Methods: Herein, we report a comprehensive study of the dynamics of H5N1 mutations by analysis of the aligned overlapping nonamer positions (1-9, 2-10, etc.) of more than 13,000 protein sequences of avian and human influenza A (H5N1) viruses, reported over at least 50 years. Entropy calculations were performed on 9,408 overlapping nonamer position of the proteome to study the diversity in the context of immune system. The nonamers represent the predominant length of the binding cores for peptides recognized by the cellular immune system. To further dissect the sequence diversity, each overlapping nonamer position was quantitatively analyzed for four patterns of sequence diversity motifs: index, major, minor and unique.
Results: Almost all of the aligned overlapping nonamer positions of each viral proteome exhibited variants (major, minor, and unique) to the predominant index sequence. Each variant motif displayed a characteristic pattern of incidence change in relation to increased total variants. The major variant exhibited a restrictive pyramidal incidence pattern, with peak incidence at 50% total variants. Post this peak incidence, the minor variants became the predominant motif for majority of the positions. Unique variants, each sequence observed only once, were present at nearly all of the nonamer positions. The diversity motifs (index and variants) demonstrated complex inter-relationships, with motif switching being a common phenomenon. Additionally, 25 highly conserved sequences were identified to be shared across viruses of both hosts, with half conserved to several other influenza A subtypes.
Discussion: The presence of distinct sequences (nonatypes) at nearly all nonamer positions represents a large repertoire of reported viral variants in the proteome, which influence the variability dynamics of the viral population. This work elucidated and provided important insights on the components that make up the viral diversity, delineating inherent patterns in the organization of sequence changes that function in the viral fitness-selection. Additionally, it provides a catalogue of all the mutational changes involved in the dynamics of H5N1 viral diversity for both avian and human host populations. This work provides data relevant for the design of prophylactics and therapeutics that overcome the diversity of the virus, and can aid in the surveillance of existing and future strains of influenza viruses.
Materials and Methods: Five treatment groups were established as follows: Group 1 (C), which was given distilled water; Group 2 (T0), which was administered with LA (10 mg/kg body weight [BW]); and Groups 3 (T1), 4 (T2), and 5 (T3), which were given LA (10 mg/kg BW) plus graded concentrations of 30, 60, and 120 mg/kg BW of EBN, respectively. Rats were euthanized at week 5 to collect blood for superoxide dismutase (SOD) assay, and uterus for histomorphological study and expression analyses of epidermal growth factor (EGF), vascular endothelial growth factor (VEGF), and proliferating cell nuclear antigen (PCNA).
Results: Results revealed that LA causes destruction of uterine lining cells and necrosis of uterine glands of exposed rats without EBN supplement while the degree of damage decreased among EBN treated groups; T3 showed the highest ameliorating effect against LA toxicity, as well as an increased number of uterine glands. Increased levels of SOD were also achieved in EBN supplemented groups than the controls. Results of immunohistochemistry showed significantly higher expressions of EGF, VEGF, and PCNA levels (p<0.05) in T3 compared to other treatments. EBN maintained upregulation of antioxidant - reactive oxygen species balance.
Conclusion: The findings showed that EBN could ameliorate the detrimental effects of LA toxicity on the uterus possibly by enhancing enzymatic antioxidant (SOD) activity as well as expressions of EGF, VEGF, and PCNA with cell proliferation roles.