Identification and comparison of point mutations associated in classic and variant infectious bursal disease viruses

Loop PDE of viral capsid protein is involved in immune escape of the emerging novel variant infectious bursal disease virus

Infectious bursa disease (IBD) is an acute, highly contactable, lethal, immunosuppressive infectious disease caused by the Infectious bursa disease virus (IBDV). Currently, the emerged novel variant IBDV (nVarIBDV) and the sustainedly prevalent very virulent IBDV (vvIBDV) are the two most prevalent strains of IBDV in China. The antigenic properties of the two prevalent strains differed significantly, which led to the escape of nVarIBDV from the immune protection provided by the existing vvIBDV vaccine. However, the molecular basis of the nVarIBDV immune escape remains unclear. In this study, we demonstrated, for the first time, that residues 252, 254, and 256 in the PDE of VP2 are involved in the immune escape of the emerging nVarIBDV. Firstly, the IFA-mediated antigen-antibody affinity assay showed that PBC and PDE of VP2 could affect the affinity of vvIBDV antiserum to VP2, of which PDE was more significant. The key amino acids of PDE influencing the antigen-antibody affinity were also identified, with G254N being the most significant, followed by V252I and I256V. Then the mutated virus with point or combined mutations was rescued by reverse genetics. it was further demonstrated that mutations of V252I, G254N, and I256V in PDE could individually or collaboratively reduce antigen-antibody affinity and interfere with antiserum neutralization, with G254N being the most significant. This study revealed the reasons for the widespread prevalence of nVarIBDV in immunized chicken flocks and provided innovative ideas for designing novel vaccines that match the antigen of the epidemic strain.

Genetic Diversity of Recent Infectious Bursal Disease Viruses Isolated From Vaccinated Poultry Flocks in Malaysia

Vaccination is an essential component in controlling infectious bursal disease (IBD), however, there is a lack of information on the genetic characteristics of a recent infectious bursal disease virus (IBDV) that was isolated from IBD vaccinated commercial flocks in Malaysia. The present study investigated 11 IBDV isolates that were isolated from commercial poultry farms. The isolates were detected using reverse transcription-polymerase chain reaction (RT-PCR) targeting the hypervariable region (HVR) of VP2. Based on the HVR sequences, five isolates (IBS536/2017, IBS624/2017, UPM766/2018, UPM1056/2018, and UPM1432/2019) were selected for whole-genome sequencing using the MiSeq platform. The nucleotide and amino acid (aa) sequences were compared with the previously characterized IBDV strains. Deduced aa sequences of VP2HVR revealed seven isolates with 94–99% aa identity to very virulent strains (genogroup 3), two isolates with 97–100% aa identity to variant strains (genogroup 2), and two strains with 100% identity to the vaccine strain (genogroup 1) of IBDV. The phylogenetic analysis also showed that the isolates formed clusters with the respective genogroups. The characteristic motifs 222T, 249K, 286I, and 318D are typical of the variant strain and were observed for UPM1219/2019 and UPM1432/2019. In comparison, very virulent residues such as 222A, 249Q, 286T, and 318G were found for the vvIBDV, except for the UPM1056/2018 strain with a A222T substitution. In addition, the isolate has aa substitutions such as D213N, G254D, S315T, S317R, and A321E that are not commonly found in previously reported vvIBDV strains. Unlike the other vvIBDVs characterized in this study, UPM766/2018 lacks the MLSL aa residues in VP5. The aa tripeptides 145/146/147 (TDN) of VP1 were conserved for the vvIBDV, while a different motif, NED, was observed for the Malaysian variant strain. The phylogenetic tree showed that the IBDV variant clustered with the American and Chinese variant viruses and are highly comparable to the novel Chinese variants, with 99.9% identity. Based on the sequences and phylogenetic analyses, this is the first identification of an IBDV variant being reported in Malaysia. Further research is required to determine the pathogenicity of the IBDV variant and the protective efficacy of the current IBD vaccines being used against the virus.

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.

Identification of Infectious Bursal Disease Virus with Atypical VP2 Amino Acid Profile in Latvia

Introduction

Infectious bursal disease virus (IBDV) is a causative agent of immunosuppressive disorder resulting in significant losses to the world poultry industry. This study describes the molecular characterisation of an atypical IBDV from a field outbreak that occurred in vaccinated chicken flocks in Latvia in 2011.

Material and Methods

Ten bursae of Fabricius from each flock were collected for laboratory examination. Virus isolation was performed in embryonated eggs and CEF culture. The RT-PCR aimed at hypervariable domain of VP2 gene combined with sequencing was performed for detection and identification of IBDV.

Results

The molecular examinations confirmed the IBDV infection. The analysis of the amino acid sequence revealed that the strain possessed four amino acids at VP2 protein (222A, 256I, 294I, and 299S), indicating a genetic relatedness to a very virulent IBDV. However, some unique or rare amino acid substitutions (219L, 220F, 254D, 279N, and 280T) were also detected.

Conclusion

The obtained results demonstrate the occurrence of IBDV with a high mutation rate within the hypervariable domain of VP2 peptide, and highlight the necessity of implementation of IBDV surveillance in Eastern European poultry industry to determine whether this strain is an exception or a new wave of IBDV with new genetic features emerged in the field.

