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Wang M, Bo Z, Zhang C, Guo M, Wu Y, Zhang X. Deciphering the Genetic Variation: A Comparative Analysis of Parental and Attenuated Strains of the QXL87 Vaccine for Infectious Bronchitis. Animals (Basel) 2024; 14:1784. [PMID: 38929403 PMCID: PMC11200882 DOI: 10.3390/ani14121784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
The QXL87 live attenuated vaccine strain for infectious bronchitis represents the first approved QX type (GI-19 lineage) vaccine in China. This strain was derived from the parental strain CK/CH/JS/2010/12 through continuous passage in SPF chicken embryos. To elucidate the molecular mechanism behind its attenuation, whole-genome sequencing was conducted on both the parental and attenuated strains. Analysis revealed 145 nucleotide mutations in the attenuated strain, leading to 48 amino acid mutations in various proteins, including Nsp2 (26), Nsp3 (14), Nsp4 (1), S (4), 3a (1), E (1), and N (1). Additionally, a frameshift mutation caused by a single base insertion in the ORFX resulted in a six-amino-acid extension. Subsequent comparison of post-translational modification sites, protein structure, and protein-protein binding sites between the parental and attenuated strains identified three potential virulence genes: Nsp2, Nsp3, and S. The amino acid mutations in these proteins not only altered their conformation but also affected the distribution of post-translational modification sites and protein-protein interaction sites. Furthermore, three potential functional mutation sites-P106S, A352T, and L472F, all located in the Nsp2 protein-were identified through PROVEAN, PolyPhen, and I-Mutant. Overall, our findings suggest that Nsp2, Nsp3, and S proteins may play a role in modulating IBV pathogenicity, with a particular focus on the significance of the Nsp2 protein. This study contributes to our understanding of the molecular mechanisms underlying IBV attenuation and holds promise for the development of safer live attenuated IBV vaccines using reverse genetic approaches.
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Affiliation(s)
- Mengmeng Wang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
| | - Zongyi Bo
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Chengcheng Zhang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
| | - Mengjiao Guo
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
| | - Yantao Wu
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Xiaorong Zhang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
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Xiong T, Xie H, Li L, Liang S, Huang M, Yu C, Zhuang T, Liang X, Liu D, Chen R. Prevalence, Genotype Diversity, and Distinct Pathogenicity of 205 Gammacoronavirus Infectious Bronchitis Virus Isolates in China during 2019-2023. Viruses 2024; 16:930. [PMID: 38932222 PMCID: PMC11209364 DOI: 10.3390/v16060930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/04/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Gammacoronavirus infectious bronchitis virus (IBV) causes a highly contagious disease in chickens and seriously endangers the poultry industry. The emergence and co-circulation of diverse IBV serotypes and genotypes with distinct pathogenicity worldwide pose a serious challenge to the development of effective intervention measures. In this study, we report the epidemic trends of IBV in China from 2019 to 2023 and a comparative analysis on the antigenic characteristics and pathogenicity of isolates among major prevalent lineages. Phylogenetic and recombination analyses based on the nucleotide sequences of the spike (S) 1 gene clustered a total of 205 isolates into twelve distinct lineages, with GI-19 as a predominant lineage (61.77 ± 4.56%) exhibiting an overall increasing trend over the past five years, and demonstrated that a majority of the variants were derived from gene recombination events. Further characterization of the growth and pathogenic properties of six representative isolates from different lineages classified four out of the six isolates as nephropathogenic types with mortality rates in one-day-old SPF chickens varying from 20-60%, one as a respiratory type with weak virulence, and one as a naturally occurring avirulent strain. Taken together, our findings illuminate the epidemic trends, prevalence, recombination, and pathogenicity of current IBV strains in China, providing key information for further strengthening the surveillance and pathogenicity studies of IBV.
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Affiliation(s)
- Ting Xiong
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510640, China
- Zhaoqing Branch of Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China
| | - Hangao Xie
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510640, China
- Zhaoqing Branch of Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China
| | - Lin Li
- Key Laboratory of Manufacture Technology of Veterinary Bioproducts, Ministry of Agriculture and Rural Affairs, Zhaoqing 526238, China
| | - Shijin Liang
- Zhaoqing Branch of Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China
| | - Meizhen Huang
- Zhaoqing Branch of Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China
| | - Chuanzhao Yu
- Zhaoqing Branch of Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China
| | - Tingting Zhuang
- Zhaoqing Branch of Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China
| | - Xuejing Liang
- Zhaoqing Branch of Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China
| | - Dingxiang Liu
- Zhaoqing Branch of Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China
- Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Ruiai Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510640, China
- Zhaoqing Branch of Guangdong Laboratory of Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China
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Song G, Zhang C, Yu X, Li J, Fan Q, Liu F, He Q, Shang C, Li X. Infectious bronchitis virus (IBV) triggers autophagy to enhance viral replication by activating the VPS34 complex. Microb Pathog 2024; 190:106638. [PMID: 38574829 DOI: 10.1016/j.micpath.2024.106638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Autophagy plays an important role in the lifecycle of viruses. However, there is currently a lack of systematic research on the relationship between Infectious Bronchitis Virus (IBV) and autophagy. This study aims to investigate the impact of IBV on autophagy and the role of autophagy in viral replication. We observed that IBV infection increased the expression of microtubule-associated protein 1 light chain 3, a marker of autophagy, decreased the expression of sequestosome 1, and led to elevated intracellular LC3 puncta levels. These findings suggest that IBV infection activates the autophagic process in cells. To investigate the impact of autophagy on the replication of IBV, we utilized rapamycin as an autophagy activator and 3-methyladenine as an autophagy inhibitor. Our results indicate that IBV promotes viral replication by inducing autophagy. Further investigation revealed that IBV induces autophagosome formation by inhibiting the mTOR-ULK1 pathway and activating the activity of vacuolar protein sorting 34 (VPS34), autophagy-related gene 14, and the Beclin-1 complex. VPS34 plays a crucial role in this process, as inhibiting VPS34 protein activity enhances cell proliferation after IBV infection. Additionally, inhibiting VPS34 significantly improves the survival rate of IBV-infected chicks, suppresses IBV replication in the kidney, and alleviates tracheal, lung, and kidney damage caused by IBV infection. In summary, IBV infection can induce autophagy by modulating the mTOR/ULK1 signaling pathway and activating the VPS34 complex, while autophagy serves to promote virus replication.
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Affiliation(s)
- Gaojie Song
- Jiangxi Provincial Key Laboratory of Systems Biomedicine, Jiujiang University, Jiujiang, China
| | - Cuiling Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xiaoyang Yu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China; College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jiaqi Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China; Shandong Normal University, Jinan, China
| | - Qinlei Fan
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Fei Liu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Qinghao He
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
| | - Chao Shang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.
| | - Xiao Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China.
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O’Dowd K, Isham IM, Vatandour S, Boulianne M, Dozois CM, Gagnon CA, Barjesteh N, Abdul-Careem MF. Host Immune Response Modulation in Avian Coronavirus Infection: Tracheal Transcriptome Profiling In Vitro and In Vivo. Viruses 2024; 16:605. [PMID: 38675946 PMCID: PMC11053446 DOI: 10.3390/v16040605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Infectious bronchitis virus (IBV) is a highly contagious Gammacoronavirus causing moderate to severe respiratory infection in chickens. Understanding the initial antiviral response in the respiratory mucosa is crucial for controlling viral spread. We aimed to characterize the impact of IBV Delmarva (DMV)/1639 and IBV Massachusetts (Mass) 41 at the primary site of infection, namely, in chicken tracheal epithelial cells (cTECs) in vitro and the trachea in vivo. We hypothesized that some elements of the induced antiviral responses are distinct in both infection models. We inoculated cTECs and infected young specific pathogen-free (SPF) chickens with IBV DMV/1639 or IBV Mass41, along with mock-inoculated controls, and studied the transcriptome using RNA-sequencing (RNA-seq) at 3 and 18 h post-infection (hpi) for cTECs and at 4 and 11 days post-infection (dpi) in the trachea. We showed that IBV DMV/1639 and IBV Mass41 replicate in cTECs in vitro and the trachea in vivo, inducing host mRNA expression profiles that are strain- and time-dependent. We demonstrated the different gene expression patterns between in vitro and in vivo tracheal IBV infection. Ultimately, characterizing host-pathogen interactions with various IBV strains reveals potential mechanisms for inducing and modulating the immune response during IBV infection in the chicken trachea.
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Affiliation(s)
- Kelsey O’Dowd
- Health Research Innovation Centre, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (K.O.); (I.M.I.)
| | - Ishara M. Isham
- Health Research Innovation Centre, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (K.O.); (I.M.I.)
| | - Safieh Vatandour
- Department of Animal and Poultry Science, Islamic Azad University, Qaemshahr Branch, Qaem Shahr 4765161964, Iran;
| | - Martine Boulianne
- Swine and Poultry Infectious Diseases Research Centre–Fonds de Recherche du Québec (CRIPA-FRQ), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada; (M.B.); (C.M.D.); (C.A.G.); (N.B.)
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Charles M. Dozois
- Swine and Poultry Infectious Diseases Research Centre–Fonds de Recherche du Québec (CRIPA-FRQ), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada; (M.B.); (C.M.D.); (C.A.G.); (N.B.)
- Institut National de Recherche Scientifique-Centre Armand-Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada
| | - Carl A. Gagnon
- Swine and Poultry Infectious Diseases Research Centre–Fonds de Recherche du Québec (CRIPA-FRQ), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada; (M.B.); (C.M.D.); (C.A.G.); (N.B.)
- Molecular Diagnostic and Virology Laboratories, Centre de Diagnostic Vétérinaire de l’Université de Montréal (CDVUM), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Neda Barjesteh
- Swine and Poultry Infectious Diseases Research Centre–Fonds de Recherche du Québec (CRIPA-FRQ), Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada; (M.B.); (C.M.D.); (C.A.G.); (N.B.)
| | - Mohamed Faizal Abdul-Careem
- Health Research Innovation Centre, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (K.O.); (I.M.I.)
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Franzo G, Faustini G, Tucciarone CM, Poletto F, Tonellato F, Cecchinato M, Legnardi M. The Effect of Global Spread, Epidemiology, and Control Strategies on the Evolution of the GI-19 Lineage of Infectious Bronchitis Virus. Viruses 2024; 16:481. [PMID: 38543846 PMCID: PMC10974917 DOI: 10.3390/v16030481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/11/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
The GI-19 lineage of infectious bronchitis virus (IBV) has emerged as one of the most impactful, particularly in the "Old World". Originating in China several decades ago, it has consistently spread and evolved, often forming independent clades in various areas and countries, each with distinct production systems and control strategies. This study leverages this scenario to explore how different environments may influence virus evolution. Through the analysis of the complete S1 sequence, four datasets were identified, comprising strains of monophyletic clades circulating in different continents or countries (e.g., Asia vs. Europe and China vs. Thailand), indicative of single introduction events and independent evolution. The population dynamics and evolutionary rate variation over time, as well as the presence and intensity of selective pressures, were estimated and compared across these datasets. Since the lineage origin (approximately in the mid-20th century), a more persistent and stable viral population was estimated in Asia and China, while in Europe and Thailand, a sharp increase following the introduction (i.e., 2005 and 2007, respectively) of GI-19 was observed, succeeded by a rapid decline. Although a greater number of sites on the S1 subunit were under diversifying selection in the Asian and Chinese datasets, more focused and stronger pressures were evident in both the European (positions 2, 52, 54, 222, and 379 and Thai (i.e., positions 10, 12, 32, 56, 62, 64, 65, 78, 95, 96, 119, 128, 140, 182, 292, 304, 320, and 323) strains, likely reflecting a more intense and uniform application of vaccines in these regions. This evidence, along with the analysis of control strategies implemented in different areas, suggests a strong link between effective, systematic vaccine implementation and infection control. However, while the overall evolutionary rate was estimated at approximately 10-3 to 10-4, a significant inverse correlation was found between viral population size and the rate of viral evolution over time. Therefore, despite the stronger selective pressure imposed by vaccination, effectively constraining the former through adequate control strategies can efficiently prevent viral evolution and the emergence of vaccine-escaping variants.
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Affiliation(s)
- Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell’Università 16, 35020 Legnaro, Italy; (G.F.); (C.M.T.); (F.P.); (F.T.); (M.C.); (M.L.)
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Xia T, Xu S, Li X, Ruan W. Avian coronavirus infectious bronchitis virus Beaudette strain NSP9 interacts with STAT1 and inhibits its phosphorylation to facilitate viral replication. Virology 2024; 590:109944. [PMID: 38141500 DOI: 10.1016/j.virol.2023.109944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 11/11/2023] [Accepted: 11/16/2023] [Indexed: 12/25/2023]
Abstract
Avian coronavirus, known as infectious bronchitis virus (IBV), is the causative agent of infectious bronchitis (IB). Viral nonstructural proteins play important roles in viral replication and immune modulation. IBV NSP9 is a component of the RNA replication complex for viral replication. In this study, we uncovered a function of NSP9 in immune regulation. First, the host proteins that interacted with NSP9 were screened. The immune-related protein signal transducer and activator of transcription 1 (STAT1) was identified and the interaction between NSP9 and STAT1 was further confirmed. Furthermore, IBV replication was inhibited in STAT1-overexpressing cells but inversely affected in STAT1 knock-down cells. Importantly, NSP9 inhibited STAT1 phosphorylation. Finally, the expression of JAK/STAT pathway downstream genes IRF7 and ISG20 was significantly decreased in NSP9-overexpressing cells. These results showed the important role of IBV NSP9 in immunosuppression.
