figure 3. . Seroconversion and percentage survival of chickens experimentally infected with infectious bronchitis virus (IBV), People’s Republic of China. A) Survival of chickens after inoculation with IBV YN strain. B) Detection of...

Clinically, some birds appeared depressed with ruffled feathers; these birds had increased water intake and huddled together in YN-inoculation group at 2 days postinfection (dpi). At 4 dpi, IB-like signs became obvious in all infected chickens, and some birds were euthanized because of severe disease. Deaths occurred until 21 dpi; the death rate reached 65% (Figure 3, panel A). No deaths or clinical signs were observed in the control group.

Figure 4

Figure 4. . Gross lesions from kidney tissues from chickens experimentally infected with infectious bronchitis virus (IBV). A) Kidney tissue of an uninfected control chicken. B) Obvious enlargement and urate deposition in the...

Slight hemorrhage with serous catarrhal exudate could be seen in the trachea of all euthanized birds. Air sac lesions also were present, characterized by marked thickening of the air sac wall and a yellow caseous exudate. All euthanized chickens showed typical kidney lesions. The affected kidneys were substantially enlarged, and deposits of pale urate were frequently observed in the tubules and ureters (Figure 4). No gross lesions were observed in any birds in the control group.

Antibody responses in birds that survived infection were measured by a commercial ELISA kit (IDEXX Laboratories). All but 1 chicken showed a positive reaction (Figure 3, panel B) by ELISA, and the mean titer induced by the YN strain was 1,250.35 at 21 dpi.

RT-PCR and Virus Isolation on Tissues

To further examine the pathogenicity of IBV YN, the tissue tropism of the strain was investigated by RT-PCR and virus isolation by using tissue suspensions from dead birds. YN strain replicated well in the various organs, including the kidneys, trachea, lungs, and bursa (Table 3; Technical Appendix).

Histopathologic and IIHC Analyses

Figure 5

Figure 5. . Histopathologic analysis (hematoxylin and eosin stain) of tissues from 30-day-old chickens infected with infectious bronchitis virus YN strain. Panels A, C, E, and G, correspond to control tissues. B) Trachea,...

Figure 6

Figure 6. . Immunohistochemical detection of avian infectious bronchitis virus (IBV) antigens in tissues after experimental infection with IBV YN strain. Panels A, C, E, and G correspond to control tissues. B) Tracheal...

Microscopic examination of the tracheal tissues revealed extensive degeneration and necrosis of the ciliated epithelial cells, sometimes with pseudoacinar structures resulting from dropout of dead cells (Figure 5, panel B). Viral antigen was detected at high levels in the epithelial cells of the tracheal mucosa (Figure 6, panel B). Lung lesions were characterized by hemorrhage, congestion, and lymphocytic infiltration in the alveolar lumen (Figure 5, panel D), and viral antigen was detected in alveolar cells (Figure 6, panel D). Severe renal lesions, including degeneration and necrosis of renal tubular epithelial cells, lymphocytic infiltration in the interstitium, exfoliated renal tubular epithelial cells, and erythrocytes were frequently observed (Figure 5, panel F). Viral antigens were detected extensively in the renal tubular epithelial cells (Figure 6, panel F). Serious atrophy of lymphoid follicles and widening of the interstitium were observed in the bursa of Fabricius (Figure 5, panel H), and viral antigens were detected widely in the mucosal epithelium of the bursa of Fabricius (Figure 6, panel H). Sporadic congestion also was observed in the liver and cerebrum.