Tracking the molecular epidemiology of Brazilian Infectious bursal disease virus (IBDV) isolates

Designing a bioadjuvant candidate vaccine targeting infectious bursal disease virus (IBDV) using viral VP2 fusion and chicken IL-2 antigenic epitope: A bioinformatics approach

Infectious Bursal Disease (IBD) is a common and contagious viral infection that significantly affects the poultry industry. This severely suppresses the immune system in chickens, thereby threating their health and well-being. Vaccination is the most effective strategy for preventing and controlling this infectious agent. The development of VP2-based DNA vaccines combined with biological adjuvants has recently received considerable attention due to their effectiveness in eliciting both humoral and cellular immune responses. In this study, we applied bioinformatics tools to design a fused bioadjuvant candidate vaccine from the full-length sequence of the VP2 protein of IBDV isolated in Iran using the antigenic epitope of chicken IL-2 (chiIL-2). Furthermore, to improve the antigenic epitope presentation and to maintain the three-dimensional structure of the chimeric gene construct, the P2A linker (L) was used to fuse the two fragments. Our in-silico analysis for the design of a candidate vaccine indicates that a continuous sequence of amino acid residues ranging from 105 to 129 in chiIL-2 is proposed as a B cell epitope by epitope prediction servers. The final 3D structure of the VP2-L-chiIL-2105-129 was subjected to physicochemical property determination, molecular dynamic simulation, and antigenic site determination. The results of these analyses led to the development of a stable candidate vaccine that is non-allergenic and has the potential for antigenic surface display potential and adjuvant activity. Finally, it is necessary to investigate the immune response induced by our proposed vaccine in avian hosts. Notably, increasing the immunogenicity of DNA vaccines can be achieved by combining antigenic proteins with molecular adjuvants using the principle of rational vaccine design.

Phylogenotyping of infectious bursal disease virus in Vietnam according to the newly unified genotypic classification scheme

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.

Evolution and Epidemic Spread of the Avian Infectious Bronchitis Virus (IBV) GI-23 in Brazil

Infectious bronchitis virus (IBV) is a pathogen affecting poultry flocks worldwide. GI-23 is an IBV lineage with a rapid spread into different continents of the world, and it was reported for the first time in South American/Brazilian broiler farms last year. This study aimed to investigate the recent introduction and epidemic spread of IBV GI-23 in Brazil. Ninety-four broiler flocks infected with this lineage were evaluated from October 2021 to January 2023. IBV GI-23 was detected using real-time RT-qPCR, and the S1 gene hypervariable regions 1 and 2 (HVR1/2) were sequenced. S1 complete and HVR1/2 nucleotide sequence datasets were used to carry out phylogenetic and phylodynamic analyses. Brazilian IBV GI-23 strains clustered into two specific subclades (SA.1 and SA.2), both in tree branches with IBV GI-23 from Eastern European poultry-producing countries, suggesting two independent and recent introductions (around 2018). Viral phylodynamic analysis showed that the IBV GI-23 population increased from 2020 to 2021, remaining constant for one year and declining in 2022. S1 amino acid sequences from Brazilian IBV GI-23 presented specific and characteristic substitutions in the HVR1/2 for subclades IBV GI-23 SA.1 and SA.2. This study brings new insights into the introduction and recent epidemiology of IBV GI-23 in Brazil.

Analysis of the global origin, evolution and transmission dynamics of the emerging novel variant IBDV (A2dB1b): The accumulation of critical aa-residue mutations and commercial trade contributes to the emergence and transmission of novel variants

The Chinese IBDV novel variant (nvIBDV), belonging to the genotype A2dB1b, an emerging pathotype that can cause subclinical disease with severe, prolonged immunosuppression, poses a new threat to the poultry industry. The process of the global origin, evolution and transmission dynamics of nvIBDV, however, is poorly understood. In this study, phylogenetic trees, site substitutions of amino acid (aa) and highly accurate protein structure modelling, selection pressure, evolutionary and transmission dynamics of nvIBDV were analysed. Interestingly, nvIBDV was classified into the same genogroup with the early US antigenic variants (avIBDV) but in a new lineage with a markedly different and specific pattern of 17 aa-residual substitutions: 13 in VP2 (77D, 213N, 221K, 222T, 249K, 252I, 253Q, 254N, 284A, 286I, 299S, 318D and 323E) and four in VP1 (141I, 163V, 240E and 508K). Importantly, the aa-residues 299S and 163V may play a key role in cell binding and polymerase activity, respectively. The effective population size of the circulating avIBDV experienced two growth phases, respectively, in the years 1999-2007 (in North America) and 2015-2021 (in Asia), which is consistent with the observed trend of the epidemic outbreaks. The most recent common ancestor (tMRCA) of avIBDV most first originated in the USA and was dated around the 1970s. After its emergence, the ancestor virus of this group probably spread to China around the 1990s and the variants experienced a long-term latent circulation with the accumulation of several critical aa-residue mutations in VP2 until re-emerging in 2016. At present, central China has become the epicentre of nvIBDV spread to other parts of China and Asian countries. Importantly, a strong correlation seems to exist between the transmission patterns of virus and the flow of commercial trade of live poultry and products. These findings provide important insights into the origin, evolution and transmission of the nvIBDV and will assist in the development of programs for control strategies for these emerging viruses.

