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

Isolation of a more aggressive GVI-1 genotype strain HX of the avian infectious bronchitis virus

The avian infectious bronchitis virus (IBV) poses a significant economic threat to the global poultry industry. Although in recent years, the GVI-1 lineage of IBV has proliferated throughout China, there is still a lack of comprehensive studies regarding the pathogenicity of this lineage, particularly with respect to infections of the digestive tract and the antigenic characteristics of the S1 gene. In this study, we investigated the effects of infecting 14-day-old chicks with the HX strain of the GVI-1 lineage over a 14-d period postinfection. Assessment of the pathogenicity of the HX strain included clinical observations; monitoring of body weight, organ viral load, viral shedding, and gross anatomy; histopathological analysis, and bioinformatics-based antigenic characterization of the S1 protein. The findings revealed that compared with previously reported GVI-1 lineage strains, the HX strain is characterized by greater virulence, with infection leading to approximately 26% mortality and extensive severe organ damage, including that of the proventriculus and kidneys. Moreover, at 14 d postinfection, 80% of oral swabs and 100% of cloacal swabs from chickens infected with the HX strain tested positive, indicating a prolonged period of viral shedding relative to that previously reported for GVI-1 lineage strains. Bioinformatic analysis of B-cell epitopes on the S1 protein revealed 7 potential antigenic epitopes. Collectively, our findings in this study provide clear evidence to indicate that compared previously reported GVI-1 lineage strains, chicks infected with the IBV GVI-1 lineage strain HX are characterized by heightened rates of mortality, more pronounced organ damage, and an extended period of viral shedding. This comprehensive characterization highlights the pathogenic potential of the GVI-1 lineage and its capacity to induce severe kidney and proventriculus damage, thereby emphasizing the imperative of early initiated preventive measures. Furthermore, on the basis of our analysis of the antigenic properties of the S1 protein, we have identified 7 potential linear B-cell epitopes, which will provide valuable insights for the development of epitope-based vaccines.

Pathogenicity and molecular characterization of a GI-19 infectious bronchitis virus isolated from East China

Infectious bronchitis virus (IBV) is responsible for avian infectious bronchitis, a disease prevalent in countries with intensive poultry farming practices. Given the presence of multiple genotypic strains in China, identifying the regionally dominant genotypes is crucial for the implementation of effective prevention and control measures. This study focuses on the IBV strain CK/CH/WJ/215, isolated from a diseased commercial chicken flock in China in 2021. The CK/CH/WJ/215 isolate was genetically characterized through complete S1 sequence analysis. Phylogenetic comparisons were made with prevalent vaccine strains (H120, LDT3-A, and 4/91). Glycosylation patterns in the S1 protein were also analyzed. Pathogenicity was assessed in 7-day-old specific-pathogen-free chicks, monitoring morbidity, mortality, and tissue tropisms. Phylogenetic analysis clustered the CK/CH/WJ/215 isolate within the GI-19 lineage. Identity with the vaccination strains H120, LDT3-A, and 4/91 was low (75.7%, 78.6%, and 77.5% respectively). Novel glycosylation sites at positions 138 and 530 were identified compared to H120 and LDT-A. The isolate demonstrated nephropathogenic characteristics, causing 100% morbidity and 73.3% mortality in SPF chicks, with broader tropisms in tissues including trachea, lungs, kidneys, and bursa of Fabricius. Comprehensive genetic and pathological investigations revealed significant differences between the CK/CH/WJ/215 isolate and common vaccine strains, including novel glycosylation sites and a strong multiorgan infective capability. These findings are crucial for understanding the evolutionary dynamics of IBV and developing more effective prevention and control strategies.

