Genetic diversity of avian infectious bronchitis virus in China in recent years

Assessing a respiratory toxic infectious bronchitis virus (IBV) strain: isolation, identification, pathogenicity, and immunological failure insights

Infectious bronchitis virus (IBV) is caused by avian coronavirus and poses a global economic threat to the poultry industry. In 2023, a highly pathogenic IBV strain, IBV/CN/GD20230501, was isolated and identified from chickens vaccinated with IBV-M41 in Guangdong, China. This study comprehensively investigated the biological characteristics of the isolated IBV strain, including its genotype, whole genome sequence analysis of its S1 gene, pathogenicity, host immune response, and serum non-targeted metabolomics. Through the analysis of the S1 gene sequence, serum neutralization tests, and comparative genomics, it was proven that IBV/CN/GD20230501 belongs to the GI-I type of strain and is serotype II. One alanine residue in the S1 subunit of the isolated strain was mutated into serine, and some mutations were observed in the ORF1ab gene and the terminal region of the genome. Animal challenge experiments using the EID50 and TCID50 calculations showed that IBV/CN/GD20230501 possesses strong respiratory pathogenicity, with early and long-term shedding of viruses and rapid viral spread. Antibody detection indicated that chickens infected with IBV/CN/GD20230501 exhibited delayed expression of early innate immune genes, while those infected with M41 showed rapid gene induction and effective viral control. Metabolomics analysis demonstrated that this virus infection led to differential expression of 291 ions in chicken serum, mainly affecting the citric acid cycle (tricarboxylic acid cycle).IMPORTANCEThis study identified an infectious bronchitis virus (IBV) strain isolated from vaccinated chickens in an immunized population that had certain sequence differences compared to IBV-M41, resulting in significantly enhanced pathogenicity and host defense. This strain has the potential to replace M41 as a more suitable challenge model for drug research. The non-targeted metabolomics analysis highlighting the citric acid cycle provides a new avenue for studying this highly virulent strain.

Protection Against Infectious Bronchitis Virus Vaccine Recombinants and Chicken-Selected Vaccine Subpopulations

Outbreaks of infectious bronchitis (IB) continue to occur from novel variants of IB virus (IBV) emerging from selection of vaccine subpopulations and/or naturally occurring recombination events. S1 sequencing of Arkansas (Ark) -type viruses obtained from clinical cases in Alabama broilers and backyard chickens shows both Ark Delmarva Poultry Industry (ArkDPI) vaccine subpopulations as well as Ark vaccine viruses showing recombination with other IB vaccine viruses. IB Ark-type isolates AL5, most similar to an ArkDPI vaccine subpopulation selected in chickens, AL4, showing a cluster of three nonsynonymous changes from ArkDPI subpopulations selected in chickens, and AL9, showing recombination with Massachusetts (Mass) -type IBV, were examined for pathogenicity and ability to break through immunity elicited by vaccination with a commercial ArkDPI vaccine. Analysis of predicted S1 protein structures indicated the changes were in regions previously shown to comprise neutralizing epitopes. Thus, they were expected to contribute to immune escape and possibly virulence. Based on clinical signs, viral load, and histopathology, all three isolates caused disease in naïve chickens, although AL9 and AL5 viral loads in trachea were statistically significantly higher (30- and 40-fold) than AL4. S1 gene sequencing confirmed the stability of the relevant changes in the inoculated viruses in the chickens, although virus in some individual chickens exhibited additional S1 changes. A single amino acid deletion in the S1 NTD was identified in some individual chickens. The location of this deletion in the predicted structure of S1 suggested the possibility that it was a compensatory change for the reduced ability of AL4 to replicate in the trachea of naïve chickens. Chickens vaccinated with a commercial ArkDPI vaccine at day of hatch and challenged at 21 days of age showed that vaccination provided incomplete protection against challenge with these viruses. Moreover, based on viral RNA copy numbers in trachea, differences were detected in the ability of the vaccine to protect against these IBV isolates, with the vaccine protecting the most poorly against AL4. These results provide additional evidence supporting that IBV attenuated vaccines, especially ArkDPI vaccines, contribute to perpetuating the problem of IB in commercial chickens.

A novel highly virulent nephropathogenic QX-like infectious bronchitis virus originating from recombination of GI-13 and GI-19 genotype strains in China

Infectious bronchitis virus (IBV) is one of the most widely spread RNA viruses, causing respiratory, renal, and intestinal damage, as well as decreased reproductive performance in hens, leading to significant economic losses in the poultry industry. In this study, a new IBV strain designated as CK/CH/GX/LA/071423 was successfully isolated from the 60-day-old Three-Yellow chicken vaccinated with H120 and QXL87 vaccines. The complete genome sequence analysis revealed that the CK/CH/GX/LA/071423 strain shared a high similarity of 96.7% with the YX10 strain belonging to the GI-19 genotype. Genetic evolution analysis based on the IBV S1 gene showed that the CK/CH/GX/LA/071423 isolate belonged to the GI-19 genotype. Recombination analysis of the virus genome using RDP and Simplot software indicated that CK/CH/GX/LA/071423 was derived from recombination events between the YX10 and 4/91 vaccine strains, which was supported by phylogenetic analysis using gene sequences from the 3 regions. Furthermore, the S1 protein tertiary structure differences were observed between the CK/CH/GX/LA/071423 and the QXL87 and H120 vaccine strains. Pathogenicity studies revealed that the CK/CH/GX/LA/071423 caused death and led to pale and enlarged kidneys with abundant urate deposits, indicative of a nephropathogenic IBV strain. High virus titers were detected in the trachea, kidneys, and cecal tonsils, demonstrating broad tissue tropism. Throughout the experimental period, the virus positive rate in throat swabs of the infected group reached to 100%. These findings highlight the continued predominance of the QX genotype IBV in Guangxi of China and the ongoing evolution of different genotypes through genetic recombination, raising concerns about the efficacy of current IBV vaccines in providing effective protection to poultry.

S2 subunit plays a critical role in pathogenesis of TW-like avian coronavirus infectious bronchitis virus

To investigate the critical role of the S gene in determining pathogenesis of TW-like avian infectious bronchitis virus (IBV), we generated two recombinant IBVs (rGDaGD-S1 and rGDaGD-S2) by replacing either the S1 or S2 region of GD strain with the corresponding regions from an attenuated vaccine candidate aGD strain. The virulence and pathogenicity of these recombinant viruses was assessed both in vitro and in vivo. Our results indicated the mutations in the S2 region led to decreased virulence, as evidenced by reduced virus replication in embryonated chicken eggs and chicken embryonic kidney cells as well as observed clinical symptoms, gross lesions, microscopic lesions, tracheal ciliary activity, and viral distribution in SPF chickens challenged with recombinant IBVs. These findings highlight that the S2 subunit is a key determinant of TW-like IBV pathogenicity. Our study established a foundation for future investigations into the molecular mechanisms underlying IBV virulence.

