Molecular cloning and sequence comparison of the S1 glycoprotein of the Gray and JMK strains of avian infectious bronchitis virus

A New Dual Fluorescence Method for Rapid Detection of Infectious Bronchitis Virus at Constant Temperature

Infectious bronchitis virus (IBV) causes infectious bronchitis in chicken, an acute, highly contagious respiratory infection. Because of genetic mutations and recombination, IBV forms many subtypes, which makes it difficult to treat the disease and apply commercial vaccines. Therefore, to detect IBV in time and stop the virus from spreading, a novel and convenient IBV detection technology based on reverse transcription recombinase-aided amplification (RT-RAA) was established in this study. According to the S1 gene of IBV CH I-V and Mass genotypes and S1 gene of IBV CH VI genotype, a set of optimal primers were designed and selected to establish a real-time dual fluorescence RT-RAA method. The lowest detection line was 10 copies/μL of RNA molecules and the method exhibited no cross-reactivity with avian reticuloendotheliosis virus (REV), infectious bursal disease virus (IBDV), avian leukosis virus (ALV), Newcastle disease virus (NDV), chicken infectious anemia virus (CIAV), infectious laryngotracheitis virus (ILTV), Marek's disease virus (MDV), and H9N2 avian influenza virus (H9N2), demonstrating high specificity. When compared to qPCR detection results, our method achieved a sensitivity of 96.67%, a specificity of 90%, and a Kappa value of 0.87 for the IBV CH I-V and Mass genotypes, and achieved a sensitivity of 100%, a specificity of 97.73%, and a Kappa value of 0.91 for the IBV CH VI genotype.

Antigenic and molecular characterization of isolates of the Brazilian genotype BR-I (GI-11) of infectious bronchitis virus supports its recognition as BR-I serotype

The antigenic and molecular characteristics of BR-I infectious bronchitis viruses (IBVs) isolated from Brazil are reported. IBVs isolated from commercial flocks with different clinical manifestations between 2003 and 2019 were submitted to antigenic and molecular characterization. The complete S1 glycoprotein gene of 11 field isolates was amplified and sequenced. The virus neutralization (VN) test showed 94.75% neutralization with a BR-I isolate and 30% or less against other worldwide reference strains. The nucleotide and amino acid sequence analyses revealed 84.3-100% and 83.5-100% identity among them, respectively. The identity values ranged from 57.1 to 82.6% for nucleotides and from 46.6-84.4% for amino acids compared with those of other genotypes. By phylogenetic tree analysis, the Brazilian isolates were branched into the BR-I genotype (lineage GI-11), which was differentiated from foreign reference strains. Selective pressure analyses of BR-I IBVs revealed evolution under purifying selection (negative pressure) for the complete S1 gene but four specific sites (87, 121, 279, and 542) under diversifying selection (positive pressure). Profiles of cleavage sites and potential N-glycosylation sites differed from those of other genotypes. The low molecular relationship among the Brazilian viruses and foreign serotypes was concordant with the VN test results. The low antigenic relatedness (ranging from 5.3-30% between Brazilian genotype BR-I and reference IBV serotypes of North America, Europe, and Asia) indicates that the BR-I genotype is a different serotype, referred to for the first time and hereafter as serotype BR-I. RESEARCH HIGHLIGHTSStrains of the BR-I genotype presented robust antigenic and molecular similarity.BR-I strains evolved under purifying selection mode (negative pressure).The BR-I genotype originated in Brazil and dispersed to other countries.BR-I genotype viruses can be referred to as the BR-I serotype.

