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Huang X, Li Y, Li J, Jiang Y, Cui W, Zhou H, Tang L. The long noncoding RNA loc107053557 acts as a gga-miR-3530-5p sponge to suppress the replication of vvIBDV through regulating STAT1 expression. Virulence 2024; 15:2333237. [PMID: 38528779 PMCID: PMC10984138 DOI: 10.1080/21505594.2024.2333237] [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: 10/18/2023] [Accepted: 03/16/2024] [Indexed: 03/27/2024] Open
Abstract
Infectious bursal disease virus (IBDV) causes immunosuppression and high mortality in young chickens. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are important regulators during viral infection. However, detailed the regulatory mechanisms of lncRNA-miRNA-mRNA have not yet been described in IBDV infection. Here, we analysed the role of lncRNA53557/gga-miR-3530-5p/STAT1 axis in very virulent IBDV (vvIBDV) infection. Evidently upregulated expression of lncRNA53557 was observed in bursa of Fabricius and DT40 cells. Meanwhile, overexpression of lncRNA53557 promoted STAT1 expression and inhibited vvIBDV replication and vice versa, indicating that the upregulation of lncRNA53557 was part of the host antiviral defence. The subcellular fractionation assay confirmed that lncRNA53557 can be localized in the cytoplasm. Further, dual-luciferase reporter, RNA pulldown, FISH and RT-qPCR assays revealed that lncRNA53557 were directly bound to gga-miR-3530-5p and had a negative regulatory relationship between them. Subsequent mechanistic analysis showed that lncRNA53557 acted as a competing endogenous RNA (ceRNA) of gga-miR-3530-5p to relieve the repressive effect of gga-miR-3530-5p on its target STAT1, as well as Mx1, OASL, and ISG15, thereby suppressing vvIBDV replication. The study reveals that a network of enriched lncRNAs and lncRNA-associated ceRNA is involved in the regulation of IBDV infection, offering new insight into the mechanisms underlying IBDV-host interaction.
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Affiliation(s)
- Xuewei Huang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, P.R. China
| | - Yue Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
| | - Jiaxuan Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
| | - Yanping Jiang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, P.R. China
| | - Wen Cui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, P.R. China
| | - Han Zhou
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, P.R. China
| | - Lijie Tang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, P.R. China
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Sajid S, Rahman SU, Mohin M, Sindhu ZUD. Development of egg yolk-based polyclonal antibodies and immunoprophylactic potential of antigen-antibody complex against infectious bursal disease. Vet Anim Sci 2024; 23:100326. [PMID: 38162251 PMCID: PMC10755096 DOI: 10.1016/j.vas.2023.100326] [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] [Indexed: 01/03/2024] Open
Abstract
A study conducted in the Faisalabad district sampled 50 cases across five IBD outbreaks, revealing an alarming 80 % infection rate among poultry. Our research focused on developing an immune complex (Antigen-antibody complex) with potential immunoprophylactic benefits to counter this formidable threat. Our study was based on producing egg yolk-derived polyclonal antibodies (IgY) targeting IBDV. Commercial layer birds were immunized with inactivated IBDV, yielding IgY antibodies extracted from their eggs exhibited substantially higher and more enduring antibody titers, with a geometric mean titer of 104. Further research involved the creation of an immune complex (ICx) where antigen was extracted from infected bursae tissues. The immunogenic response of ICx was assessed in poultry birds after a challenge with a virulent strain of IBD virus and compared to a conventional IBDV vaccine in poultry. Results revealed significantly higher and more enduring antibody titers induced by the ICx, offering enhanced protective immunity against the IBDV challenge, as evidenced by lower Bursa to bodyweight ratios in vaccinated birds.
