Characterization of an avian infectious bronchitis virus isolated in China from chickens with nephritis

Detection and Molecular Characterization of Enteric Viruses in Poultry Flocks in Hebei Province, China

Simple Summary

Enteric viruses act as etiological agents for a series of health disturbances that pose a threat to commercial chickens worldwide. The affected chickens exhibit stunted growth, low feed conversion, etc. On a global scale, research on enteric virus diversity has been performed in countries such as India, South Korea and Brazil, yet at present, there have been no conclusive reports of avian enteric viruses in China. In the present study, the virus species, infection types, clinical symptoms, and relationships among the virus species were studied in 145 positive enteric virus samples. Additionally, the evolutionary relationship and recombination of the viruses were also further studied. The results of this study can be used to define the distribution and infection type of enteric viruses in poultry, and to analyze the classification of and evolutionary relationship between certain viruses.

Abstract

Enteric viruses, as a potential pathogen, have been found to be vital causes of economic losses in poultry industry worldwide. The enteric viruses widely studied to date mainly include avian nephritis virus (ANV), avian reovirus (ARe), chicken astrovirus (CAstV), chicken parvovirus (ChPV), fowl adenovirus group I (FAdV-1), infectious bronchitis virus (IBV), and avian rotavirus (ARoV). This paper aimed to identify single and multiple infections of the seven enteric viruses using the data obtained from positive 145 enteric virus samples in poultry flocks from different areas in Hebei Province, throughout the period from 2019 to 2021. Next, the correlation between bird age and clinical signs was investigated using PCR and RT-PCR techniques. Furthermore, the whole genomes of seven parvovirus strains and open reading frame 2 (ORF2) of six CAstV strains and eight ANV strains were sequenced for phylogenetic analysis and recombination analysis, to characterize the viruses and evaluate species correlation and geographic patterns. A total of 11 profiles of virus combinations were detected; 191 viruses were detected in 145 samples; 106 single infections were reported in 73.1% of the samples; and multiple infections were detected in the remaining 26.9%. For viruses, 69% of ChPV was correlated with single infection, while ANV (61.4%) and CAstV (56.1%) were correlated with multiple infections. However, IBV and ARe were not detected in any of the samples. Recombination events were reported in parvovirus, and all CAstV sequences investigated in this paper were included within genotype Bii. The eight ANV strains pertained to different subtypes with significant differences. The above results revealed for the first time the complexity of enteric viruses over the past several years, thus contributing to disease prevention and control in the future.

Construction of an infectious bronchitis virus vaccine strain carrying chimeric S1 gene of a virulent isolate and its pathogenicity analysis

Abstract

Infectious bronchitis virus (IBV) is a member of genus gamma-coronavirus in the family Coronaviridae, causing serious economic losses to the poultry industry. Reverse genetics is a common technique to study the biological characteristics of viruses. So far, there is no BAC reverse genetic system available for rescue of IBV infectious clone. In the present study, a new strategy for the construction of IBV infectious cDNA clone was established. The full-length genomic cDNA of IBV vaccine strain H120 was constructed in pBAC vector from four IBV fragment subcloning vectors by homologous recombination, which contained the CMV promoter at the 5′ end and the hepatitis D virus ribozyme (HDVR) sequence and bovine growth hormone polyadenylation (BGH) sequence after the polyA tail at the 3′ end of the full-length cDNA. Subsequently, using the same technique, another plasmid pBAC-H120/SCS1 was also constructed, in which S1 gene from IBV H120 strain was replaced with that of a virulent SC021202 strain. Recombinant virus rH120 and rH120/SCS1 were rescued by transfecting the plasmids into BHK cells and passaged in embryonated chicken eggs. Finally, the pathogenicity of both the recombinant virus strains rH120 and rH120/SCS1 was evaluated in SPF chickens. The results showed that the chimeric rH120/SCS1 strain was not pathogenic compared with the wild-type IBV SC021202 strain and the chickens inoculated with rH120/SCS1 could resist challenge infection by IBV SC021202. Taken together, our results indicate that BAC reverse genetic system could be used to rescue IBV in vitro and IBV S1 protein alone might not be the key factor for IBV pathogenicity.