Avian infectious bronchitis virus (AIBV) review by continent

Infectious bronchitis virus (IBV) is a positive-sense, single-stranded, enveloped RNA virus responsible for substantial economic losses to the poultry industry worldwide by causing a highly contagious respiratory disease. The virus can spread quickly through contact, contaminated equipment, aerosols, and personal-to-person contact. We highlight the prevalence and geographic distribution of all nine genotypes, as well as the relevant symptoms and economic impact, by extensively analyzing the current literature. Moreover, phylogenetic analysis was performed using Molecular Evolutionary Genetics Analysis (MEGA-6), which provided insights into the global molecular diversity and evolution of IBV strains. This review highlights that IBV genotype I (GI) is prevalent worldwide because sporadic cases have been found on many continents. Conversely, GII was identified as a European strain that subsequently dispersed throughout Europe and South America. GIII and GV are predominant in Australia, with very few reports from Asia. GIV, GVIII, and GIX originate from North America. GIV was found to circulate in Asia, and GVII was identified in Europe and China. Geographically, the GVI-1 lineage is thought to be restricted to Asia. This review highlights that IBV still often arises in commercial chicken flocks despite immunization and biosecurity measures because of the ongoing introduction of novel IBV variants and inadequate cross-protection provided by the presently available vaccines. Consequently, IB consistently jeopardizes the ability of the poultry industry to grow and prosper. Identifying these domains will aid in discerning the pathogenicity and prevalence of IBV genotypes, potentially enhancing disease prevention and management tactics.

Antigenic Characterization of Infectious Bronchitis Virus in the South China during 2021-2022

Avian infectious bronchitis is a serious and highly contagious disease that is caused by the infectious bronchitis virus (IBV). From January 2021 to June 2022, 1008 chicken tissue samples were collected from various regions of southern China, and 15 strains of the IBV were isolated. Phylogenetic analysis revealed that the strains mainly comprised the QX type, belonging to the same genotype as the currently prevalent LX4 type, and identified four recombination events in the S1 gene, among which lineages GI-13 and GI-19 were most frequently involved in recombination. Further study of seven selected isolates revealed that they caused respiratory symptoms, including coughing, sneezing, nasal discharge, and tracheal sounds, accompanied by depression. Inoculation of chicken embryos with the seven isolates resulted in symptoms such as curling, weakness, and bleeding. Immunization of specific pathogen-free (SPF) chickens with inactivated isolates produced high antibody levels that neutralized the corresponding strains; however, antibodies produced by vaccine strains were not effective in neutralizing the isolates. No unambiguous association was found between IBV genotypes and serotypes. In summary, a new trend in IBV prevalence has emerged in southern China, and currently available vaccines do not provide protection against the prevalent IBV strains in this region, facilitating the continued spread of IBV.

Identification of Host Proteins Interacting with IBV S1 Based on Tracheal Organ Culture

Infectious bronchitis virus (IBV) belongs to the gamma-coronavirus genus of Coronaviridae and causes serious infectious diseases in the poultry industry. However, only a few IBV strains can infect avian passage cell lines, seriously hindering the progress of basic research on IBV pathogenesis. Whereas IBV field strains can replicate in tracheal ring organ culture (TOC) without any previous adaptation in chicken embryos or primary cells. In this study, to investigate the potential use of TOC as an in vitro infection model for the study of IBV-host interaction, we first established a chicken embryo TOC culture system and carried out an investigation on the IBV replication kinetics in the system. We found that the selected strains of the IBV GI-1, GI-7, GI-13, GI-19, and GI-22 genotypes could successfully replicate in TOC and bring about damage to the infected trachea. Next, we identified host proteins of the chicken embryo trachea that interact with the IBV S1 protein by immunoprecipitation and protein mass spectrometry. A total of 127 candidate proteins were initially identified with major involvement in cell adhesion pathways and apoptosis- and autophagy-related pathways. The heat shock protein 70 (HSP70) was selected for further investigation in the interaction with IBV viral proteins. Our results showed that HSP70 interacted with IBV S1 in both TOC and CEK cells, whereas HSP70 overexpression inhibited viral replication. This study indicates that TOC is a good system for the elucidation of IBV-host interactions and HSP70 is a potential host antiviral factor.

Which strain of the avian coronavirus vaccine will become the prevalent one in China next?

Infectious bronchitis virus (IBV) is a vital pathogen in poultry farms, which can induce respiratory, nephropathogenic, oviduct, proventriculus, and intestinal diseases. Based on the phylogenetic classification of the full-length S1 gene, IBV isolates have been categorized into nine genotypes comprising 38 lineages. GI (GI-1, GI-2, GI-3, GI-4, GI-5, GI-6, GI-7, GI-13, GI-16, GI-18, GI-19, GI-22, GI-28, and GI-29), GVI-1 and GVII-1 have been reported in China in the past 60 years. In this review, a brief history of IBV in China is described, and the current epidemic strains and licensed IBV vaccine strains, as well as IBV prevention and control strategies, are highlighted. In addition, this article presents unique viewpoints and recommendations for a more effective management of IBV. The recombinant Newcastle Disease virus (NDV) vector vaccine expressed S gene of IBV QX-like and 4/91 strains may be the dominant vaccine strains against NDV and IBV.

Insights on genetic characterization and pathogenesis of a GI-19 (QX-like) infectious bronchitis virus isolated in China

Infectious bronchitis virus (IBV) causes respiratory diseases in chickens, incurring great losses to the poultry industry worldwide. In this study, we isolated an IBV strain, designated as AH-2020, from the chickens vaccinated with H120 and 4/91 in Anhui, China. The sequence homology analysis based on the S1 gene revealed that AH-2020 shares low similarities with the 3 vaccine strains, namely, H120, LDT3-A, and 4/91 (78.19, 80.84, and 81.6%, respectively). Phylogenetic analysis based on the S1 gene revealed that AH-2020 clustered with the GI-19 type. Furthermore, protein modeling revealed that the mutations in the amino acids in AH-2020 were mainly located in the N-terminal domain of S1 (S1-NTD), and the pattern of deletion and insertion mutations in the S1 protein may have influenced the structural changes on the surface of S1. Further, approximately 7-day-old SPF chickens were inoculated with AH-2020 at 10^6.0 EID₅₀. These chickens exhibited clinical signs of the infection such as listlessness, huddling, and head-shaking, accompanied by depression and 40% mortality. Serum antibody test demonstrated that in response to the AH-2020 infection, the antibody level increased the fastest at 7 dpi, with virus shedding rate of cloaca being 100% at 14 dpi. The viral titer in various tissues was detected using hematoxylin and eosin staining and immunohistochemistry, which revealed that AH-2020 infection can damage the kidney, trachea, lung, cecal tonsil, and bursa of Fabricius. Our study provided evidence that the GI-19-type IBV is undergoing more complex mutations, and effective measures are urgently needed to prevent the spread of these variant strains.

Development of SYBR green RT-qPCR assay for titrating bivalent live infectious bronchitis vaccines

Infectious bronchitis (IB) is a highly contagious viral disease of chickens caused by IB virus (IBV) that can cause substantial economic losses in the poultry industry. IBV variant infections have been continuously reported since the initial description in the 1930s. QX-like IBVs are the predominant circulating genotype globally. A homologous QX vaccine has superior protection efficacy compared with that of other available vaccines, and the combination of Massachusetts (Mass)-like and QX-like strains is being used to combat QX-like IBV infections. Inoculation of embryonated chicken eggs is the standard method for the titration of IBV, and the titer is expressed as 50% egg infectious dose (EID₅₀)_. However, this method cannot effectively distinguish or quantify different genotypic strains in a mixture of different viruses, especially in the absence of neutralizing monoclonal antibodies. In this study, quantitative real-time PCR (RT-qPCR) was applied using specific primers for the QX- and Mass-like strains to quantitate IBV infection and for comparison with the conventional virus titration quantitative method. A strong positive correlation was observed between RT-qPCR cycle threshold values and the different EID₅₀ concentrations. This method was further used to titrate bivalent IB vaccines, and the amount of individual genotype virus was determined based on specific primers. Thus, this RT-qPCR assay may be used as a highly specific, sensitive, and rapid alternative to the EID₅₀ assay for titering IBVs.

