Avian influenza A (H9N2): computational molecular analysis and phylogenetic characterization of viral surface proteins isolated between 1997 and 2009 from the human population

Abstract

Background: H9N2 avian influenza A viruses have become panzootic in Eurasia over the last decade and have caused several human infections in Asia since 1998. To study their evolution and zoonotic potential, we conducted an in silico analysis of H9N2 viruses that have infected humans between 1997 and 2009 and identified potential novel reassortments.

Results: A total of 22 hemagglutinin (HA) and neuraminidase (NA) nucleotide and deduced amino acid sequences were retrieved from the NCBI flu database. It was identified that mature peptide sequences of HA genes isolated from humans in 2009 had glutamine at position 226 (H3) of the receptor binding site, indicating a preference to bind to the human α (2-6) sialic acid receptors, which is different from previously isolated viruses and studies where the presence of leucine at the same position contributes to preference for human receptors and presence of glutamine towards avian receptors. Similarly, strains isolated in 2009 possessed new motif R-S-N-R in spite of typical R-S-S-R at the cleavage site of HA, which isn't reported before for H9N2 cases in humans. Other changes involved loss, addition, and variations in potential glycosylation sites as well as in predicted epitopes. The results of phylogenetic analysis indicated that HA and NA gene segments of H9N2 including those from current and proposed vaccine strains belong to two different Eurasian phylogenetic lineages confirming possible genetic reassortments.

Conclusions: These findings support the continuous evolution of avian H9N2 viruses towards human as host and are in favor of effective surveillance and better characterization studies to address this issue.

Figure 1

Phylogenetic relationships of HA genes in H9N2 influenza viruses isolated from humans between 1997 and 2009. A phylogenetic tree was generated using minimum evolution analysis with maximum composite likelihood using the Tamura-Nei model with MEGA software version 4.0.2. Numbers below branches indicate bootstrap value percentages from 1000 replicates. The scale bar represents the distance unit between sequence pairs. Representative prototype viruses for different Eurasian lineages are indicated as red. The sequences of H9N2 influenza viruses isolated from the human population are indicated as blue.

Figure 2

Phylogenetic relationships of NA genes in H9N2 influenza viruses isolated from humans between 1997 and 2009. The phylogenetic methods and abbreviations were as described for figure 1.