Key points

• BAC vector was used to construct IBV full-length cDNA by homologous recombination.

• Based on four subcloning vectors, a recombinant chimeric IBV H120/SCS1 was constructed and rescued.

• Pathogenicity of H120/SCS1 was similar to that of H120, but different to that of SC021202.

Development and application of nsp5-ELISA for the detection of antibody to infectious bronchitis virus

Infectious bronchitis virus (IBV) continues to be one of the most important poultry pathogens worldwide. The current commercially available enzyme-linked immunosorbent assay (ELISA) kits for IBV specific antibody detection are mostly based on the whole virion, and few serological tests based on nonstructural proteins of IBV have been developed. Herein, an alternative indirect ELISA for detection of IBV antibody was developed with IBV nonstructural protein 5 (nsp5) produced by Escherichia coli. Using an indirect immunofluorescence assay (IFA) and a commercial ELISA kit as reference, we optimized the nsp5-ELISA and determined its cut-off as 0.12. The diagnostic sensitivity (DSN), specificity (DSP) and accuracy of the nsp5-ELISA were 93.11%, 95.38% and 93.33%, respectively, compared with IFA in 660 field serum samples, and were 98.11%, 95.00% and 97.62%, respectively, compared with the commercial IBV ELISA kit (IDEXX) in 126 field sera samples. Furthermore, a time course of IBV specific antibody level detected by nsp5-ELISA following IBV infection and vaccination is consistent with that of IBV antibody detected by the commercial ELISA kit. The results presented in this study indicate that nsp5-ELISA has the potential to serve as a rapid, reliable and cost-effective method for IBV antibody detection. This study is the first to report the development of an nsp-based ELISA to detect an antibody to IBV.

Isolation of a novel serotype strain of infectious bronchitis virus ZZ2004 from ducks in China

In chickens, the infectious bronchitis virus (IBV) often causes respiratory distress, a decrease in egg production, poor egg quality, and occasional nephritis. However, ZZ2004, a Chinese isolate of IBV, was obtained from ducks with clinical growth suppression and mild respiratory symptoms that had been reared with chickens in the central region of China. Virus isolation, virus neutralization testing, and RT-PCR were employed to identify the causative pathogen, while sequence alignment was used to analyze gene variations of the S1 subunit and M genes. The results showed that the ducks were infected with IBV due to the emergence of a dwarfing phenotype and the death of embryos between 48 and 144 h post-inoculation. RT-PCR also confirmed the presence of the expected fragment sizes of the S1 subunit and M genes by RT-PCR. Meanwhile, the results of the virus neutralization test indicated that the strains of JX/99/01, GD, SAIBK, LDT3 showed cross-reactivity with the ZZ2004 isolate, and hardly any cross-neutralization of IBV ZZ2004 was observed with the strains of M41, H120, Gray, Holte, or Aust-T. Phylogenetic analysis suggested that there were large differences between ZZ2004 and other IBV reference strains on the S1 subunit. Meanwhile, homologies in the nucleotide and amino acid sequences of the M gene of IBV ZZ2004 were 86.9–92.0 % and 91.1–93.9 %, respectively, compared with 35 other IBV reference strains derived from different regions. This result revealed that there were conspicuous variations among the selected strains. Furthermore, the results showed that the prevalent strains of IBV in ducks had no antigen homology with the vaccine strains widely used in China except the LDT3-strain, making it urgent to explore and develop new IBV vaccines.

Complete genome sequence of a nephropathogenic infectious bronchitis virus strain isolated in china

Infectious bronchitis virus (IBV) causes tremendous economic losses to the poultry industry. Here, we report the complete genome analysis results for a new natural recombination nephropathogenic IBV strain named SAIBK, which was isolated in the Sichuan province of China in 2005.