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Affiliation(s)
- Sanaullah Sajid
- Institute of Microbiology, University of Agriculture Faisalabad, Pakistan
| | - Sajjad ur Rahman
- Institute of Microbiology, University of Agriculture Faisalabad, Pakistan
| | - Mashkoor Mohin
- Institute of Microbiology, University of Agriculture Faisalabad, Pakistan
| | - Zia ud Din Sindhu
- Department of Parasitology, University of Agriculture Faisalabad, Pakistan
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Setta A, Yehia N, Shaheen M, Shami A, Al-Saeed FA, Alsamghan A, Amin R, El-Saadony MT, El-Tarabily KA, Salem HM. Continuous clinicopathological and molecular recognition of very virulent infectious bursal disease virus in commercial broiler chickens. Poult Sci 2024; 103:103306. [PMID: 38228049 PMCID: PMC10823078 DOI: 10.1016/j.psj.2023.103306] [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: 08/03/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 01/18/2024] Open
Abstract
Gumboro virus is one of the most dangerous immunosuppressant viruses that infect chickens and causes massive financial losses worldwide. The current study aims to conduct a molecular characterization of chicken farms for the infectious bursal disease virus (IBDV). Based on postmortem (PM) lesions, 125 bursal samples from 25 farms were collected from clinically diseased commercial chicken farms with increased mortality and suspected Gumboro virus infection. Pooled bursal samples from suspected IBD-vaccinated flocks were tested for IBDV by reverse transcriptase polymerase chain reaction (RT-PCR). Fifteen out of 25 pooled specimens were found positive for IBDV, with a 60% detection rate, and confirmed positive for very virulent IBDV (vvIBDV) by sequence analysis. Nucleotide phylogenetic analysis of VP1 and VP2 genes was employed to compare the 5 chosen isolates with strains representing different governorates in Egypt during 2022. All strains were clustered with vvIBDV with no evidence of reassortment in the VP1 gene. The VP1 and VP2 genes are divided into groups (I, II). The strains in our study were related to group II, and it acquired a new mutation in the VP2 gene that clustered it into new subgroup B. By mutation analysis, the VP2 gene of all strains had a characteristic mutation to vvIBDV. It acquired new mutations in HVRs compared with HK46 in Y220F, A222T/V in all strains in our study, and Q221K that was found in IBD-EGY-AH5 and AH2 in the loop PBC in addition to G254S in all strains in our study and Q249k that found in IBD-EGY-AH1 and AH3 in the loop PDE. These mutations are important in the virulency and antigenicity of the virus. The VP1 had 242E, 390M, and 393D which were characteristic of vvIBDV and KpnI restriction enzyme (777GGTAC/C782) in addition to a new mutation (F243Y and N383H) in IBD-EGY-AH1 and AH4 strains. According to the current study, the strains were distinct from the vaccinal strain; they could be responsible for the most recent IBDV outbreaks observed in flocks instead of received vaccinations. The current study highlighted the importance of molecular monitoring to keep up to date on the circulating IBDV for regular evaluation of commercial vaccination programs against circulating field viruses.
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Affiliation(s)
- Ahmed Setta
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt; Ceva Sante Animale, Al Sheikh Zayed, Giza, Egypt
| | - Nahed Yehia
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
| | - Momtaz Shaheen
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
| | - Ashwag Shami
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Fatimah A Al-Saeed
- Department of Biology, College of Science, King Khalid University, Abha 61413, Saudi Arabia
| | - Awad Alsamghan
- Family and Community Medicine Department, College of Medicine, King Khalid University, Abha 61413, Saudi Arabia
| | | | - Mohamed T El-Saadony
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain 15551, United Arab Emirates.
