Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions

Abstract

Background: Variations in the influenza Hemagglutinin protein contributes to antigenic drift resulting in decreased efficiency of seasonal influenza vaccines and escape from host immune response. We performed an in silico study to determine characteristics of novel variable and conserved motifs in the Hemagglutinin protein from previously reported H3N2 strains isolated from Hong Kong from 1968-1999 to predict viral motifs involved in significant biological functions.

Highly conserved influenza A virus epitope sequences as candidates of H3N2 flu vaccine targets

“…One study discovered 19 universal conserved functional motifs and accessible regions for functional mapping and annotation [14]. Another study reported motifs within the HA protein and correlated them with a high number of potential post-translational modification sites that overlap antigenic and receptor binding sites [15,16]. A third study performed phylogenic analysis and addressed the evolution of influenza A viral segments [16].…”

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

“…Molecular modelling studies have in addition provided mechanistic explanations for such questions like drug modes of action, virus-receptor interaction, and virus-host interactions. In these lines of research, conserved regions found in viruses, extrapolated from multiple sequence alignments of different strains, were essential in functional prediction through the identification of epitopes and motifs [ 15 - 17 ].…”

“…Additionally, methodical analysis of the whole genome has identified co-occurrence of mutation networks and other properties, such as relative codon usage (rscu) and codon usage patterns (cup), as features of Influenza evolution [ 19 ]. Motif prediction in the HA influenza genes and proteins has been previously conducted [ 17 ].…”