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Affiliation(s)
- Ting Xia
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Shengkui Xu
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Xueyan Li
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Wenke Ruan
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.
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Hassan MSH, Ali A, Mahmoud ME, Altakrouni D, Najimudeen SM, Abdul-Careem MF. Protection of laying chickens against the Canadian DMV/1639 infectious bronchitis virus infection through priming with heterologous live vaccine and boosting with heterologous or homologous inactivated vaccine. Virus Res 2024; 339:199281. [PMID: 37995965 PMCID: PMC10751723 DOI: 10.1016/j.virusres.2023.199281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023]
Abstract
The emergence of the Canadian Delmarva (DMV)/1639 infectious bronchitis virus (IBV) type strains was associated with egg production disorders in Eastern Canadian layer operations. While developing vaccines for novel IBV variants is not typically a reasonable approach, the consideration of an autogenous vaccine becomes more appealing, particularly when the new variant presents significant economic challenges. The current study aimed to compare the efficacies of two vaccination programs that included heterologous live priming by Massachusetts (Mass) and Connecticut (Conn) type vaccines followed by either a commercial inactivated Mass type vaccine or a locally prepared autogenous inactivated DMV/1639 type vaccine against DMV/1639 IBV challenge. The protection parameters evaluated were egg production, viral shedding, dissemination of the virus in tissues, gross and microscopic lesions, and immunological responses. The challenge with the DMV/1639 caused severe consequences in the non-vaccinated laying hens including significant drop in egg production, production of low-quality eggs, serious damage to the reproductive organs, and yolk peritonitis. The two vaccination programs protected the layers from the poor egg-laying performance and the pathology. The vaccination program incorporating the autogenous inactivated DMV/1639 type vaccine was more effective in reducing vial loads in renal and reproductive tissues. This was associated with a higher virus neutralization titer compared to the group that received the commercial inactivated Mass type vaccine. Additionally, the autogenous vaccine boost led to a significant reduction in the viral shedding compared to the non-vaccinated laying hens. However, both vaccination programs induced significant level of protection considering all parameters examined. Overall, the findings from this study underscore the significance of IBV vaccination for protecting laying hens.
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Affiliation(s)
- Mohamed S H Hassan
- Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Department of Avian and Rabbit Medicine, Faculty of Veterinary Medicine, Assiut University, Assiut 71515, Egypt
| | - Ahmed Ali
- Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Department of Pathology, Faculty of Veterinary Medicine, Beni-Suef University, Beni Suef 62521, Egypt
| | - Motamed Elsayed Mahmoud
- Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada; Department of Animal Husbandry, Faculty of Veterinary Medicine, Sohag University, Sohag 84524, Egypt
| | - Danah Altakrouni
- Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Shahnas M Najimudeen
- Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
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Bhuiyan MSA, Sarker S, Amin Z, Rodrigues KF, Bakar AMSA, Saallah S, Md. Shaarani S, Siddiquee S. Seroprevalence and molecular characterisation of infectious bronchitis virus (IBV) in broiler farms in Sabah, Malaysia. Vet Med Sci 2023; 10:e1153. [PMID: 38151844 PMCID: PMC10807952 DOI: 10.1002/vms3.1153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 10/01/2022] [Accepted: 04/18/2023] [Indexed: 12/29/2023] Open
Abstract
BACKGROUND Infectious bronchitis virus (IBV) is classified as a highly contagious viral agent that causes acute respiratory, reproductive and renal system pathology in affected poultry farms. Molecular and serological investigations are crucial for the accurate diagnosis and management of IBV. OBJECTIVES The purpose of this study was to determine the seroprevalence of IBV and to characterise the circulating IBV in poultry farms in Sabah Province, Malaysia. METHODS To determine IBV antibodies, a total of 138 blood samples and 50 organ samples were collected from 10 commercial broiler flocks in 3 different farms by using the enzyme-linked immunosorbent assay (ELISA) (IDEXX Kit) and reverse transcription-polymerase chain reaction (RT-PCR) followed by sequencing. RESULTS A total of 94.2% (130/138) of the samples were seropositive for IBV in the vaccinated flock, and 38% (52/138) of the birds was the IBV titre for infection. The selected seropositive samples for IBV were confirmed by RT-PCR, with 22% (11/50) being IBV positive amplified and sequenced by targeted highly conserved partial nucleocapsid (N) genes. Subsequently, phylogenetic analysis constructed using amplified sequences again exposed the presence of Connecticut, Massachusetts, and Chinese QX variants circulating in poultry farms in Sabah, Malaysia. CONCLUSIONS The unexpectedly increasing mean titres in serology indicated that post infection of IBV and highly prevalent IBV in selected farms in this study. The sequencing and phylogenetic analysis revealed the presence of multiple IBV variants circulating in Malaysian chicken farms in Sabah, which further monitoring of genetic variation are needed to better understand the genetic diversity.
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Affiliation(s)
| | - Subir Sarker
- Department of MicrobiologyAnatomyPhysiology and PharmacologySchool of AgricultureBiomedicine and EnvironmentLa Trobe UniversityMelbourneVictoriaAustralia
| | - Zarina Amin
- Biotechnology Research InstituteUniversiti Malaysia SabahKota KinabaluSabahMalaysia
| | | | | | - Suryani Saallah
- Biotechnology Research InstituteUniversiti Malaysia SabahKota KinabaluSabahMalaysia
| | - Sharifudin Md. Shaarani
- Food Biotechnology ProgramFaculty of Science and TechnologyUniversitiSains Islam MalaysiaNilaiSembilanMalaysia
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Domańska-Blicharz K, Miłek-Krupa J, Pikuła A. Gulls as a host for both gamma and deltacoronaviruses. Sci Rep 2023; 13:15104. [PMID: 37704675 PMCID: PMC10499781 DOI: 10.1038/s41598-023-42241-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023] Open
Abstract
The coronaviruses (CoV) are ubiquitous pathogens found in wide variety of hosts that constantly pose a threat to human and animal health as a result of their enormous capacity to generate genetic changes. Constant monitoring of virus reservoirs can constitute an early-warning tool and control the spread and evolution of the virus. Coronaviruses are common in wild birds, globally, and birds of the Charadriiformes in particular have been demonstrated to be carriers of delta- (dCoV) and gammacoronaviruses (gCoV). In this paper, we present the genetic characterisation of five CoV strains from black-headed (Chroicocephalus ridibundus) and common (Larus canus) gulls. Whole genome sequence analysis showed high similarity of detected dCoV in gulls to previously identified strains from falcon, houbara, pigeon and gulls from Asia (UAE, China). However, phylogenetic analysis revealed bifurcation within a common branch. Furthermore, the accumulation of numerous amino acid changes within the S-protein was demonstrated, indicating further evolution of dCoV within a single gull host. In turn, phylogenetic analysis for the most of the structural and non-structural genes of identified gCoV confirmed that the strain belongs to the duck coronavirus 2714 (DuCoV2714) species within Igacovirus subgenera, while for the spike protein it forms a separate branch not closely related to any gCoV species known to date. The current study provides new and significant insights into the evolution and diversification of circulating coronaviruses in members of Laridae family.
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Affiliation(s)
- Katarzyna Domańska-Blicharz
- Department of Poultry Diseases, National Veterinary Research Institute, al. Partyzantow 57, 24-100, Pulawy, Poland.
| | - Justyna Miłek-Krupa
- Department of Poultry Diseases, National Veterinary Research Institute, al. Partyzantow 57, 24-100, Pulawy, Poland
- Holy Cross Cancer Center, Stefana Artwińskiego 3, 25-734, Kielce, Poland
| | - Anna Pikuła
- Department of Poultry Diseases, National Veterinary Research Institute, al. Partyzantow 57, 24-100, Pulawy, Poland
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François S, Nazki S, Vickers SH, Fournié G, Perrins CM, Broadbent AJ, Pybus OG, Hill SC. Genetic diversity, recombination and cross-species transmission of a waterbird gammacoronavirus in the wild. J Gen Virol 2023; 104. [PMID: 37589541 DOI: 10.1099/jgv.0.001883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
Viruses emerging from wildlife can cause outbreaks in humans and domesticated animals. Predicting the emergence of future pathogens and mitigating their impacts requires an understanding of what shapes virus diversity and dynamics in wildlife reservoirs. In order to better understand coronavirus ecology in wild species, we sampled birds within a coastal freshwater lagoon habitat across 5 years, focussing on a large population of mute swans (Cygnus olor) and the diverse species that they interact with. We discovered and characterised the full genome of a divergent gammacoronavirus belonging to the Goose coronavirus CB17 species. We investigated the genetic diversity and dynamics of this gammacoronavirus using untargeted metagenomic sequencing of 223 faecal samples from swans of known age and sex, and RT-PCR screening of 1632 additional bird samples. The virus circulated persistently within the bird community; virus prevalence in mute swans exhibited seasonal variations, but did not change with swan age-class or epidemiological year. One whole genome was fully characterised, and revealed that the virus originated from a recombination event involving an undescribed gammacoronavirus species. Multiple lineages of this gammacoronavirus co-circulated within our study population. Viruses from this species have recently been detected in aquatic birds from both the Anatidae and Rallidae families, implying that host species habitat sharing may be important in shaping virus host range. As the host range of the Goose coronavirus CB17 species is not limited to geese, we propose that this species name should be updated to 'Waterbird gammacoronavirus 1'. Non-invasive sampling of bird coronaviruses may provide a tractable model system for understanding the evolutionary and cross-species dynamics of coronaviruses.
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Affiliation(s)
- Sarah François
- Department of Biology, University of Oxford, South Park Road, Oxford, OX1 3SY, UK
| | - Salik Nazki
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FZ, UK
- The Pirbright Institute, Ash Rd, Pirbright, Woking GU24 0NF, UK
| | - Stephen H Vickers
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
| | - Guillaume Fournié
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Gènes-Champanelle, France
| | | | - Andrew J Broadbent
- The Pirbright Institute, Ash Rd, Pirbright, Woking GU24 0NF, UK
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD20742, USA
| | - Oliver G Pybus
- Department of Biology, University of Oxford, South Park Road, Oxford, OX1 3SY, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
| | - Sarah C Hill
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
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11
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Wang C, Hou B. A pathogenic and recombinant infectious bronchitis virus variant (CK/CH/GX/202109) with multiorgan tropism. Vet Res 2023; 54:54. [PMID: 37400928 DOI: 10.1186/s13567-023-01182-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/26/2023] [Indexed: 07/05/2023] Open
Abstract
Despite vaccine use, novel strains and variants of infectious bronchitis virus (IBV) have emerged continuously, leading to economic losses to the poultry industry worldwide. This study aimed to characterize the IBV isolate CK/CH/GX/202109 from three yellow broilers in Guangxi, China. Recombination was shown to have occurred in regions of the 1ab gene. Compared to the whole genome of ck/CH/LGX/130530, which is genotypically related to tl/CH/LDT3-03, the 202109 strain had 21 mutations. The pathological assessment showed that this variant caused 30% and 40% mortality in 1-day-old chicks infected with oral and ocular inoculum, respectively. Nephritis, enlarged proventriculus, inflammation of the gizzard, and atrophy of the bursa of Fabricius were also observed at both 7 and 14 days post-infection (dpi). Viral loads in the trachea, proventriculus, gizzard, kidney, bursa, and cloacal swabs were higher at 7 dpi than at 14 dpi. Clinicopathological and immunohistochemical analyses revealed that this virus exhibited multiple organ tropisms capable of infecting the trachea, proventriculus, gizzard, kidney, bursa, ileum, jejunum, and rectum. Almost none of the 1-day-old infected chicks seroconverted until 14 dpi. While the virus was found in the ileum, jejunum, and rectum in the 28-day-old ocular group, the majority of 28-day-old infected chickens seroconverted at 10 dpi. These study findings demonstrate that recombination events and mutations during the evolution of IBV may greatly alter tissue tropism and emphasize the need for the continued surveillance of novel strains and variants in order to control this infection.
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Affiliation(s)
- Chenyan Wang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences/Fujian Animal Disease Control Technology Development Center, Fuzhou, 350013, Fujian Province, China
| | - Bo Hou
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences/Fujian Animal Disease Control Technology Development Center, Fuzhou, 350013, Fujian Province, China.
