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Nour I, Blakey JR, Alvarez-Narvaez S, Mohanty SK. Whole Genome Sequencing of Infectious Bursal Disease Viruses Isolated from a Californian Outbreak Unravels the Underlying Virulence Markers and Highlights Positive Selection Incidence. Viruses 2023; 15:2044. [PMID: 37896821 PMCID: PMC10612053 DOI: 10.3390/v15102044] [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: 09/12/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
Outbreaks of the immunosuppressive infectious bursal disease (IBD) are frequently reported worldwide, despite the vaccination regimes. A 2009 Californian IBD outbreak caused by rA and rB isolates was described as very virulent (vv) IBD virus (IBDV); however, molecular factors beyond this virulence were not fully uncovered. Therefore, segments of both isolates were amplified, successfully cloned, whole genome sequenced by Next Generation Sequencing, genotyped, and the leading virulence factors were entirely investigated in terms of phylogenetic and amino acid analysis and protein modeling for positive selection orientation and interaction analysis. rA and rB isolates displayed the highest amino acid identity (97.84-100%) with Genotype 3 strains. Interestingly, rA and rB contained all virulence hallmarks of hypervariable (HVR), including 222A, 242I, 249Q, 256I, 284A, 286T, 294I, 299S, and 318G, as well as the serine-rich heptapeptide sequence. Moreover, we pinpointed the A3B2 genotype of rA and rB, predominant in non-reassortants, and we highlighted the absence of recombination events. Furthermore, gene-wise phylogenetic analysis showed the entire genes of rA and rB clustered with the vvIBDVs and emphasized their share in IBDV virulence. VP5 showed a virulence marker, MLSL (amino acid sequence). VP2 encountered three significant novel mutations apart from the HVR, including G163E in rA and Y173C and V178A in rB, all residing within interacting motifs. VP4 contained 168Y, 173N, 203S, and 239D characteristic for the vv phenotype. A235V mutation was detected at the dsRNA binding domain of VP3. In VP1, the TDN triplet and the mutation (V4I) were detected, characteristic of hypervirulence occurring at the N-terminus responsible for protein priming. Although selection analysis revealed seven sites, codon 222 was the only statistically significant selection site. The VP2 modeling of rA and rB highlighted great structure fitness, with 96.14% Ramachandran favored positioning including the 222A, i.e., not influencing the structure stability. The 222A was found to be non-interface surface residue, associated with no interaction with the attachment-mediated ligand motif. Our findings provide pivotal insights into the evolution and underlying virulence factors and will assist in the development of control strategies via sequence-based continuous monitoring for the early detection of novel vv strains.
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Affiliation(s)
| | | | | | - Sujit K. Mohanty
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), US National Poultry Research Center, Athens, GA 30605, USA; (I.N.); (J.R.B.); (S.A.-N.)
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Junnu S, Pohuang T. Full -length coding sequence analysis of genome segments A and B of infectious bursal disease virus in Thailand: identification of Chinese-like and recombinant virus in the field. Avian Pathol 2023; 52:339-350. [PMID: 37357759 DOI: 10.1080/03079457.2023.2230164] [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: 09/26/2022] [Revised: 05/22/2023] [Accepted: 06/21/2023] [Indexed: 06/27/2023]
Abstract
RESEARCH HIGHLIGHTS For the first time, this work demonstrated a recombinant IBDV strain in Thailand.Two genogroups of IBDV were found in Thailand: including HLJ-504-like and recombinant virus.Analysis of the full coding sequence is essential for monitoring emerging variant IBDV.
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Affiliation(s)
- Sucheeva Junnu
- Division of Livestock Medicine, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research Group for Emerging and Re-emerging Infectious Diseases in Animals and Zoonotic Diseases, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Tawatchai Pohuang
- Division of Livestock Medicine, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research Group for Emerging and Re-emerging Infectious Diseases in Animals and Zoonotic Diseases, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand
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Le XTK, Do RT, Doan HTT, Nguyen KT, Pham LTK, Le TH. Phylogenotyping of infectious bursal disease virus in Vietnam according to the newly unified genotypic classification scheme. Arch Virol 2023; 168:201. [PMID: 37402052 DOI: 10.1007/s00705-023-05830-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/02/2023] [Indexed: 07/05/2023]
Abstract
Since 1987, infectious bursal disease virus (IBDV) has circulated and evolved in Vietnam, but little is known about the genotypes present. IBDV samples were collected in 1987, 2001-2006, 2008, 2011, 2015-2019, and 2021 in 18 provinces. We conducted phylogenotyping analysis based on an alignment of 143 VP2-HVR (hypervariable region) sequences from 64 Vietnamese isolates (26 previous and 38 additional sequences and two vaccines, and alignment of 82 VP1 B-marker sequences, including one vaccine and four Vietnamese field strains. The analysis identified three A-genotypes, A1, A3, and A7, and two B-genotypes, B1 and B3, among the Vietnamese IBDV isolates. The lowest average evolutionary distance (8.6%) was seen between the A1 and A3 genotypes, and the highest (21.7%) was between A5 and A7, while there was a distance of 14% between B1 and B3 and 17% between B3 and B2. Unique signature residues were observed for genotypes A2, A3, A5, A6, and A8, which could be used for genotypic discrimination. A timeline statistical summary revealed that the A3-genotype predominated (79.8% presence) in Vietnam from 1987 to 2021 and that it remained the dominant IBDV genotype over the last five years (2016-2021). The current study contributes to a better understanding of the circulating genotypes and evolution of IBDV in Vietnam and worldwide.