Amino acids contributing to antigenic drift in the infectious bursal disease Birnavirus (IBDV)

We examined the effect of amino acids 222 and 254 on antigenicity of the variant Del-E strain of infectious bursal disease virus (IBDV). Using molecular epidemiology, we identified a virus designated as Del-E-222 that was identical to Del-E except for alanine at position 222. A second virus was generated using reverse genetics of the Del-E backbone to create Del-E-254 that contained an asparagine at amino acid 254. The Del-E-222 and Del-E-254 viruses were tested for their ability to escape neutralizing immunity provided by parenteral vaccination. The bursas from birds vaccinated with parental Del-E and challenged with Del-E-222 or Del-E-254 had macroscopic lesions typical of an IBDV infection, and their B-BW ratios were significantly smaller than the controls. Microscopic lesions included lymphocyte depletion and confirmed the ability of Del-E-222 and Del-E-254 to break through the immunity induced by the parental Del-E virus vaccination. Both mutations appear to be contributing to antigenic drift.

Genotyping of Canadian field strains of infectious bursal disease virus

For this retrospective study, infectious bursal disease virus (IBDV) was detected in 134 bursal samples that originated from flocks with conditions such as airsacculitis, tracheitis, pneumonia, septicaemia, inclusion body hepatitis, coccidiosis, and/or a history of production problems without overt clinical symptoms. Samples were from seven Canadian provinces: Ontario, Quebec, Manitoba, British Columbia, Nova Scotia, Alberta, and Newfoundland and Labrador. Viral RNA was identified in bursae with moderate to severe and acute to chronic bursal damage. The ages of the flocks from which samples were collected ranged from 3 to 63 days. Following reverse transcriptase-polymerase chain reaction the nucleotide sequence of the VP2 hypervariable region was determined and compared with sequences available in GenBank. The most common Canadian IBDV field strains were North-American variant viruses. Forty-four viruses were highly related (97.5% to 100.0%) to the US IBDV strain NC171. Moreover, 16 field viruses whose VP2 sequences were 99.2% to 100% identical to the South African 05SA8 IBDV strain appeared closely related to the NC171 group. Delaware E-related field viruses, 98.3% to 100.0% identical to the prototype virus, were identified in 33 samples. Thirty-four Canadian IBDVs showed the highest identity, 94.2% to 98.3%, to US IBDV strain 586. Five samples contained vaccine-related viruses, while two field strains showed the best match to Del A (United States) and IBDV strains SP_04_02 (Spain). Very virulent IBDVs were not detected in Canada.

Molecular characteristics of infectious bursal disease viruses from asymptomatic broiler flocks in Europe

Infectious bursal disease virus (IBDV) exists in several different antigenic and pathogenic forms. The immune suppression caused by this virus in young chickens is not always associated with clinical signs of disease. The antigenic variant viruses originally described in the United States typically do not cause clinical signs of disease but can cause a marked immune suppression via the destruction of B lymphocytes. Using a reverse transcription-polymerase chain reaction (RT-PCR) assay we conducted a survey of asymptomatic broiler chicken flocks in Europe for IBDV. Restriction fragment length polymorphisms in the viral protein 2 (VP2) gene of four isolates from Spain and four isolates from France indicated they may be different from the classic and very virulent (vv) IBDV strains found throughout Europe. Nucleotide sequence and phylogenetic analysis of the hypervariable region of the VP2 gene indicated that all eight viruses were more similar to U.S. variant viruses than classic viruses. In two viruses, one from France and one from Spain, threonine was observed at amino acid position 222 and serine was found at position 254. These two substitution mutations are characteristic of Delaware variant viruses. In addition, all eight viruses had mutated amino acid position 318 from glycine to aspartic acid, another substitution mutation commonly found in U.S. variant viruses. Although importation restrictions prevented us from directly testing the antigenicity of these viruses, their nucleotide and predicted amino acid sequences suggest they could be antigenically distinctive compared to classic and vvIBDV commonly found in Europe. Confirmation of the presence of antigenic variant IBDV strains in Europe requires additional immunologic studies to elucidate the exact nature of the viral epitopes. Our data support the need for these immunologic studies.

Restriction fragment length polymorphism analysis of the VP2 gene of Australian strains of infectious bursal disease virus

Twenty-four Australian strains of infectious bursal disease virus (IBDV) were characterized by reverse transcription/polymerase chain reaction-restriction fragment length polymorphism and compared with previously published overseas strains. A primer pair designed to amplify a 743 base pair fragment of the VP2 gene was used and restriction fragment length polymorphism profiles were determined for each strain using three restriction enzymes, Bst NI, MboI and SspI. Australian strains comprised 12 molecular groups that were unique and distinct from overseas IBDV strains. A specific SspI site that is used to predict a very virulent IBDV phenotype was absent from all Australian strains, contrary to a previous finding by Jackwood and Sommer (1999). One Australian strain (N1/99) contained an SspI site; however, this was located at a different position than that found in very virulent IBDV strains. The results demonstrate that restriction fragment length polymorphism can be used to rapidly differentiate Australian IBDV strains from overseas strains. However, the existence of a large number of molecular groups might preclude its effectiveness for inter-strain differentiation.

Storage of viruses on filter paper for genetic analysis

The purpose of this study was to develop a method to store viruses on filter paper without the need for special conditions for future use of the genetic material. Two non-enveloped viruses were used as models. Infectious bursal disease virus (IBDV), a double-stranded RNA virus that infects chickens, belongs to the Birnaviridae family. Hemorrhagic enteritis virus (HEV), with double-stranded DNA, belongs to the Adenoviridae family. Three different solutions were found suitable for loading the virus. The viruses were stored at room temperature or at 37 degrees C for periods of 5-30 days. Direct reverse transcription-polymerase chain reaction (RT-PCR) (without previous extraction of the RNA) was carried out on filter paper loaded with IBDV, and fragments of the expected size were detected. HEV DNA was extracted from filter paper loaded with purified virus or crude tissue. PCR fragments were found to be of similar intensity to those of control virus that was kept in a tube at -20 degrees C. This method permits the storage and transport of viruses from the field or from clinics to a regional laboratory or any laboratory elsewhere, without the need for prior treatment or special environmental conditions.