Avian infectious bronchitis and deep pectoral myopathy - a case control study

Infectious bronchitis is caused by a coronavirus, infectious bronchitis virus (IBV). Infectious bronchitis is an acute and highly contagious disease of economic importance due to the reduction in weight gain observed with infected broilers and the drop in egg quality and production associated with infected laying hens. The presence of deep pectoral myopathy has been associated with IBV variants. This lesion is detected at slaughterhouses and is characterized by paleness and atrophy of the deep pectoral muscle, including necrosis of the region, leading to condemnations of the breast muscle, a valuable meat cut in the market. This work aimed to study the relationship between deep pectoral myopathy and IBV by describing tracheal and muscle lesions and comparing the frequency of IBV detection via reverse-transcription (RT) PCR in muscle, tracheal, and cecal tonsil samples from broilers with and without myopathy. A case-control study was conducted in 40 broiler flocks vaccinated with the Massachusetts strain. The case group consisted of 23 flocks that presented myopathic lesions under sanitary inspection and a control group of 17 flocks without myopathic lesions. The tracheal, cecal tonsil, and supracoracoid muscle (with and without lesions) samples from the 40 broiler flocks were screened by RT-PCR to detect IBV. Histopathology of muscle and tracheal tissue was carried out. Upon microscopic examination, the muscle samples from the case group presented extensive necrosis, intense mononuclear inflammatory infiltration, muscle fiber fragmentation, and fibrotic tissue, confirming myopathy, whereas muscles from the control group showed no alterations. The tracheal samples presented a large number of infiltrated mononuclear inflammatory cells that in some areas formed submucosal nodules. A total of 25 flocks tested IBV positive by RT-PCR: 14 from the case group and 11 from the control group. The IBV was detected by RT-PCR directly in muscle samples. Despite that, the relationship between deep pectoral myopathy and IBV was not established. The higher positive IBV RT-PCR percentage noted in the cecal tonsil samples demonstrates how important the choice of organs is for diagnostic purposes.

Bioinformatics and evolutionary insight on the spike glycoprotein gene of QX-like and Massachusetts strains of infectious bronchitis virus

Background

Infectious bronchitis virus (IBV) is a Gammacoronavirus of the family Coronaviridae and is a causative agent of an economically important disease in poultry. The spike glycoprotein of IBV is essential for host cell attachment, neutralization, and is involved in the induction of protective immunity. Previously obtained sequence data of the spike gene of IBV QX-like and Massachusetts strains were subjected to bioinformatics analysis.

Findings

On analysis of potential phosphorylation sites, the Ser542 and Ser563 sites were not present in Massachusetts strains, while QX-like isolates did not have the Ser534 site. Massachusetts and QX-like strains showed different cleavage site motifs. The N-glycosylation sites ASN-XAA-SER/THR-55, 147, 200 and 545 were additionally present in QX-like strains. The leucine-rich repeat regions in Massachusetts strains consisted of stretches of 63 to 69 amino acids, while in the QX-like strains they contained 59 amino acids in length. An additional palmitoylation site was observed in CK/SWE/082066/2010 a QX-like strain. Primary structure data showed difference in the physical properties and hydrophobic nature of both genotypes. The comparison of secondary structures revealed no new structural domains in the genotypic variants. The phylogenetic analyses based on avian and mammalian coronaviruses showed the analysed IBV as closely related to turkey coronaviruses and distantly related to thrush and munia coronaviruses.

Conclusion

The study demonstrated that spike glycoprotein of the Massachusetts and the QX-like variants of IBV are molecularly distinct and that this may reflect in differences in the behavior of these viruses in vivo.