Pathogenicity evaluation of GVI-1 lineage infectious bronchitis virus and its long-term effects on reproductive system development in SPF hens

Infectious bronchitis virus (IBV) has gained increasing attention in the poultry industry due to its ability to cause tissue injuries not only in the respiratory system and kidney but also in the reproductive system of layers. Recently, the GVI-1 lineage IBVs have spread widely in China, whereas their pathogenicity in egg-laying chickens has rarely been studied, especially its long-term influence in egg production upon the early infection in chicks. In this study, 10-day-old SPF chicks were infected with the GVI-1 lineage JX181 strain and monitored over a 170-day period after infection. The pathogenicity evaluation of the JX181 strain included clinical observations, immunohistochemical assay, viral load, viral shedding, gross autopsy, and laying rate. The results showed that JX181 has a high pathogenicity, causing severe system lesions, and the decrease in egg production. In summary, this study describes the long-term damages caused by the early infection with the IBV GVI-1 lineage on the reproductive system of hens, providing a comprehensive understanding of the pathogenicity of the IBV GVI-1 lineage and emphasizing the importance of its early prevention.

Molecular Characterization Analysis of Prevalent Infectious Bronchitis Virus and Pathogenicity Assessment of Recombination Strain in China

Avian coronavirus infectious bronchitis virus (IBV) is a respiratory pathogen of chickens, resulting in severe economic losses in the poultry industry. This study aimed to monitor and isolate the molecular identity of IBV in broiler flocks with respiratory symptoms in eight provinces of China. In total, 910 samples (oropharyngeal and cloacal mixed swabs) from broiler flocks showed IBV positive rates of 17.6% (160/910) using PCR assay. Phylogenetic analysis of the complete S1 genes of 160 IBV isolates was performed and revealed that QX-type (GI-19), TW-type (GI-7), 4/91-type (GI-13), HN08-type (GI-22),TC07-2-type (GVI-1), and LDT3-type (GI-28) exhibited IBV positive rates of 58.15, 25, 8.12, 1.86, 5.62, and 1.25%. In addition, recombination analyses revealed that the four newly IBV isolates presented different recombination patterns. The CK/CH/JS/YC10-3 isolate likely originated from recombination events between strain YX10 (QX-type) and strain TW2575-98 (TW-type), the pathogenicity of which was assessed, comparing it with strain GZ14 (TW-type) and strain CK/CH/GD/JR07-7 (QX-type). The complete S1 gene data from these isolates indicate that IBV has consistently evolved through genetic recombination or mutation, more likely changing the viral pathogenicity and leading to larger outbreaks in chick populations, in China.

Phylogenetic and Spatiotemporal Analyses of the Complete Genome Sequences of Avian Coronavirus Infectious Bronchitis Virus in China During 1985-2020: Revealing Coexistence of Multiple Transmission Chains and the Origin of LX4-Type Virus

Infectious bronchitis (IB) virus (IBV) causes considerable economic losses to poultry production. The data on transmission dynamics of IBV in China are limited. The complete genome sequences of 212 IBV isolates in China during 1985–2020 were analyzed as well as the characteristics of the phylogenetic tree, recombination events, dN/dS ratios, temporal dynamics, and phylogeographic relationships. The LX4 type (GI-19) was found to have the highest dN/dS ratios and has been the most dominant genotype since 1999, and the Taiwan-I type (GI-7) and New type (GVI-1) showed an increasing trend. A total of 59 recombinants were identified, multiple recombination events between the field and vaccine strains were found in 24 isolates, and the 4/91-type (GI-13) isolates were found to be more prone to being involved in the recombination. Bayesian phylogeographic analyses indicated that the Chinese IBVs originated from Liaoning province in the early 1900s. The LX4-type viruses were traced back to Liaoning province in the late 1950s and had multiple transmission routes in China and two major transmission routes in the world. Viral phylogeography identified three spread regions for IBVs (including LX4 type) in China: Northeastern China (Heilongjiang, Liaoning, and Jilin), north and central China (Beijing, Hebei, Shanxi, Shandong, and Jiangsu), and Southern China (Guangxi and Guangdong). Shandong has been the epidemiological center of IBVs (including LX4 type) in China. Overall, our study highlighted the reasons why the LX4-type viruses had become the dominant genotype and its origin and transmission routes, providing more targeted strategies for the prevention and control of IB in China.

Molecular characterization of infectious bronchitis virus in Southwestern China for the protective efficacy evaluation of four live vaccine strains

The high mutation rate of infectious bronchitis virus (IBV) poses a significant threat to the protective efficacy of vaccines. This study aimed at analyzing the S1 genes of IBV field strains isolated in Southwestern China from 2018 to 2020, assessing the pathogenicity of four dominating strains, and evaluating the protective efficacy of four commercial vaccine strains against the endemic representative strains. Thirty-two field strains of IBV were isolated in Southwestern China from 2018 to 2020. Phylogenetic analysis of their S1 genes revealed the nucleotide homology ranged from 64.6% to 100%, and belonged to five genotypes [GI-19 (QX, 53.13%), GI-28 (LDT3-A,15.63%), GI-7 (TW, 12.50%), GI-1 (Mass, 6.23%), GVI-1 (TC07-2, 6.25%)], and two variant groups [variant-3 (3.13%) and variant-5 (3.13%)]. Recombination events between field and vaccine strains or between field strains were identified in the S1 genes of eight IBV field strains. The CK/CH/YNKM/191128 and CK/CH/CQBS/191203 strains of GI-19 showed morbidity rates of 66.7% and 73.7%, respectively, and mortality rates of 13.3% and 33.3%, respectively. Besides, the CK/CH/SCYC/191030 and CK/CH/GZGY/191021 strains of GI-28 caused morbidity rates of 60% and 86.7%, respectively, and mortality rates of 33.3%. The protective efficacy of the four commercial live vaccine strains (4/91, FNO-E55, LDT3-A, and QXL87) ranged from 70% - 100% and reduced tissue lesions against CK/CH/GZGY/191021 and CK/CH/CQBS/191203 strains. LDT3-A strain was the most effective one but still could not completely prohibit IBV shedding. These findings provide a reference for IBV molecular evolution analysis and control of IB.

Identification of Novel T-Cell Epitopes on Infectious Bronchitis Virus N Protein and Development of a Multi-epitope Vaccine