Characterization and pathogenicity of a naturally reassortant and recombinant infectious bursal disease virus in China

Infectious bursal disease virus (IBDV), an Avibirnavirus, is the pathogen of infectious bursal disease, which is a severely immunosuppressive disease in 3-15-week-old chickens. Different phenotypes of IBDV, including classical, variant, very virulent (vv) and attenuated IBDV, have been reported in many chicken-rearing countries worldwide. Here, we isolated and identified a naturally reassortant and recombinant IBDV (designated GXB02) from 20-day-old chickens with clinicopathological changes of infectious bursal disease (IBD) in Guangxi Province, China. Whole genomic sequencing showed that the strain GXB02 simultaneously has both reassortant and recombinant characteristics with segments A and B being derived from recombinant intermediate vaccine strain and classic strains of IBDV. Segment A of strain GXB02 was incorporated into the skeleton of an intermediate IBDV vaccine strain (W2512), where the breakpoints of two recombinant events located at nucleotide positions 1468 and 1648 were replaced by reassortant vvIBDV (PK2) and vvIBDV (D6948) of segment A, respectively. We used this GXB02 strain to inoculate 21-day-old specific-pathogen-free chickens to evaluate its pathogenicity. Strain GXB02 has clinicopathologic characteristics of IBD with severe bursal lesions, as evidenced by necrosis, depletion of lymphocytes, and follicle atrophy, indicating that reassortment with classical strains in segment B or/and recombination with very virulent strains increased pathogenicity of the strain GXB02 in chickens. These findings provide important insights into the genetic exchange between classic and attenuated strains of IBDV with two recombinant events occurring at the intermediate derivative segment A with vvIBDV strains, thereby increasing the difficulty of prevention and control of IBD due to novel reassortant-recombinant strains.

Assessing the antigenicity of different VP3 regions of infectious bursal disease virus in chickens from South Brazil

Background

Infectious bursal disease (IBD), also known as Gumboro disease, is a viral infection that causes mortality and immunosuppression in chickens (Gallus gallus). VP2 and VP3 are the major structural viral capsid components and are the most immunogenic proteins of IBD virus (IBDV). Reliable diagnostic tests using VP2 and VP3 produced in heterologous systems are important tools to control this infection. One advantage of an IBD diagnostic based on VP3, over those that use VP2, is that VP3 has linear epitopes, enabling its production in bacteria.

Results

We tested the suitability of recombinant VP3 (rVP3) as a diagnostic reagent in an enzyme-linked immunosorbent assay (ELISA). Compared with a commercial test, rVP3 ELISA showed high sensitivity and specificity as a diagnostic tool for vaccinated animals. In addition, rVP3, but not the commercial ELISA, was able to detect antibodies in nonvaccinated chickens, probably developed against circulating IBDV strains. It was possible the assessment of VP3 regions antigenicity using chicken antisera.

Conclusions

The full-length recombinant VP3 can be used to assess post vaccination immunological status of chickens and its production is feasible and inexpensive. The evaluation of VP3 regions as candidates for general use in the diagnosis of IBD in chickens should be conducted with caution. Our work was the first to identify several regions of VP3 recognized by chicken antibodies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-021-02956-0.