Genome Variability of Infectious Bronchitis Virus in Mexico: High Lineage Diversity and Recurrent Recombination

The avian infectious bronchitis virus (IBV) is a coronavirus that mutates frequently, leading to a contagious and acute disease that results in economic losses to the global poultry industry. Due to its genetic and serological diversity, IBV poses a challenge in preventing and controlling the pathogen. The full-length S1 sequence analysis identifies seven main genotypes (GI-GVII) comprising 35 viral lineages. In addition to the previously described lineage, a new GI lineage (GI-30) and two lineages from novel genotypes (GVIII-1 and GIX-1) have been described in Mexico. To prevent the spread of IBV outbreaks in a specific geographic location and select the suitable vaccine, it is helpful to genetically identify the circulating IBV types. Moreover, sequencing genomes can provide essential insights into virus evolution and significantly enhance our understanding of IBV variability. However, only genomes of previously described lineages (GI-1, GI-9, GI-13, and GI-17) have been reported for Mexican strains. Here, we sequenced new genomes from Mexican lineages, including the indigenous GI-30, GVIII-1, and GIX-1 lineages. Comparative genomics reveals that Mexico has relatively homogenous lineages (i.e., GI-13), some with greater variability (i.e., GI-1 and GI-9), and others extremely divergent (GI-30, GVIII-1, and GIX-1). The circulating lineages and intra-lineage variability support the unique diversity and dynamic of Mexican IBV.

Infectious Bronchitis Virus in Egypt: Genetic Diversity and Vaccination Strategies

Infectious bronchitis virus (IBV) is a highly evolving avian pathogen that has increasingly imposed a negative impact on poultry industry worldwide. In the last 20 years, IBV has been continuously circulating among chicken flocks in Egypt causing huge economic losses to poultry production. Multiple IBV genotypes, namely, GI-1, GI-13, GI-16, and GI-23 have been reported in Egypt possessing different genetic and pathogenic features. Different vaccine programs are being used to control the spread of the disease in Egypt. However, the virus continues to spread and evolve where multiple IBV variants and several recombination evidence have been described. In this review, we highlight the current knowledge concerning IBV circulation, genesis, and vaccination strategies in Egypt. In addition, we analyze representative Egyptian IBV strains from an evolutionary perspective based on available data of their S1 gene. We also provide insight into the importance of surveillance programs and share our perspectives for better control of IBV circulating in Egypt.

Genetic characterisation and analysis of infectious bronchitis virus isolated from Brazilian flocks between 2010 and 2015

1. Infectious bronchitis virus (IBV) variants in Brazil were isolated during 2010-2015 for epidemiological and molecular analysis to characterise the different variants and perform a bioinformatic analysis to compare with sequences of variants collected over the previous 40 years. 2. Of the 453 samples examined, 61.4% were positive for IBV and 75.9% of these were considered to have the BR-I genotype and were detected in birds of all ages distributed in all five Brazilian regions. 3. The ratio of non-synonymous substitutions per non-synonymous site (dN) to synonymous substitutions per synonymous site (dS), i.e. dN/dS, revealed a predominance of codons with non-synonymous substitutions in the first third of the S1 gene and a dN/dS ratio of 0.67. Additionally, prediction of N-glycosylation sites showed that most of the BR-I variants (from 2003 to early 2014) had an extra site at amino acid position 20, whereas the newest variants lacked this extra site. 4. These results suggest that Brazilian IBV variants probably underwent drastic mutations at various points between 1983 and 2003 and that the selection processes became silent after achieving a sufficiently effective antigenic structure for invasion and replication in their hosts. Brazilian IBV genotype BR-I is currently the predominant genotype circulating in Brazil and South America.

A Real-Time Reverse-Transcription Polymerase Chain Reaction for Differentiation of Massachusetts Vaccine and Brazilian Field Genotypes of Avian Infectious Bronchitis Virus