| | - Heba M Salem
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
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Sajid S, Rahman SU, Mohsin Gilani M, Sindhu ZUD, Ali MB, Hedfi A, Almalki M, Mahmood S. Molecular Characterization and Demographic Study on Infectious Bursal Disease Virus in Faisalabad District. PLoS One 2021; 16:e0254605. [PMID: 34398875 PMCID: PMC8366999 DOI: 10.1371/journal.pone.0254605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/29/2021] [Indexed: 11/19/2022] Open
Abstract
The re-emergence of virulent strains of the Infectious Bursal Disease Virus (IBDV) leads to significant economic losses of poultry industry in Pakistan during last few years. This disease causes the infection of bursa, which leads to major immune losses. A total number of 30 samples from five IBD outbreaks during the period of 2019-20 were collected from different areas of Faisalabad district, Pakistan and assayed by targeting the IBD virus VP2 region through RT-PCR. Among all the outbreaks, almost 80% of poultry birds were found positive for the IBDV. The bursa tissues were collected from the infected birds and histopathological examination of samples revealed severe lymphocytic depletion, infiltration of inflammatory cells, and necrosis of the bursa of Fabricius (BF). Positive samples were subjected to re-isolation and molecular characterization of IBDV. The Pakistan IBDV genes were subjected to DNA sequencing to determine the virus nucleotide sequences. The sequences of 100 Serotype-I IBDVs showing nearest homology were compared and identified with the study sequence. The construction of the phylogenetic tree for nucleotide sequences was accomplished by the neighbor-joining method in MEGA-6 with reference strains. The VP2 segment reassortment of IBDVs carrying segment A were identified as one important type of circulating strains in Pakistan. The findings indicated the molecular features of the Pakistan IBDV strains playing a role in the evolution of new strains of the virus, which will contribute to the vaccine selection and effective prevention of the disease.
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Affiliation(s)
- Sanaullah Sajid
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Sajjad ur Rahman
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | | | - Zia ud Din Sindhu
- Department of Parasitology, University of Agriculture, Faisalabad, Pakistan
| | - Manel Ben Ali
- Department of Biology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Amor Hedfi
- Department of Biology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Mohammed Almalki
- Department of Biology, College of Sciences, Taif University, Taif, Saudi Arabia
| | - Shahid Mahmood
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
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Huang X, Xu Y, Lin Q, Guo W, Zhao D, Wang C, Wang L, Zhou H, Jiang Y, Cui W, Qiao X, Li Y, Ma G, Tang L. Determination of antiviral action of long non-coding RNA loc107051710 during infectious bursal disease virus infection due to enhancement of interferon production. Virulence 2021; 11:68-79. [PMID: 31865850 PMCID: PMC6961729 DOI: 10.1080/21505594.2019.1707957] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The functions and profiles of lncRNAs during infectious bursal disease virus (IBDV) infection have not been determined, yet. The objectives of this study were to determine the antiviral action of loc107051710 lncRNA during IBDV infection by investigating the relationship between loc107051710 and IRF8, Type I IFN, STATs, and ISGs. DF-1 cells were either left untreated as non-infected controls (n = 1) or infected with IBDV (n = 3). RNA sequencing was applied for analysis of mRNAs and lncRNAs expression. Differentially expressed genes were verified by RT-qPCR. Then identification, of 230 significantly different expressed genes (182 mRNAs and 48 lncRNA) by pairwise comparison of the infected and control groups, was carried out. The functions of differentially expressed lncRNAs were investigated by selection of lncRNAs and mRNAs significantly enriched in the aforementioned biological processes and signaling pathways for construction of lncRNA-mRNA co-expression networks. The techniques of gene ontology and Kyoto Encyclopedia of Genes and Genomes pathways were applied. It was suggested that these differentially expressed genes were involved in the interaction between the host and IBDV. Loc107051710 was found to have potential antiviral effects. RT-qPCR and western blot were applied and revealed that loc107051710 was required for induction of IRF8, type I IFN, STAT, and ISG expression, and its knockdown promoted IBDV replication. By fluorescence in situ hybridization, it was found that loc107051710 was translocated from the nucleus to the cytoplasm after infection with IBDV. Overall, loc107051710 promoted the production of IFN-α and IFN-β by regulating IRF8, thereby promoting the antiviral activity of ISGs.