Cellular immune responses play a key role in the control of viral infection. The nucleocapsid (N) protein of infectious bronchitis virus (IBV) is a major immunogenic protein that can induce protective immunity. To screen for potential T-cell epitopes on IBV N protein, 40 overlapping peptides covering the entirety of the N protein were designed and synthesized. Four T-cell epitope peptides were identified by gamma interferon (IFN-γ) enzyme-linked immunosorbent spot (ELISpot), intracellular cytokine staining, and carboxyfluorescein succinimidyl ester (CFSE) lymphocyte proliferation assays; among them, three peptides (N_211-230, N_271-290, and N_381-400) were cytotoxic T lymphocyte (CTL) epitopes, and one peptide (N_261-280) was a dual-specific T-cell epitope, which can be recognized by both CD8⁺ and CD4⁺ T cells. Multi-epitope gene transcription cassettes comprising four neutralizing epitope domains and four T-cell epitope peptides were synthesized and inserted into the genome of Newcastle disease virus strain La Sota between the P and M genes. Recombinant IBV multi-epitope vaccine candidate rLa Sota/SBNT was generated via reverse genetics, and its immune protection efficacy was evaluated in specific-pathogen-free chickens. Our results show that rLa Sota/SBNT induced IBV-specific neutralizing antibody and T-cell responses and provided significant protection against homologous and heterologous IBV challenge. Thus, the T-cell epitope peptides identified in this study could be good candidates for IBV vaccine development, and recombinant Newcastle disease virus-expressing IBV multi-epitope genes represent a safe and effective vaccine candidate for controlling infectious bronchitis. IMPORTANCE T-cell-mediated immune responses are critical for the elimination of IBV-infected cells. To screen conserved T-cell epitopes in the IBV N protein, 40 overlapping peptides covering the entirety of the N protein were designed and synthesized. By combining IFN-γ ELISpot, intracellular cytokine staining, and CFSE lymphocyte proliferation assays, we identified three CTL epitopes and one dual-specific T-cell epitope. The value of T-cell epitope peptides identified in the N protein was further verified by the design of an IBV multi-epitope vaccine. Results show that IBV multi-epitope vaccine candidate rLa Sota/SBNT provided cross protection against challenges with a QX-like or a TW-like IBV strain. So, T-cell-mediated immune responses play an important role in the control of viral infection, and conserved T-cell epitopes serve as promising candidates for use in multi-epitope vaccine construction. Our results provide a new perspective for the development of a safer and more effective IBV vaccine.

Two newly isolated GVI lineage infectious bronchitis viruses in China show unique molecular and pathogenicity characteristics

During 2016 to 2020, GVI-1 type infectious bronchitis virus (IBV) strains were sporadically reported across China, indicating a new epidemic trend of the virus. Here we investigated the molecular characteristics and pathogenicity of two newly isolated GVI-1 type IBV virus strains (CK/CH/TJ1904 and CK/CH/NP2011) from infected chicken farms in China. Genetic evolution analysis of the S1 gene showed the highest homology with the GVI-1 representative strain, TC07-2. Phylogenetic analysis and recombination analysis of the virus genomes indicated that newly isolated strains in China may be independently derived from recombination events that occurred between GI-19 and GI-22 strains and early GVI-1 viruses. Interestingly, unlike the deduced parental GI-19 or GI-22 strains, CK/CH/TJ1904 and CK/CH/NP2011 showed affinity for the trachea rather than the kidney and were less pathogenic. This difference may be because of recombination events that occurred during the long co-existence of the GVI-1 viruses with prevalent GI-19 and GI-22 strains. Considering the new trend, it is very important to permanently monitor circulating strains and to develop new vaccines to counteract emerging new-type IBVs.

Infectious bronchitis virus in Australia: a model of coronavirus evolution - a review

Infectious bronchitis virus (IBV) was first isolated in Australia in 1962. Ongoing surveillance and characterization of Australian IBVs have shown that they have evolved separately from strains found throughout the rest of the world, resulting in the evolution of a range of unique strains and changes in the dominant wild-type strains, affecting tissue tropism, pathogenicity, antigenicity, and gene arrangement. Between 1961 and 1976 highly nephropathogenic genotype GI-5 and GI-6 strains, causing mortalities of 40% to 100%, predominated, while strains causing mainly respiratory disease, with lower mortality rates, have predominated since then. Since 1988, viruses belonging to two distinct and novel genotypes, GIII and GV, have been detected. The genome organization of the GIII strains has not been seen in any other gammacoronavirus. Mutations that emerged soon after the introduction of vaccination, incursion of strains with a novel lineage from unknown sources, recombination between IBVs from different genetic lineages, and gene translocations and deletions have contributed to an increasingly complex IBV population. These processes and the consequences of this variation for the biology of these viruses provide an insight into the evolution of endemic coronaviruses during their control by vaccination and may provide a better understanding of the potential for evolution of other coronaviruses, including SARS-CoV-2. Furthermore, the continuing capacity of attenuated IBV vaccines developed over 40 years ago to provide protection against viruses in the same genetic lineage provides some assurance that coronavirus vaccines developed to control other coronaviruses may continue to be effective for an extended period.

Genomic Analysis of Avian Infectious Bronchitis Viruses Recently Isolated in South Korea Reveals Multiple Introductions of GI-19 Lineage (QX Genotype)

Infectious bronchitis virus (IBV) was first identified in the 1930s and it imposes a major economic burden on the poultry industry. In particular, GI-19 lineage has spread globally and has evolved constantly since it was first detected in China. In this study, we analyzed S1 gene sequences from 60 IBVs isolated in South Korea. Two IBV lineages, GI-15 and GI-19, were identified in South Korea. Phylogenetic analysis suggested that there were six distinct subgroups (KM91-like, K40/09-like, and QX-like I to IV) of the South Korean GI-19 IBVs. Among them, QX-type III and IV subgroups, which are phylogenetically different from those reported in South Korea in the past, accounted for more than half of the total. Moreover, the phylogeographic analysis of the QX-like subgroups indicated at least four distinct introductions of GI-19 IBVs into South Korea during 2001–2020. The efficacy of commercialized vaccines against the recently introduced QX-like subgroups should be verified, and continuous international surveillance efforts and quarantine procedures should be enhanced to prevent the incursion of viruses.

Genetic and pathogenic characterization of a novel recombinant avian infectious bronchitis virus derived from GI-1, GI-13, GI-28, and GI-19 strains in Southwestern China

Avian infectious bronchitis (IB), caused by avian infectious bronchitis virus (IBV), is an acute and highly contagious disease that is extremely harmful to the poultry industry throughout the world. The cross-using of different attenuated live vaccine strains has led to the occurrence of diverse IBV serotypes. In this study, we isolated an IBV strain from a chicken farm in southwest China and designated it CK/CH/SCMY/160315. Construction of a phylogenetic tree based on full S1 gene sequence analysis suggested that CK/CH/SCMY/160315 bears similarity to GI-28, and further comparison of S1 amino acid residues revealed that CK/CH/SCMY/160315 showed mutations and deletions in many key positions between LDT3-A and other GI-28 reference strains. Importantly, CK/CH/SCMY/160315 was identified as a novel recombinant virus derived from live attenuated vaccine strains H120 (GI-1), 4/91 (GI-13), LDT3-A (GI-28), and the field strain LJL/08-1 (GI-19), identifying at least 5 recombination sites in both structural and accessory genes. Pathogenicity analysis indicated that CK/CH/SCMY/160315 caused listlessness, sneezing, huddling, head shaking, and increased antibody levels in the inoculated chickens. To further describe pathogenicity of this novel strain, we assessed viral load in different tissues and conducted hematoxylin and eosin (HE) staining of the trachea, lungs and kidneys. Our results provide evidence for the continuing evolution of IBV field strains via genetic recombination and mutation, leading to outbreaks in the vaccinated chicken populations in China.