The avian infectious bronchitis virus is classified into serotypes or genotypes (or both) in different poultry-producing countries of the world. In Brazil, Massachusetts type (Mass), used as a live vaccine, and local field Brazilian variants (genotypes; BR) predominate in the commercial poultry flocks. This study describes the development and validation of two real-time reverse-transcription polymerase chain reactions (RT-qPCR) for the specific detection of Mass and BR genotypes in allantoic fluids and clinical samples. Genotype-specific primers, combined with a generic probe targeted to the S1 gene, originated Mass RT-qPCR and BR RT-qPCR-specific assays. Analytical sensitivity and linearity of these assays were determined in comparison with an IBV generic real-time RT-PCR based on the 5' untranslated region (5'UTR RT-qPCR). Mass RT-qPCR detected five Mass field isolates, three vaccine samples, and one coinfected sample (BR and Mass) while BR RT-qPCR detected 16 BR field isolates. Both assays were linear (R(2) > 0.98), reproducible, and as sensitive as the classical 5'UTR RT-qPCR used to detect IBV. In the analysis of 141 IBV clinical samples, 8 were positive for Mass RT-qPCR, 76 for BR RT-qPCR, and 2 for both assays. In the remaining 55 samples, 25 were positive only for 5'UTR RT-qPCR and 30 were negative for the three assays. In conclusion, both assays were able to detect Mass and BR genotypes, allowing rapid and easy IBV molecular typing from allantoic fluids and clinical samples.

S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification

Infectious bronchitis virus (IBV) is the causative agent of a highly contagious disease that results in severe economic losses to the global poultry industry. The virus exists in a wide variety of genetically distinct viral types, and both phylogenetic analysis and measures of pairwise similarity among nucleotide or amino acid sequences have been used to classify IBV strains. However, there is currently no consensus on the method by which IBV sequences should be compared, and heterogeneous genetic group designations that are inconsistent with phylogenetic history have been adopted, leading to the confusing coexistence of multiple genotyping schemes. Herein, we propose a simple and repeatable phylogeny-based classification system combined with an unambiguous and rationale lineage nomenclature for the assignment of IBV strains. By using complete nucleotide sequences of the S1 gene we determined the phylogenetic structure of IBV, which in turn allowed us to define 6 genotypes that together comprise 32 distinct viral lineages and a number of inter-lineage recombinants. Because of extensive rate variation among IBVs, we suggest that the inference of phylogenetic relationships alone represents a more appropriate criterion for sequence classification than pairwise sequence comparisons. The adoption of an internationally accepted viral nomenclature is crucial for future studies of IBV epidemiology and evolution, and the classification scheme presented here can be updated and revised novel S1 sequences should become available.

Sequence analysis of infectious bronchitis virus isolates from the 1960s in the United States

To better understand the molecular epidemiology of infectious bronchitis virus (IBV) in the United States following the introduction of commercial IBV vaccines, we sequenced the S1 and N structural protein genes of thirteen IBV field isolates collected in the 1960s. Analysis of the S1 sequence showed that seven isolates were of the Massachusetts (Mass) genotype, five were SE17, and one was of the Connecticut (Conn) genotype, suggesting that these three IBVs were circulating in commercial poultry raised in different regions in the United States during the 1960s. The S1 genes of Mass-type isolates had high levels of sequence variation, representing 81.3-81.9 % nucleotide (nt) and 77.3-78.7 % amino acid (aa) identity when compared to those of the SE17-type isolates. In contrast, the N genes from the same isolates were less variable (>92 % nt and >93 % aa identity) when compared to those of the SE17-type isolates. Phylogenetic analysis based on the S1 gene indicated that one isolate (L748) was more closely related to the Mass type. In contrast, phylogenetic analysis based on the N gene showed that L748 was more closely related to the SE17 type, indicating that there had been exchange of S1 genetic materials between Mass- and SE17-like viruses. In addition, the Mass-type isolates had high levels of sequence identity in the S1 gene compared with widely used modified live vaccines (Mass41, Ma5 and H120) and modern field strains from the USA and other countries, suggesting a common ancestor.