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Affiliation(s)
- Xuewei Huang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
| | - Yigang Xu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
| | - Qingyu Lin
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
| | - Weilong Guo
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
| | - Dongfang Zhao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
| | - Chunmei Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
| | - Li Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
| | - Han Zhou
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
| | - Yanping Jiang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
| | - Wen Cui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
| | - Xinyuan Qiao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
| | - Yijing Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
| | - Guangpeng Ma
- Agricultural High Technology Department, China Rural Technology Development Center, Beijing China
| | - Lijie Tang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, P.R. China
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6
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Huang X, Liu W, Zhang J, Liu Z, Wang M, Wang L, Zhou H, Jiang Y, Cui W, Qiao X, Xu Y, Li Y, Tang L. Very virulent infectious bursal disease virus-induced immune injury is involved in inflammation, apoptosis, and inflammatory cytokines imbalance in the bursa of fabricius. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 114:103839. [PMID: 32898577 DOI: 10.1016/j.dci.2020.103839] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Infectious bursal disease virus (IBDV) can cause a highly contagious disease in young chickens, resulting in bursal necrosis that causes severe damage to the immune system. The effects of various IBDV strains on the bursa of Fabricius (BF) have been extensively studied; however, few studies have investigated the effects of IBDV strain LJ-5, a newly discovered very virulent IBDV (vvIBDV), infection on young chicken BF. In this study, three-week-old specific pathogen-free (SPF) chickens were infected with vvIBDV for one to five days. LJ-5 decreased the bursa index, B lymphocyte viability and immunoglobulin (Ig) levels, including IgM and IgA in the bursa and IgY in the sera. Histopathological analysis revealed necrosis and depletion of the lymphoid cells and complete loss of bursal architecture in the BF, and transmission electron microscopy revealed mitochondrial vacuoles, cristae breaks, and nuclear damage in vvIBDV-infected bursa tissue. The number of terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling-positive nuclei significantly increased following IBDV infection. Cytokine levels increased in the bursa after IBDV infection, promoting inflammation and causing an inflammatory imbalance. Apoptotic gene expression confirmed that vvIBDV infection promotes the apoptosis of bursal cells. These results suggest that vvIBDV infection attenuate immune responses by reducing B lymphocyte activity of secretion Ig in the bursa or sera and triggers inflammation, apoptosis, and an imbalance of inflammatory cytokines in the BF, resulting in immune injury in SPF chickens, which offered basic data for further study of vvIBDV pathogenesis.
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Affiliation(s)
- Xuewei Huang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Wei Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Junyan Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Zengsu Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Meng Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China
| | - Li Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China; Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, PR China
| | - Han Zhou
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China; Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, PR China
| | - Yanping Jiang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China; Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, PR China
| | - Wen Cui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China; Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, PR China
| | - Xinyuan Qiao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China; Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, PR China
| | - Yigang Xu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China; Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, PR China
| | - Yijing Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China; Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, PR China
| | - Lijie Tang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, PR China; Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, PR China.
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Huang X, Zhang J, Liu Z, Wang M, Fan X, Wang L, Zhou H, Jiang Y, Cui W, Qiao X, Xu Y, Li Y, Tang L. Genome-wide analysis of differentially expressed mRNAs, lncRNAs, and circRNAs in chicken bursae of Fabricius during infection with very virulent infectious bursal disease virus. BMC Genomics 2020; 21:724. [PMID: 33076825 PMCID: PMC7574500 DOI: 10.1186/s12864-020-07129-1] [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: 07/01/2020] [Accepted: 10/08/2020] [Indexed: 12/13/2022] Open
Abstract
Background Infectious bursal disease virus (IBDV) causes acute, highly contagious, immunosuppressive, and lethal infectious disease in young chickens and mainly infects the bursa of Fabricius (BF). To investigate interactions between IBDV and its host, RNA sequencing was applied to analyze the responses of the differentially expressed transcriptional profiles of BF infected by very virulent IBDV (vvIBDV). Results In total, 317 upregulated and 94 downregulated mRNAs were found to be significantly differentially expressed in infected chickens, compared to controls. Long non-coding RNA (lncRNA) and circular RNA (circRNA) alterations were identified in IBDV-infected chickens, and significantly different expression was observed in 272 lncRNAs and 143 circRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed to assess the functions of significantly dysregulated genes, which showed that the JAK-STAT signaling pathway, the NOD-like receptor signaling pathway, and apoptosis may be activated by IBDV infection. We predicted interactions between differentially expressed genes and produced lncRNA-mRNA and circRNA-miRNA-mRNA regulator network. Conclusions The present study identified the expression profiles of mRNAs, lncRNAs, and circRNAs during vvIBDV infection and provides new insights into the pathogenesis of IBDV and antiviral immunity of the host.