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Affiliation(s)
- Xuyen Thi Kim Le
- Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet Rd, Cau Giay, Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet Rd, Cau Giay, Hanoi, Vietnam
| | - Roan Thi Do
- Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet Rd, Cau Giay, Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet Rd, Cau Giay, Hanoi, Vietnam
| | - Huong Thi Thanh Doan
- Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet Rd, Cau Giay, Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet Rd, Cau Giay, Hanoi, Vietnam
| | - Khue Thi Nguyen
- Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet Rd, Cau Giay, Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet Rd, Cau Giay, Hanoi, Vietnam
| | - Linh Thi Khanh Pham
- Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet Rd, Cau Giay, Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet Rd, Cau Giay, Hanoi, Vietnam
| | - Thanh Hoa Le
- Immunology Department, Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet Rd, Cau Giay, Hanoi, Vietnam.
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18. Hoang Quoc Viet Rd, Cau Giay, Hanoi, Vietnam.
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Wang C, Hou B, Shao G, Wan C. Development of a One-Step Real-Time TaqMan Reverse Transcription Polymerase Chain Reaction (RT-PCR) Assay for the Detection of the Novel Variant Infectious Bursal Disease Virus (nVarIBDV) Circulating in China. Viruses 2023; 15:1453. [PMID: 37515141 PMCID: PMC10383243 DOI: 10.3390/v15071453] [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: 05/23/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
The novel variant IBDV (nVarIBDV, especially genotype A2dB1) mainly affects broilers in China. It causes an infection characterized by the atrophy of the bursa, a decrease in the level of lymphocytes, proliferation of fibrous tissue around the follicle, and severe atrophy of the follicle in the bursa. Poultry vaccinated with live IBDV vaccines do not have the challenge present with bursa atrophy, which is misdiagnosed for nVarIBDV because of the lack of other gross clinical symptoms. The present study sought to explore the potential and reliability of the real-time TaqMan analysis method for the detection and discrimination of the nVarIBDV genotype from that of the non-nVarIBDV, especially in live vaccine strains. This method will help monitor vaccinated poultry to control and manage infection with the nVarIBDV IBDVs. The nucleotide polymorphism in the 5'-UTR region and the vp5/vp2 overlapping region of the segment A sequences of IBDV were used to establish a one-step real-time TaqMan reverse transcription polymerase chain reaction (RT-PCR) method in this study. The results showed that the method accurately distinguished the nVarIBDV and non-nVarIBDV strains (especially live vaccine strains), and there were no cross-reactions with the infectious bronchitis virus (IBV), Newcastle disease virus (NDV), avian influenza virus (AIV), infectious laryngotracheitis virus (ILTV), fowlpox virus (FPV), Mycoplasma gallisepticum (M. gallisepticum), Mycoplasma synoviae (M. synoviae), and IBDV-negative field samples. The method showed a linear dynamic range between 102 and 107 DNA copies/reaction, with an average R2 of 0.99 and an efficiency of 93% for nVarIBDV and an average R2 of 1.00 and an efficiency of 94% for non-nVarIBDV. The method was also used for the detection of 84 clinical bursae of chickens vaccinated with the live vaccine. The results showed that this method accurately distinguished the nVarIBDV and non-nVarIBDV strains (vaccine strains), compared with a strategy based on the sequence analysis of HVRs at the vp2 gene or the reverse transcription PCR (RT-PCR) for the vp5 gene. These findings showed that this one-step real-time TaqMan RT-PCR method provides a rapid, sensitive, specific, and simple approach for detection of infections caused by nVarIBDV and is a useful clinical diagnostic tool for identifying and distinguishing nVarIBDV from non-nVarIBDV, especially live vaccine strains.
