Dynamics of Influenza A (H5N1) virus protein sequence diversity

PeerJ
Hadia Syahirah Abd RamanAsif M Khan

Abstract

Influenza A (H5N1) virus is a global concern with potential as a pandemic threat. High sequence variability of influenza A viruses is a major challenge for effective vaccine design. A continuing goal towards this is a greater understanding of influenza A (H5N1) proteome sequence diversity in the context of the immune system (antigenic diversity), the dynamics of mutation, and effective strategies to overcome the diversity for vaccine design. 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. Almost all of the aligned overlapping nonamer positions of each viral proteome ex...Continue Reading

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Citations

Jul 3, 2021·Proteomes·Eleni I KatsarouAngeliki I Katsafadou

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Software Mentioned

NetCTL
LBtope
NetMHCII
Bepipred
Ggplot2
R
JalView
Clustal Omega

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