Epidemiological survey and molecular characterization of avian infectious bronchitis virus in Brazil between 2003 and 2009

As part of an epidemiological study of infectious bronchitis virus (IBV) in Brazil, 252 samples from IBV-suspect flocks were tested and the IBV-positive samples were analysed by sequencing of hypervariable regions 1 and 2 of the S1 gene. A high prevalence of IBV variants was found and the sequence analysis of 41 samples revealed a high molecular similarity among the Brazilian isolates (from 90.2 to 100% and from 85.3 to 100% nucleotide and amino acid identity, respectively). The Brazilian isolates showed low genetic relationship with Massachusetts (63.4 to 70.7%), European (45.9 to 75.6%), American (49.3 to 76.4%) and other reference serotypes (67.5 to 78.8%). The Brazilian isolates branched into one unique cluster, separate from the reference serotypes used for infectious bronchitis control in other countries. The variants analysed in this work had a high similarity with all previously published Brazilian IBV isolates, suggesting the presence and high prevalence of a unique or predominant genotype circulating in Brazil. In addition, the virus neutralization test showed that the three Brazilian isolates analysed in the present study are antigenically related to one another but are different from the Massachusetts serotype. The present study shows that IBVs of a unique genotype can be associated with different clinical diseases, and that low genetic variation was detected in this genotype over a long period of time. The molecular characterization of the Brazilian variants isolated from 2003 to 2009 from different geographic regions of the country shows that only one predominant genotype is widespread in the Brazilian territory, denominated in this study as BR-I genotype.

Complete genomic sequence analysis of infectious bronchitis virus Ark DPI strain and its evolution by recombination

An infectious bronchitis virus Arkansas DPI (Ark DPI) virulent strain was sequenced, analyzed and compared with many different IBV strains and coronaviruses. The genome of Ark DPI consists of 27,620 nucleotides, excluding poly (A) tail, and comprises ten open reading frames. Comparative sequence analysis of Ark DPI with other IBV strains shows striking similarity to the Conn, Gray, JMK, and Ark 99, which were circulating during that time period. Furthermore, comparison of the Ark genome with other coronaviruses demonstrates a close relationship to turkey coronavirus. Among non-structural genes, the 5'untranslated region (UTR), 3C-like proteinase (3CL^pro) and the polymerase (RdRp) sequences are 100% identical to the Gray strain. Among structural genes, S1 has 97% identity with Ark 99; S2 has 100% identity with JMK and 96% to Conn; 3b 99%, and 3C to N is 100% identical to Conn strain. Possible recombination sites were found at the intergenic region of spike gene, 3'end of S1 and 3a gene. Independent recombination events may have occurred in the entire genome of Ark DPI, involving four different IBV strains, suggesting that genomic RNA recombination may occur in any part of the genome at number of sites. Hence, we speculate that the Ark DPI strain originated from the Conn strain, but diverged and evolved independently by point mutations and recombination between field strains.

Molecular characterization of infectious bronchitis virus strains isolated from the enteric contents of Brazilian laying hens and broilers

Infectious bronchitis virus (IBV) is the causative agent of avian infectious bronchitis, which is characterized by respiratory, reproductive, and renal signs. However, the role of IBV as an enteric pathogen in still controversial. In Brazil, antigenic groups of IBV divergent from the Massachusetts serotype used for vaccination schedules in that country have already been demonstrated. The present study aimed to assess the different genotypes of IBV in Brazilian commercial poultry flocks by partial sequencing of the S1 amino-terminus coding region using enteric contents as samples and examine their relationship with the vaccine serotype currently in use. Samples of enteric contents were taken as pools of five birds from each of 18 poultry farms (17 broiler and one laying farm) from five Brazilian states between 2002 and 2006. Birds were presenting watery diarrhea and poor general condition but were without respiratory, renal, or reproductive signs. Conventional antibacterial and anticoccidial therapies were unsuccessful and, furthermore, all samples proved negative for rotavirus, reovirus, and astrovirus. Eleven IBV samples were isolated in embryonated eggs and resulted in S1 sequences. Phylogenetic analysis showed that these segregated into an exclusive cluster, close to serotype D274, but distant from Massachusetts. Mean amino acid identity amongst these Brazilian strains was 94.07%; amongst these and serotypes D274, 4/91, and Massachusetts, mean amino acid identity was 77.17%, 69.94%, and 68.93%, respectively. In conclusion, the presence of genotype variant strains of IBV in Brazilian poultry flocks has been demonstrated and might be the reason for the unsuccessful control of IBV in Brazil. Furthermore, these results also strengthen the implications of IBV in enteric diseases of poultry.