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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, China
| | - Bo Hou
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China
| | - Guoqing Shao
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, National Research Center for Engineering and Technology of Veterinary Bio-Products, Nanjing 210014, China
| | - Chunhe Wan
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fujian Animal Disease Control Technology Development Center, Fuzhou 350013, China
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Nwagbo I, Milani A, Salviato A, Zamperin G, Sulaiman L, Maurice N, Meseko C, Fusaro A, Shittu I. Genomic Analysis of Infectious Bursal Disease Virus in Nigeria: Identification of Unique Mutations of Yet Unknown Biological Functions in Both Segments A and B. Vaccines (Basel) 2023; 11:vaccines11040867. [PMID: 37112779 PMCID: PMC10144922 DOI: 10.3390/vaccines11040867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Infectious bursal disease (IBD) is a viral poultry disease known worldwide for impacting the economy and food security. The disease is endemic in Nigeria, with reported outbreaks in vaccinated poultry flocks. To gain insight into the dynamics of infectious bursal disease virus (IBDV) evolution in Nigeria, near-complete genomes of four IBDVs were evaluated. Amino acid sequences in the hypervariable region of the VP2 revealed conserved markers (222A, 242I, 256I, 294I and 299S) associated with very virulent (vv) IBDV, including the serine-rich heptapeptide motif (SWSASGS). Based on the newly proposed classification for segments A and B, the IBDVs clustered in the A3B5 group (where A3 are IBDVs with vvIBDV-like segment A, and where B5 are from non-vvIBDV-like segment B) form a monophyletic subcluster. Unique amino acid mutations with yet-to-be-determined biological functions have been observed in both segments. Amino acid sequences of the Nigerian IBDVs showed that they are reassortant viruses. Circulation of reassortant IBDVs may be responsible for the vaccination failures observed in the Nigerian poultry population. Close monitoring of changes in the IBDV genome is recommended to nip deleterious changes in the bud through the identification and introduction of the most appropriate vaccine candidates and advocacy/extension programs for properly implementing disease control.
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Affiliation(s)
- Ijeoma Nwagbo
- National Veterinary Research Institute, Vom 930010, Nigeria
| | - Adelaide Milani
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
| | - Annalisa Salviato
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
| | - Gianpiero Zamperin
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
| | - Lanre Sulaiman
- National Veterinary Research Institute, Vom 930010, Nigeria
| | - Nanven Maurice
- National Veterinary Research Institute, Vom 930010, Nigeria
| | - Clement Meseko
- National Veterinary Research Institute, Vom 930010, Nigeria
| | - Alice Fusaro
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
| | - Ismaila Shittu
- National Veterinary Research Institute, Vom 930010, Nigeria
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Pikuła A, Lisowska A, Domańska-Blicharz K. Epidemiology of Infectious Bursal Disease Virus in Poland during 2016-2022. Viruses 2023; 15:v15020289. [PMID: 36851502 PMCID: PMC9963850 DOI: 10.3390/v15020289] [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: 12/09/2022] [Revised: 01/04/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
Infectious bursal disease virus is an immunosuppressive ubiquitous pathogen that causes serious economic losses in poultry production. The virus is prone to genetic changes through mutations and reassortment, which drive the emergence of new variants and lead to a change in the epidemiological situation in a field. Such a situation is currently being reported due to a large wave of IBDV A3B1 reassortant infections in northwestern Europe. On the other hand, in Poland, which is the largest producer of chicken meat in the EU, the IBDVs of genotypes A3B2 and A3B4 were circulating just before the emergence of A3B1 reassortants. The purpose of the presented study was to update the IBDV epidemiological situation. The performed molecular survey based on the sequence of both genome segments showed the presence of very virulent strains (A3B2) and reassortants of genotypes A3B4 and A3B1; moreover, two of these genotypes are newly introduced IBDV lineages. In addition, a number of amino acid substitutions were demonstrated, including within antigenic epitopes and virulence determinants. In conclusion, the results obtained indicated a dynamic epidemiological situation in Poland, which highlights the need for further monitoring studies in the region and verification of protection conferred by the vaccines used against infection with detected IBDV.