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12
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Pawlak JB, Hsu JCC, Xia H, Han P, Suh HW, Grove TL, Morrison J, Shi PY, Cresswell P, Laurent-Rolle M. CMPK2 restricts Zika virus replication by inhibiting viral translation. PLoS Pathog 2023; 19:e1011286. [PMID: 37075076 PMCID: PMC10150978 DOI: 10.1371/journal.ppat.1011286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 05/01/2023] [Accepted: 03/09/2023] [Indexed: 04/20/2023] Open
Abstract
Flaviviruses continue to emerge as global health threats. There are currently no Food and Drug Administration (FDA) approved antiviral treatments for flaviviral infections. Therefore, there is a pressing need to identify host and viral factors that can be targeted for effective therapeutic intervention. Type I interferon (IFN-I) production in response to microbial products is one of the host's first line of defense against invading pathogens. Cytidine/uridine monophosphate kinase 2 (CMPK2) is a type I interferon-stimulated gene (ISG) that exerts antiviral effects. However, the molecular mechanism by which CMPK2 inhibits viral replication is unclear. Here, we report that CMPK2 expression restricts Zika virus (ZIKV) replication by specifically inhibiting viral translation and that IFN-I- induced CMPK2 contributes significantly to the overall antiviral response against ZIKV. We demonstrate that expression of CMPK2 results in a significant decrease in the replication of other pathogenic flaviviruses including dengue virus (DENV-2), Kunjin virus (KUNV) and yellow fever virus (YFV). Importantly, we determine that the N-terminal domain (NTD) of CMPK2, which lacks kinase activity, is sufficient to restrict viral translation. Thus, its kinase function is not required for CMPK2's antiviral activity. Furthermore, we identify seven conserved cysteine residues within the NTD as critical for CMPK2 antiviral activity. Thus, these residues may form an unknown functional site in the NTD of CMPK2 contributing to its antiviral function. Finally, we show that mitochondrial localization of CMPK2 is required for its antiviral effects. Given its broad antiviral activity against flaviviruses, CMPK2 is a promising potential pan-flavivirus inhibitor.
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Affiliation(s)
- Joanna B. Pawlak
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Jack Chun-Chieh Hsu
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Patrick Han
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Hee-Won Suh
- Department of Biomedical Engineering, Yale University School of Engineering and Applied Science, New Haven, Connecticut, United States of America
| | - Tyler L. Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Juliet Morrison
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, Texas, United States of America
- Sealy Institute for Drug Discovery, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Peter Cresswell
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Maudry Laurent-Rolle
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
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13
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Gul I, Hassan A, Haq E, Ahmad SM, Shah RA, Ganai NA, Chikan NA, Abdul-Careem MF, Shabir N. An Investigation of the Antiviral Potential of Phytocompounds against Avian Infectious Bronchitis Virus through Template-Based Molecular Docking and Molecular Dynamics Simulation Analysis. Viruses 2023; 15:v15040847. [PMID: 37112828 PMCID: PMC10144825 DOI: 10.3390/v15040847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/17/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Vaccination is widely used to control Infectious Bronchitis in poultry; however, the limited cross-protection and safety issues associated with these vaccines can lead to vaccination failures. Keeping these limitations in mind, the current study explored the antiviral potential of phytocompounds against the Infectious Bronchitis virus using in silico approaches. A total of 1300 phytocompounds derived from fourteen botanicals were screened for their potential ability to inhibit the main protease, papain-like protease or RNA-dependent RNA–polymerase of the virus. The study identified Methyl Rosmarinate, Cianidanol, Royleanone, and 6,7-Dehydroroyleanone as dual-target inhibitors against any two of the key proteins. At the same time, 7-alpha-Acetoxyroyleanone from Rosmarinus officinalis was found to be a multi-target protein inhibitor against all three proteins. The potential multi-target inhibitor was subjected to molecular dynamics simulations to assess the stability of the protein–ligand complexes along with the corresponding reference ligands. The findings specified stable interactions of 7-alpha-Acetoxyroyleanone with the protein targets. The results based on the in silico study indicate that the phytocompounds can potentially inhibit the essential proteins of the Infectious Bronchitis virus; however, in vitro and in vivo studies are required for validation. Nevertheless, this study is a significant step in exploring the use of botanicals in feed to control Infectious Bronchitis infections in poultry.
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Affiliation(s)
- Irfan Gul
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India; (I.G.)
- Department of Biotechnology, University of Kashmir, Srinagar 190006, India
| | - Amreena Hassan
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India; (I.G.)
- Department of Biotechnology, University of Kashmir, Srinagar 190006, India
| | - Ehtishamul Haq
- Department of Biotechnology, University of Kashmir, Srinagar 190006, India
| | - Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India; (I.G.)
| | - Riaz Ahmad Shah
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India; (I.G.)
| | - Nazir Ahmad Ganai
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India; (I.G.)
| | - Naveed Anjum Chikan
- Division of Computational Biology, Daskdan Innovations, Pvt. Ltd., Kashmir 190006, India
| | - Mohamed Faizal Abdul-Careem
- Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
- Correspondence: (M.F.A.-C.); (N.S.)
| | - Nadeem Shabir
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190006, India; (I.G.)
- Correspondence: (M.F.A.-C.); (N.S.)
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14
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Icochea E, González R, Castro-Sanguinetti G, Maturrano L, Alzamora L, Sesti L, Chacón J, More-Bayona J. Genetic Analysis of Infectious Bronchitis Virus S1 Gene Reveals Novel Amino Acid Changes in the GI-16 Lineage in Peru. Microorganisms 2023; 11:microorganisms11030691. [PMID: 36985264 PMCID: PMC10051523 DOI: 10.3390/microorganisms11030691] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 03/30/2023] Open
Abstract
Infectious bronchitis is a highly contagious viral disease that represents an economic threat for poultry despite the wide use of vaccination. To characterize the virus circulating in Peru, we analyzed 200 samples, including nasopharyngeal swabs and multiple tissues collected from animals suspected of being infected with infectious bronchitis virus (IBV) between January and August in 2015. All animals had at least one positive sample for IBV by RT-PCR. Out of these positive samples, eighteen (18) were selected for viral isolation and a partial S1 sequencing. Phylogenetic analysis showed that sixteen isolates clustered with members of GI-16 lineage, also known as Q1, with nucleotide homology ranging from 93% to 98%. The two remaining isolates grouped with members of the GI-1 lineage. Our study reveals circulation of GI-16 lineage during this period in poultry systems in Peru, along with GI-1 lineage (vaccine-derived). Moreover, those IBV GI-16 isolates showed unique nucleotide and amino acid changes compared to their closest relatives. Altogether, these findings reveal the circulation of GI-16 lineage while describing changes at key regions of the S protein that might be of relevance for vaccine evasion. These results highlight the importance of genetic surveillance for improving vaccination strategies against infectious bronchitis.
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Affiliation(s)
- Eliana Icochea
- Laboratory of Avian Pathology, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalación 2800, Lima 15081, Peru
| | - Rosa González
- Laboratory of Avian Pathology, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalación 2800, Lima 15081, Peru
| | - Gina Castro-Sanguinetti
- Laboratory of Avian Pathology, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalación 2800, Lima 15081, Peru
| | - Lenin Maturrano
- Laboratory of Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalación 2800, Lima 15081, Peru
| | - Luis Alzamora
- CEVA Animal Health, 3461 Av. República de Panamá Dpto. 1102, San Isidro, Lima 15047, Peru
| | - Luiz Sesti
- CEVA Animal Health, 3461 Av. República de Panamá Dpto. 1102, San Isidro, Lima 15047, Peru
| | - Jorge Chacón
- CEVA Animal Health, 3461 Av. República de Panamá Dpto. 1102, San Isidro, Lima 15047, Peru
| | - Juan More-Bayona
- Laboratory of Avian Pathology, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalación 2800, Lima 15081, Peru
- Laboratory of Virology, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Av. Circunvalación 2800, Lima 15081, Peru
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15
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Ma P, Gu K, Wen R, Li C, Zhou C, Zhao Y, Li H, Lei C, Yang X, Wang H. Guanylate-binding protein 1 restricts avian coronavirus infectious bronchitis virus-infected HD11 cells. Poult Sci 2023; 102:102398. [PMID: 36580763 PMCID: PMC9731647 DOI: 10.1016/j.psj.2022.102398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/23/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
The Infectious Bronchitis Virus (IBV), a coronavirus, is a key avian pathogen that causes acute and highly infectious viral respiratory diseases. IBV is an enveloped, positive-sense RNA virus, and the host factors that restrict infection and replication of the virus remain poorly understood. Guanylate-binding protein 1 (GBP1), an interferon-gamma (IFN-γ)-inducible guanosine triphosphatase (GTPase), is a major player in host immunity and provides defense against viral replication. However, the role of chicken GBP1 (chGBP1) in the IBV-life cycle is not well understood. Therefore, this study aimed to reveal the potential role of IFN-γ-induced chGBP1 in mediating host anti-IBV infection responses. We identified the host restriction factor, chGBP1, in IBV-infected chicken macrophages HD11 cell lines. We showed that chGBP1 was upregulated by treatment with both IFN-γ and IBV in HD11 cells. chGBP1 inhibited IBV replication in a dose-dependent manner and enhanced IFN-γ anti-IBV activity. Importantly, the GTPase domain of chGBP1 played a pivotal role in its anti-IBV activity. Furthermore, chGBP1 interacts with IBV Nucleocapsids protein to degrade IBV-N protein through the autophagy pathway. Taken together, our results demonstrate a critical role of chGBP1 in anti-IBV in macrophages HD11 cells.
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Affiliation(s)
- Peng Ma
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Kui Gu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Renqiao Wen
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Chao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Changyu Zhou
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Yu Zhao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Hao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Changwei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Xin Yang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, 610064, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610064, China.
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16
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Molecular Detection and Characterization of Coronaviruses in Migratory Ducks from Portugal Show the Circulation of Gammacoronavirus and Deltacoronavirus. Animals (Basel) 2022; 12:ani12233283. [PMID: 36496804 PMCID: PMC9736399 DOI: 10.3390/ani12233283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/11/2022] [Accepted: 11/23/2022] [Indexed: 11/26/2022] Open
Abstract
Coronaviruses (CoVs) are part of the Coronaviridae family, and the genera Gamma (γ) and Delta (δ) are found mostly in birds. Migratory birds have an enormous potential for dispersing pathogenic microorganisms. Ducks (order Anseriformes) can host CoVs from birds, with pathogenic expression and high economic impact. This study aimed to identify and characterize the diversity of CoVs in migratory ducks from Portugal. Duck stool samples were collected using cloacal swabs from 72 individuals (Anas platyrhynchos, Anas acuta, and Anas crecca). Among the 72 samples tested, 24 showed amplicons of the expected size. Twenty-three were characterized as Gammacoronavirus and one as Deltacoronavirus (accession numbers ON368935-ON368954; ON721380-ON721383). The Gammacoronaviruses sequences showed greater similarities to those obtained in ducks (Anas platyrhynchos) from Finland and Poland, Anas crecca duck from the USA, and mute swans from Poland. Birds can occupy many habitats and therefore play diverse ecological roles in various ecosystems, especially given their ability to migrate exceptional distances, facilitating the dispersal of microorganisms with animal and/or human impact. There are a considerable number of studies that have detected CoVs in ducks, but none in Portugal. The present study assessed the circulation of CoVs in wild ducks from Portugal, being the first description of CoVs for these animals in Portugal.
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17
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Pinto SC, Aleixo J, Camela K, Chilundo AG, Bila CG. Seroprevalence of infectious bronchitis virus and avian reovirus in free backyard chickens. Onderstepoort J Vet Res 2022; 89:e1-e4. [PMID: 36453824 PMCID: PMC9724075 DOI: 10.4102/ojvr.v89i1.2042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/14/2022] [Accepted: 10/06/2022] [Indexed: 12/11/2023] Open
Abstract
Infectious bronchitis virus (IBV) and avian reovirus (ARV) cause significant losses in the poultry industry throughout the world. A cross-sectional study was conducted in four villages in Manjacaze district, Southern Mozambique, to determine the seroprevalence of IBV and ARV. A total of 467 serum samples from adult unvaccinated backyard chickens were screened using commercial and competitive enzyme-linked immunoabsorbent assay kits. Our results showed anti-IBV and anti-ARV antibodies in all surveyed households and villages. The overall seroprevalence was 89.5% (95% confidence interval [CI]: 77.2-97.4) and 95.7% (95% CI: 88.0-99.2) for IBV and ARV, respectively. The risk of becoming exposed to IBV was lower in Chidenguele village compared with the other three villages (p 0.05). However, no statistically significant differences were observed for becoming exposed to ARV between villages (p 0.05). The backyard chickens tested in this study had no previous history of vaccination, outbreaks or typical clinical signs of IB and AR diseases. Therefore, the presence of antibodies to IBV and ARV was considered clear evidence that the birds have been naturally exposed to those two infectious agents, and the infection was of subclinical type. It is concluded that IBV and ARV are widespread in backyard chickens in the studied area. These obtained data are essential for design and implementation of chicken health development programmes.Contribution: The epidemiology of IBV and ARV of backyard chicken in Mozambique is unknown. This study determined the seroprevalence of IBV and ARV in backyard chicken health. The obtained data are essential for design and implementation of chicken health development programmes.