Infectious bursal disease in Nigeria: continuous circulation of reassortant viruses

Outbreaks of infectious bursal disease (IBD), a highly contagious immunosuppressive disease of young chickens, are still reported globally despite vaccination efforts. This study investigated the genetic characteristics of infectious bursal disease virus (IBDV) from 26 reported outbreaks in 2019 in Nigeria. Nucleotide sequences of VP2 hypervariable (hvVP2) region (n=26) and VP1 (n=23) of Nigerian IBDVs were determined. Our results revealed the detection of reassortant strains with segment A related to very virulent IBDV (vvIBDV) having virulence marker (222A, 242I, 256I, 294I and 299S), whereas their segment B were closely related to previously detected IBDV strains having QEG substitution at positions 145-147. Phylogenetic analysis of the hvVP2 region revealed that all the Nigerian IBDV clustered with vvIBDV (genogroup 3) and were independent of the Asian/European lineage. Interestingly, in the hvVP2, all the viruses had a G-S substitution at residue 254. Additionally, one isolate had an A321T substitution at the P_HI loop, which has been suggested to play a key role in antigenicity. Four of the viruses (Bauchi=3 and Plateau=1) had a unique A-T substitution at residue 144 on the VP1 region. We also observed a T174S substitution in nine of the Nigerian viruses from Bauchi and Plateau state that were not found in any outbreak viruses from Oyo and Akwa Ibom. This report demonstrates the circulation of reassortant strains in commercial and backyard poultry farms in Nigeria despite sustained vaccination efforts. Our data suggest that the Nigerian outbreak viruses have mutations that may affect antigenicity and contribute to antigenic drift.

The Novel Genetic Background of Infectious Bursal Disease Virus Strains Emerging from the Action of Positive Selection

The circulation in Europe of novel reassortant strains of infectious bursal disease virus (IBDV), containing a unique genetic background composition, represents a serious problem for animal health. Since the emergence of this novel IBDV mosaic was first described in Poland, this scenario has become particularly attractive to uncover the evolutionary forces driving the genetic diversity of IBDV populations. This study additionally addressed the phenotypic characterization of these emergent strains, as well as the main features affecting the viral fitness during the competition process of IBDV lineages in the field. Our results showed how different evolutionary mechanisms modulate the genetic diversity of co-existent IBDV lineages, leading to the error catastrophe effect, Muller ratchet effect, or prevalence, depending on their genetic compositions. We also determined that the action of the positive selection pressure, depending on the genomic segment on which it is acting, can drive two main phenotypes for IBDV: immune-escaping strains from the selection on segment A or strains with functional advantages from the selection on segment B. This last group seems to possess an increased fitness landscape in the viral quasispecies composition, presenting better adaptability to dissimilar environmental conditions and likely becoming the dominant population. The reassortant strains also exhibited a lower mortality rate compared with the well-known vvIBDV strains, which can facilitate their spreading.

In Ovo and Day of Hatch Application of a Live Infectious Bursal Disease Virus Vaccine to Commercial Broilers

Infectious bursal disease (IBD) is an economically important disease of young chickens caused by an Avibirnavirus, the infectious bursal disease virus (IBDV). The causative virus is highly resilient in poultry environments and vaccination is the most effective measure for IBDV control. However, both the suspected neutralization of highly attenuated strains by maternal antibodies and the assumed virulence of partly attenuated strains have limited the implementation of conventional live IBDV vaccine strains in pre- and posthatch chicks. Nevertheless, preliminary data have raised questions about the validity of this prevailing dogma. To investigate the possible application of a live IBDV intermediate plus vaccine strain, the IBDV MB-1, to maternally immunized chicken embryos and day-of-hatch chicks, four large-scale field trials have been conducted in distinct global locations. The four trials have measured the relative safety, IBDV immunization parameters, and production performances of MB-1 vs. the established live and immune complex IBDV vaccines in a variety of commercial broiler systems. The overall health and production performances in all four trials have been similar or better in the MB-1 groups. The results challenge the prevailing notion that live IBDV strains may be neutralized or break through maternal immunity and induce permanent damage to the young broiler chick's immune response. A delayed replication phenomenon following parenteral administration of the live IBDV vaccine strain has been observed, while the delayed replication mechanism remains to be elucidated. This study's findings warrant further investigation of conventional live IBDV vaccine strains as an alternative for pre- and posthatch broilers active immunization.