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Affiliation(s)
- Xuewei Huang
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Road No. 600, Xiang Fang District, Harbin, People's Republic of China
| | - Junyan Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Road No. 600, Xiang Fang District, Harbin, People's Republic of China
| | - Zengsu Liu
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Road No. 600, Xiang Fang District, Harbin, People's Republic of China
| | - Meng Wang
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Road No. 600, Xiang Fang District, Harbin, People's Republic of China
| | - Xiaolong Fan
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Road No. 600, Xiang Fang District, Harbin, People's Republic of China
| | - Li Wang
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Road No. 600, Xiang Fang District, Harbin, People's Republic of China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, People's Republic of China
| | - Han Zhou
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Road No. 600, Xiang Fang District, Harbin, People's Republic of China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, People's Republic of China
| | - Yanping Jiang
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Road No. 600, Xiang Fang District, Harbin, People's Republic of China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, People's Republic of China
| | - Wen Cui
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Road No. 600, Xiang Fang District, Harbin, People's Republic of China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, People's Republic of China
| | - Xinyuan Qiao
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Road No. 600, Xiang Fang District, Harbin, People's Republic of China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, People's Republic of China
| | - Yigang Xu
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Road No. 600, Xiang Fang District, Harbin, People's Republic of China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, People's Republic of China
| | - Yijing Li
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Road No. 600, Xiang Fang District, Harbin, People's Republic of China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, People's Republic of China
| | - Lijie Tang
- College of Veterinary Medicine, Northeast Agricultural University, Changjiang Road No. 600, Xiang Fang District, Harbin, People's Republic of China. .,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, People's Republic of China.
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Abstract
Because of their replication mode and segmented dsRNA genome, homologous recombination is assumed to be rare in the rotaviruses. We analyzed 23,627 complete rotavirus genome sequences available in the NCBI Virus Variation database, and found 109 instances of homologous recombination, at least eleven of which prevailed across multiple sequenced isolates. In one case, recombination may have generated a novel rotavirus VP1 lineage. We also found strong evidence for intergenotypic recombination in which more than one sequence strongly supported the same event, particularly between different genotypes of segment 9, which encodes the glycoprotein, VP7. The recombined regions of many putative recombinants showed amino acid substitutions differentiating them from their major and minor parents. This finding suggests that these recombination events were not overly deleterious, since presumably these recombinants proliferated long enough to acquire adaptive mutations in their recombined regions. Protein structural predictions indicated that, despite the sometimes substantial amino acid replacements resulting from recombination, the overall protein structures remained relatively unaffected. Notably, recombination junctions appear to occur nonrandomly with hot spots corresponding to secondary RNA structures, a pattern seen consistently across segments. In total, we found strong evidence for recombination in nine of eleven rotavirus A segments. Only segments 7 (NSP3) and 11 (NSP5) did not show strong evidence of recombination. Collectively, the results of our computational analyses suggest that, contrary to the prevailing sentiment, recombination may be a significant driver of rotavirus evolution and may influence circulating strain diversity.