Amachawadi R, Dash AP, Yadav MP, Prasad KS, P S, Jain AS, Shivamallu C. COVID-19 PANDEMIC: A SYSTEMATIC REVIEW ON THE CORONAVIRUSES OF ANIMALS AND SARS-CoV-2

Coronaviruses (CoVs), classified into four genera, viz., alpha-, beta-, gamma-, and Delta- CoV, represent an important group of diverse transboundary pathogens that can infect a variety of mammalian and avian species including humans, animals, poultry, and non-poultry birds. CoVs primarily infect lung and gut epithelial cells, besides monocytes and macrophages. CoVs have high mutation rates causing changes in host specificity, tissue tropism, and mode of virus excretion and transmissions. The recent CoV zoonoses are SARS, MERS, and COVID-19 that are caused by the transmission of beta-CoVs of bats to humans. Recently, reverse zoonoses of the COVID-19 virus have been detected in dogs, tigers, and minks. Beta-CoV strains also infect bovine (BCoV) and canine species (CRCoV); both these beta-CoVs might have originated from a common ancestor. Despite the high genetic similarity between BCoV, CRCoV, and HCoV-OC43, these differ in species specificity. Alpha-CoV strains infect canine (CCoV), feline (FIPV), swine (TGEV and PEDV), and humans (HCoV229E and NL63). Six coronavirus species are known to infect and cause disease in pigs, seven in human beings, and two in dogs. The high mutation rate in CoVs is attributed to error-prone 3′-5′ exoribonuclease (NSP 14), and genetic recombination to template shift by the polymerase. The present compilation describes the important features of the CoVs and diseases caused in humans, animals, and birds that are essential in surveillance of diverse pool of CoVs circulating in nature, and monitoring interspecies transmission, zoonoses, and reverse zoonoses.

Identification and analysis of long non-coding RNAs and mRNAs in chicken macrophages infected with avian infectious bronchitis coronavirus

BACKGROUND

Avian infectious bronchitis virus (IBV) is a gamma coronavirus that severely affects the poultry industry worldwide. Long non-coding RNAs (lncRNAs), a subset of non-coding RNAs with a length of more than 200 nucleotides, have been recently recognized as pivotal factors in the pathogenesis of viral infections. However, little is known about the function of lncRNAs in host cultured cells in response to IBV infection.

RESULTS

We used next-generation high throughput sequencing to reveal the expression profiles of mRNAs and lncRNAs in IBV-infected HD11 cells. Compared with the uninfected cells, we identified 153 differentially expressed (DE) mRNAs (106 up-regulated mRNAs, 47 down-regulated mRNAs) and 181 DE lncRNAs (59 up-regulated lncRNAs, 122 down-regulated lncRNAs) in IBV-infected HD11 cells. Moreover, gene ontology (GO) and pathway enrichment analyses indicated that DE mRNAs and lncRNAs were mainly involved in cellular innate immunity, amino acid metabolism, and nucleic acid metabolism. In addition, 2640 novel chicken lncRNAs were identified, and a competing endogenous RNA (ceRNAs) network centered on gga-miR-30d and miR-146a-5p was established.

CONCLUSIONS

We identified expression profiles of mRNAs and lncRNAs during IBV infection that provided new insights into the pathogenesis of IBV.

Design and Characterization of a DNA Vaccine Based on Spike with Consensus Nucleotide Sequence against Infectious Bronchitis Virus

Avian coronavirus infectious bronchitis virus (IBV) causes severe economic losses in the poultry industry, but its control is hampered by the continuous emergence of new genotypes and the lack of cross-protection among different IBV genotypes. We designed a new immunogen based on a spike with the consensus nucleotide sequence (S_con) that may overcome the extraordinary genetic diversity of IBV. S_con was cloned into a pVAX1 vector to form a new IBV DNA vaccine, pV-S_con. pV-S_con could be correctly expressed in HD11 cells with corresponding post-translational modification, and induced a neutralizing antibody response to the Vero-cell-adapted IBV strain Beaudette (p65) in mice. To further evaluate its immunogenicity, specific-pathogen-free (SPF) chickens were immunized with the pV-S_con plasmid and compared with the control pVAX1 vector and the H120 vaccine. Detection of IBV-specific antibodies and cell cytokines (IL-4 and IFN-γ) indicated that vaccination with pV-S_con efficiently induced both humoral and cellular immune responses. After challenge with the heterologous strain M41, virus shedding and virus loading in tissues was significantly reduced both by pV-S_con and its homologous vaccine H120. Thus, pV-S_con is a promising vaccine candidate for IBV, and the consensus approach is an appealing method for vaccine design in viruses with high variability.

Genotyping of infectious bronchitis viruses isolated in Japan during 2008-2019

Seventeen isolates of infectious bronchitis virus (IBV) were obtained from various prefectures of Japan during 2008-2019 and genetically analyzed. The IBV isolates were classified into six genetic groups, based on phylogenetic analysis of the S1 gene. The S1 genotypes were distinguishable by a newly developed restriction fragment length polymorphism (RFLP) method using three endonucleases, Hae II, Hpa I, and Fok I. Moreover, the isolates were classified into four genetic groups, based on phylogenetic analysis of the S2 gene. However, novel genetic groups based on a combination of S1 and S2 genotypes, which were undetected previously, were confirmed in this study, indicating that various recombinant IBV strains were prevalent in poultry in Japan.

Phylogenetic analysis of infectious bronchitis virus circulating in southern China in 2016-2017 and evaluation of an attenuated strain as a vaccine candidate

Avian infectious bronchitis (IB) is a highly contagious viral respiratory disease, caused by infectious bronchitis virus (IBV), that poses an important economic threat to the poultry industry. In recent years, genotypes GI-7, GI-13, and GI-19 have been the most prevalent IBV strains in China. However, in this study, we found that most IBV strains from southern China in 2016-2017 belonged to genotype GVI-1. This genotype, for which there is no vaccine, has been reported sporadically in the region. The GDTS13 strain, which caused severe IB outbreaks on the farms where it was isolated, was evaluated as a candidate vaccine strain. GDTS13 was serially passaged in specific-pathogen-free embryonated chicken eggs for 100 generations to produce GDTS13-F100. Safety testing indicated that GDTS13-F100 had no pathogenic effect on chickens. Additionally, GDTS13-F100 showed an excellent protective effect against GDTS13, with no clinical signs or virus shedding observed in immunized chickens challenged with the parent strain. These findings indicate that GVI-1 has become the most prevalent IBV genotype in southern China and that GDTS13-F100 may serve as an attenuated vaccine to protect against infection with this genotype.

Genetic, Antigenic, and Pathogenic Characteristics of Infectious Bronchitis Virus GI-7/TW-II in China

Nine infectious bronchitis virus (IBV) strains belonging to the GI-7 lineage were isolated between 2009 and 2017 in China. Phylogenetic analysis and comparisons of full-length sequences of the S1 gene suggested that the GI-7 lineage should be further classified as Taiwan (TW)-I and TW-II sublineages, which correspond to the previous TW-I and TW-II genotypes. The nine IBV strains were clustered in the TW-II sublineage. Further investigation revealed that viruses in the TW-I and TW-II were not only genetically but also antigenically different. Moreover, the TW-II sublineage contained various clades and recombinants. A recombinant was found to originate from recombination events between field strains (TW-II ck/CH/LJL/090608- and GI-19 ck/ CH/LDL/091022-like viruses) in which the recombination in the S1 subunit coding sequences had led to changes in antigenicity of the viruses. A more in-depth investigation demonstrated that TW-II viruses appear to have undergone a significant evolution following introduction in mainland China, which resulted in the viruses diverging into different clades. The viruses between the different clades in TW-II sublineage exhibited a significant change in genetic and antigenic characteristics. In addition, the five TW-II viruses selected on the basis of the results of S1 nucleotide sequence phylogenetic trees showed different pathogenicity to specific-pathogen-free chickens, although they could induce nephritis in the infected chickens and thus were identified as nephropathogenic strains.