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Affiliation(s)
- Sonia C Pinto
- Department of Animal Health and Epidemiology, Faculty of Veterinary Medicine, Eduardo Mondlane University, Maputo.
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18
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Kariithi HM, Volkening JD, Leyson CM, Afonso CL, Christy N, Decanini EL, Lemiere S, Suarez DL. Genome Sequence Variations of Infectious Bronchitis Virus Serotypes From Commercial Chickens in Mexico. Front Vet Sci 2022; 9:931272. [PMID: 35903135 PMCID: PMC9315362 DOI: 10.3389/fvets.2022.931272] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/20/2022] [Indexed: 11/16/2022] Open
Abstract
New variants of infectious bronchitis viruses (IBVs; Coronaviridae) continuously emerge despite routine vaccinations. Here, we report genome sequence variations of IBVs identified by random non-targeted next generation sequencing (NGS) of vaccine and field samples collected on FTA cards from commercial flocks in Mexico in 2019–2021. Paired-ended sequencing libraries prepared from rRNA-depleted RNAs were sequenced using Illumina MiSeq. IBV RNA was detected in 60.07% (n = 167) of the analyzed samples, from which 33 complete genome sequences were de novo assembled. The genomes are organized as 5'UTR-[Rep1a-Rep1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b]-3'UTR, except in eight sequences lacking non-structural protein genes (accessory genes) 4b, 4c, and 6b. Seventeen sequences have auxiliary S2' cleavage site located 153 residues downstream the canonically conserved primary furin-specific S1/S2 cleavage site. The sequences distinctly cluster into lineages GI-1 (Mass-type; n = 8), GI-3 (Holte/Iowa-97; n = 2), GI-9 (Arkansas-like; n = 8), GI-13 (793B; n = 14), and GI-17 (California variant; CAV; n = 1), with regional distribution in Mexico; this is the first report of the presence of 793B- and CAV-like strains in the country. Various point mutations, substitutions, insertions and deletions are present in the S1 hypervariable regions (HVRs I-III) across all 5 lineages, including in residues 38, 43, 56, 63, 66, and 69 that are critical in viral attachment to respiratory tract tissues. Nine intra-/inter-lineage recombination events are present in the S proteins of three Mass-type sequences, two each of Holte/Iowa-97 and Ark-like sequence, and one each of 793B-like and CAV-like sequences. This study demonstrates the feasibility of FTA cards as an attractive, adoptable low-cost sampling option for untargeted discovery of avian viral agents in field-collected clinical samples. Collectively, our data points to co-circulation of multiple distinct IBVs in Mexican commercial flocks, underscoring the need for active surveillance and a review of IBV vaccines currently used in Mexico and the larger Latin America region.
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Affiliation(s)
- Henry M. Kariithi
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, USDA-ARS, Athens, GA, United States
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Nairobi, Kenya
- *Correspondence: Henry M. Kariithi
| | | | - Christina M. Leyson
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, USDA-ARS, Athens, GA, United States
| | | | - Nancy Christy
- Boehringer Ingelheim Animal Health, Guadalajara, Mexico
| | | | | | - David L. Suarez
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, USDA-ARS, Athens, GA, United States
- David L. Suarez
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19
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Infectious Bronchitis Coronavirus: Genome Evolution in Vaccinated and Non-Vaccinated SPF Chickens. Viruses 2022; 14:v14071392. [PMID: 35891373 PMCID: PMC9319055 DOI: 10.3390/v14071392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 12/04/2022] Open
Abstract
Infectious Bronchitis virus (IBV) continues to cause significant economic losses for the chicken industry despite the use of many live IBV vaccines around the world. Several authors have suggested that vaccine-induced partial protection may contribute to the emergence of new IBV strains. In order to study this hypothesis, three passages of a challenge IBV were made in SPF chickens sham inoculated or vaccinated at day of age using a live vaccine heterologous to the challenge virus. All birds that were challenged with vaccine heterologous virus were positive for viral RNA. NGS analysis of viral RNA in the unvaccinated group showed a rapid selection of seven genetic variants, finally modifying the consensus genome of the viral population. Among them, five were non-synonymous, modifying one position in NSP 8, one in NSP 13, and three in the Spike protein. In the vaccinated group, one genetic variant was selected over the three passages. This synonymous modification was absent from the unvaccinated group. Under these conditions, the genome population of an IBV challenge virus evolved rapidly in both heterologous vaccinated and non-vaccinated birds, while the genetic changes that were selected and the locations of these were very different between the two groups.
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20
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Wasberg A, Raghwani J, Li J, Pettersson JHO, Lindahl JF, Lundkvist Å, Ling J. Discovery of a Novel Coronavirus in Swedish Bank Voles ( Myodes glareolus). Viruses 2022; 14:1205. [PMID: 35746677 PMCID: PMC9230040 DOI: 10.3390/v14061205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
The unprecedented pandemic COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with bats as original reservoirs, has once again highlighted the importance of exploring the interface of wildlife diseases and human health. In this study, we identified a novel Betacoronavirus from bank voles (Myodes glareolus) in Grimsö, Sweden, and this virus is designated as Grimso virus. Repeated detection over three years and an overall prevalence of 3.4% suggest that the virus commonly occurs in bank voles. Furthermore, phylogenetic analyses indicate that the Grimso virus belongs to a highly divergent Embecovirus lineage predominantly associated with bank voles. Given that bank voles are one of the most common rodent species in Sweden and Europe, our findings indicate that Grimso virus might be circulating widely in bank voles and further point out the importance of sentinel surveillance of coronaviruses in wild small mammalian animals, especially in wild rodents.
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Affiliation(s)
- Anishia Wasberg
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden; (A.W.); (J.H.-O.P.); (J.F.L.); (Å.L.)
| | - Jayna Raghwani
- Department of Zoology, University of Oxford, Oxford OX1 4BH, UK;
| | - Jinlin Li
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden;
| | - John H.-O. Pettersson
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden; (A.W.); (J.H.-O.P.); (J.F.L.); (Å.L.)
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Johanna F. Lindahl
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden; (A.W.); (J.H.-O.P.); (J.F.L.); (Å.L.)
- Department of Biosciences, International Livestock Research Institute, Nairobi 00100, Kenya
- Department of Clinical Sciences, Swedish University of Agricultural Research, 750 07 Uppsala, Sweden
| | - Åke Lundkvist
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden; (A.W.); (J.H.-O.P.); (J.F.L.); (Å.L.)
| | - Jiaxin Ling
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden; (A.W.); (J.H.-O.P.); (J.F.L.); (Å.L.)
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21
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Domańska-Blicharz K, Lisowska A, Opolska J, Pikuła A, Sajewicz-Krukowska J. Molecular Epidemiology of Turkey Coronaviruses in Poland. Viruses 2022; 14:v14051023. [PMID: 35632765 PMCID: PMC9148103 DOI: 10.3390/v14051023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 02/04/2023] Open
Abstract
The only knowledge of the molecular structure of European turkey coronaviruses (TCoVs) comes from France. These viruses have a quite distinct S gene from North American isolates. The aim of the study was to estimate the prevalence of TCoV strains in a Polish turkey farm during a twelve-year period, between 2008 and 2019, and to characterize their full-length S gene. Out of the 648 flocks tested, 65 (10.0%, 95% CI: 7.9–12.6) were positive for TCoV and 16 of them were molecularly characterized. Phylogenetic analysis showed that these strains belonged to two clusters, one formed by the early isolates identified at the beginning of the TCoV monitoring (from 2009 to 2010), and the other, which was formed by more recent strains from 2014 to 2019. Our analysis of the changes observed in the deduced amino acids of the S1 protein suggests the existence of three variable regions. Moreover, although the selection pressure analysis showed that the TCoV strains were evolving under negative selection, some sites of the S1 subunit were positively selected, and most of them were located within the proposed variable regions. Our sequence analysis also showed one TCoV strain had recombined with another one in the S1 gene. The presented investigation on the molecular feature of the S gene of TCoVs circulating in the turkey population in Poland contributes interesting data to the current state of knowledge.
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22
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Eriani G, Martin F. Viral and cellular translation during SARS‐CoV‐2 infection. FEBS Open Bio 2022; 12:1584-1601. [PMID: 35429230 PMCID: PMC9110871 DOI: 10.1002/2211-5463.13413] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/30/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022] Open
Abstract
SARS‐CoV‐2 is a betacoronavirus that emerged in China in December 2019 and which is the causative agent of the Covid‐19 pandemic. This enveloped virus contains a large positive‐sense single‐stranded RNA genome. In this review, we summarize the current knowledge on the molecular mechanisms for the translation of both viral transcripts and cellular messenger RNAs. Non‐structural proteins are encoded by the genomic RNA and are produced in the early steps of infection. In contrast, the structural proteins are produced from subgenomic RNAs that are translated in the late phase of the infectious program. Non‐structural protein 1 (NSP1) is a key molecule that regulates both viral and cellular translation. In addition, NSP1 interferes with multiple steps of the interferon I pathway and thereby blocks host antiviral responses. Therefore, NSP1 is a drug target of choice for the development of antiviral therapies.
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Affiliation(s)
- Gilbert Eriani
- Université de Strasbourg Institut de Biologie Moléculaire et Cellulaire Architecture et Réactivité de l’ARN CNRS UPR9002 2, allée Konrad Roentgen F‐67084 Strasbourg France
| | - Franck Martin
- Université de Strasbourg Institut de Biologie Moléculaire et Cellulaire Architecture et Réactivité de l’ARN CNRS UPR9002 2, allée Konrad Roentgen F‐67084 Strasbourg France
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23
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Peng S, Wang Y, Zhang Y, Song X, Zou Y, Li L, Zhao X, Yin Z. Current Knowledge on Infectious Bronchitis Virus Non-structural Proteins: The Bearer for Achieving Immune Evasion Function. Front Vet Sci 2022; 9:820625. [PMID: 35464391 PMCID: PMC9024134 DOI: 10.3389/fvets.2022.820625] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
Infectious bronchitis virus (IBV) is the first coronavirus discovered in the world, which is also the prototype of gamma-coronaviruses. Nowadays, IBV is widespread all over the world and has become one of the causative agent causing severe economic losses in poultry industry. Generally, it is believed that the viral replication and immune evasion functions of IBV were modulated by non-structural and accessory proteins, which were also considered as the causes for its pathogenicity. In this study, we summarized the current knowledge about the immune evasion functions of IBV non-structural and accessory proteins. Some non-structural proteins such as nsp2, nsp3, and nsp15 have been shown to antagonize the host innate immune response. Also, nsp7 and nsp16 can block the antigen presentation to inhibit the adapted immune response. In addition, nsp13, nsp14, and nsp16 are participating in the formation of viral mRNA cap to limit the recognition by innate immune system. In conclusion, it is of vital importance to understand the immune evasion functions of IBV non-structural and accessory proteins, which could help us to further explore the pathogenesis of IBV and provide new horizons for the prevention and treatment of IBV in the future.
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24
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Wang K, Cui P, Ni R, Gong H, Li H, Yan W, Fu X, Chen L, Lei C, Wang H, Yang X. Chicken-Derived Pattern Recognition Receptor chLGP2 Inhibits the Replication and Proliferation of Infectious Bronchitis Virus. Front Microbiol 2022; 12:810215. [PMID: 35145497 PMCID: PMC8824401 DOI: 10.3389/fmicb.2021.810215] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 12/17/2021] [Indexed: 12/03/2022] Open
Abstract
The widespread nature and economic importance of Infectious bronchitis virus (IBV) and interactions between IBV and the host immune response remain poorly understood. Understanding the mechanism of virus recognition via innate immunity can help resist IBV invasion. Retinoic acid-induced gene I-like receptor (RLRs) recognize virus RNA in virus infection, and LGP2 is a member of RLRs. According to the current studies, LGP2 exhibited certain inhibition in the virus, and there is a lack of investigation for chicken’s LGP2. It is important to figure out the role of chLGP2 in host immune recognition of IBV. Our results showed that chLGP2 inhibited the proliferation of IBV Beaudette in cells. Also, chLGP2 can identify and combine with IBV RNA. The domains of chLGP2 were separately expressed and inspired by related literature, and the chLGP2 K30A mutant was constructed. Our results suggested its structural integrity and the adenosine triphosphatase (ATPase) activity are critical for IBV inhibiting activity. chTRBP was selected after CO-IP and Mass spectrometry test. We found chTRBP and chLGP2 are the interacting partners and promote mutual expression. Our study showed that chTRBP could also suppress IBV infections via chLGP2, which provided a basis for future innate immunity research for IBV.