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Affiliation(s)
- Irene Hoxie
- Biology Department, Queens College of The City University of New York, 65-30 Kissena Blvd, Queens, NY 11367, USA.,The Graduate Center of The City University of New York, Biology Program, 365 5th Ave, New York, NY 10016, USA
| | - John J Dennehy
- Biology Department, Queens College of The City University of New York, 65-30 Kissena Blvd, Queens, NY 11367, USA.,The Graduate Center of The City University of New York, Biology Program, 365 5th Ave, New York, NY 10016, USA
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Molini U, Aikukutu G, Kabajani J, Khaiseb S, Cattoli G, Dundon WG. Molecular characterisation of infectious bursal disease virus in Namibia, 2017. ACTA ACUST UNITED AC 2019; 86:e1-e6. [PMID: 31291734 PMCID: PMC6620521 DOI: 10.4102/ojvr.v86i1.1676] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 01/16/2023]
Abstract
Between July and September 2017, samples collected from six unvaccinated chickens in Namibia were shown to be positive for infectious bursal disease virus (IBDV) by RT-PCR. Partial sequence and phylogenetic analysis of the VP1 and VP2 genes from six viruses revealed that they all belong to the very virulent pathotype (Genogroup 3) and are genetically very similar to IBDVs identified in neighbouring Zambia. This is the first molecular characterisation of IBDV in Namibia and has implications on the control and management of the disease in the country.
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Affiliation(s)
- Umberto Molini
- Department of Pathobiology, School of Veterinary Medicine, Faculty of Agriculture and Natural Resources, University of Namibia, Neudamm Campus.
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de Fraga AP, Gräf T, Coltro VP, Ikuta N, Fonseca ASK, Majó N, Lunge VR. Phylodynamic analyses of Brazilian antigenic variants of infectious bursal disease virus. INFECTION GENETICS AND EVOLUTION 2019; 73:159-166. [PMID: 31022473 DOI: 10.1016/j.meegid.2019.04.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/27/2019] [Accepted: 04/21/2019] [Indexed: 12/18/2022]
Abstract
Infectious bursal disease virus (IBDV) is a very important pathogen to poultry production and it is classified into three main groups: classical virulent (cvIBDV), very virulent (vvIBDV) and antigenic variants (avIBDV). This last group is composed by five different genetic lineages (recently classified in genogroups G2, G4, G5, G6, and G7) distributed in specific regions around the world. Brazil is one of the biggest poultry producers in the world and the present study aimed to investigate the evolutionary history of avIBDVs of the genogroup G4 in Brazil. A total of 5331 IBDV positive bursa samples, from different Brazilian poultry flocks, were genotyped in a period of ten years (2005 to 2014) and 1888 (35.42%) were identified as local avIBDVs. The highly variable region of the viral protein 2 (hvvp2) gene of 28 avIBDVs was sequenced and used in phylogenetic analyses and evaluation of local amino acid signatures. In addition, all complete and partial IBDV vp2 gene sequences, with local and year of collection information available on GenBank, were retrieved. Phylogenetic analyses were carried out based on a maximum likelihood method for the classification of genogroups occurring in Brazil. Based on a Maximum Likelihood (ML) phylogenetic tree, all Brazilian avIBDVs grouped into the genogroup 4. Bayesian phylodynamics analysis demonstrated the ancestor virus of this group was probably introduced in South America in 1968 (1960 to 1974, 95% HPD) and in Brazil in 1974 (1968 to 1977, 95% HPD) and the most likely source was East Europe (Hungary or Poland). All Brazilian avIBDV sequences, as well as the other genogroup 4 sequences, showed a specific pattern of amino acid: S222, T272, P289, I290, and F296. This report brings new insights about the IBDV epidemiology in Brazil and South America.
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Affiliation(s)
- Aline Padilha de Fraga
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil.
| | - Tiago Gräf
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Nilo Ikuta
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil; Simbios Biotecnologia, Cachoeirinha, Rio Grande do Sul, Brazil
| | | | - Natàlia Majó
- Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain; Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Vagner Ricardo Lunge
- Laboratório de Diagnóstico Molecular, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil; Simbios Biotecnologia, Cachoeirinha, Rio Grande do Sul, Brazil
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Computational Comparison and Visualization of Viruses in the Perspective of Clinical Information. Interdiscip Sci 2019; 11:86-94. [PMID: 28391493 PMCID: PMC7090701 DOI: 10.1007/s12539-017-0229-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/17/2017] [Accepted: 03/25/2017] [Indexed: 01/13/2023]
Abstract
This paper addresses the visualization of complex information using multidimensional scaling (MDS). MDS is a technique adopted for processing data with multiple features scattered in high-dimensional spaces. For illustrating the proposed techniques, the case of viral diseases is considered. The study evaluates the characteristics of 21 viruses in the perspective of clinical information. Several new schemes are proposed for improving the visualization of the MDS charts. The results follow standard clinical practice, proving that the method represents a valuable tool to study a large number of viruses.