Molecular epidemiology of infectious bronchitis virus in eastern and southern China during 2021-2023

As a highly infectious and contagious pathogen in chickens, infectious bronchitis virus (IBV) is currently grouped into nine genotypes (GI to GIX). However, the classification of serotypes of IBV is still not clear. In this study, 270 field strains of IBV were isolated from dead or diseased chicken flocks in eastern and southern China during January 2021 to April 2023. These isolated IBV strains could be classified into 2 genotypes, GI (including 5 lineages GI-1, GI-13, GI-19, GI-22, and GI-28) and GVI based on the complete S1 sequence. Further analysis showed that the GI-19, GI-13, GI-22, GI-28, and GVI were the dominant genotypes with the proportions of 61.48, 8.89, 8.89, 7.78, and 8.89% respectively, and the homology of S1 protein of these isolates ranged from 86.85 to 100% in GI-19, 92.22 to 100% in GI-13, 83.1 to 100% in GI-22, 94.81 to 100% in GI-28 and 90.0 to 99.8% in GVI, respectively. Moreover, cross-neutralization test with sera revealed that these isolates in GI-19 lineage could be classified into at least 3 serotypes according to the antigenic relationship. In addition, structure assay using PyMOL indicated that one mutation such as S120 in receptor binding site (RBD) of GI-19 might alter the antigenicity and conformation of S protein of IBV. Overall, our data demonstrate that not only multiple genotypes, but also multiple serotypes in a single genotype or lineage have been co-circulated in eastern and southern China, providing novel insights into the molecular evolution of the antigenicity of IBV and highlighting the significance of the selection of the dominant isolate for vaccine development in IBV endemic region.

Development of a colloidal gold immunochromatographic strip for rapid detection of avian coronavirus infectious bronchitis virus

Avian infectious bronchitis virus (IBV) still causes serious economic losses in the poultry industry. Currently, there are multiple prevalent genotypes and serotypes of IBVs. It is imperative to develop a new diagnosis method that is fast, sensitive, specific, simple, and broad-spectrum. A monoclonal hybridoma cell, N2D5, against the IBV N protein was obtained after fusion of myeloma SP2/0 cells with spleen cells isolated from the immunized Balb/c mice. The N2D5 monoclonal antibody (mAb) and the previously prepared mouse polyclonal antibody against the IBV N protein were used to target IBV as a colloidal gold-mAb conjugate and a captured antibody, respectively, in order to develop an immunochromatographic strip. The optimal pH and minimum antibody concentration in the reaction system for colloidal gold-mAb N2D5 conjugation were pH 6.5 and 30 μg/mL, respectively. Common avian pathogens were tested to evaluate the specificity of the strip and no cross-reaction was observed. The sensitivity of the strip for detecting IBV was 10-1.4522 EID50/mL. The strip showed a broad-spectrum cross-reactive capacity for detecting IBV antigens, including multiple IBV genotypes in China and all of the seven serotypes of IBV that are currently prevalent in southern China. Additionally, the result can be observed within 2 min without any equipment. The throat and cloacal swab samples of chickens that were artificially infected with three IBV strains were tested using the developed strip and the qPCR method; the strip test demonstrated a high consistency in detecting IBV via qPCR gene detection. In conclusion, the immunochromatographic strip that was established is rapid, sensitive, specific, simple, practical, and broad-spectrum; additionally, it has the potential to serve as an on-site rapid detection method of IBV and can facilitate the surveillance and control of the disease, especially in resource-limited areas.

Molecular and Serological Investigation of Infectious Bronchitis Virus in the East Shewa, Central Ethiopia

Background

Infectious bronchitis (IB) is an economically important disease in poultry with worldwide distribution. The occurrence of IB has been reported both in commercial and backyard poultry in Ethiopia, although comprehensive information lacks available prevalence of the disease and the circulating serotypes.

Methods

A cross-sectional study was conducted from November 2021 to June 2022 in seven commercial farms found in East Shewa, Central Ethiopia. Serological assay using indirect ELISA, virus isolation techniques in embryonated eggs, and molecular techniques such as one-step reverse transcriptase polymerase chain reaction (RT-PCR) and nested polymerase chain reaction (PCR) targeting a 466 bp S1 gene were employed.

Results

A total of 196 blood samples, 7 pools (35) of swab samples, and 5 pools of tracheal samples were investigated. The results of serological analysis revealed that 97.96% (192/196; 95% CI: 94.86-99.44) of the sera samples were found to be positive for antibodies against IBV. Out of the 7 pools of swab and 5 pools of tracheal tissue samples analyzed using RT-PCR 33.3% (4/12) of them gave positive results all from swab samples. The RT-PCR-positive samples were subjected to a nested PCR yielding 295bp and 154bp indicating the circulation of Mass and 793/B (4/91) strains of IBV, respectively. The 12 pools of samples inoculated into embryonated egg showed cytopathic changes such as congestion, bleeding, and deformation only after three passages.