Origin and global spreading of an ancestral lineage of the infectious bursal disease virus

Infectious bursal disease virus (IBDV) is an economically relevant and widespread pathogen that produces immunosuppression in young chickens. IBDV is genetically classified into seven genogroups (G1-G7), where the traditional classic, variant and very virulent strains correspond to G1, G2 and G3, respectively. The G4 strains, also known as 'distinct' (dIBDV), have recently acquired increased relevance because of their prevalence and notorious impair to the poultry industry in South America. Here, worldwide dIBDV strains were studied using phylogenetic and phylodynamic approaches. The phylogenetic analyses performed using partial and complete sequences of both viral segments (A and B) consistently clustered the dIBDV strains in a monophyletic group. The analyses of the VP5, polyprotein and VP1 coding regions identified amino acid residues that act as markers for the identification of the entire dIBDV group or different sub-populations. The phylodynamic analyses performed using the hypervariable region of VP2 indicated that the dIBDV strains emerged in the early 1930s in Eastern Europe, shortly after the emergence of classic strains (1927) and before variant (1949) and very virulent strains (1967). The analysis of the migration routes indicated that after its emergence, the dIBDV strains spread to Eastern Asia around 1959, to Brazil around 1963, and to Argentina around 1990. These inter-continental migrations resulted in three sub-populations that are currently represented by strains from (a) Brazil, (b) Eastern Asia and Canada, and (c) Eastern Europe, Argentina and Uruguay. Taken together, our results highlight the complex evolutionary history of IBDV and the importance of new phylodynamic data to unravel and nearly follow the different evolutionary pathways taken by this important poultry pathogen.

Feline coronavirus isolates from a part of Brazil: insights into molecular epidemiology and phylogeny inferred from the 7b gene

The Feline coronavirus (FCoV) can lead to Feline infectious peritonitis (FIP), which the precise cause is still unknown. The theory of internal mutation suggests that a less virulent biotype of FCoV (FECV) would lead to another more pathogenic biotype (FIPV) capable of causing FIP. In this work, the 7b gene was amplified from 51 domestic cat plasma samples by semi-nested PCR and tested through phylogenetic and phylogeographical approaches. The 7b gene of Brazilian isolates displayed high conservation, a strong correlation between the geographic origin of the viral isolates and their genealogy, and its evolution was possibly shaped by a combination of high rates of nucleotide substitution and purifying selection.

Molecular characterization of field isolates of infectious bursal disease virus from three decades, 1987-2018, reveals a distinct genotypic subgroup in Vietnam

The complete nucleotide sequence of the viral protein 2 (VP2) ORF was determined for 26 Vietnamese infectious bursal disease isolates collected from clinical outbreaks in vaccinated flocks from 1987 to 2018 and two commercial vaccine specimens. These sequences were compared for molecular classification with 42 reference strains representing all four main classes of serotype 1, including very virulent (vvIBDV), classical (cvIBDV), antigenic variant (avIBDV) and attenuated (atIBDV) strains, and serotype 2 strains. Amino acids at nine key positions in the VP2-HVR in 20 Vietnamese isolates, A222, I242, Q253, I256, D279, A284, I294, S299, A329, which are typical of the vvIBDV class, were found to be identical in all of the isolates. Eighteen of these isolates had a unique change at residue 212 (D212N) located in the P_AB loop. Phylogenetic analysis revealed a distinct lineage/subclade with strong nodal support (96%) that included recent Chinese IBDV strains that were distinct from typical vvIBDVs. Six isolates contained the amino acid substitutions P222, V242, Q253, V256, D279, A284, I294, N299, A329, which are present in two vaccine strains derived from strain 2512 and these isolates were also closely related to the classical virulent STC strain. Data from this study show that there is considerable genetic diversity among vvIBDVs, which vary according to geographic region. Antigenic drift and differences in genetic characteristics between virulent strains and IBDV vaccine strains may be the cause of vaccine failure. Better antigenic matching of vaccines to the strains circulating in Vietnam is therefore required.

Phylodynamic analyses of Brazilian antigenic variants of infectious bursal disease virus

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.

Phylogeny and evolution of infectious bursal disease virus circulating in Turkish broiler flocks