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Affiliation(s)
- Kailu Wang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Pengfei Cui
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Ruiqi Ni
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Huiling Gong
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Hao Li
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Wenjun Yan
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Xue Fu
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Liang Chen
- Deyang Animal Disease Control Center, Deyang, China
| | - Changwei Lei
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Hongning Wang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Xin Yang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
- *Correspondence: Xin Yang,
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25
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Evaluation of viral load and transcriptome changes in tracheal tissue of two hybrids of commercial broiler chickens infected with avian infectious bronchitis virus: a comparative study. Arch Virol 2022; 167:377-391. [PMID: 34981169 PMCID: PMC8723822 DOI: 10.1007/s00705-021-05322-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 10/19/2021] [Indexed: 01/13/2023]
Abstract
Infectious bronchitis virus (IBV) is one of the major threats to the poultry industry, with significant economic consequences. Despite strict measures, the disease is difficult to control worldwide. Experimental evidence demonstrates that the severity of IBV is affected by the genetic background of the chicken, and the selection of appropriate breeds can increase production efficiency. Therefore, the aim of the present study was to assess the strength of the immune response to IBV in tracheal tissues of Ross 308 and Cobb 500 broiler chickens by evaluating transcriptome changes, focusing on immune responses and the viral load in tracheal tissues two days after IBV infection. We identified 899 and 1350 differentially expressed genes (DEGs) in the Cobb 500 and Ross 308 experimental groups compared to their respective control groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated the involvement of signaling pathways (Toll-like receptor [TLR], NOD-like receptor [NLR], and RIG-I-like receptor [RLR] signaling pathways). Interestingly, the RLR signaling pathway appears to be affected only in the Cobb hybrid. Furthermore, the viral loads in tracheal samples obtained from the Ross challenged group were significantly higher than those of the Cobb challenged group. The results of this study indicated that the host transcriptional response to IBV infection as well as the viral load can differ by hybrid. Furthermore, genes such as TLR-3, ChIFN-α, MDA5, LGP2, IRF-7, NF-κB, and TRIM25 may interfere with IBV proliferation.
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26
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Genetic and Pathogenic Characteristics of a Novel Infectious Bronchitis Virus Strain in Genogroup VI (CK/CH/FJ/202005). Vet Microbiol 2022; 266:109352. [DOI: 10.1016/j.vetmic.2022.109352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 11/19/2022]
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27
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Inayoshi Y, Oguro S, Tanahashi E, Lin Z, Kawaguchi Y, Kodama T, Sasakawa C. Bacterial artificial chromosome-based reverse genetics system for cloning and manipulation of the full-length genome of infectious bronchitis virus. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100155. [PMID: 35909616 PMCID: PMC9325906 DOI: 10.1016/j.crmicr.2022.100155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Reverse genetics system to clone attenuated IBV C-78 full-length genome in a BAC. Rescued virus from BAC-cloned C-78 show parental virus properties. Genetic manipulation of BAC-cloned C-78 using Red-mediated recombination in E. coli. Construction of S gene recombinant C-78 by swapping with the S gene of virulent IBV. S gene determines neutralization specificity but not virulence and tissue-tropism.
Avian infectious bronchitis virus (IBV) causes highly contagious respiratory reproductive and renal system diseases in chickens, and emergence of serotypic variants resulting from mutations in the viral S gene hampers vaccine management for IBV infection. In this study, to facilitate the molecular analysis of IBV pathogenesis and the development of a new-generation IBV vaccine, we established a reverse genetics system (RGS) for cloning the full-length cDNA of the IBV C-78E128 attenuated strain in a bacterial artificial chromosome (BAC). The BAC-cloned C-78E128 cDNA generated infectious viruses with biological properties of the parental C-78E128 strain with regard to an avirulent phenotype, tissue tropism and induction of virus neutralizing (VN) antibody in vivo. To assess the feasibility of genetic manipulation of the IBV genome using the BAC-based RGS, the S gene of the BAC-cloned C-78E128 cDNA was replaced with that of the IBV S95E4 virulent strain, which differs from the C-78E128 strain in serotype and tissue tropism, by bacteriophage lambda Red-mediated homologous recombination in Escherichia coli (E. coli). The resultant S gene recombinant virus was found to be avirulent and fully competent to induce a serotype-specific VN antibody against the S95 strain; however, the S gene recombinant virus did not fully recapitulate the tissue tropism of the S95E4 strain. These data imply that serotype-specific VN immunogenicity, but not tissue-tropism and pathogenicity, of IBV is determined by the viral S gene. The IBV BAC-based RGS that enables cloning and manipulation of the IBV virus genome entirely in E. coli provides a useful platform for the molecular analyses of IBV pathogenesis and the development of rationally designed IBV recombinant vaccines.
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Pathogenicity of the Canadian Delmarva (DMV/1639) Infectious Bronchitis Virus (IBV) on Female Reproductive Tract of Chickens. Viruses 2021; 13:v13122488. [PMID: 34960757 PMCID: PMC8703381 DOI: 10.3390/v13122488] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/25/2021] [Accepted: 12/09/2021] [Indexed: 01/29/2023] Open
Abstract
Infectious bronchitis virus (IBV) infection causes significant economic losses to various sectors of the poultry industry worldwide. Over the past few years, the incidence of false layer syndrome in Eastern Canadian layer flocks has been associated with the increased prevalence of the IBV Delmarva (DMV)/1639 strain. In this study, 1-day-old specific-pathogen-free (SPF) hens were infected with the Canadian DMV/1639 strain and observed until 16 weeks of age in order to determine if the IBV DMV/1639 strain is causing false layer syndrome. Early after infection, the virus showed a wide tissue distribution with characteristic gross and histopathological lesions in the respiratory tract and kidney. Around 60–70% of the infected hens demonstrated continuous cloacal viral shedding until the end of the experiment (at 16 weeks) which was associated with high IBV genome loads detected in the cecal tonsils. The experiment confirmed the field observations that the Canadian DMV/1639 strain is highly pathogenic to the female reproductive tract causing marked cystic lesions in the oviduct. Moreover, significant histopathological damage was observed in the ovary. Our study provides a detailed description of the pathological consequences of the IBV DMV/1639 strain circulating in an important poultry production sector.
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29
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Jackwood MW, Jordan BJ. Molecular Evolution of Infectious Bronchitis Virus and the Emergence of Variant Viruses Circulating in the United States. Avian Dis 2021; 65:631-636. [DOI: 10.1637/aviandiseases-d-21-00104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 11/05/2022]
Affiliation(s)
- Mark W. Jackwood
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, Athens, GA 30602
| | - Brian J. Jordan
- Department of Population Health, Poultry Diagnostic and Research Center, College of Veterinary Medicine, Athens, GA 30602
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30
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Zhou Z, Qiu Y, Ge X. The taxonomy, host range and pathogenicity of coronaviruses and other viruses in the Nidovirales order. ANIMAL DISEASES 2021; 1:5. [PMID: 34778878 PMCID: PMC8062217 DOI: 10.1186/s44149-021-00005-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/04/2021] [Indexed: 12/17/2022] Open
Abstract
The frequent emergence of coronavirus (CoV) epidemics has seriously threatened public health and stock farming. The major hosts for CoVs are birds and mammals. Although most CoVs inhabit their specific natural hosts, some may occasionally cross the host barrier to infect livestock and even people, causing a variety of diseases. Since the beginning of the new century, increasing attention has been given to research on CoVs due to the emergence of highly pathogenic and genetically diverse CoVs that have caused several epidemics, including the recent COVID-19 pandemic. CoVs belong to the Coronaviridae family of the Nidovirales order. Recently, advanced techniques for viral detection and viral genome analyses have enabled characterization of many new nidoviruses than ever and have greatly expanded the Nidovirales order with new classification and nomenclature. Here, we first provide an overview of the latest research progress in the classification of the Nidovirales order and then introduce the host range, genetic variation, genomic pattern and pathogenic features of epidemic CoVs and other epidemic viruses. This information will promote understanding of the phylogenetic relationship and infectious transmission of various pathogenic nidoviruses, including epidemic CoVs, which will benefit virological research and viral disease control.
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Affiliation(s)
- Zhijian Zhou
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan China
| | - Ye Qiu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan China
| | - Xingyi Ge
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan China
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31
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Houta MH, Hassan KE, Legnardi M, Tucciarone CM, Abdel-Moneim AS, Cecchinato M, El-Sawah AA, Ali A, Franzo G. Phylodynamic and Recombination Analyses of Avian Infectious Bronchitis GI-23 Reveal a Widespread Recombinant Cluster and New Among-Countries Linkages. Animals (Basel) 2021; 11:ani11113182. [PMID: 34827914 PMCID: PMC8614413 DOI: 10.3390/ani11113182] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/31/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Infectious bronchitis virus (IBV) is one of the main infectious agents affecting the avian industry. The remarkable evolutionary rate of this virus represents an often unsurmountable challenge to its control, leading to the emergence of different lineages featured by different biological properties and limited cross-protection. In the present study, the origin, spreading and evolution of GI-23, one of the most important IBV emerging lineages, has been reconstructed using a phylodynamic approach. To this purpose, the broadest available collection of complete and partial S1 sequences was downloaded from GenBank and merged with specifically sequenced European strains. After a likely ancient origin, GI-23 circulated undetected in the Middle East for a considerable time, thereafter emerging as a threat in parallel with the intensification of the poultry industry and its introduction in other countries. An intensive viral circulation affecting mainly neighbouring countries or those with strong economic and political relationships was demonstrated, even though some nations appear to play a major role as a “bridge” among less related locations. Of note, a big recombinant cluster, likely originating in the Middle East but spreading thereafter, especially to Europe through Turkey, demonstrated a much-marked increase in viral population size, and potentially fitness, compared to previously circulating variants. Abstract Infectious bronchitis virus GI-23 lineage, although described approximately two decades ago in the Middle East, has recently drawn remarkable attention and is considered an “emerging” lineage due to its current spread to several other regions, including Europe. Despite the relevance, no comprehensive studies are available investigating its epidemiologic and evolutionary pattern. The present phylodynamic study was designed to fill this gap, benefitting from a collection of freely available GI-23 sequences and ad-hoc generated European ones. After a relatively ancient origin in the Middle East, likely in the first half of the previous century, GI-23 circulated largely undetected or underdiagnosed for a long time in this region, likely causing little damage, potentially because of low virulence coupled with limited development of avian industry in the considered years and regions and insufficient diagnostic activity. The following development of the poultry industry and spread to other countries led to a progressive but slow increase of viral population size between the late ‘90s and 2010. An increase in viral virulence could also be hypothesized. Of note, a big recombinant cluster, likely originating in the Middle East but spreading thereafter, especially to Europe through Turkey, demonstrated a much-marked increase in viral population size compared to previously circulating variants. The extensive available GI-23 sequence datasets allowed to demonstrate several potential epidemiological links among African, Asian, and European countries, not described for other IBV lineages. However, differently from previously investigated IBV lineages, its spread appears to primarily involve neighbouring countries and those with strong economic and political relationships. It could thus be speculated that frequent effective contacts among locations are necessary for efficient strain transmission. Some countries appear to play a major role as a “bridge” among less related locations, being Turkey the most relevant example. The role of vaccination in controlling the viral population was also tentatively evaluated. However, despite some evidence suggesting such an effect, the bias in sequence and data availability and the variability in the applied vaccination protocols prevent robust conclusions and warrant further investigations.
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Affiliation(s)
- Mohamed H. Houta
- Poultry Diseases Department, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef 62511, Egypt; (M.H.H.); (K.E.H.); (A.A.E.-S.)
| | - Kareem E. Hassan
- Poultry Diseases Department, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef 62511, Egypt; (M.H.H.); (K.E.H.); (A.A.E.-S.)
| | - Matteo Legnardi
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, 35020 Legnaro, Italy; (M.L.); (C.M.T.); (M.C.)
| | - Claudia M. Tucciarone
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, 35020 Legnaro, Italy; (M.L.); (C.M.T.); (M.C.)
| | - Ahmed S. Abdel-Moneim
- Microbiology Department, Virology Division, College of Medicine, Taif University, Taif 21944, Saudi Arabia;
| | - Mattia Cecchinato
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, 35020 Legnaro, Italy; (M.L.); (C.M.T.); (M.C.)
| | - Azza A. El-Sawah
- Poultry Diseases Department, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef 62511, Egypt; (M.H.H.); (K.E.H.); (A.A.E.-S.)
| | - Ahmed Ali
- Poultry Diseases Department, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef 62511, Egypt; (M.H.H.); (K.E.H.); (A.A.E.-S.)
- Correspondence: (A.A.); (G.F.)
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, 35020 Legnaro, Italy; (M.L.); (C.M.T.); (M.C.)
- Correspondence: (A.A.); (G.F.)