Conclusion

Two serotypes of IBV are circulating in Ethiopian chickens, and molecular identification of the Massachusetts serotype is the first report in Ethiopia. Further epidemiological investigation is needed in order to devise effective control measures.

Adjuvant effects of novel water/oil emulsion formulations on immune responses against infectious bronchitis (IB) vaccine in mice

Vaccines have long made use of adjuvants to boost the immune response of the body and reduce the amount of vaccine needed as well as the expense of producing the vaccine. Many vaccine adjuvants are in development, but their application in veterinary vaccinations is restricted due to their lack of efficacy or undesirable side effects. For this reason, it is essential to develop novel adjuvants. To address the issue that the currently available infectious bronchitis (IB) vaccine often fails to produce sufficient immune responses, Coral Biotechnology tested two of their newly developed water-in-oil (W/O) type emulsion adjuvants (Coralvac RZ 528 and Coralvac RZ 506) in the IB vaccine. These adjuvants were tested in a mouse model to determine whether it worked with an inactive IBV H120 vaccine. Vaccine formulations were prepared by combining a virus concentration of 1 × 106 EID50/0.1 ml with an emulsion of the W/O type in a specific ratio. Once the formulations were ready, it was injected intramuscularly as a single dosage, and the mice were monitored for 21 days afterwards. The results showed that anti-IB antibody titer (IgG and IgG1), CD3+ CD8+ T cell responses as well as IFN- γ cytokine production, and splenocyte proliferation were all considerably higher in the IBV H120 with Coralvac RZ 528 and IBV H120 with Coralvac RZ 506 formulation groups than in the viral control group. According to our findings, the humoral and cellular immune responses of mice were significantly enhanced by these novel vaccine adjuvants. Thus, our results provide evidence that the W/O type emulsion adjuvants developed by Coral Biotechnology may be a useful adjuvant in IBV vaccines.

Genotyping and phylogeography of infectious bronchitis virus isolates from Pakistan show unique linkage to GI-24 lineage

Infectious bronchitis virus (IBV) is prevalent in Pakistan causing enormous economic losses. To date no clear data are available on circulating genotypes and phylogeographic spread of the virus. Hence current study assessed these parameters for all available IBV Pakistani isolates, based on the 9 new sequences, with respect to other Asian and non-Asian countries. Results indicated that all Pakistani isolates belonged to genotype I (GI), with more than half of them (16/27) belonging to the GI-24 lineage, against which no vaccine is available. Three possible introduction events of the GI-13 IBV lineage into Pakistan, based on the estimated IBV population using isolates from this study, were observed possibly from Afghanistan, China, and/or Egypt. These events were further analyzed on the S1 amino acid level which showed unique alterations (S250H, T270K, and Q298S) in 1 isolate (IBV4, GI-13) when compared to GI-1 lineage. Both GI-1 and GI-13 Pakistani strains showed close homology with homologous vaccine strains that are used in Pakistan. For GI-24 strains, none of the used vaccines showed substantial homology, necessitating the need for further exploration of this lineage and vaccine design. In addition, our findings highlight the importance of genomic surveillance to support phylogeographical studies on IBV in genotyping and molecular epidemiology.

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.

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.

The conserved L1089 in the S2 subunit of avian infectious bronchitis virus determines viral kidney tropism by disrupting virus-cell fusion

The virulence of avian gamma-coronavirus infectious bronchitis viruses (IBV) for the kidney has led to high mortality in dominant-genotype isolations, but the key sites of viral protein that determine kidney tropism are still not fully clear. In this study, the amino acid sequences of the S2 subunit of IBVs with opposing adaptivity to chicken embryonic kidney cells (CEKs) were aligned to identify putative sites associated with differences in viral adaptability. The S2 gene and the putative sites of the non-adapted CN strain were introduced into the CEKs-adapted SczyC30 strain to rescue seven mutants. Analysis of growth characteristics showed that the replacement of the entire S2 subunit and the L1089I substitution in the S2 subunit entirely abolished the proliferation of recombinant IBV in CEKs as well as in primary chicken oviduct epithelial cells. Pathogenicity assays also support the decisive role of this L1089 for viral nephrotropism, and this non-nephrotropic L1089I substitution significantly attenuates pathogenicity. Analysis of the putative cause of proliferation inhibition in CEKs suggests that the L1089I substitution affects neither virus attachment nor endocytosis, but instead fails to form double-membrane vesicles to initiate the viral replication and translation. Position 1089 of the IBV S2 subunit is conservative and predicted to lie in heptad repeat 2 domains. It is therefore reasonable to conclude that the L1089I substitution alters the nephrotropism of parent strain by affecting virus-cell fusion. These findings provide crucial insights into the adaptive mechanisms of IBV and have applications in the development of vaccines and drugs against IB.