Genetic and antigenic heterogeneity of GI-1/Massachusetts lineage infectious bronchitis virus variants recently isolated in China

Four GI-1/Massachusetts-type (GI-1/Mass-type) infectious bronchitis virus (IBV) strains were isolated and the complete genomes of these isolates, coupled with the Mass-type live-attenuated vaccine H120 and the Mass-type pathogenic M41 strains, were sequenced in the present study. Our results show that isolates LJL/140820 and I0306/17 may be derived from the Ma5 (another Mass-type live-attenuated vaccine strain) and H120 vaccine strains, respectively. The I1124/16 strain was found to be a M41 variant that likely resulted from nucleotide accumulated mutations in the genome. Consistently, the results of the virus neutralization test showed that isolate I1124/16 was antigenically related but slight different from the M41. Our results from the protection experiments pointed out that chickens immunized with H120 failed to eliminate viral shedding after infection with the isolate I1124/16, which was different from that of M41; this result was consistent to the field observation and further implicated that the variant IBV isolate I1124/16 was antigenic different from the M41 strain. Furthermore, the I1124/16 was found to have comparable but slightly lower pathogenicity with the M41 strain. More studies based on the reverse genetic techniques are needed to elucidate the amino acids in the S1 subunit of spike protein contributing to the altered antigenicity of the isolate I1124/16. In addition, an IBV isolate, LJL/130609, was found to be originated from recombination events between the I1124/16- and Connecticut-like strains. Our results from the virus neutralization test also showed that isolates LJL/130609 and I1124/16 were antigenic closely related. Hence, there are at least 3 different genetic evolution patterns for the circulation of the GI-1/Mass-type IBV field strains in China. The differences of vaccines used, the field conditions and genetic pressures between different flocks, likely account for the emergence, evolution patterns, and characteristics of the Mass-type IBV strains.

A highly pathogenic GI-19 lineage infectious bronchitis virus originated from multiple recombination events with broad tissue tropism

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The GI-19 strain was shown to be the dominant IBV lineage worldwide.

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Isolate I0305/19 belongs to GI-19 lineage.

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Isolate I0305/19 emerged through recombination events.

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Isolate I0305/19 is a highly nephropathogenic strain.

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Isolate I0305/19 showed broad tissue tropism in infected chickens.

In the present study, an IBV strain I0305/19 was isolated from a diseased commercial broiler flock in 2019 in China with high morbidity and mortality. The isolate I0305/19 was clustered together with viruses in sublineage D of GI-19 lineage on the basis of the complete S1 sequence analysis. Isolate I0305/19 and other GI-19 viruses isolated in China have the amino acid sequence MIA at positions 110–112 in the S protein. Further analysis based on the complete genomic sequence showed that the isolate emerged through at least four recombination events between GI-19 ck/CH/LJS/120848- and GI-13 4/91-like strains, in which the S gene was found to be similar to that of the GI-19 ck/CH/LJS/120848-like strain. Pathological assessment showed the isolate was a nephropathogenic IBV strain that caused high morbidity of 100 % and mortality of 80 % in 1-day-old specific-pathogen-free (SPF) chicks. The isolate I0305/19 exhibited broader tropisms in different tissues, including tracheas, lungs, bursa of Fabricius, spleen, liver, kidneys, proventriculus, small intestines, large intestines, cecum, and cecal tonsils. Furthermore, subpopulations of the virus were found in tissues of infected chickens; this finding is important in understanding how the virulent IBV strains can potentially replicate and evolve to cause disease. This information is also valuable for understanding the mechanisms of replication and evolution of other coronaviruses such as the newly emerged SARS-CoV-2.

Epidemiological investigation of avian infectious bronchitis and locally determined genotype diversity in central China: a 2016-2018 study

Infectious bronchitis (IB), caused by avian IB virus (IBV), is an acute and highly contagious disease of chickens. From 2016 to 2018, 56 IBV strains were isolated and identified from clinical samples obtained from various chicken farms located in central China. The S1 sequencing of these strains revealed nucleotide and amino acid identities of 70.2 to 100% and 62.6 to 100%, respectively, compared with those of reference strains. Phylogenetic analysis indicated that the genotypes of the isolates included GI-13 (4/91), GI-7 (TW-I), GI-24 (Mass), GI-19 (QX), and GI-18 (LDT3-A), with GI-19 (QX) being the predominant genotype. Meanwhile, GI-13 (4/91) was the second most dominant genotype in Henan Province, whereas it was GI-7 (TW-I) in Hunan and Hubei provinces. Recombination analysis of 3 variant strains showed that CK/CH/HeN/20160113 might be a recombination of LDT3-A- and QX-type strains and that CK/CH/HeN/20160316 might be a recombination of Italy-02-type strain and CK-CH-LJS08II. The predicted tertiary structure between CK/CH/HeN/20160113 and LDT3-A-type strain revealed that the novel 336 (L-P) and 455 (S-A) mutations changed the structure from an alpha helix to a random crimp. In addition, the 275 (Y-F) site reduced the length of the β-sheet, whereas the site 353 (A-T) extended the β-sheet. These findings suggested that GI-19 (QX) remains the predominant genotype in central China, and a locally determined complex genotype associated with variable clinical symptoms exists related to gene recombination and mutations.

Multiple recombination events between field and vaccine strains resulted in the emergence of a novel infectious bronchitis virus with decreased pathogenicity and altered replication capacity

In this study, we isolated and identified 2 infectious bronchitis virus (IBV) strains from layer chickens soon after vaccination with the Massachusetts-Connecticut bivalent vaccine (Conn) and H120 and 4/91 booster vaccines in China in 2011. The results of cross-virus-neutralization tests and phylogenetic analysis of the S1 subunit of spike gene of these vaccine strains and other reference strains showed that strain LJL/110302 was of GI-19 lineage, whereas LLN/111169 was of the GI-1 lineage of the Conn serotype. Further comparative genomic analysis revealed that LLN/111169, an IBV strain with novel traits, originated from multiple recombination events (at least 3 recombination sites) between GI-19 and the Conn and 4/91 vaccine strains. LLN/111169 was pathogenic to specific pathogen-free (SPF) chickens. This is of prime importance because while IBV prevention measures worldwide are mainly dependent on modified live vaccine strains, our results showed that recombination between field and vaccine strains has produced a novel pathogenic IBV strain. In addition, LLN/111169 showed relatively broad tissue tropism (trachea, lungs, kidneys, and cecal tonsils) in infected SPF chickens. These results emphasize the importance of IBV surveillance in chicken flocks.

Genetic characterization of infectious bronchitis viruses in Thailand, 2014-2016: identification of a novel recombinant variant

Infectious bronchitis (IB) causes severe economic losses to the poultry industry worldwide owing to frequent emergence of novel infectious bronchitis virus (IBV) variants, which potentially affect the effectiveness of the currently used IBV vaccine. Therefore, continuous monitoring of IBV genotypes and lineages recently circulating in chickens worldwide is essential. In this study, we characterized the complete S1 gene from 120 IBVs circulating in chickens in Thailand from 2014 to 2016. Phylogenetic analysis of the complete S1 gene of 120 Thai IBVs revealed that the 2014–2016 Thai IBVs were divided into 3 lineages (GI-1, GI-13, and GI-19) and a novel IBV variant. Our results also showed that GI-19 lineage has become the predominant lineage of IBV circulating in chicken flocks in Thailand from 2014 to 2016. It is interesting to note that a novel IBV variant, which was genetically different from the established IBV lineages, was identified in this study. The recombination analysis demonstrated that this novel IBV variant was a recombinant virus, which was originated from the GI-19 and GI-13 lineage viruses. In conclusion, our data demonstrate the circulation of different lineages of IBV and the presence of a novel recombinant IBV variant in chicken flocks in Thailand. This study highlights the high genetic diversity and continued evolution of IBVs in chickens in Thailand, and the importance of continued IBV surveillance for effective control and prevention of IB.