S1 gene sequence analysis of a nephropathogenic strain of avian infectious bronchitis virus in Egypt

BACKGROUND

Infectious bronchitis is highly contagious and constitutes one of the most common and difficult poultry diseases to control. IBV is endemic in probably all countries that raise chickens. It exists as dozens of serotypes/genotypes. Only a few amino acid differences in the S1 protein of vaccine and challenge strains of IBV may result in poor protection. Tropism of IBV includes the respiratory tract tissues, proventriculus and caecal tonsils of the alimentary tract, the oviduct and the kidney.

RESULTS

Infectious bronchitis virus (IBV) strain closely related to Massachusetts (Mass) serotype was isolated from broiler chickens suffering from severe renal and respiratory distresses. The isolate was serologically identified by Dot-ELISA and further characterized by RT-PCR then genotyped using S1 gene sequence analysis. Alignment of the S1 sequence of the isolate with 16 IBV strains revealed high homology to isolates related to Mass serotype. Inoculation with the strain reproduced the disease in experimental 1-day-old chickens and resulted in 20% mortality, severe renal and moderate respiratory distresses. Marked histopathological changes in both kidney and trachea were observed in experimentally infected chickens. A protection study using the H120 live attenuated vaccine showed low protection rate in spite of high S1 sequence homology (97%). Protection based criteria were: virus re-isolation attempts from trachea, tracheal and renal histopathology as well as IBV antigens detection by immunofluorescent antibody technique in kidney sections.

CONCLUSION

Periodical evaluation of cross-protective capabilities of IBV vaccine(s) versus recently recovered field isolates should be performed to ensure optimum control of IBV.

Genetic diversity of avian infectious bronchitis coronavirus strains isolated in China between 1995 and 2004

Twenty-six avian infectious bronchitis (IB) viruses (IBV) were isolated from outbreaks in chickens in China between 1995 and 2004. They were characterized by comparison with twenty-six Chinese reference strains and five other IBV strains. Chinese IBVs, which were mainly nephropathogenic, were placed into seven genotypes. Fourteen Chinese IBV isolates were placed in genotype I, having small evolutionary distances from each other. Genotype II included 6 strains that were isolated in the 1990s in China. Genotype III consisted of eight Chinese isolates that showed close relationship with Korean IBV isolates. Another eight IBV isolates clustered in genotype IV and showed larger evolutionary distances. The Massachusetts serotype was present in China in 1990s and was in a separate genotype. Two isolates, HN99 and CK/CH/LHN/00I, which might be a reisolation of vaccine strains, clustered into genotype VI. Four Chinese IBV isolates formed another genotype and showed larger evolutionary distances from other Chinese IBV genotypes (genotype VII). IBVs in same genotypes showed more than 90% amino acid sequence similarities, whereas most of the viruses in different genotypes showed less than 90%. The results showed that IBVs in China came from genetic changes both in IBV populations that existed before the advent of vaccination and in the viruses that were introduced through live vaccines. IBVs showing various genetic differences are cocirculating in China.