Emergence of novel strains of avian infectious bronchitis virus in Sweden

Infectious bronchitis virus (IBV) causes avian infectious bronchitis, an important disease that produces severe economic losses in the poultry industry worldwide. Recent IBV infections in Sweden have been associated with poor growth in broilers, drop in egg production and thin egg shells in layers. The complete spike gene of selected isolates from IBV cases was amplified and sequenced using conventional RT-PCR. Nucleotide and amino acid sequence comparisons have shown that the recent isolates bear 98.97% genetic similarity with strains of the QX-like genotype. The phylogenetic analysis revealed that strains predominant in the nineties, which were of the Massachusetts type, have been replaced by D388/QX-like strains, however the evolutionary link could not be established. The homology between the two genotypes was 79 and 81%. Remarkably, a strong positive selection pressure was determined, mostly involving the S1 subunit of the S gene. This strong selective pressure resulted in recombination events, insertions and deletions in the S gene. Two new isolates generated from recombination were found with nucleotide sequence diverging 1.7–2.4% from the D388/QX-like branch, indicating the emergence of a new lineage. The study demonstrates a constant evolution of IBV that might be in relation to increased poultry farming, trade and vaccine pressure. The findings underscore the importance of continuous monitoring to control spread of infections, as well as to timely adjust diagnostic methods, molecular epidemiological studies, development and use of vaccines that are adapted to the changing disease scenario.

Detection of avian nephritis virus in Australian chicken flocks

Avian nephritis virus (ANV) is thought to infect poultry flocks worldwide, but no confirmed case has been reported in Australia. The first such case is described in this study. Cases of young chickens with clinical signs of dehydration and diarrhea were submitted to our laboratory and histopathology detected interstitial nephritis. Vaccine strains of infectious bronchitis virus were detected in some of these cases but were not considered to be the causative agent. A total of seven fresh submissions from broiler chicken flocks were collected at 8-11 days of age. Degenerate PCR primers were designed based on published ANV polymerase gene sequences and used to analyze historic cases as well as the fresh submissions. Six of the seven fresh submissions, and one historic case, were positive for ANV with nucleotide sequencing confirming these results. These results establish ANV as an infectious pathogen circulating in Australian poultry.

Characterization of a new genotype and serotype of infectious bronchitis virus in Western Africa

Between 2002 and 2007, more than 1000 chickens from commercial farms, live bird markets and backyard farms in Nigeria and Niger were tested for the presence of the infectious bronchitis virus (IBV) genome. Phylogenetic analysis of full-length sequences of the spike 1 (S1) gene revealed a new genotype of IBV that we refer to as ‘IBADAN’. The minimum genetic distance to the closest ‘non-IBADAN’ strains (UK/7/93 at the nucleotide level; H120 and M41 at the amino acid level) reached 24 and 32 % at the nucleotide and amino acid levels, respectively. The full genome of the IBADAN reference strain (NGA/A116E7/2006) had a genetic distance of 9.7–16.4 % at the nucleotide level with all available fully sequenced strains. As IBV S1 plays a major role in antigenicity, the antigenic relatedness of NGA/A116E7/2006 was compared with strains of other serotypes. NGA/A116E7/2006 did not cross-react with antisera against IT02, M41, D274, Connecticut or 793/B strains in virus neutralization assays. NGA/A116E7/2006 cross-reacted with the QX-like strain ITA/90254/2005 but only to a low level (antigenic relatedness of 33 %), suggesting that IBADAN also represents a new serotype. A comparison of S1 sequences identified several amino acids that may play a role in IBV antigenicity. Despite the absence of obvious clinical signs in poultry infected by IBADAN strains, it is important to test the cross-protection of current vaccine strains.

Sequence and phylogenetic analysis of S1, S2, M, and N genes of infectious bronchitis virus isolates from Malaysia

Two Malaysian infectious bronchitis virus isolates, MH5365/95 and V9/04 were characterized based on sequence and phylogenetic analyses of S1, S2, M, and N genes. Nucleotide sequence alignments revealed many point mutations, short deletions, and insertions in S1 region of both IBV isolates. Phylogenetic analysis of S1 gene and sequences analysis of M gene indicated that MH5365/95 and V9/04 belong to non-Massachusetts strain. However, both isolates share only 77% identity. Analysis based on S1 gene showed that MH5365/95 shared more than 87% identity to several Chinese strains. Meanwhile, V9/04 showed only 67-77% identity to all the previously studied IBV strains included in this study suggesting it is a variant of IBV isolate that is unique to Malaysia. Phylogenetic analysis suggests, although both isolates were isolated 10 years apart from different states in Malaysia, they shared a common origin. Analysis based on S2 and N genes indicated that both strains are highly related to each other, and there are fewer mutations which occurred in the respective genes.