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Pikuła A, Lisowska A. Genetics and Pathogenicity of Natural Reassortant of Infectious Bursal Disease Virus Emerging in Latvia. Pathogens 2022; 11:pathogens11101081. [PMID: 36297138 PMCID: PMC9612254 DOI: 10.3390/pathogens11101081] [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] [Received: 08/24/2022] [Revised: 09/19/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
Infectious bursal disease virus is an immunosuppressive pathogen that, despite applied vaccination, is affecting the poultry industry worldwide. This report presents the genetic and pathotypic characterization of a natural reassortant emerging in Europe (Latvia). Genetic characterization showed that strain 25/11/Latvia/2011 represents genotype A3B1, whose segment A is derived from very virulent strains, while segment B is from the classic-like genogroup. Phylogenetic maximum likelihood inference of the B-segment sequence clustered the reassortant strain together with the US antigenic variant E strain. However, the obtained full-length sequence of 25/11/Latvia/2011 revealed that not only reassortment but also dozens of mutations shaped the unique genetic makeup. Phenotypic characterization showed no mortality and no clinical signs of disease but a severe bursa of Fabricius atrophy and splenomegaly in the convalescent birds at 10 days post infection. The results obtained indicate that the acquired genetic constellation contributed to a decrease in virulence; nevertheless, the infection causes severe damage to lymphoid organs, which can lead to impaired immune responses.
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Lachheb J, Jbenyeni A, Nsiri J, Larbi I, Ammouna F, El Behi I, Ghram A. Full-length genome sequencing of a very virulent infectious bursal disease virus isolated in Tunisia. Poult Sci 2020; 100:496-506. [PMID: 33518102 PMCID: PMC7858174 DOI: 10.1016/j.psj.2020.11.035] [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: 06/12/2020] [Revised: 11/10/2020] [Accepted: 11/22/2020] [Indexed: 11/29/2022] Open
Abstract
Infectious bursal disease (IBD), an acute, highly contagious, and immunosuppressive avian disease, is caused by infectious bursal disease virus (IBDV) and constitutes one of the main threats to the poultry industry, worldwide. This study was performed to isolate and characterize IBDV isolates circulating in Tunisia. Eleven collected bird samples were identified using an SYBR Green–based one-step real-time reverse transcriptase polymerase chain reaction. The full-length genome sequencing of 7 of the 11 IBDV isolates has been realized. VP2 gene data showed limited sequence variations for all the 7 tested samples. The few nucleotide changes were silent and the deduced amino acid sequences were identical with the exception of a unique and characteristic nonsilent mutation (C1203) detected for the TN37/19 isolate, with a change of amino acid (L) to (F) at position 401. In addition, the serine-rich heptapeptide SWSASGS, characteristic of virulent IBDV, as well the amino acid residues, conserved in most very virulent IBDV (vvIBDV) strains, were detected in all the Tunisian tested isolates. Nucleotide sequences of VP5 gene revealed the presence of 5 substitutions leading to changes in the amino acid sequences of the virus. Two of these mutations were unique and characteristic of the Tunisian isolates. Besides, the alternative AUG start codon, characteristic of vvIBDV, was observed in all obtained VP5 gene sequences. The Tunisian protein sequences of VP1 showed E242 and the TDN triplet at positions 145, 146, and 147, a motif specific of vvIBDV. Phylogenetic analyses of the 5 genes confirmed the sequence alignment results and showed that the Tunisian strains are closely related to the very virulent Algerian IBDV strains.
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Affiliation(s)
- Jihene Lachheb
- Laboratory of Epidemiology and Veterinary Microbiology LR0020, Institut Pasteur of Tunis, Tunis El Manar University, Tunis Belvedere 1002, Tunisia.
| | - Adam Jbenyeni
- Veterinary Practice El Intilaka, Canal Street 20, 2097 Ben Arous, Tunisia
| | - Jihene Nsiri
- Laboratory of Epidemiology and Veterinary Microbiology LR0020, Institut Pasteur of Tunis, Tunis El Manar University, Tunis Belvedere 1002, Tunisia
| | - Imen Larbi
- Laboratory of Epidemiology and Veterinary Microbiology LR0020, Institut Pasteur of Tunis, Tunis El Manar University, Tunis Belvedere 1002, Tunisia
| | - Faten Ammouna
- Laboratory of Epidemiology and Veterinary Microbiology LR0020, Institut Pasteur of Tunis, Tunis El Manar University, Tunis Belvedere 1002, Tunisia
| | - Imen El Behi
- Laboratory of Epidemiology and Veterinary Microbiology LR0020, Institut Pasteur of Tunis, Tunis El Manar University, Tunis Belvedere 1002, Tunisia
| | - Abdeljelil Ghram
- Laboratory of Epidemiology and Veterinary Microbiology LR0020, Institut Pasteur of Tunis, Tunis El Manar University, Tunis Belvedere 1002, Tunisia
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