The emergence of new infectious bursal disease virus (IBDV) variants can threaten poultry health and production all over the world causing significant economic losses. Therefore, this study was performed to determine IBDV molecular epidemilogy, VP2 gene variation, and corresponding pathological lesions in IBDV infected chickens in Turkey. For this, 1855 bursa of Fabricius samples were collected from 371 vaccinated broiler flocks. Atrophia and haemorrhages were seen in the bursa Fabricius of very virulent IBDV (vvIBDV) infected chickens. Partial VP2 gene was sequenced and phylogenetic, recombination, and evolutionary analyses were performed. 1548 (83.5%) out of 1855 of bursa of Fabricius samples were IBDV positive and 1525 of those could be sequenced. The recombination analysis did not detect occurrence of any recombination event among the Turkish strains. Among 1525 sequenced samples, 1380 of them were found to be classical strains. Among 1380 classical strains, 1317 were similar to IBDV 2512, 11 to Faragher 52/70, 40 to 228 E, and 12 to Lukert strain. Out of 1525 reverse transcriptase ploymerase chain reaction positive samples, 144 of them were found to be similar to vvIBDV-VP2 gene reported to GenBank previously. The phylogenetic tree performed on a broad sequence dataset demonstrated grouping of vvIBDV Turkish strains in three different clusters, including sequences collected also from Iraq and Kuwait (Cluster 1), Indian (Cluster 2), and a distinct Turkish-only cluster (Cluster 3). The evolutionary rate estimation on branches/clades including Turkish strain mirrored the expected one for RNA viruses and no significant differences were found among different considered branches. In conclusion, results of this study indicate that vvIBDV strains similar to those circulating in various countries in the Middle East are present and undergoing evolution in chickens from Turkish broiler flocks. This point needs to be taken into account in planning adequate control strategies.

Molecular epidemiological study on Infectious Pancreatic Necrosis Virus isolates from aquafarms in Scotland over three decades

In order to obtain an insight into genomic changes and associated evolution and adaptation of Infectious Pancreatic Necrosis Virus (IPNV), the complete coding genomes of 57 IPNV isolates collected from Scottish aquafarms from 1982 to 2014 were sequenced and analysed. Phylogenetic analysis of the sequenced IPNV strains showed separate clustering of genogroups I, II, III and V. IPNV isolates with genetic reassortment of segment A/B of genogroup III/II were determined. About 59 % of the IPNV isolates belonged to the persistent type and 32 % to the low-virulent type, and only one highly pathogenic strain (1.79 %) was identified. Codon adaptation index calculations indicated that the IPNV major capsid protein VP2 has adapted to its salmonid host. Under-representation of CpG dinucleotides in the IPNV genome to minimize detection by the innate immunity receptors, and observed positive selection in the virulence determination sites of VP2 embedded in the variable region of the main antigenic region, suggest an immune escape mechanism driving virulence evolution. The prevalence of mostly persistent genotypes, together with the assumption of adaptation and immune escape, indicates that IPNV is evolving with the host.

Low evolutionary rate of infectious pancreatic necrosis virus (IPNV) in Italy is associated with reduced virulence in trout

Infectious pancreatic necrosis virus (IPNV) is a naked double-stranded RNA virus with a bi-segmented genome that is classified within the family Birnaviridae, genus Aquabirnavirus. IPNV was first detected in Italian trout farms in the late 1970s and ultimately became endemic. To characterize the evolution of IPNV circulating in Italy, particularly whether there is a link between evolutionary rate and virulence, we obtained and analyzed the VP1 (polymerase) and the pVP2 (major capsid protein precursor) sequences from 75 IPNV strains sampled between 1978 and 2017. These data revealed that the Italian IPNV exhibit relatively little genetic variation over the sampling period, falling into four genetic clusters within a single genogroup (group 2 for VP1 and genogroup V for pVP2) and contained one example of inter-segment reassortment. The mean evolutionary rates for VP1 and pVP2 were estimated to be 1.70 and 1.45 × 10⁻⁴ nucleotide substitutions per site, per year, respectively, and hence significantly lower than those seen in other Birnaviruses. Similarly, the relatively low ratios of non-synonymous (d_N) to synonymous (d_S) nucleotide substitutions per site in both genes indicated that IPNV was subject to strong selective constraints, again in contrast to other RNA viruses infecting salmonids that co-circulate in the same area during the same time period. Notably, all the Italian IPNV harbored a proline at position 217 (P₂₁₇) and a threonine at position 221 (T₂₂₁) in pVP2, both of which are associated with a low virulence phenotype. We therefore suggest the lower virulence of IPNV may have resulted in reduced rates of virus replication and hence lower rates of evolutionary change. The data generated here will be of importance in understanding the factors that shape the evolution of Aquabirnaviruses in nature.