Characterization and membrane gene-based phylogenetic analysis of avian infectious bronchitis virus Chinese strain HH06

A Chinese isolate of avian infectious bronchitis virus (IBV) designated HH06 was isolated from the kidney tissues of a chicken flock experiencing an outbreak of nephritis. In vivo pathogenicity of the IBV isolate HH06 was determined by inoculating specific pathogen-free (SPF) chickens. The clinical signs and related gross lesions of HH06 infected chickens were similar with those of the field-infected chickens. SPF embryonated eggs were inoculated with virus suspension for serial passage and their genomic RNA was extracted. RT-PCR technique was utilized to amplify the M gene sequence encoding membrane protein of IBV. Recombinant plasmid named T-vector-M was constructed via inserting the M gene into the TA cloning vector, pMD 18-T. The sequenced M gene and its deduced amino acid (aa) sequences were compared with the published sequences of reference strains. The M gene is of 687 bp in length encoding the M protein of 228 amino acids with a predicted molecular weight of 25.4 kDa. The sequences of the M gene and M protein share 83.9-97.9% and 83.6-96.5% homologous identities, respectively, compared with 29 IBV reference strains derived from different regions or countries, which revealed that there are still significant variations between strains. Furthermore, a phylogenetic tree based on these M DNA sequences was generated, and the tree topology suggests that some Chinese IBV strains may have a common ancestor; however, HH06 is a new local IBV isolate that is responsible for the field outbreak of nephritis.

Identification of a newly isolated avian infectious bronchitis coronavirus variant in China exhibiting affinity for the respiratory tract

Twelve infectious bronchitis virus (IBV) isolates obtained from commercial chickens in China between 2005 and 2006 were characterized by reverse transcriptase-polymerase chain reaction (RT-PCR) and the sequencing of the entire S1 gene. CK/CH/LSD/05I--an IBV variant, which was unlike the nephropathogenic IBV isolates found in China--exhibited an affinity for the respiratory tract. The variant was identified by phylogenic analysis and basic local alignment search tool (BLAST) searches of the entire S1 gene and by the vaccination-challenge test that was performed using heterologous strains. Further, it was demonstrated that the commercially used H120 vaccine did not provide sufficient protection against this variant; however, the attenuated heterologous IBV tl/CH/LDT3/03 P120, whose parent virus was isolated in China, showed a better efficacy of protection against CK/CH/LSD/05I. This study thus may demonstrate that the use of a combination of commercially available vaccines or of attenuated heterologous strains would provide satisfactory protection against the variant CK/CH/LSD/05I. In addition, the study also revealed that IBV strains exhibiting different pathogenicities were found cocirculating in the chicken flock in China.

Molecular epizootiology of avian infectious bronchitis in Russia

Molecular characterization of infectious bronchitis viruses (IBVs) isolated between 1998 and 2002 from chickens in Russia was performed. More than 250 field samples were tested by reverse transcriptase-polymerase chain reaction using two sets of primers corresponding to the most conserved 3'-untranslated region and the most variable S1 gene region of the viral genome. Ninety-one IBV isolates were characterized by phylogenetic analysis of the S1 gene hypervariable region comprising 136 to 558 nucleotides. The major group of isolates (38 viruses) showed very close sequence relationship with strains of the Massachusetts genotype circulating in Russia since the early 1970s. The analysed region of the other 22 Russian IBVs was similar (from 89 to 98% identity) to that from the strains of European genotypes including D274 (nine isolates), 793/B (10 isolates), and B1648, 624/I and Italy-02 (one isolate in each group). Two isolates from very distant geographic locations in Russia (Far East and the European part) clustered together with Chinese strains of QXIBV genotype. None of the remaining 27 Russian isolates showed a close sequence relationship with known IBV strains available in sequence databases. The majority of these variant viruses clustered into the six novel Russian genotypes, often correlating with their geographic location. The remaining five of them were placed outside these unique groups, also representing new genotypes. These data for the first time demonstrated the high genetic diversity of IBV isolates circulating in Russia.