A novel low virulent respiratory infectious bronchitis virus originating from the recombination of QX, TW and 4/91 genotype strains in China

In China, variants of infectious bronchitis virus (IBV) evolve continually and diverse recombinant strains have been reported. Here, an IBV strain, designated as ck/CH/LJX/2017/07 (referred as JX17) was isolated from chicken vaccinated with H120 and 4/91 in Jiangxi, China, in 2017. Sequence analysis reveals of the S1 gene of JX17 the highest nucleotide identity of 98.15% with that of GI-7 genotype TW2575/98 strain. Furthermore, whole genome analysis among JX17 and other 18 IBV strains demonstrates that JX17 has the highest nucleotide identity of 95.94% with GI-19 genotype YX10 strain. Among all genes of JX17 except the S1 gene, the N gene and 3' UTR have the highest identity to GI-13 genotype 4/91 strain and the rest genes are the most identical to GI-19 genotype YX10 strain. Analyzed by the RDP and SimPlot, the recombination of JX17 strain was shown to occur in regions which include 5'-terminal S1 gene (20,344 to 22,447 nt), most N gene and 3' UTR (26,163 to 27,648 nt). The pathogenicity study shows that JX17 is a natural low virulent IBV variant which caused respiratory symptoms but no death. Taken together, these results indicate that IBV strains continue to evolve through genetic recombination and three prevalent genotypes in China including QX, TW and 4/91 have started to recombine.

Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure

The high mutation rates of infectious bronchitis virus (IBV) pose economic threats to the poultry industry. In order to track the genetic evolutionary of IBV isolates circulating in yellow chickens, we continued to conduct the genetic analyses of the structural genes S1, E, M, and N from 64 IBV isolates in southern China during 2009–2017. The results showed that the dominant genotypes based on the four genes had changed when compared with those during 1985–2008. Based on the S1 gene phylogenetic tree, LX4-type (GI-19) was the most dominant genotype, which was different from that during 1985–2008. The second most dominant genotype was LDT3-A-type, but this genotype disappeared after 2012. New-type 1 (GVI-1) isolates showed increasing tendency and there were four aa (QKEP) located in the hypervariable region (HVR) III and one aa (S) insertion in all the New-type 1 isolates. Both the analyses of amino acid entropy and molecular evolutionary rate revealed that the variations from large to small were S1, E, M, and N. Purifying selection was detected in the S1, E, M, and N gene proteins, which was different from the positive selection during 1985–2008. Six isolates were confirmed to be recombinants, possibly generated from a vaccine virus of the 4/91-type or LDT3-A-type and a circulating virus. The estimated times for the most recent common ancestors based on the S1, E, M, and N genes were the years of 1744, 1893, 1940, and 1945, respectively. Bayesian skyline analysis revealed a sharp decrease in genetic diversity of all the four structural genes after 2010 and since late 2015, the viral population rapidly rose. In conclusion, the IBVs circulating in southern China over the past decade have experienced a remarkable change in genetic diversity, dominant genotypes, and selection pressure, indicating the importance of permanent monitoring of circulating strains and the urgency for developing new vaccines to counteract the emerging LX4-type and New-type IBVs.

Molecular and Antigenic Characterization of GI-13 and GI-16 Avian Infectious Bronchitis Virus Isolated in Chile from 2009 to 2017 Regarding 4/91 Vaccine Introduction

Simple Summary

The high adaptation and recombination abilities of infectious bronchitis virus (IB) have been proven. This study aims to verify the genetic and antigenic variation of eight field IB strains regarding the 4/91 strain vaccination in Chilean chickens. Phylogenetic, serologic and challenge studies were carried out to accomplish this goal. The genetic analyses indicate that all the viruses isolated prior to the 4/91 introduction belong to the genetic group GI-16 (three isolates from 2009). On the other hand, just one of the viruses isolated after the 4/91 strain vaccine introduction in Chile (in 2015) showed relationship with GI-16 lineage. The remaining four viruses (from 2017) belong to GI-13, the group where the strain 4/91 has been previously classified. Three viruses were chosen to perform antigenic and protective studies. Antigenically, the high relationship between the 4/91 vaccine with the isolate from 2017 is remarkable and could not be observed with isolates from 2009 and 2015. The 4/91 vaccine also showed better protection against the isolate from 2017 than isolates from 2009 and 2015. These results suggest that the introduction of the 4/91 vaccine in Chile could imply a change in some viruses, showing its ability to interact with field viruses, so it is important to monitor the circulating viruses and include these results in future governmental decisions.

Abstract

The introduction of the 4/91 vaccine against infectious bronchitis in Chile, a lineage not described until that time in the country, led to looking for changes induced by this action. This study considers eight isolates obtained from 2009, 2015 and 2017 and uses a maximum likelihood approach to classify the field isolates. Three isolates were selected to analyze antigenic relationships through a virus neutralization test and to perform protection tests measured trough an RT-qPCR. The isolates from 2009 and 2015 showed a relationship with GI-16 while those from 2017 were related to GI-13. Though the field isolates were classified in two different phylogenetic lineages, all of them showed only minor variations in subtype. The 13885R-17 isolate from 2017 exhibited high antigenic relatedness to the 4/91 vaccine. As expected, 4/91 and Massachusetts vaccines were not antigenically related. Vaccinated birds with the 4/91 vaccine showed less tracheal virus replication for the 13885R-17 from 2017 challenge than for the 12101SP-09 from 2009 and 13347SP-15 from 2015 isolates. The results indicated genetic and antigenic diversity in the most recent infectious bronchitis virus (IBV) isolates in Chile. Moreover, the 4/91 vaccine would be involved in the generation of some current field viruses, which must be considered in vaccination programs and public policies.

Molecular and biological characteristics of the infectious bronchitis virus TC07-2/GVI-1 lineage isolated in China

In the present study, a thorough comparison of the infectious bronchitis virus (IBV) TC07–2/GVI-1 linage was conducted by comparing the S1 gene sequences of GVI-1 viruses with those of viruses representing the established genotypes and lineages. IBV GVI-1 strains were found to be closely genetically related to each other, irrespective of where the viruses were isolated, and differed from other known IBV genotypes and lineages; thus, it was confirmed that GVI represents a novel genotype. However, the GVI-1 viruses exhibited variable antigenicity when compared to each other. Further analysis found that strains CO8089L and CO8091L, which were isolated in Colombia in 2003, were closely related to GVI-1 viruses, suggesting that GVI-1 viruses likely originated from Colombia and are prevalent in at least five countries (Colombia, China, the Republic of Korea, Japan, and Vietnam). Analysis of the complete GVI-1 virus genomes suggested that the GVI-1 strains in China may be independently derived from recombination events that occurred between GI-19 strains and CO8089L/CO8091L-like viruses following the introduction of the viruses from Colombia. Similar to the viruses isolated in the Republic of Korea, GVI-1 viruses isolated in China also showed an affinity for the respiratory tract of chickens, which differed from one of the deduced parental viruses, the GI-19 strain. This difference may be due to recombination events that occurred in the genomes of the GVI-1 viruses, resulting in the replacement of the spike gene sequences in an YX10-like strain of GI-19 lineage.

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GVI-1 viruses likely originated from Columbia.

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GVI-1 strains isolated in China may be derived from recombination events between GI-19 and CO8089L/CO8091L-like viruses.

