Genetic Characterization of Infectious Bursal Disease Viruses from Field Outbreaks of the North East Region of India

Continuous clinicopathological and molecular recognition of very virulent infectious bursal disease virus in commercial broiler chickens

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.

VP2 gene sequencing based Geno-grouping of infectious bursal disease viruses isolated from Gujarat and Maharashtra state (India)

Infectious bursal disease (IBD), caused by infectious bursal disease virus (IBDV), has recently been reported in chickens vaccinated with classical or intermediate types of vaccines from various regions of India due to the emergence of novel very virulent strains of infectious bursal disease virus (vvIBDV). In the present study, suspected samples of IBD were collected from poultry flocks of districts of Gujarat and Nagpur (Maharashtra), identified using PCR and grouped as per traditional and new genogrouping pattern. Out of 54 bursa samples, 21 (38.89%) yielded the expected amplicon of 743 bp (701-1444 bp), and were found positive for IBDV. Among these 21 positive flocks, 11 (52.38%) were already vaccinated. Upon nucleotide sequencing of amplicon and its deduction into amino acids, it was found that all the sequences of present study were related to vvIBDV according to old classification pattern. Considering the new genogrouping pattern, nine and four sequences of this study fell within G3a and G3b lineage, respectively. These sequences revealed important differences at key amino acid positions with respect to classical (G1 genogroup), variant (G2 genogroup) type of IBDV and classical vaccines. Further divergence from prototypic vvIBDV strains was revealed as, D-N at 212 position (N = 9) and 279 position (N = 1). In sequences from Maharashtra (group 2 of G3a lineage), occurrence of V instead of P/T/A at 222 position was recorded as a novel and conspicuous substitution in the immunodominant peak A of VP2 hypervariable region. Additional changes at 270 (3 sequences) and 272 positions (4 sequences) could be attributed to reverse mutation or recombination with vaccine strains. In conclusion, both point mutation and genetic reassortment with intermediate type of vaccines were found to be responsible for generation of novel vvIBDV strains in this area which belonged to G3a and G3b genogroups.

Genetic variability in VP1 gene of infectious bursal disease virus from the field outbreaks of Kerala, India

Infectious bursal disease (IBD) is considered as menace as it affects poultry industry globally causing immunosuppression, high mortality and heavy economic loss. Outbreaks of IBD were reported in many states of India including Kerala. VP1 gene acts as an important factor in the process of virus encapsidation and its involvement in viral virulence and viral replication indicates its importance in infectious bursal disease virus (IBDV). The present study was conducted to carry out the molecular characterization of VP1 gene of virulent IBDV in Kerala. A total of 42 samples were processed for the detection and analysis of VP1 gene of IBDV. Out of 42 samples, 21 samples were positive for VP1 gene of IBD. The phylogenetic analysis of the partial VP1 gene sequences reveals the clustering of IBDV isolates into very virulent IBDV (vvIBDV) and non-virulent IBDV (vIBDV). Eighteen isolates (11 isolates from vaccinated flock and 7 from non-vaccinated flocks) clustered with very virulent strains. Three isolates (2 isolates were from vaccinated flock and 1 from non-vaccinated flock) clustered with non-virulent IBDV strains, showing more evolutionarily similarity to south Indian strain VCN14/ABT/MVC/India. It is observed that vvIBDV isolates from this study have common ancestor with the south Indian strain PY12 but showed 9-10% divergence from this strains. The amino acid analysis of these 21 isolates revealed that 17 isolates possessed the characteristic vvIBDV TDN amino acid triplet, while the three isolates had non-vIBDV NEG amino acid triplet at 145/146/147 position. The remaining isolate 1/CVASP/IBDV/VP1 shows unique PDN triplet instead of TDN. Two vvIBDV isolates (15/CVASP/IBDV/VP1 and 18/CVASP/IBDV/VP1) showed 100% nucleotide and amino acid similarity with intermediate plus vaccine strain. Four vvIBDV isolates showed neutral amino acid substitution K251R which was earlier reported in Indian strains but first time in south Indian isolates. The most common unique amino acid substitution observed in our study was neutral E269D amino acid substitution in 12 isolates, neutral amino acid substitution T329S in five isolates, neutral T174N and non-polar to polar amino acid substitution A178T in isolate 10/CVASP/IBDV/VP1, non-polar to polar amino acid substitution P360R in isolate 17/CVASP/IBDV/VP1 and non-polar to polar amino acid substitution P188S in isolate 1/CVASP/IBDV/VP1. These novel mutations in our study reveal the role of genetic drift in the evolution of vvIBDV strains. The isolate 2/CVASP/IBDV/VP1 from non-vaccinated flock shows VP1 gene of non-vIBDV, but possessing VP2 of vvIBDV type indicates this is evolved by genetic shift of segments A and B. This is the first genetic characterization study of field VP1 gene of IBDV isolates in Kerala, India.

Identification and genetic analysis of infectious bursal disease viruses from field outbreaks in Kerala, India

Recurrent infectious bursal disease (IBD) outbreaks were reported in different regions of Kerala, India. This paper reports the comparative genetic analysis of the hypervariable region of the VP2 gene of IBD virus isolates from the field outbreaks in Kerala. In phylogenetic analysis, the obtained field isolates fall into genogroup 1 and 3. In genogroup 3, all vvIBDV isolates shared a common ancestor with other south Indian isolates but isolates 9/CVASP/IBDV, 10/CVASP/IBDV, 12/CVASP/IBDV, 14/CVASP/IBDV and 17/CVASP/IBDV are most recently evolved and are diverged from the south Indian isolates. The amino acid sequence of 22 isolates was analysed, out of which 18 had conserved amino acids which were characteristic of vvIBDV. All the vvIBDV isolates obtained in the study had phenylalanine and valine at the position 240 and 294, respectively, similar to recently evolved Indian IBDV isolate (MDI14). But we observed T269A and S299N mutations in the isolate 6/CVASP/IBDV, and it is the first report of such mutations at these positions in India IBDV isolates. The isolate 11/CVASP/IBDV had a unique mutation of V225A which is not yet reported in IBDV isolates. Two isolates (15/CVASP/IBDV and 18/CVASP/IBDV) were 100% amino acid similar to intermediate plus vaccine strain. The isolates 8/CVASP/IBDV/VP2 and 19/CVASP/IBDV had amino acids unique for the intermediate vaccine with mutations observed at H253Q and V256I in 19/CVASP/IBDV, T270A and novel mutation N279Y in isolate 8/CVASP/IBDV. These two isolates had non-virulent classical heptapeptide sequence 'SWSARGS'; nevertheless, they produce field outbreaks of IBD. This is the first report of genetic characterisation of IBDV in Kerala, India.