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Van Borm S, Steensels M, Mathijs E, Vandenbussche F, van den Berg T, Lambrecht B. Metagenomic sequencing determines complete infectious bronchitis virus (avian Gammacoronavirus) vaccine strain genomes and associated viromes in chicken clinical samples. Virus Genes 2021; 57:529-540. [PMID: 34626348 PMCID: PMC8501334 DOI: 10.1007/s11262-021-01872-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/24/2021] [Indexed: 12/24/2022]
Abstract
Infectious bronchitis virus (IBV, genus Gammacoronavirus) causes an economically important and highly contagious disease in chicken. Random primed RNA sequencing was applied to two IBV positive clinical samples and one in ovo-passaged virus. The virome of a cloacal swab pool was dominated by IBV (82% of viral reads) allowing de novo assembly of a GI-13 lineage complete genome with 99.95% nucleotide identity to vaccine strain 793B. In addition, substantial read counts (16% of viral reads) allowed the assembly of a near-complete chicken astrovirus genome, while lower read counts identified the presence of chicken calicivirus and avian leucosis virus. Viral reads in a respiratory/intestinal tissue pool were distributed between IBV (22.53%), Sicinivirus (Picornaviridae, 24%), and avian leucosis virus (37.04%). A complete IBV genome with 99.95% nucleotide identity to vaccine strain H120 (lineage GI-1), as well as a near-complete avian leucosis virus genome and a partial Sicinivirus genome were assembled from the tissue sample data. Lower read counts identified chicken calicivirus, Avibirnavirus (infectious bursal disease virus, assembling to 98.85% of segment A and 69.66% of segment B closely related to D3976/1 from Germany, 2017) and avian orthoreovirus, while three avian orthoavulavirus 1 reads confirmed prior real-time RT-PCR result. IBV sequence variation analysis identified both fixed and minor frequency variations in the tissue sample compared to its in ovo-passaged virus. Metagenomic methods allow the determination of complete coronavirus genomes from clinical chicken samples while providing additional insights in RNA virus sequence diversity and coinfecting viruses potentially contributing to pathogenicity.
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Affiliation(s)
- Steven Van Borm
- Department of Animal Infectious Diseases, Sciensano, Brussels, Belgium.
| | - Mieke Steensels
- Department of Animal Infectious Diseases, Sciensano, Brussels, Belgium
| | - Elisabeth Mathijs
- Department of Animal Infectious Diseases, Sciensano, Brussels, Belgium
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Complete Genome Sequence of Infectious Bronchitis Virus Strain JP/KH/64, Isolated in Japan. Microbiol Resour Announc 2021; 10:e0066521. [PMID: 34617789 PMCID: PMC8496369 DOI: 10.1128/mra.00665-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Here, we report the complete genome sequence of infectious bronchitis virus (IBV) strain JP/KH/64, which is the reference strain for the JP-I genotype in Japan. This information should be useful for an in-depth understanding of the evolution of the JP-I genotype.
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Islam A, Ferdous J, Islam S, Sayeed MA, Dutta Choudhury S, Saha O, Hassan MM, Shirin T. Evolutionary Dynamics and Epidemiology of Endemic and Emerging Coronaviruses in Humans, Domestic Animals, and Wildlife. Viruses 2021; 13:1908. [PMID: 34696338 PMCID: PMC8537103 DOI: 10.3390/v13101908] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/12/2021] [Accepted: 09/17/2021] [Indexed: 12/21/2022] Open
Abstract
Diverse coronavirus (CoV) strains can infect both humans and animals and produce various diseases. CoVs have caused three epidemics and pandemics in the last two decades, and caused a severe impact on public health and the global economy. Therefore, it is of utmost importance to understand the emergence and evolution of endemic and emerging CoV diversity in humans and animals. For diverse bird species, the Infectious Bronchitis Virus is a significant one, whereas feline enteric and canine coronavirus, recombined to produce feline infectious peritonitis virus, infects wild cats. Bovine and canine CoVs have ancestral relationships, while porcine CoVs, especially SADS-CoV, can cross species barriers. Bats are considered as the natural host of diverse strains of alpha and beta coronaviruses. Though MERS-CoV is significant for both camels and humans, humans are nonetheless affected more severely. MERS-CoV cases have been reported mainly in the Arabic peninsula since 2012. To date, seven CoV strains have infected humans, all descended from animals. The severe acute respiratory syndrome coronaviruses (SARS-CoV and SARS-CoV-2) are presumed to be originated in Rhinolopoid bats that severely infect humans with spillover to multiple domestic and wild animals. Emerging alpha and delta variants of SARS-CoV-2 were detected in pets and wild animals. Still, the intermediate hosts and all susceptible animal species remain unknown. SARS-CoV-2 might not be the last CoV to cross the species barrier. Hence, we recommend developing a universal CoV vaccine for humans so that any future outbreak can be prevented effectively. Furthermore, a One Health approach coronavirus surveillance should be implemented at human-animal interfaces to detect novel coronaviruses before emerging to humans and to prevent future epidemics and pandemics.
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Affiliation(s)
- Ariful Islam
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Burwood, VIC 3216, Australia
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Jinnat Ferdous
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
- School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia
| | - Shariful Islam
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Md. Abu Sayeed
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Shusmita Dutta Choudhury
- EcoHealth Alliance, New York, NY 10001-2320, USA; (J.F.); (S.I.); (M.A.S.); (S.D.C.)
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
| | - Otun Saha
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh;
| | - Mohammad Mahmudul Hassan
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh;
| | - Tahmina Shirin
- Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka 1212, Bangladesh;
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Tucciarone CM, Franzo G, Legnardi M, Fortin A, Valastro V, Lazzaro E, Terregino C, Cecchinato M. Effect of assay choice, viral concentration and operator interpretation on infectious bronchitis virus detection and characterization. Avian Pathol 2021; 50:357-365. [PMID: 34313501 DOI: 10.1080/03079457.2021.1959897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Despite the efforts to achieve a consistent classification scheme based on the complete S1 gene, the genetic characterization of infectious bronchitis virus (IBV) is often performed on partial S1 regions due to economic and time constraints in the diagnostic routine. Sanger sequencing remains the most common and cost-effective option even if the analysis of samples where multiple field and vaccine strain populations coexist can lead to partial or misleading results. The present study aimed to evaluate the different diagnostic outcomes of three commonly used RT-PCR methods targeting two regions of the S1 gene. A possible bias in IBV detection and characterization was investigated in relation to the adopted method, the strain concentration as well as their ratio in mixed samples. Thirty samples were prepared by artificially mixing two vaccine strains, combined at different ratios and selected among four different IBV lineages, i.e. GI-1 (Mass), GI-13 (793/B), GI-19 (QX), GI-23 (Israeli Variant 2). Sequence analysis was conducted both manually and with bioinformatic methods. The result agreement among methods, replicates and analysis approaches was statistically evaluated. Consistent results emerged among the three assays, with a few discrepancies likely caused by primer affinity and target amount. This study confirms the complexity of IBV strain identification and highlights the importance of evaluating and updating the available diagnostic assays for a reliable detection of all circulating IBV strains.
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Affiliation(s)
- Claudia Maria Tucciarone
- Department of Animal Medicine, Production and Health (MAPS), Università degli Studi di Padova, Viale dell'Università, Legnaro PD, Italy
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), Università degli Studi di Padova, Viale dell'Università, Legnaro PD, Italy
| | - Matteo Legnardi
- Department of Animal Medicine, Production and Health (MAPS), Università degli Studi di Padova, Viale dell'Università, Legnaro PD, Italy
| | - Andrea Fortin
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università, Legnaro PD, Italy
| | - Viviana Valastro
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università, Legnaro PD, Italy
| | - Elena Lazzaro
- Department of Animal Medicine, Production and Health (MAPS), Università degli Studi di Padova, Viale dell'Università, Legnaro PD, Italy
| | - Calogero Terregino
- Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università, Legnaro PD, Italy
| | - Mattia Cecchinato
- Department of Animal Medicine, Production and Health (MAPS), Università degli Studi di Padova, Viale dell'Università, Legnaro PD, Italy
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Verheije MH, Coorens M, Weerts EAWS, Berends AJ, Harten RM, Angel M, Kooij J, Ordonez SR, Beurden SJ, Dijk A, Haagsman HP, Veldhuizen EJA. Antiviral activity of selected cathelicidins against infectious bronchitis virus. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- M. Hélène Verheije
- Department of Biomolecular Health Sciences, Division Pathology, Faculty of Veterinary Medicine Utrecht University The Netherlands
| | - Maarten Coorens
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Section Molecular Host Defence, Faculty of Veterinary Medicine Utrecht University The Netherlands
| | - Erik A. W. S. Weerts
- Department of Biomolecular Health Sciences, Division Pathology, Faculty of Veterinary Medicine Utrecht University The Netherlands
| | - Alinda J. Berends
- Department of Biomolecular Health Sciences, Division Pathology, Faculty of Veterinary Medicine Utrecht University The Netherlands
| | - Roel M. Harten
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Section Molecular Host Defence, Faculty of Veterinary Medicine Utrecht University The Netherlands
| | - Marloes Angel
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Section Molecular Host Defence, Faculty of Veterinary Medicine Utrecht University The Netherlands
| | - Jannetje Kooij
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Section Molecular Host Defence, Faculty of Veterinary Medicine Utrecht University The Netherlands
| | - Soledad R. Ordonez
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Section Molecular Host Defence, Faculty of Veterinary Medicine Utrecht University The Netherlands
| | - Steven J. Beurden
- Department of Biomolecular Health Sciences, Division Pathology, Faculty of Veterinary Medicine Utrecht University The Netherlands
| | - Albert Dijk
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Section Molecular Host Defence, Faculty of Veterinary Medicine Utrecht University The Netherlands
| | - Henk P. Haagsman
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Section Molecular Host Defence, Faculty of Veterinary Medicine Utrecht University The Netherlands
| | - Edwin J. A. Veldhuizen
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Section Immunology, Faculty of Veterinary Medicine Utrecht University The Netherlands
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Yan W, Qiu R, Wang F, Fu X, Li H, Cui P, Zhai Y, Li C, Zhang L, Gu K, Zuo L, Lei C, Wang H, Yang X. 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. Poult Sci 2021; 100:101210. [PMID: 34116353 PMCID: PMC8192866 DOI: 10.1016/j.psj.2021.101210] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 11/19/2022] Open
Abstract
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.
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Affiliation(s)
- Wenjun Yan
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province; Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science Sichuan University, Chengdu 610064, China
| | - Rongbin Qiu
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Fuyan Wang
- Sichuan Sundaily Farm Ecological Food Co., Ltd., Mianyang 621010, China
| | - Xue Fu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province; Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science Sichuan University, Chengdu 610064, China
| | - Hao Li
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province; Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science Sichuan University, Chengdu 610064, China
| | - Pengfei Cui
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province; Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science Sichuan University, Chengdu 610064, China
| | - Yaru Zhai
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province; Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science Sichuan University, Chengdu 610064, China
| | - Chun Li
- Sichuan Animal Disease Control Center, Chengdu, 610041, China
| | - Lan Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province; Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science Sichuan University, Chengdu 610064, China
| | - Kui Gu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province; Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science Sichuan University, Chengdu 610064, China
| | - Lei Zuo
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province; Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science Sichuan University, Chengdu 610064, China
| | - Changwei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province; Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science Sichuan University, Chengdu 610064, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province; Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science Sichuan University, Chengdu 610064, China
| | - Xin Yang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province; Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science Sichuan University, Chengdu 610064, China.
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Lisowska A, Pikuła A, Opolska J, Jasik A, Kycko A, Domańska-Blicharz K. Virulence Properties of GI-23 Infectious Bronchitis Virus Isolated in Poland and Efficacy of Different Vaccination strategies. Pathogens 2021; 10:pathogens10050522. [PMID: 33926018 PMCID: PMC8145137 DOI: 10.3390/pathogens10050522] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 11/16/2022] Open
Abstract
Infectious bronchitis virus (IBV) is one of the most important poultry pathogens, leading significant economic losses worldwide. IBV is characterised by highly genetic, serotype, and pathotypic variability. Despite extensive immunoprophylaxis strategies, the emergence of new genetic lineages is frequently observed in the field, causing disease control to be more complicated. In the last decade, the spread of variants assigned to the GI-23 lineage of IBV (formerly known as Var2) started from Middle-Eastern countries and reached Europe in the last few years. Recently, the introduction and fast spread of Var2-like IBVs in Poland was reported. In this study, the virulence properties and efficacy of different vaccination programmes were evaluated against infection with the IBV GI-23 strain gammaCoV/Ck/Poland/G052/2016. The pathogenicity of the Var2 isolate was conducted in one-day-old and three-week-old SPF chickens and showed that the course of the disease is age dependent. Seven vaccination programmes using Mass, 793B, QX alone or in combination, and Var2 live vaccines were tested against the GI-23 infectious bronchitis virus challenge. All groups were scored according to the ciliostasis test at 5 days post challenge. Two immunoprophylaxis strategies generated full protection against gammaCoV/Ck/Poland/G052/2016 infection-Var2 and Mass used in one-day-old chickens boosted by a combination of the QX and 793B vaccine (both with a ciliostasis score of 0 and 100% protection).
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Affiliation(s)
- Anna Lisowska
- Department of Poultry Diseases, National Veterinary Research Institute, Partyzantów 57, 24-100 Puławy, Poland; (A.L.); (J.O.)
| | - Anna Pikuła
- Department of Poultry Diseases, National Veterinary Research Institute, Partyzantów 57, 24-100 Puławy, Poland; (A.L.); (J.O.)