Characterization of field infectious bursal disease viruses in Zambia: evidence of co-circulation of multiple genotypes with predominance of very virulent strains

Infectious bursal disease (IBD) is a highly contagious, immunosuppressive disease of chickens and causes substantial economic losses to the poultry industry globally. This study investigated the genetic characteristics and pathological lesions induced by IBD viruses (IBDVs) that were associated with 60 suspected outbreaks in chickens during 2015-2016 in Lusaka Province, Zambia. Nucleotide sequences of VP2 hypervariable region (VP2-HVR) (n = 38) and part of VP1 (n = 37) of Zambian IBDVs were phylogenetically analysed. Phylogenetic analysis of the VP2-HVR and VP1 revealed that most viruses (n = 31 of each genome segment) clustered with the very virulent (vv) strains. The rest of the viruses clustered with the classical strains, with two of the viruses being closely related to attenuated vaccine isolates. Two of the viruses that belonged to the vv genotype had a unique amino acid (aa) substitution Q324L whereas one virus had two unique changes, N280S and E300A in the VP2-HVR aa sequence. Although Zambian strains with a vv genotype possessed virulence marker aa within VP1 at 145T, 146D and 147N, two viruses showed unique substitutions, with one virus having 147T while the other had 147H. Pathologically, it was noted that only viruses with a vv genotype appeared to be associated with inducing pathological lesions in non-lymphoid organs (proventriculus and gizzard). Whilst documenting for the first time the presence of classical virulent IBDVs, this study demonstrates the involvement of multiple genotypes, with predominance of vvIBDVs in the epidemiology of IBD in Zambia.

Infectious bursal disease virus in poultry: current status and future prospects

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.

Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent

Background

Infectious bursal disease (IBD) is a highly contagious and acute viral disease, which has caused high mortality rates in birds and considerable economic losses in different parts of the world for more than two decades and it still represents a considerable threat to poultry. The current study was designed to rigorously measure the reliability of a phylogenetic marker included into segment B. This marker can facilitate molecular epidemiology studies, incorporating this segment of the viral genome, to better explain the links between emergence, spreading and maintenance of the very virulent IBD virus (vvIBDV) strains worldwide.

Methodology/Principal Findings

Sequences of the segment B gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank Database; Cuban sequences were obtained in the current work. A phylogenetic marker named B-marker was assessed by different phylogenetic principles such as saturation of substitution, phylogenetic noise and high consistency. This last parameter is based on the ability of B-marker to reconstruct the same topology as the complete segment B of the viral genome. From the results obtained from B-marker, demographic history for both main lineages of IBDV regarding segment B was performed by Bayesian skyline plot analysis. Phylogenetic analysis for both segments of IBDV genome was also performed, revealing the presence of a natural reassortant strain with segment A from vvIBDV strains and segment B from non-vvIBDV strains within Cuban IBDV population.

Conclusions/Significance

This study contributes to a better understanding of the emergence of vvIBDV strains, describing molecular epidemiology of IBDV using the state-of-the-art methodology concerning phylogenetic reconstruction. This study also revealed the presence of a novel natural reassorted strain as possible manifest of change in the genetic structure and stability of the vvIBDV strains. Therefore, it highlights the need to obtain information about both genome segments of IBDV for molecular epidemiology studies.

Spatiotemporal Phylogenetic Analysis and Molecular Characterisation of Infectious Bursal Disease Viruses Based on the VP2 Hyper-Variable Region

Background

Infectious bursal disease is a highly contagious and acute viral disease caused by the infectious bursal disease virus (IBDV); it affects all major poultry producing areas of the world. The current study was designed to rigorously measure the global phylogeographic dynamics of IBDV strains to gain insight into viral population expansion as well as the emergence, spread and pattern of the geographical structure of very virulent IBDV (vvIBDV) strains.

Methodology/Principal Findings

Sequences of the hyper-variable region of the VP2 (HVR-VP2) gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank database; Cuban sequences were obtained in the current work. All sequences were analysed by Bayesian phylogeographic analysis, implemented in the Bayesian Evolutionary Analysis Sampling Trees (BEAST), Bayesian Tip-association Significance testing (BaTS) and Spatial Phylogenetic Reconstruction of Evolutionary Dynamics (SPREAD) software packages. Selection pressure on the HVR-VP2 was also assessed. The phylogeographic association-trait analysis showed that viruses sampled from individual countries tend to cluster together, suggesting a geographic pattern for IBDV strains. Spatial analysis from this study revealed that strains carrying sequences that were linked to increased virulence of IBDV appeared in Iran in 1981 and spread to Western Europe (Belgium) in 1987, Africa (Egypt) around 1990, East Asia (China and Japan) in 1993, the Caribbean Region (Cuba) by 1995 and South America (Brazil) around 2000. Selection pressure analysis showed that several codons in the HVR-VP2 region were under purifying selection.

Conclusions/Significance

To our knowledge, this work is the first study applying the Bayesian phylogeographic reconstruction approach to analyse the emergence and spread of vvIBDV strains worldwide.