Cross-species transmission, evolution and zoonotic potential of coronaviruses

Coronaviruses (CoVs) continuously evolve, crossing species barriers and spreading across host ranges. Over the last two decades, several CoVs (HCoV-229E, HCoV-NL63, HCoV-HKU1, HCoV-OC43, SARS-CoV, MERS-CoV, and SARS-CoV-2) have emerged in animals and mammals, causing significant economic and human life losses. Due to CoV cross-species transmission and the evolution of novel viruses, it is critical to identify their natural reservoiurs and the circumstances under which their transmission occurs. In this review, we use genetic and ecological data to disentangle the evolution of various CoVs in wildlife, humans, and domestic mammals. We thoroughly investigate several host species and outline the epidemiology of CoVs toward specific hosts. We also discuss the cross-species transmission of CoVs at the interface of wildlife, animals, and humans. Clarifying the epidemiology and diversity of species reservoirs will significantly impact our ability to respond to the future emergence of CoVs in humans and domestic animals.

The relation between avian coronaviruses and SARS-CoV-2 coronavirus

The coronaviruses (CoVs) are a family of ribonucleic acid viruses that are present in both mammals and birds. SARS-CoV and MERS-CoV originated in bats, and there is a possibility that this could be the case for SARS-CoV-2 as well. There is already evidence that a probable intermediary host is responsible for the emergence of viruses in humans as was the case for SARS-CoVs and MERS-CoV. As the SARS-CoV-2 originated from a live animal market, there is always the question if domestic animals are susceptible to these viruses and the possible risk of zoonotic transmission with mammals, including humans. This uncertainty of the transmission of the COVID-19 virus between humans and animals is of great significance worldwide. Hence, this paper focuses on the avian CoVs and their possible relation and interaction with SARS-CoV-2.

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.

The N1038S Substitution and 1153EQTRPKKSV1162 Deletion of the S2 Subunit of QX-Type Avian Infectious Bronchitis Virus Can Synergistically Enhance Viral Proliferation

The S2 subunit of infectious bronchitis virus (IBV) plays a critical role in the process of IBV infection. A comparison between the S2 subunit sequence of chicken embryo kidney cell (CEK) adapted virulent QX-like IBV strain SczyC30 (hereafter referred to as zy30) and its CEK-attenuated strain, SczyC100, revealed an N1038S substitution in S2 subunit and a ¹¹⁵⁴EQTRPKKSV¹¹⁶² residue deletion in the C-terminus of the S2 subunit. In order to explore whether these two mutations are related to changes in the biological characteristics of IBV, we firstly constructed an infectious clone of zy30 using a bacterial artificial chromosome (BAC), which combines the transcription of infectious IBV genomic RNA in non-susceptible BHK-21 cells with the amplification of rescued virus rzy30 in CEK cells. Then, three recombinant viruses, including an rzy30S2-N1038S strain that contained the N1038S substitution, an rzy30S2-CT9^△ strain that contained the ¹¹⁵⁴EQTRPKKSV¹¹⁶² deletion, and an rzy30S2-N1038S-CT9^△ strain that contained both mutations, were constructed using rescued virus rzy30 as the backbone. The results showed that each mutation did not significantly affect the replication titer in CEK cells but reduced pathogenicity in chickens, while in combination, the N1038S substitution and ¹¹⁵⁴EQTRPKKSV¹¹⁶² deletion improved the proliferation efficiency in CEK cells and reduced pathogenicity, compared to rzy30 strain. The contribution made by the ¹¹⁵⁴EQTRPKKSV¹¹⁶² deletion in reducing pathogenicity was higher than that of N1038S substitution. Our results revealed that the N1038S substitution and ¹¹⁵⁴EQTRPKKSV¹¹⁶² deletion in S2 subunit were deeply involved in the replication efficiency of IBV and contributed to reduction of viral pathogenicity.