- Correspondence: (A.P.); (K.D.-B.)
| | - Justyna Opolska
- Department of Poultry Diseases, National Veterinary Research Institute, Partyzantów 57, 24-100 Puławy, Poland; (A.L.); (J.O.)
| | - Agnieszka Jasik
- Department of Pathology, National Veterinary Research Institute, Partyzantów 57, 24-100 Puławy, Poland; (A.J.); (A.K.)
| | - Anna Kycko
- Department of Pathology, National Veterinary Research Institute, Partyzantów 57, 24-100 Puławy, Poland; (A.J.); (A.K.)
| | - Katarzyna Domańska-Blicharz
- Department of Poultry Diseases, National Veterinary Research Institute, Partyzantów 57, 24-100 Puławy, Poland; (A.L.); (J.O.)
- Correspondence: (A.P.); (K.D.-B.)
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Franzo G, Tucciarone CM, Legnardi M, Cecchinato M. Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues. BMC Genomics 2021; 22:244. [PMID: 33827429 PMCID: PMC8025453 DOI: 10.1186/s12864-021-07559-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 03/26/2021] [Indexed: 11/10/2022] Open
Abstract
Background Infectious bronchitis virus (IBV) is one of the most relevant viruses affecting the poultry industry, and several studies have investigated the factors involved in its biological cycle and evolution. However, very few of those studies focused on the effect of genome composition and the codon bias of different IBV proteins, despite the remarkable increase in available complete genomes. In the present study, all IBV complete genomes were downloaded (n = 383), and several statistics representative of genome composition and codon bias were calculated for each protein-coding sequence, including but not limited to, the nucleotide odds ratio, relative synonymous codon usage and effective number of codons. Additionally, viral codon usage was compared to host codon usage based on a collection of highly expressed genes in IBV target and nontarget tissues. Results The results obtained demonstrated a significant difference among structural, non-structural and accessory proteins, especially regarding dinucleotide composition, which appears under strong selective forces. In particular, some dinucleotide pairs, such as CpG, a probable target of the host innate immune response, are underrepresented in genes coding for pp1a, pp1ab, S and N. Although genome composition and dinucleotide bias appear to affect codon usage, additional selective forces may act directly on codon bias. Variability in relative synonymous codon usage and effective number of codons was found for different proteins, with structural proteins and polyproteins being more adapted to the codon bias of host target tissues. In contrast, accessory proteins had a more biased codon usage (i.e., lower number of preferred codons), which might contribute to the regulation of their expression level and timing throughout the cell cycle. Conclusions The present study confirms the existence of selective forces acting directly on the genome and not only indirectly through phenotype selection. This evidence might help understanding IBV biology and in developing attenuated strains without affecting the protein phenotype and therefore immunogenicity. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07559-5.
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Affiliation(s)
- Giovanni Franzo
- Microbiology and Infectious Diseases, Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16 - 35020 Legnaro, Padua, Italy.
| | - Claudia Maria Tucciarone
- Microbiology and Infectious Diseases, Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16 - 35020 Legnaro, Padua, Italy
| | - Matteo Legnardi
- Microbiology and Infectious Diseases, Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16 - 35020 Legnaro, Padua, Italy
| | - Mattia Cecchinato
- Microbiology and Infectious Diseases, Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16 - 35020 Legnaro, Padua, Italy
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Colina SE, Serena MS, Echeverría MG, Metz GE. Clinical and molecular aspects of veterinary coronaviruses. Virus Res 2021; 297:198382. [PMID: 33705799 PMCID: PMC7938195 DOI: 10.1016/j.virusres.2021.198382] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/20/2020] [Accepted: 03/04/2021] [Indexed: 12/12/2022]
Abstract
Coronaviruses are a large group of RNA viruses that infect a wide range of animal species. The replication strategy of coronaviruses involves recombination and mutation events that lead to the possibility of cross-species transmission. The high plasticity of the viral receptor due to a continuous modification of the host species habitat may be the cause of cross-species transmission that can turn into a threat to other species including the human population. The successive emergence of highly pathogenic coronaviruses such as the Severe Acute Respiratory Syndrome (SARS) in 2003, the Middle East Respiratory Syndrome Coronavirus in 2012, and the recent SARS-CoV-2 has incentivized a number of studies on the molecular basis of the coronavirus and its pathogenesis. The high degree of interrelatedness between humans and wild and domestic animals and the modification of animal habitats by human urbanization, has favored new viral spreads. Hence, knowledge on the main clinical signs of coronavirus infection in the different hosts and the distinctive molecular characteristics of each coronavirus is essential to prevent the emergence of new coronavirus diseases. The coronavirus infections routinely studied in veterinary medicine must be properly recognized and diagnosed not only to prevent animal disease but also to promote public health.
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Affiliation(s)
- Santiago Emanuel Colina
- Virology, Faculty of Veterinary Sciences, National University of La Plata, La Plata, Argentina; CONICET (National Scientific and Technical Research Council), CCT La Plata, Argentina
| | - María Soledad Serena
- Virology, Faculty of Veterinary Sciences, National University of La Plata, La Plata, Argentina; CONICET (National Scientific and Technical Research Council), CCT La Plata, Argentina
| | - María Gabriela Echeverría
- Virology, Faculty of Veterinary Sciences, National University of La Plata, La Plata, Argentina; CONICET (National Scientific and Technical Research Council), CCT La Plata, Argentina
| | - Germán Ernesto Metz
- Virology, Faculty of Veterinary Sciences, National University of La Plata, La Plata, Argentina; CONICET (National Scientific and Technical Research Council), CCT La Plata, Argentina.
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Domanska-Blicharz K, Sajewicz-Krukowska J. Recombinant turkey coronavirus: are some S gene structures of gammacoronaviruses especially prone to exchange? Poult Sci 2021; 100:101018. [PMID: 33662661 PMCID: PMC7937746 DOI: 10.1016/j.psj.2021.101018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 12/30/2020] [Accepted: 01/19/2021] [Indexed: 01/16/2023] Open
Abstract
The objective of the present study was to characterize the atypical turkey coronavirus strain detected in a commercial meat turkey farm in Poland. Using the viral metagenomics approach, we obtained a complete genome sequence of coronavirus, isolated from duodenum samples of animals suffering from acute enteritis. The nearly full-length genome consisted of 27,614 nucleotides and presented a typical genetic organization similar to that of Polish infectious bronchitis virus (IBV) or French turkey coronavirus/guinea fowl coronavirus strains. Phylogenetic analysis based on both the full-length genome and the whole S gene suggested that gCoV/Tk/Poland/G160/2016 is related to turkey and guinea fowl coronavirus and not IBV strains. Sequence analysis of the genome revealed unique genetic characteristics of the present strain, demonstrating that the virus emerged as a result of the exchange of the S gene of IBV GI-19 lineage with the S gene related to the North American turkey coronaviruses and French guinea fowl coronaviruses. Analysis of earlier, similar recombinations suggests that both the S gene structures may be particularly mobile, willingly switching between different gammacoronavirus genomic backbones. The identified recombinant caused a severe course of the disease, which may imply that it is in the first phase of breaking the barriers between different bird species.
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42
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Karpiński TM, Ożarowski M, Seremak-Mrozikiewicz A, Wolski H, Wlodkowic D. The 2020 race towards SARS-CoV-2 specific vaccines. Theranostics 2021; 11:1690-1702. [PMID: 33408775 PMCID: PMC7778607 DOI: 10.7150/thno.53691] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/08/2020] [Indexed: 12/13/2022] Open
Abstract
The global outbreak of a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlighted a requirement for two pronged clinical interventions such as development of effective vaccines and acute therapeutic options for medium-to-severe stages of "coronavirus disease 2019" (COVID-19). Effective vaccines, if successfully developed, have been emphasized to become the most effective strategy in the global fight against the COVID-19 pandemic. Basic research advances in biotechnology and genetic engineering have already provided excellent progress and groundbreaking new discoveries in the field of the coronavirus biology and its epidemiology. In particular, for the vaccine development the advances in characterization of a capsid structure and identification of its antigens that can become targets for new vaccines. The development of the experimental vaccines requires a plethora of molecular techniques as well as strict compliance with safety procedures. The research and clinical data integrity, cross-validation of the results, and appropriated studies from the perspective of efficacy and potently side effects have recently become a hotly discussed topic. In this review, we present an update on latest advances and progress in an ongoing race to develop 52 different vaccines against SARS-CoV-2. Our analysis is focused on registered clinical trials (current as of November 04, 2020) that fulfill the international safety and efficacy criteria in the vaccine development. The requirements as well as benefits and risks of diverse types of SARS-CoV-2 vaccines are discussed including those containing whole-virus and live-attenuated vaccines, subunit vaccines, mRNA vaccines, DNA vaccines, live vector vaccines, and also plant-based vaccine formulation containing coronavirus-like particle (VLP). The challenges associated with the vaccine development as well as its distribution, safety and long-term effectiveness have also been highlighted and discussed.
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Affiliation(s)
- Tomasz M. Karpiński
- Chair and Department of Medical Microbiology, Poznań University of Medical Sciences, Wieniawskiego 3, 61-712 Poznań, Poland
| | - Marcin Ożarowski
- Department of Biotechnology, Institute of Natural Fibres and Medicinal Plants, Poznań, Poland
| | - Agnieszka Seremak-Mrozikiewicz
- Division of Perinatology and Women's Disease, Poznań University of Medical Sciences, Poznań, Poland
- Laboratory of Molecular Biology in Division of Perinatology and Women's Diseases, Poznań University of Medical Sciences, Poznań, Poland
- Department of Pharmacology and Phytochemistry, Institute of Natural Fibres and Medicinal Plants, Poznań, Poland
| | - Hubert Wolski
- Division of Perinatology and Women's Disease, Poznań University of Medical Sciences, Poznań, Poland
- Division of Obstetrics and Gynecology, Tytus Chałubiński's Hospital, Zakopane, Poland
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Abozeid HH, Naguib MM. Infectious Bronchitis Virus in Egypt: Genetic Diversity and Vaccination Strategies. Vet Sci 2020; 7:vetsci7040204. [PMID: 33348570 PMCID: PMC7766096 DOI: 10.3390/vetsci7040204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
Infectious bronchitis virus (IBV) is a highly evolving avian pathogen that has increasingly imposed a negative impact on poultry industry worldwide. In the last 20 years, IBV has been continuously circulating among chicken flocks in Egypt causing huge economic losses to poultry production. Multiple IBV genotypes, namely, GI-1, GI-13, GI-16, and GI-23 have been reported in Egypt possessing different genetic and pathogenic features. Different vaccine programs are being used to control the spread of the disease in Egypt. However, the virus continues to spread and evolve where multiple IBV variants and several recombination evidence have been described. In this review, we highlight the current knowledge concerning IBV circulation, genesis, and vaccination strategies in Egypt. In addition, we analyze representative Egyptian IBV strains from an evolutionary perspective based on available data of their S1 gene. We also provide insight into the importance of surveillance programs and share our perspectives for better control of IBV circulating in Egypt.
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Affiliation(s)
- Hassanein H. Abozeid
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt;
| | - Mahmoud M. Naguib
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 21 Uppsala, Sweden
- Correspondence:
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Hemida MG, Ba Abduallah MM. The SARS-CoV-2 outbreak from a one health perspective. One Health 2020; 10:100127. [PMID: 32292814 PMCID: PMC7102578 DOI: 10.1016/j.onehlt.2020.100127] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/12/2020] [Accepted: 03/14/2020] [Indexed: 01/04/2023] Open
Abstract
The severe acute respiratory syndrome cornavirus (SARS-CoV-2) is a new human coronavirus candidate recently detected in China that is now reported in people on inhabited continents. The virus shares a high level of identity with some bat coronaviruses and is recognised as a potentially zoonotic virus. We are utilizing the One Health concept to understand the emergence of the virus, as well as to point to some possible control strategies that might reduce the spread of the virus across the globe; thus, containment of such virus would be possible.
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Affiliation(s)
- Maged Gomaa Hemida
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Egypt
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45
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Tegegne D, Deneke Y, Sori T, Abdurahaman M, Kebede N, Cecchinato M, Franzo G. Molecular Epidemiology and Genotyping of Infectious Bronchitis Virus and Avian Metapneumovirus in Backyard and Commercial Chickens in Jimma Zone, Southwestern Ethiopia. Vet Sci 2020; 7:vetsci7040187. [PMID: 33255570 PMCID: PMC7711717 DOI: 10.3390/vetsci7040187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 01/26/2023] Open
Abstract
Poultry production plays a relevant role in the Ethiopian economy and represents a source of poverty alleviation for several social classes. Infectious diseases can therefore significantly impact the economy and welfare. Despite infectious bronchitis virus (IBV) and avian metapneumovirus (aMPV) being present, the knowledge of their epidemiology and impact is extremely limited. In the present work, a cross-sectional study based on 500 tracheal swabs collected from 50 intensive and backyard unvaccinated flocks of the Jimma Zone was performed to investigate the circulation of these viruses and molecularly characterize them. IBV and aMPV presence was tested by molecular assays, and genotyping was carried out on positive samples. Accordingly, 6% (95% CI 2.06% to 16.22%) and 8% (95% CI 3.15% to 18.84%) of flocks tested IBV and aMPV positive, respectively. Particularly, IBV 793B (GI-13) strains were detected in backyard flocks only, and identical or closely related sequences (p-distance <2%) were detected in distantly spaced flocks, suggesting relevant viral circulation. On the contrary, both backyard and intensive flocks were affected by aMPV subtype B. Potential epidemiological links associated to the importation of parental birds from foreign countries could be established. These results highlight non-negligible circulation of these viruses, warranting further epidemiological studies and the evaluation of control measure implementation.