Production and characterization of monoclonal antibodies to (poly100)S1 protein of avian infectious bronchitis virus

Fragments within S1 genes ((poly100)S1) of infectious bronchitis virus (IBV) strains ZJ971, M41 and SC021202 (SC) were subcloned into a prokaryotic expression vector and expressed in Escherichia coli. Monoclonal antibodies (mAbs) against the recombinant (poly100)S1 proteins were produced, characterized and used to analyse epitopes on the S1 subunit of IBV. Nine mAbs raising from the three (poly100)S1 proteins recognized five different epitopes of the S1 subunit, designated as S1-A, B, C, D and E. Epitopes S1-C and S1-D are common for the three IBV strains, while S1-A and S1-B exist on ZJ971 and M41 strains, and S1-E was a strain-specific epitope for SC strain. Immunocytochemistry indicated that all the mAbs to the (poly100)S1 proteins can react with the homologous S1 glycoprotein expressed in Vero cells. Moreover neutralization test demonstrated that only mAbs 6E2, 4F9 and 6G4 had neutralization activity for the homologous IBV. These mAbs to (poly100)S1 protein were potential candidates for detecting and distinguishing IBV strains, and also used to examine antigenic variation of the S1 protein.

Molecular analysis of Brazilian infectious bronchitis field isolates by reverse transcription-polymerase chain reaction, restriction fragment length polymorphism, and partial sequencing of the N gene

Molecular analysis of 15 Brazilian infectious bronchitis virus (IBV) isolates, obtained from clinical outbreaks of the disease in chickens (broilers or layers) in the state of Minas Gerais (Brazil) between 1972 and 1989, is reported. Using the N protein gene as target, IBVs were analyzed by reverse transcription-polymerase chain reaction/restriction fragment length polymorphism (RT-PCR/RFLP) with the restriction enzymes AvaII, HphI, Sau96I, and Tsp509I and cDNA sequencing. Results obtained from those isolates were compared to 19 sequences available in GenBank. N gene RFLP profiles, cDNA sequences, and predicted amino acid composition were used for the construction of dendrograms. Brazilian isolates were grouped into one distinct group. Identity of predicted N protein amino acid composition varied from 45% (between isolates G and 208) up to 99% (PM 1 and PM2), and, when compared to the other IBVs, the amino acid identity was from 42% (Q3/88 and G) up to 97% (D41 and PM1). The great genetic diversity was shown to occur before the official use of vaccination in Brazil and has remained thereafter.

Isolation and characterization of a coronavirus from pigeons with pancreatitis

OBJECTIVE

To identify and partially characterize a coronaviruslike virus isolated from naturally infected pigeons.

ANIMALS

50 specific pathogen-free (SPF) embryonated chicken eggs, 30 White Leghorn SPF chickens, and 12 clinically normal pigeons.

PROCEDURES

Pancreatic tissue specimens from sick pigeons were inoculated into SPF embryonated chicken eggs for viral isolation and investigation of morphologic and hemagglutinating properties of the isolate, called PSH050513. Furthermore, virulence studies in SPF chickens and experimental pigeons were performed. The spike (S) glycoprotein gene of PSH050513 was further sequenced and analyzed.

RESULTS

PSH050513 was isolated and identified from the experimentally infected pigeons by a routine method, which was in accordance with Koch's postulates. The complete S protein (1,167 amino acids) was compared with published S protein sequences of other avian and mammalian coronaviruses. A high degree of sequence identity (79.3% to 99.6%) was observed between the S protein sequence of PSH050513 and published sequences of avian infectious bronchitis virus (IBV); only limited identity (< 37.8%) was observed with turkey coronavirus and mammalian coronaviruses. Furthermore, when the virus was inoculated into SPF chickens, pancreatitis developed.

CONCLUSIONS AND CLINICAL RELEVANCE

PSH050513 has been tentatively identified as a novel member of group 3 coronaviruses that have close genetic relationships with IBV strains.