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.

Near-Complete Genome Sequence of GI-17 Lineage Infectious Bronchitis Virus, Circulating in Iowa

Avian infectious bronchitis virus (AvIBV) is the causative agent of a highly contagious respiratory disease in chickens which results in significant economic losses in the poultry industry. Here, we report a near-complete genome sequence of the strain, designated IA1162/2020, identified in tracheal swabs from chickens in Iowa in 2020.

Avian infectious bronchitis virus (AvIBV) is the causative agent of a highly contagious respiratory disease in chickens which results in significant economic losses in the poultry industry. Here, we report a near-complete genome sequence of the strain, designated IA1162/2020, identified in tracheal swabs from chickens in Iowa in 2020.

Coronaviruses in farm animals: Epidemiology and public health implications

Coronaviruses (CoVs) are documented in a wide range of animal species, including terrestrial and aquatic, domestic and wild. The geographic distribution of animal CoVs is worldwide and prevalences were reported in several countries across the five continents. The viruses are known to cause mainly gastrointestinal and respiratory diseases with different severity levels. In certain cases, CoV infections are responsible of huge economic losses associated or not to highly public health impact. Despite being enveloped, CoVs are relatively resistant pathogens in the environment. Coronaviruses are characterized by a high mutation and recombination rate, which makes host jumping and cross-species transmission easy. In fact, increasing contact between different animal species fosters cross-species transmission, while agriculture intensification, animal trade and herd management are key drivers at the human-animal interface. If contacts with wild animals are still limited, humans have much more contact with farm animals, during breeding, transport, slaughter and food process, making CoVs a persistent threat to both humans and animals. A global network should be established for the surveillance and monitoring of animal CoVs.

Construction and Immunogenicity Comparison of Three Virus-Like Particles Carrying Different Combinations of Structural Proteins of Avian Coronavirus Infectious Bronchitis Virus

Infectious bronchitis virus (IBV) poses massive economic losses in the global poultry industry. Here, we firstly report the construction and immunogenicity comparison of virus-like particles (VLPs) carrying the S, M and E proteins (SME-VLPs); VLPs carrying the S and M proteins (SM-VLPs); and VLPs carrying the M and E proteins (ME-VLPs) from the dominant serotype representative strain GX-YL5 in China. The neutralizing antibody response induced by the SME-VLPs was similar to that induced by the inactivated oil vaccine (OEV) of GX-YL5, and higher than those induced by the SM-VLPs, ME-VLPs and commercial live vaccine H120. More importantly, the SME-VLPs elicited higher percentages of CD4⁺ and CD8⁺ T lymphocytes than the SM-VLPs, ME-VLPs and OEV of GX-YL5. Compared with the OEV of GX-YL5, higher levels of IL-4 and IFN-γ were also induced by the SME-VLPs. Moreover, the mucosal immune response (sIgA) induced by the SME-VLPs in the tear and oral swabs was comparable to that induced by the H120 vaccine and higher than that induced by the OEV of GX-YL5. In the challenge experiment, the SME-VLPs resulted in significantly lower viral RNA levels in the trachea and higher protection scores than the OEV of GX-YL5 and H120 vaccines, and induced comparable viral RNA levels in the kidneys, and tear and oral swabs to the OEV of GX-YL5. In summary, among the three VLPs, the SME-VLPs carrying the S, M and E proteins of IBV could stimulate the strongest humoral, cellular and mucosal immune responses and provide effective protection, indicating that it would be an attractive vaccine candidate for IB.

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.