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Affiliation(s)
- Dechassa Tegegne
- School of Veterinary Medicine, Jimma University College of Agriculture and Veterinary Medicine, P.O. Box 307 Jimma, Ethiopia; (D.T.); (Y.D.); (T.S.); (M.A.)
| | - Yosef Deneke
- School of Veterinary Medicine, Jimma University College of Agriculture and Veterinary Medicine, P.O. Box 307 Jimma, Ethiopia; (D.T.); (Y.D.); (T.S.); (M.A.)
| | - Takele Sori
- School of Veterinary Medicine, Jimma University College of Agriculture and Veterinary Medicine, P.O. Box 307 Jimma, Ethiopia; (D.T.); (Y.D.); (T.S.); (M.A.)
| | - Mukarim Abdurahaman
- School of Veterinary Medicine, Jimma University College of Agriculture and Veterinary Medicine, P.O. Box 307 Jimma, Ethiopia; (D.T.); (Y.D.); (T.S.); (M.A.)
| | - Nigatu Kebede
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 1176 Addis Ababa, Ethiopia;
| | - Mattia Cecchinato
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, 35020 Legnaro (PD), Italy;
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, 35020 Legnaro (PD), Italy;
- Correspondence:
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Farjana M, Moni A, Sohag AAM, Hasan A, Hannan MA, Hossain MG, Uddin MJ. Repositioning Vitamin C as a Promising Option to Alleviate Complications associated with COVID-19. Infect Chemother 2020; 52:461-477. [PMID: 33263242 PMCID: PMC7779993 DOI: 10.3947/ic.2020.52.4.461] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/05/2020] [Indexed: 02/07/2023] Open
Abstract
Vitamin C, also known as L-ascorbic acid, is an essential vitamin with pleiotropic functions, ranging from antioxidant to anti-microbial functions. Evidence suggests that vitamin C acts against inflammation, oxidative stress, autophagy chaos, and immune dysfunction. The ability to activate and enhance the immune system makes this versatile vitamin a prospective therapeutic agent amid the current situation of coronavirus disease 2019 (COVID-19). Being highly effective against the influenza virus, causing the common cold, vitamin C may also function against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and its associated complications. Severe infections need higher doses of the vitamin to compensate for the augmented inflammatory response and metabolic demand that commonly occur during COVID-19. Compelling evidence also suggests that a high dose of vitamin C (1.5 g/kg body weight) in inflammatory conditions can result in effective clinical outcomes and thus can be employed to combat COVID-19. However, further studies are crucial to delineate the mechanism underlying the action of vitamin C against COVID-19. The current review aims to reposition vitamin C as an alternative approach for alleviating COVID-19-associated complications.
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Affiliation(s)
| | - Akhi Moni
- ABEx Bio-Research Center, East Azampur, Dhaka, Bangladesh
| | - Abdullah Al Mamun Sohag
- Department of Biochemistry and Molecular Biology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Adeba Hasan
- ABEx Bio-Research Center, East Azampur, Dhaka, Bangladesh
| | - Md Abdul Hannan
- ABEx Bio-Research Center, East Azampur, Dhaka, Bangladesh.,Department of Biochemistry and Molecular Biology, Bangladesh Agricultural University, Mymensingh, Bangladesh.,Department of Anatomy, Dongguk University College of Medicine, Gyeongju, Korea
| | - Md Golzar Hossain
- Division of Virology, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md Jamal Uddin
- ABEx Bio-Research Center, East Azampur, Dhaka, Bangladesh.,Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, Korea.
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Al-Jallad T, Kassouha M, Salhab M, Alomar A, Al-Masalma M, Abdelaziz F. Molecular characterization of isolated infectious bronchitis viruses from affected vaccinated broiler flocks in Syria. BMC Vet Res 2020; 16:449. [PMID: 33213457 PMCID: PMC7678145 DOI: 10.1186/s12917-020-02672-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 11/09/2020] [Indexed: 11/29/2022] Open
Abstract
Background Avian Infectious Bronchitis Virus (IBV) is a highly contagious disease that imposes a huge economic burden on the global poultry industry. IBV contains numerous serotypes and variants with incomplete tenuous cross immunological protection. The failure of currently used vaccines to protect against diverse, circulating IBV strains that are specific to a given region poses a major problem for the poultry industry. Thus, there is an urgent need to conduct studies aimed at genotyping field IB viruses. In this study, we have determined the molecular characteristics of circulating IBV by sequencing the S1 gene of viral isolates from affected previously vaccinated broiler flocks suffering from the disease. Results Ten isolates propagated in embryonated eggs showed an ability to induce typical IBV lesions after three successive viral passages. We performed a nested RT–PCR assay that targeted the hypervariable region 3 (HVR-3) of the S1 gene, and identified the isolates as IBV through sequence analysis. The IBV isolates showed sequence similarity between the Syrian isolates that vary from 96.20 to 100%, and those being closer to the Variant-2 strain IS/1494/06 (EU780077.2) with 97.5 to 99.4% similarities. However, less nucleotide identity was found with sequences belonging to the used vaccine strains such as H120, Mass5, and 4/91. Conclusions This study showed the presence of the Variant-2 strain circulating in Syrian broiler flocks showing signs of IBV disease. Currently, there is no commercial effective vaccine which protects birds against the Variant-2 strain. Continuous monitoring procedures should be taken to control and limit the spread of the IBV Variant-2 strain. This research emphasizes both the importance of epidemiological monitoring in intensive poultry farming for novel pathogens and the use of local isolates as future vaccine targets.
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Affiliation(s)
- Tamara Al-Jallad
- The General Commission for Scientific Agricultural Research, Lattakia, Syria.,Department of Animal Production, Tishreen University, Lattakia, Syria
| | - Morshed Kassouha
- Department of Microbiology, Faculty of Veterinary Medicine, Hama University, Hama, Syria.
| | - Mohamad Salhab
- The General Commission for Scientific Agricultural Research, Lattakia, Syria
| | - Anouar Alomar
- Faculty of Sciences, Al-Baath University, Homs, Syria
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Bovine Coronavirus: Variability, Evolution, and Dispersal Patterns of a No Longer Neglected Betacoronavirus. Viruses 2020; 12:v12111285. [PMID: 33182765 PMCID: PMC7697035 DOI: 10.3390/v12111285] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022] Open
Abstract
Bovine coronavirus (BoCV) is an important pathogen of cattle, causing severe enteric disease and playing a role in the bovine respiratory disease complex. Similar to other coronaviruses, a remarkable variability characterizes both its genome and biology. Despite their potential relevance, different aspects of the evolution of BoCV remain elusive. The present study reconstructs the history and evolution of BoCV using a phylodynamic approach based on complete genome and spike protein sequences. The results demonstrate high mutation and recombination rates affecting different parts of the viral genome. In the spike gene, this variability undergoes significant selective pressures—particularly episodic pressure—located mainly on the protein surface, suggesting an immune-induced selective pressure. The occurrence of compensatory mutations was also identified. On the contrary, no strong evidence in favor of host and/or tissue tropism affecting viral evolution has been proven. The well-known plasticity is thus ascribable to the innate broad viral tropism rather than mid- or long-term adaptation. The evaluation of the geographic spreading pattern clearly evidenced two clusters: a European cluster and an American–Asian cluster. While a relatively dense and quick migration network was identified in the former, the latter was dominated by the primary role of the United States (US) as a viral exportation source. Since the viral spreading pattern strongly mirrored the cattle trade, the need for more intense monitoring and preventive measures cannot be underestimated as well as the need to enforce the vaccination of young animals before international trade, to reduce not only the clinical impact but also the transferal and mixing of BoCV strains.
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Moharam I, Sultan H, Hassan K, Ibrahim M, Shany S, Shehata AA, Abo-ElKhair M, Pfaff F, Höper D, EL Kady M, Beer M, Harder T, Hafez H, Grund C. Emerging infectious bronchitis virus (IBV) in Egypt: Evidence for an evolutionary advantage of a new S1 variant with a unique gene 3ab constellation. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104433. [PMID: 32622080 PMCID: PMC7327463 DOI: 10.1016/j.meegid.2020.104433] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/05/2020] [Accepted: 06/16/2020] [Indexed: 12/21/2022]
Abstract
Infectious bronchitis virus (IBV), a gamma-coronavirus, causes infectious bronchitis (IB), a major respiratory disease of chicken. Its high mutation rate in conjunction with recombination of the RNA genome constantly creates IBV variants that are difficult to control by currently available vaccines. In this study, we addressed the question whether small-scale holdings might harbor IBV variants that serve as a reservoir for newly emerging variants. Egyptian IBV isolate EGY/NR725/2016 (NR725/16) from a small-scale broiler farm was assigned to genotype I, clade 23 (S1:GI-23), based on partial S1 gene sequences and corroborated by full genome sequencing. Analysis of the S1 gene established three subclades for historical IBV strains (S1:GI-23.1, S1:GI-23.2.1 and S1:GI-23.2.2) and confirmed NR725/16 as being part of a separate fourth subclade (S1:GI-23.3). Samples from the years 2018 and 2019 revealed that the new subclade prevails in Egypt, carrying fixed mutations within the hypervariable regions (HVR) 1-3 of the S1 protein that affect two neutralization sensitive epitopes at sites 294F, 297S and 306Y (48.2) and 329R (62.1). In addition, recombination was recognized in isolate NR 725/16, with intra-subtype mixing for the entire genes 3ab and E and inter-subtype mixing for the entire gene 6b with a close match to QX like viruses of genotype GI-19. Further analysis of gene 3ab detected the homologous gene pool to NR725/16 in samples from 2013 (3ab:C) and closely related 3ab genotypes in IBV Egyptian isolates from 2016, 2018 and 2019. These data prove a flourishing exchange between poultry holdings with a common gene pool. The continued circulation of viruses harboring genes S1:GI-23.3 and 3ab:C indicates an evolutionary advantage of this combination possibly by combining antigenic escape with modulated pathogenicity to facilitate IBV spread in the vaccinated poultry population in Egypt.
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Affiliation(s)
- Ibrahim Moharam
- Institute of Diagnostic Virology Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Germany,Department of Birds and Rabbits Medicine, University of Sadat City, Monufia, Egypt
| | - Hesham Sultan
- Department of Birds and Rabbits Medicine, University of Sadat City, Monufia, Egypt
| | - K. Hassan
- Institute of Diagnostic Virology Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Germany,Department of Poultry Diseases, Beni-Suef University, Beni-Suef, Egypt
| | - Mahmoud Ibrahim
- Department of Birds and Rabbits Medicine, University of Sadat City, Monufia, Egypt
| | - Salama Shany
- Department of Poultry Diseases, Beni-Suef University, Beni-Suef, Egypt
| | - Awad A. Shehata
- Department of Birds and Rabbits Medicine, University of Sadat City, Monufia, Egypt
| | | | - Florian Pfaff
- Institute of Diagnostic Virology Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Germany
| | - Magdy EL Kady
- Department of Poultry Diseases, Beni-Suef University, Beni-Suef, Egypt
| | - Martin Beer
- Institute of Diagnostic Virology Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Germany
| | - Timm Harder
- Institute of Diagnostic Virology Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Germany
| | - Hafez Hafez
- Institute of Poultry Disease, Freie Universität Berlin, Germany
| | - Christian Grund
- Institute of Diagnostic Virology Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Germany.
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50
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Emergence of Avian coronavirus genotype GI-11 in Colombia. Braz J Microbiol 2020; 52:455-459. [PMID: 33104974 PMCID: PMC7586380 DOI: 10.1007/s42770-020-00394-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/17/2020] [Indexed: 11/16/2022] Open
Abstract
Avian coronavirus (AvCoV/IBV) is a virus with high morbidity, which can cause respiratory, digestive, renal, and reproductive diseases in chickens. Molecular detection and sequencing are the main tool for identification and classification of AvCoV. Thirty-six samples were collected in three broiler farms from different regions in Colombia, due to mortality increase; ten samples were positive using RT-qPCR targeted to the 5′ UTR of AvCoV, and one sample was positive and had its partial S gene sequenced. Phylogenetic analysis revealed that this strain belongs to the GI-11 lineage, similar to the Brazilian cluster. Several lineages have already been described in Colombia but, to the best of our knowledge, this is the first time that GI-11 has been detected in this country, which suggests that this subtype may be more widespread in South America than previously thought.
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