Nephropathogenesis of chickens experimentally infected with various strains of infectious bronchitis virus

Four-day-old specific-pathogen-free chickens were inoculated by eyedrop with four different strains (Gray, JMK, CV56b, and Wolgemuth) of infectious bronchitis virus (IBV). Birds were monitored clinically and euthanatized at 1, 4, 7, and 14 days postinfection and tissues were collected for virus isolation, histopathologic examination, in situ hybridization (ISH), and immunohistochemistry (IHC). Clinical disease was severe in chickens infected with Wolgemuth, but no overt disease was observed with the other strains. Virus was isolated from the kidneys of chickens infected with the Gray-, CV56b-, and Wolgemuth-strains of IBV. Histologically, interstitial nephritis was evident in chickens infected with these same 3 strains. However, viral nucleic acid and antigen were detected only with Wolgemuth-infected kidneys by ISH and IHC. These results indicate that the pathological changes in kidneys from chickens infected with Gray and CV56b may not have resulted from the cytolytic action of the virus.

Complete nucleotide sequences of S1 and N genes of infectious bronchitis virus isolated in Japan and Taiwan

The complete nucleotide sequences of the S1 and N genes of three Japanese and one Taiwanese field strains of IBV are reported. These Japanese strains were found to have S1 sequences most similar to those of Australian strains and N sequences most similar to those of North American strains. This result suggested that these Japanese strains might all be recombinant viruses derived from recombination of Australia- and North America-related viruses. Moreover, the S1 proteins of all these Japanese and Taiwanese strains exhibit only a limited sequence homology to strains of Massachusetts and Connecticut serotypes that have been commonly used as vaccine strains. This result high lightens the importance of development of vaccines based on the local strains of IBV.

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

One IBV isolate, SC021202, was isolated from the kidneys of the infected young chickens by inoculating embryonated eggs, and its morphology, physiochemical and haemagglutonating properties were detected. Virulence of the isolate SC021202 was determined with specific pathogen‐free (SPF) chicken inoculation. Nucleotide acid sequence of S1 gene of the isolate SC021202 was further sequenced and analysed. The physiochemical and morphological properties of the isolate SC021202 were in accordance to that of typical infectious bronchitis virus (IBV). In a pathogenicity experiment, the clinical signs and related gross lesions resembling those of field outbreak were reproduced and the virus isolate SC021202 was re‐isolated from the kidneys of the infected chicken. Sequence data demonstrated that the full length of the amplified S1 gene of the isolate SC021202 was composed of 1931 nucleotides, coding a polypeptide of 543 amino acid residues. Compared with IBV strains from GenBank, the nucleotide and deduced amino acid sequence of S1 gene of the isolate SC021202 shared 60.0–91.4% and 49.1–88.9% identities, respectively. A nucleotide fragment of ′CTTTTTAATTATACTAACGGA′ was inserted at nucleotide site 208 in the S1 gene of the isolate. These results indicated that IBV isolate SC021202 was a new variant IBV isolate and responsible for field outbreak of nephritis.

Comparisons of envelope through 5B sequences of infectious bronchitis coronaviruses indicates recombination occurs in the envelope and membrane genes

A 1.78 kb sequence, including the E, M, 5a and 5b genes, and the intergenic region between the M and 5a genes, of six US strains of infectious bronchitis (corona)virus (IBV) were sequenced and compared to the published sequences for two additional strains. The overall identities as determined through pairwise analyses of nucleotide sequences of the entire 1.78 kb region ranged from 90 to 99%, with the 5b open reading frame (ORF) having the greatest identity (94–99%) while the identities of the E, 5a and M ORFs ranged from 87 to 100%. Nucleotide sequencing of recent field isolates from Alabama (Ala1) and California (Cal3) revealed distinct shifts in homology in the M gene, indicating two apparent recombination events between the Holland 52/Mass41-like strain and an Ark-like strain, both origins of commonly used vaccine strains. Putative sites of recombination could also be identified in both the E and M ORFs of laboratory strains of IBV.