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12
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Shehata AA, Sultan H, Halami MY, Talaat S, Vahlenkamp TW. Molecular characterization of very virulent infectious bursal disease virus strains circulating in Egypt from 2003 to 2014. Arch Virol 2017; 162:3803-3815. [PMID: 28921008 DOI: 10.1007/s00705-017-3554-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/22/2017] [Indexed: 11/28/2022]
Abstract
In the present study, four very virulent infectious bursal disease virus (vvIBDV) isolates from flocks of chickens with vaccination failure in Egypt in 2003, 2007, 2010 and 2014 were characterized. The four viruses, designated USC2003, USC2007, USC2010 and USC2014, were detected by reverse transcription PCR, subjected to sequencing of both genomic segments (A and B) and compared with geographically and phylogenetically diverse IBDV strains. Phylogenetic analysis of segment A (complete) and B (partial) revealed a close relationship between Egyptian and vvIBDV reference strains of European and Asian origin. The sequences of segments of A and B the current Egyptian isolates were 96.1-98.2% and 96.5-98.7% identical, respectively, to those of other known vvIBDV isolates. The deduced amino acid sequences of VP1, polyprotein (pVP2-VP4-VP3) and VP5 revealed the presence of putative virulence determinants of Egyptian isolates compared with vvIBDV and less virulent (classical and variant) strains. The Egyptian isolates also possess unique amino acids substitutions within the hypervariable region of VP2 that differ from those of other reference IBDV strains. Further studies may be necessary to determine the pathogenic significance of these amino acid substitutions to fully understand the molecular epidemiology and evolution of IBDV.
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Affiliation(s)
- Awad A Shehata
- Faculty of Veterinary Medicine, Center for Infectious Diseases, Institute of Virology, Leipzig University, An den Tierkliniken 29, 04103, Leipzig, Germany. .,Avian and Rabbit Diseases Department, Faculty of Veterinary Medicine, University of Sadat City, 22857, Sadat, Minoufiya, Egypt.
| | - Hesham Sultan
- Avian and Rabbit Diseases Department, Faculty of Veterinary Medicine, University of Sadat City, 22857, Sadat, Minoufiya, Egypt
| | - Mohammed Y Halami
- Faculty of Veterinary Medicine, Center for Infectious Diseases, Institute of Virology, Leipzig University, An den Tierkliniken 29, 04103, Leipzig, Germany
| | - Shaimaa Talaat
- Avian and Rabbit Diseases Department, Faculty of Veterinary Medicine, University of Sadat City, 22857, Sadat, Minoufiya, Egypt
| | - Thomas W Vahlenkamp
- Faculty of Veterinary Medicine, Center for Infectious Diseases, Institute of Virology, Leipzig University, An den Tierkliniken 29, 04103, Leipzig, Germany
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13
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Lin J, Xia J, Zhang K, Yang Q. Genome-wide profiling of chicken dendritic cell response to infectious bursal disease. BMC Genomics 2016; 17:878. [PMID: 27816055 PMCID: PMC5097849 DOI: 10.1186/s12864-016-3157-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 10/12/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Avian infectious bursal disease virus (IBDV) is a highly contagious, immunosuppressive disease of young chickens, which causes high mortality rates and large economic losses in the poultry industry. Dendritic cells (DCs), which are antigen-presenting cells, have the unique ability to induce both innate and acquired immune responses and may significantly influence virus pathogenicity. To understand the interaction between IBDV and DCs, a microarray was used to analyse the response of DCs infected by IBDV. RESULTS IBDV infection induced 479 upregulated and 466 downregulated mRNAs in chicken DCs. Analysis of Gene Ontology suggested that transcription from the RNA polymerase II promoter and the RNA biosynthetic process were enriched, and pathway analyses suggested that oxidative phosphorylation, as well as the T cell receptor and Interleukin-17 (IL-17) signalling pathways might be activated by IBDV infection. Moreover, microRNA (miRNA) and long non-coding RNA (lncRNA) alterations in IBDV-infected chicken DCs were observed. A total of 18 significantly upregulated or downregulated miRNAs and 441 significantly upregulated or downregulated lncRNAs were identified in IBDV-stimulated DCs. We constructed 42 transcription factor (TF)-miRNA-mRNA interactions involving 1 TF, 3 miRNAs, and 42 mRNAs in IBDV-stimulated DCs. Finally, we predicted the target genes of differentially expressed lncRNAs, and constructed lncRNA-mRNA regulatory networks. CONCLUSIONS The results of this study suggest a mechanism to explain how IBDV infection triggers an effective immune response in chicken DCs.
