Open Access Highly Accessed Research

Identification of novel conserved functional motifs across most Influenza A viral strains

Mahmoud ElHefnawi12*, Osama AlAidi3*, Nafisa Mohamed2, Mona Kamar2, Iman El-Azab4, Suher Zada25 and Rania Siam25

Author Affiliations

1 Informatics and Systems Department and Biomedical Informatics and chemo informatics group, Division of Engineering Research and Centre of Excellence for Advanced Sciences, National Research Centre, Tahrir Street, 12311 Cairo, Egypt

2 Yousef Jameel Science and technology Research Center, The American University in Cairo, New Cairo, Egypt

3 Department of Biochemistry, University of Saskatchewan, Canada

4 Faculty of Computers & Information, Cairo University, Ahmed Zowail Street, Cairo, Egypt

5 Biology Department, American University in Cairo, Cairo, Egypt

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Virology Journal 2011, 8:44  doi:10.1186/1743-422X-8-44

Published: 27 January 2011



Influenza A virus poses a continuous threat to global public health. Design of novel universal drugs and vaccine requires a careful analysis of different strains of Influenza A viral genome from diverse hosts and subtypes. We performed a systematic in silico analysis of Influenza A viral segments of all available Influenza A viral strains and subtypes and grouped them based on host, subtype, and years isolated, and through multiple sequence alignments we extrapolated conserved regions, motifs, and accessible regions for functional mapping and annotation.


Across all species and strains 87 highly conserved regions (conservation percentage > = 90%) and 19 functional motifs (conservation percentage = 100%) were found in PB2, PB1, PA, NP, M, and NS segments. The conservation percentage of these segments ranged between 94 - 98% in human strains (the most conserved), 85 - 93% in swine strains (the most variable), and 91 - 94% in avian strains. The most conserved segment was different in each host (PB1 for human strains, NS for avian strains, and M for swine strains). Target accessibility prediction yielded 324 accessible regions, with a single stranded probability > 0.5, of which 78 coincided with conserved regions. Some of the interesting annotations in these regions included sites for protein-protein interactions, the RNA binding groove, and the proton ion channel.


The influenza virus has evolved to adapt to its host through variations in the GC content and conservation percentage of the conserved regions. Nineteen universal conserved functional motifs were discovered, of which some were accessible regions with interesting biological functions. These regions will serve as a foundation for universal drug targets as well as universal vaccine design.