Tissue distribution of avian infectious bronchitis virus following in ovo inoculation of chicken embryos examined by in situ hybridization with antisense digoxigenin-labeled universal riboprobe

Chicken embryos were inoculated with 8 different strains of infectious bronchitis virus (IBV) representing 7 different serotypes at 17 days of embryonation. At 2 and 5 days postinfection (dpi), tissues were collected for in situ hybridization using an antisense digoxigenin-labeled riboprobe corresponding to the sequence of the mRNA coding for the membrane protein. Extensive antigen staining in the cytoplasm of epithelial cells in the trachea, lung, bursa, and intestine was detected at 2 dpi with all 8 strains of IBV. At 5 dpi, little or no positive staining was observed in these tissues. However, tubular cells of the kidney showed multifocal positive staining with the Wolgemuth strain-, Gray strain-, JMK strain-, and Mass41 strain-infected chickens. No viral RNA was detected in the spleen at any time point. The results demonstrated strict epitheliotropic nature and wide tissue tropism of strains of IBV in the chicken embryo and the universality of our riboprobe. In situ hybridization with this probe will be useful for understanding the tissue tropism and the pathogenesis of IBV in vivo.

Nephropathogenic infectious bronchitis in Pennsylvania chickens 1997-2000

Nephropathogenic infectious bronchitis (NIB) was diagnosed in 28 infectious bronchitis virus (IBV)-vaccinated commercial chicken flocks in Pennsylvania from December 1997 to July 2000. Early dinical signs were increased flock mortality and urinary water loss (polyuria and pollakiuria) leading to wet litter. Daily mortality ranged from 0.01% in layers to 2.45% in broilers, with total broiler mortality as high as 23%. Severe renal swelling and accumulation of urates in the tubules were commonly seen. Visceral gout and urolithiasis were less frequently observed. Histopathologic changes included characteristic tubular epithelial degeneration and sloughing with lymphoplasmacytic interstitial nephritis. Minimal respiratory disease signs were noted in broilers. Egg production and shell quality declined in layers. Confirmatory diagnosis of NIB was made by IBV antigen-specific immunohistochemical staining of the renal tubular epithelium and virus isolation. Sequencing of the S1 subunit gene of 21 IBV isolates showed the NIB outbreak to be associated with two unique genotypes, PA/Wolgemuth/98 and PA/171/99. The cases from which the genotypes were isolated were clinically indistinguishable. The NIB viruses were unrelated to previously recognized endemic strains in Pennsylvania and were also dissimilar to each other. Genotype PA/Wolgemuth/98 was isolated almost exclusively during the first 14 mo of the outbreak, whereas PA/171/99 was recovered during the final 18 mo. The reason for the apparent replacement of PA/Wolgemuth/98 by PA/171/99 is not known.

Genetic and antigenic diversity in avian infectious bronchitis virus isolates of the 1940s

In order to verify a commonly held assumption that only Massachusetts (Mass) serotype of infectious bronchitis virus (IBV) was prevalent in the United States between the 1930s (when IBV was first isolated) and the 1950s (when the use of commercial IBV vaccines began), we examined 40 IBV field isolates from the 1940s. Thirty-eight of those isolates were recognized as Mass serotype viruses based on their reactivity to Mass-specific monoclonal antibody (Mab) and neutralization by Mass-specific chicken serum. The remaining two isolates, N-M24 and N-M39, that did not react with Mass-specific Mab, resisted neutralization by Mass-specific chicken serum, and were neutralized only by homologous chicken antibody were identified as non-Mass IBV. When the first 900 nucleotides (nt) from the 5'-end of the spike (S1) glycoprotein gene and their deduced amino acid (aa) sequences were compared, the two non-Mass isolates differed from each other by 24% and 28%, respectively. In a similar comparison, the non-Mass viruses N-M24 and N-M39 differed from M28, a Mass-type isolate from the 1940s, by 21% and 22% (nt) and 28% and 27% (aa), respectively. These data indicate that antigenic and genetic diversity among IBV isolates existed even in the 1940s. Interestingly, when the N-terminal region of the S1 of M28 was compared to that of M41, a prototype Mass virus that has undergone countless number of in vivo and in vitro host passages, the two viruses differed by only 2% (nt) and 4% (aa). This finding suggests that frequent genetic changes are not inherent in all IBV genomes.

