Epitope Peptide-Based Predication and Other Functional Regions of Antigenic F and HN Proteins of Waterfowl and Poultry Avian Avulavirus Serotype-1 Isolates From Uganda

Abstract

Uganda is a Newcastle disease (ND) endemic country where the disease is controlled by vaccination using live LaSota (genotype II) and I2 (genotype I) vaccine strains. Resurgent outbreak episodes call for an urgent need to understand the antigenic diversity of circulating wild Avian Avulavirus serotype-1 (AAvV-1) strains. High mutation rates and the continuous emergence of genetic and antigenic variants that evade immunity make non-segmented RNA viruses difficult to control. Antigenic and functional analysis of the key viral surface proteins is a crucial step in understanding the antigen diversity between vaccine lineages and the endemic wild ND viruses in Uganda and designing ND peptide vaccines. In this study, we used computational analysis, phylogenetic characterization, and structural modeling to detect evolutionary forces affecting the predicted immune-dominant fusion (F) and hemagglutinin-neuraminidase (HN) proteins of AAvV-1 isolates from waterfowl and poultry in Uganda compared with that in LaSota vaccine strain. Our findings indicate that mutational amino acid variations at the F protein in LaSota strain, 25 poultry wild-type and 30 waterfowl wild-type isolates were distributed at regions including the functional domains of B-cell epitopes or N-glycosylation sites, cleavage site, fusion site that account for strain variations. Similarly, conserved regions of HN protein in 25 Ugandan domestic fowl isolates and the representative vaccine strain varied at the flanking regions and potential linear B-cell epitope. The fusion sites, signal peptides, cleavage sites, transmembrane domains, potential B-cell epitopes, and other specific regions of the two protein types in vaccine and wild viruses varied considerably at structure by effective online epitope prediction programs. Cleavage site of the waterfowl isolates had a typical avirulent motif of 111GGRQGR'L117 with the exception of one isolate which showed a virulent motif of 111GGRQKR'F117. All the poultry isolates showed the 111GRRQKR'F117 motif corresponding to virulent strains. Amino acid sequence variations in both HN and F proteins of AAvV-1 isolates from poultry, waterfowl, and vaccine strain were distributed over the length of the proteins with no detectable pattern, but using the experimentally derived 3D structure data revealed key-mapped mutations on the surfaces of the predicted conformational epitopes encompassing the experimental major neutralizing epitopes. The phylogenic tree constructed using the full F gene and partial F gene sequences of the isolates from poultry and waterfowl respectively, showed that Ugandan ND aquatic bird and poultry isolates share some functional amino acids in F sequences yet do remain unique at structure and the B-cell epitopes. Recombination analyses showed that the C-terminus and the rest of the F gene in poultry isolates originated from prevalent velogenic strains. Altogether, these could provide rationale for antigenic diversity in wild ND isolates of Uganda compared with the current ND vaccine strains.

Newcastle Disease Genotype VII Prevalence in Poultry and Wild Birds in Egypt

“…Few amino acid (aa) substitutions (N30S, T90A, N258S, and R480K) were found in the entire length of F protein in APMV-1 isolates from chicken, duck, and wild birds, as compared with each other. Such substitutions have been proposed to influence the antigenicity as well as a change in the fusion protein confirmation [ 10 , 60 , 71 , 72 , 73 , 74 , 75 , 76 ]. The substitution particularly in the surface-exposed aa residues in the signal peptide cleavage site of NDV F protein (position: 30) is considered to be highly variable as this region must undergo constant positive selection [ 71 ].…”

“…Such substitutions have been proposed to influence the antigenicity as well as a change in the fusion protein confirmation [ 10 , 60 , 71 , 72 , 73 , 74 , 75 , 76 ]. The substitution particularly in the surface-exposed aa residues in the signal peptide cleavage site of NDV F protein (position: 30) is considered to be highly variable as this region must undergo constant positive selection [ 71 ]. Orabi et al [ 72 ] detected that the N30 residue appears to be conserved in all vaccine and Egyptian field strains clustered within genotype II; two isolates from this study “NDV/Duck/Egypt/DAK/ZU-NM09/2019” and “NDV/Chicken/Egypt/ALEX/ZU-NM97/2019” shared such residue.…”

Newcastle Disease Genotype VII Outbreaks in Poultry across Egypt are associated with Enzootic Prevalence of the Virus in Wild Birds

“…Few amino acid (aa) substitutions (N30S, T90A, N258S, and R480K) were found in the entire length of F protein in APMV-1 isolates from chicken, duck, and wild birds as compared with each other. The substitution particularly in the surface-exposed aa residues in the signal peptide cleavage site of NDV F protein (position: 30) is considered to be highly variable as this region must undergo constant positive selection [86]. Orabi et al, [87] detected that the N30 residue appears to be conserved in all vaccine and Egyptian field strains clustered within genotype II; two isolates from this study "NDV/Duck/Egypt/DAK/ZU-NM09/2019" and "NDV/Chicken/Egypt/ALEX/ZU-NM97/2019" shared such residue.…”

“…Being F protein is considered two subunits (F1 and F2), the F1 subunit is included in the position (117 → 533), and the F2 subunit is in the position (32 → 116), in which the cleavage site present at position 112-116 [86,87]. In the current study, there are two aa substitutions in the F2 subunit (position: 90) and F1 subunit (position: 258) which might initiate a change in the fusion protein.…”

“…The hypervariable regions of the fusion peptide unsurprisingly had three-heptad repeat regions HRa, HRb, and HRc spanning at positions 143-185, 268-299, and 471-500, respectively [86,91]. Three isolates (NDV/Chicken/Egypt/NOR/ZU-NM76/2019, NDV/Black-crowned night heron/Egypt/POR/ZU-NM85/2019, and NDV/Chicken/Egypt/ALEX/ZU-NM99/2019) showed the substitution R480K within the HRc, a domain essential for virus fusion together with HRa and HRb.…”