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GVI-1 viruses exhibited variable antigenicity.

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GVI viruses showed an affinity for the respiratory tract of chickens.

Pathogenicity of a GI-22 genotype infectious bronchitis virus isolated in China and protection against it afforded by GI-19 vaccine

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A GI-22 genotype IBV strain LGD was isolated in northern China in 2018.

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We investigated the molecular characteristics and pathogenecity of LGD.

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The GI-19 type vaccine was efficacious against LGD challenge.

Avian infectious bronchitis (IB) is a globally circulating bird disease caused by infectious bronchitis virus (IBV). In China, the most prevalent IBV genotype is GI-19/QX-like because the protective efficiency of the classical IBV vaccine is low, and new GI-19 vaccines are under development. In 2018, a GI-22 genotype strain CK/CH/LGD/2018 (abbreviated ‘LGD’) was isolated in northern China, which caused 10%–30% morality in H120-vaccinated chickens. A phylogenetic analysis showed that this new isolate displays novel features compared with other earlier-isolated reference strains. To monitor the epidemic trend of IBV in China, the pathogenicity of LGD was first evaluated in 1-day-old specific-pathogen-free chickens. LGD induced classical IBV damage in the trachea and kidney, whereas it also infected and damaged the bursa of Fabricius, an important immune organ of chickens. The efficacy of our earlier-developed GI-19 vaccine, strain SZ200, against LGD was also evaluated in this study. The GI-19 genotype vaccine provided sufficient protection against the new GI-22 genotype strain, and may be a promising candidate vaccine with which to control both wild GI-19 and GI-22 strains in the future.

Viral infection detection using metagenomics technology in six poultry farms of eastern China

With rapidly increasing animal pathogen surveillance requirements, new technologies are needed for a comprehensive understanding of the roles of pathogens in the occurrence and development of animal diseases. We applied metagenomic technology to avian virus surveillance to study the main viruses infecting six poultry farms in two provinces in eastern China. Cloacal/throat double swabs were collected from 60 birds at each farm according to a random sampling method. The results showed that the method could simultaneously detect major viruses infecting farms, including avian influenza virus, infectious bronchitis virus, Newcastle disease virus, rotavirus G, duck hepatitis B virus, and avian leukemia virus subgroup J in several farms. The test results were consistent with the results from traditional polymerase chain reaction (PCR) or reverse transcription-PCR analyses. Five H9N2 and one H3N8 avian influenza viruses were detected at the farms and were identified as low pathogenic avian influenza viruses according to HA cleavage sites analysis. One detected Newcastle disease virus was classified as Class II genotype I and avirulent type according to F0 cleavage sites analysis. Three avian infectious bronchitis viruses were identified as 4/91, CK/CH/LSC/99I and TC07-2 genotypes by phylogenetic analysis of S1 genes. The viral infection surveillance method using metagenomics technology enables the monitoring of multiple viral infections, which allows the detection of main infectious viruses.

Novel genotype of infectious bronchitis virus isolated in China

Recombination events are known to contribute to the emergence of novel infectious bronchitis virus (IBV) genotypes. In this study, we carried out detailed phylogenetic analysis and sequence comparisons based on 74 complete nucleotide sequences of the IBV S1 gene, including strain I0636/16 and 73 representative sequences from each genotype and lineage. The results showed that strain I0636/16 represented a novel genotype, designated as lineage 1 within genotype VII (GVII-1). Further comparative genomic analysis revealed at least two recombination sites that replaced the spike gene in a lineage 18 within genotype I (GI-18)-like virus with an as-yet-unidentified sequence, likely derived from another IBV strain, resulting a novel serotype with a lower affinity to the respiratory tract in chickens. To the best of our knowledge, this provides the first evidence for recombination leading to replacement of the complete spike gene and the emergence of a novel genotype/serotype with a lower affinity to the respiratory tract in chickens comparing to one of its parental virus ck/CH/LGX/111119. These results emphasize the importance of limiting exposure to novel IBVs that may serve as a source of genetic material for emerging viruses, as well as the importance of IBV surveillance in chicken flocks.

Genetic and biological characteristics of four novel recombinant avian infectious bronchitis viruses isolated in China

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Two IBV strains were proved to be originated from multiple recombination events.

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Viruses with very similar S1 gene sequences showed varying biological features.

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Point mutations were observed in the RBD and HVRs of the recombinant viruses.

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Point mutations likely have an effect on these differences in biological characteristics.

Infectious bronchitis viruses (IBVs) of GI-13 (793/B) and GI-19 (QX/LX4) lineages have been frequently detected in China in recent years. Naturally recombinant IBVs originating from the GI-13 and GI-19 lineages have also been isolated from chicken flocks with respiratory and renal problems in China. Thorough genetic and biological investigations of these recombinant viruses have led to speculation regarding their origin, evolution, and control. In order to confirm the previous results and further extend our understanding about the characteristics of the four recombinant IBV strains we had previously identified (I0718/17, I0722/17, I0724/17, and I0737/17), we conducted phylogenetic analysis by comparing their complete S1 gene sequences with those of 71 reference strains of different genotypes and lineages. We identified a close relationship between the S1 sequences of the four strains and those of GI-13 strains. The results of complete genome sequence analysis confirmed the previously identified recombination events in the four IBV strains and revealed additional recombination events in different genomic regions of strains I0718/17 and I0724/17, suggesting that the two strains originated from multiple recombination events between 4/91-like and YX10-like viruses. We comparatively evaluated the antigenicity, pathogenicity, and affinity of the four recombinant viruses and their deduced parental strains in the trachea and kidneys. Some of the strains showed comparable antigenic relatedness, pathogenicity, and affinity for the trachea and kidneys among each other and with their parental viruses; however, some of them showed varying biological characteristics. Point mutations observed in the receptor-binding domain and hypervariable region of the S1 subunit of the spike protein likely have an effect on these differences in biological characteristics, although the influence of other factors—such as host innate-immune responses and changes in genomic regions beyond the S1 protein—might also be responsible for such changes.

Genetics, antigenicity and virulence properties of three infectious bronchitis viruses isolated from a single tracheal sample in a chicken with respiratory problems

Three different IBV genotypes/serotypes, designated ck/CH/LDL/150434–I (LDL/150434–I), ck/CH/LDL/150434–II (LDL/150434–II) and ck/CH/LDL/150434–III (LDL/150434–III), were detected in a single tracheal sample from a chicken showing signs of respiratory disease. The viruses were isolated using a cross-neutralization test and limiting dilution in embryonated specific-pathogen-free (SPF) eggs. Isolate LDL/150434–I was a re-isolation of H120 vaccine strain that was introduced into the chicken flock by vaccination, transmitted between chickens, and later accumulated several genomic mutations. Isolate LDL/150434–II was a novel variant that originated from recombination events between H120 and ck/CH/LDT3/03-like viruses. The widespread use of H120 vaccine, which offered incomplete protection against heterotypic IBVs in the fields, may play important roles in the emergence of such a novel genetic variant. Based on the analysis of S1 and complete genomic sequence, isolate LDL/150434–III was related genetically but distinct from the established strains of nrTW I type viruses of GI-7 lineage circulating in Mainland China since 2009. The three IBV isolates were avirulent when they infected SPF chickens. Furthermore, synergistic effects on pathogenicity were not observed when the different types co-infected the SPF chickens. However, the isolates persisted in the respiratory tracts longer in combined infected birds than those in individual infected birds. The results provide insights into the evolution of the viruses and co-infection of chickens with different virus serotypes.