Sequence comparison of avian infectious bronchitis virus S1 glycoproteins of the Florida serotype and five variant isolates from Georgia and California

The infectious bronchitis virus (IBV) spike glycoprotein S1 subunit is required to initiate infection and contains virus-neutralizing and serotype-specific epitope(s). Reported are the S1 gene nucleotide and predicted amino acid sequences for the Florida 18288 strain and isolates GA-92, CV-56b, CV-9437, CV-1686, and 1013. These sequences were compared with previously published gene sequences of IBV strains, and phylogenetic relationships are reported. The S1 amino acid sequence of Florida 18288 was 94.9% similar to the Connecticut strain, and GA-92 was 92.8% similar to the Arkansas 99 strain. S1 amino acid sequences of the California variants, CV-56b, CV-9437, and CV-1686, were 97.6-99.3% similar to one another and only 76.6%-76.8% similar to the Arkansas-type strains. Isolate 1013, also from California, was 84.0% similar to Ark DPI and 77.9% similar to CV-56b. When comparing 19 viruses isolated from the United States, sequence variations were observed between amino acids 55-96, 115-149, 255-309, and 378-395. Similar regions are reported to be involved in virus-neutralizing and/or serotype-specific epitopes. These data demonstrate that variant IBV strains continue to emerge, and unique variants may circulate among poultry in geographically isolated areas.

Infectious bronchitis virus: Immunopathogenesis of infection in the chicken

The immunopathogenesis of infectious bronchitis virus (IBV) infection in the chicken is reviewed. While infectious bronchitis (IB) is considered primarily a disease of the respiratory system, different IBV strains may show variable tissue tropisms and also affect the oviduct and the kidneys, with serious consequences. Some strains replicate in the intestine but apparently without pathological changes. Pectoral myopathy has been associated with an important recent variant. Several factors can influence the course of infection with IBV, including the age, breed and nutrition of the chicken, the environment and intercurrent infection with other infectious agents. Immunogenic components of the virus include the S (spike) proteins and the N nucleoprotein. The humoral, local and cellular responses of the chicken to IBV are reviewed, together with genetic resistance of the chicken. In long-term persistence of IBV, the caecal tonsil or kidney have been proposed as the sites of persistence. Antigenic variation among IBV strains is related to relatively small differences in amino acid sequences in the S1 spike protein. However, antigenic studies alone do not adequately define immunological relationships between strains and cross-immunisation studies have been used to classify IBV isolates into 'protectotypes'. It has been speculated that changes in the S1 protein may be related to differences in tissue tropisms shown by different strains. Perhaps in the future, new strains of IBV may arise which affect organs or systems not normally associated with IB.

Analysis of the serotype-specific epitopes of avian infectious bronchitis virus strains Ark99 and Mass41

The Ark and Mass serotype-specific epitopes of infectious bronchitis virus were studied by immunofluorescence and immunoprecipitation of mutant and recombinant spike glycoproteins (S protein) expressed in mouse L cells. Serotype-specific monoclonal antibodies could bind to the recombinant proteins of Ark99 and Mass41 expressed from the chimeras in which the N-terminal thirds of the S1 sequences were reciprocally exchanged. Therefore, it appears that the respective serotype-specific epitopes of both strains were localized within the C-terminal two-thirds of the S1 proteins. Deletion and insertion of a five-amino-acid fragment on the S1 proteins of Ark99 and Mass41, altered the serotype-specific epitopes. This result implies that the five-amino-acid insertion on the S1 protein of the Ark serotype was involved in determining the conformation of the protein, probably acting as a spacer. In addition, it appears that an interaction between sequences of the N-terminal third and the remaining portion of the S1 protein determines the tertiary structure of the protein as well as the conformation of the serotype-specific epitope.