Sunflower seed oil containing ginseng stem-leaf saponins (E515-D) is a safe adjuvant for Newcastle disease vaccine

Vaccination is an effective method to prevent Newcastle disease (ND) in chickens. Marcol 52 and #10 white oil are mineral-based adjuvants and can be found in commercial inactivated ND virus vaccines. The present study demonstrated that a vegetable origin oil E515-D had lower polycyclic aromatic hydrocarbons and higher flash point than the commercial products Marcol 52 and #10 white oil. E515-D could be mixed with an aqueous phase containing ND virus antigen to form a stable water-in-oil vaccine emulsion and exhibited more potent adjuvant effects on the immune response than Marcol 52 and #10 white oil. Moreover, the absorption of E515-D-adjuvanted vaccine was faster than absorption of Marcol 52- and #10 white oil-adjuvanted vaccines when ND virus vaccines were injected in broilers. Therefore, E515-D was safe and could be a suitable adjuvant used in vaccines for food animals. In addition，E515-D is not easy to be flammable during shipping and storage owing to its higher flash point.

Full-length cDNA sequence analysis of 85 avian leukosis virus subgroup J strains isolated from chickens in China during the years 1988-2018: coexistence of 2 extremely different clusters that are highly dependent upon either the host genetic background or the geographic location

During the process of transmission and spread of avian leukosis virus subgroup J (ALV-J) in chickens worldwide, the viral genome is constantly changing. A comprehensive and systematic study of the evolutionary process of ALV-J in China is needed. In this study, we amplified the full-length viral cDNA sequences of 16 ALV-J isolates of Yellow-chicken origin and analyzed and compared these sequences with another 69 ALV-J strains isolated during the years 1988–2018. These isolates were then sorted into 2 clusters: cluster I included isolates that mainly originated from the layers and White-feather broilers from northern China; cluster II included isolates mainly from the Yellow-chicken, most of them being from southern China. According to the sequence homologies of the whole genome and gag, pol, gp85, and gp37 genes, the ALV-J strains are more likely to randomly change in different directions from the original strain HPRS-103 as time passes. The results of entropy analysis of the sequences of gag, pol, and env revealed that the env gene had the largest variation, and the gag gene nonconserved sites are mainly concentrated in p19, p10, and p12. In addition, 84.71% (72/85) of the isolates had the 205-nucleotide (nt) deletion in the 3′UTR region, and 30.59% (26/85) of the isolates had the 125-nt to 127-nt deletion in the E element. Our study provides evidence for the coexistence of 2 extremely different clusters of ALV-J prevailing in China and in some other countries during the period of 1988–2018 and implies that the clusters are highly dependent on the host genetic background and the geographic location.

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.

Vertical transmission of ALV from ALV-J positive parents caused severe immunosuppression and significantly reduced marek's disease vaccine efficacy in three-yellow chickens

In order to evaluate the influence of the vertical transmission of avian leukosis virus (ALV) from J subgroup (ALV-J) positive parents on the vaccine efficacy of Marek's disease virus (MDV), ALV-J positive male breeders × female breeders of Three-yellow chickens and the ALV negative male breeder × the negative female breeders were used respectively for crossbreeding to produce eggs and the hatching offspring. The commercial CVI988/Rispens vaccine was used to vaccinate the crossbred offspring at 1-day-old. At 7-days-old, the birds were inoculated with the inactivated oil-emulsion vaccines (OEVs) AIV-H5 monovalent and NDV + AIV-H9 bivalent, respectively. Then the birds were challenged with a Chinese very virulent (vv) MDV field strain GXY2 at 14-day-old. The results showed that the viral load of the challenged GXY2 in the offspring from the ALV-J positive breeders was significantly higher than that from the ALV-negative breeders' (P < 0.05), and the mortality and tumor incidence of offspring from the ALV-J positive breeders were higher than those of the ALV-negative breeders. Also the offspring of the ALV-J positive breeders exhibited a significant negative effect on the development of the immune organs (P < 0.05) and lower antibody responses to the vaccinations with the commercial OEVs (P<0.05). The MD vaccine protective index in the offspring from the ALV-J positive breeders was lower than that from the ALV-negative breeders. The results of the study demonstrated that the vertical transmission of ALV from the ALV-J positive parents caused severe immunosuppression and significantly reduced the Marek's disease vaccine efficacy in Three-yellow chickens.

Special Issue "Emerging Viruses: Surveillance, Prevention, Evolution, and Control"

Emerging viruses represent a major concern for public health offices. Climate changes, the international migration of people and products, deforestation, and other anthropogenic activities (and their consequences) have been historically and continuously related to the emerging and re-emerging of new viruses, triggering an increasing number of notified outbreaks, epidemics, and pandemics. [...].