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Affiliation(s)
- Jian Lin
- College of Life Science, Nanjing Agricultural University, Weigang 1, Nanjing, Jiangsu 210095 People’s Republic of China
| | - Jing Xia
- College of Life Science, Nanjing Agricultural University, Weigang 1, Nanjing, Jiangsu 210095 People’s Republic of China
| | - Keyun Zhang
- College of Life Science, Nanjing Agricultural University, Weigang 1, Nanjing, Jiangsu 210095 People’s Republic of China
| | - Qian Yang
- College of Life Science, Nanjing Agricultural University, Weigang 1, Nanjing, Jiangsu 210095 People’s Republic of China
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14
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Lopes AM, Andrade JP, Tenreiro Machado JA. Multidimensional scaling analysis of virus diseases. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2016; 131:97-110. [PMID: 27265052 PMCID: PMC7114580 DOI: 10.1016/j.cmpb.2016.03.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 02/26/2016] [Accepted: 03/30/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND OBJECTIVE Viruses are infectious agents that replicate inside organisms and reveal a plethora of distinct characteristics. Viral infections spread in many ways, but often have devastating consequences and represent a huge danger for public health. It is important to design statistical and computational techniques capable of handling the available data and highlighting the most important features. METHODS This paper reviews the quantitative and qualitative behaviour of 22 infectious diseases caused by viruses. The information is compared and visualized by means of the multidimensional scaling technique. RESULTS The results are robust to uncertainties in the data and revealed to be consistent with clinical practice. CONCLUSIONS The paper shows that the proposed methodology may represent a solid mathematical tool to tackle a larger number of virus and additional information about these infectious agents.
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Affiliation(s)
- António M Lopes
- UISPA-LAETA/INEGI, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
| | - José P Andrade
- Department of Anatomy, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - J A Tenreiro Machado
- Institute of Engineering, Department of Electrical Engineering, Polytechnic of Porto, Rua Dr. António Bernardino de Almeida, 431, 4249-015 Porto, Portugal
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15
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Alkie TN, Rautenschlein S. Infectious bursal disease virus in poultry: current status and future prospects. VETERINARY MEDICINE-RESEARCH AND REPORTS 2016; 7:9-18. [PMID: 30050833 PMCID: PMC6055793 DOI: 10.2147/vmrr.s68905] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Infectious bursal disease virus (IBDV) affects immature B lymphocytes of the bursa of Fabricius and may cause significant immunosuppression. It continues to be a leading cause of economic losses in the poultry industry. IBDV, having a segmented double-stranded RNA genome, is prone to genetic variation. Therefore, IBDV isolates with different genotypic and phenotypic diversity exist. Understanding these features of the virus and the mechanisms of protective immunity elicited thereof is necessary for developing vaccines with improved efficacy. In this review, we highlighted the pattern of virus evolution and new developments in prophylactic strategies, mainly the development of new generation vaccines, which will continue to be of interest for research as well as field application in the future.
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Affiliation(s)
- Tamiru Negash Alkie
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Canada
| | - Silke Rautenschlein
- Clinic for Poultry, University of Veterinary Medicine Hannover, Hannover, Germany,
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