Identification of hemagglutinin structural domain and polymorphisms which may modulate swine H1N1 interactions with human receptor

Abstract

Background: The novel A/H1N1 influenza virus, which recently emerged in North America is most closely related to North American H1N1/N2 swine viruses. Until the beginning of 2009, North American swine H1N1/N2 viruses have only sporadically infected humans as dead-end hosts. In 2009 the A/H1N1 virus acquired the capacity to spread efficiently by human to human transmission. The novel A/H1N1 influenza virus has struck thousands of people in more than 70 countries and killed more than 140, representing a public health emergency of international concern. Here we have studied properties of hemagglutinin of A/H1N1 which may modulate virus/receptor interaction.

Results: Analyses by ISM bioinformatics platform of the HA1 protein of North American swine H1N1/N2 viruses and the new A/H1N1 showed that both groups of viruses differed in conserved characteristics that reflect a distinct propensity of these viruses to undergo a specific interaction with swine or human host proteins or receptors. Swine H1N1/N2 viruses that sporadically infected humans featured both the swine and the human interaction pattern. Substitutions F71S, T128S, E302K, M314L in HA1 of swine H1N1 viruses from North America are identified as critical for the human interaction pattern of A/H1N1 and residues D94, D196 and D274 are predicted to be "hot-spots" for polymorphisms which could increase infectivity of A/H1N1 virus. At least one of these residues has already emerged in the A/H1N1 isolates from Spain, Italy and USA. The domain 286-326 was identified to be involved in virus/receptor interaction.

Conclusion: Our results (i) contribute to better understanding of the origin of the novel A/H1N1 influenza virus, (ii) provide a tool for monitoring its molecular evolution (iii) predicts hotspots associated with enhanced infectivity in humans and (iv) identify therapeutic and diagnostic targets for prevention and treatment of A/H1N1 infection.

Figure 1

Phylogeny of HA gene sequences of H1N1 and H1N2 viruses infecting humans. Human cases of H1 swine that infected humans between 1976 and 2007 (black square); avian species (H1); seasonal human H1N1 influenza (black triangle), representative strains of Novel A/H1N1 influenza and H1N2 viruses (asterisk).

Figure 2

The ISM analysis of HA1 proteins. (a) CIS of swine H1N1 and H1N2 influenza viruses found in North America between 1931 and 2008, (b) CIS of swine H1N1 viruses infecting humans in US during 2005-2007, A/Iowa/01/2006; A/Wisconsin/87/2005; A/Ohio/01/2007; A/Ohio/02/2007, (c) CIS of A/H1N1 viruses presented in Figure 4. (d) IS of a representative swine H1N2 HA1 (A/swine/Minnesota/1192/2001), (e) IS of a representative swine H1N1 HA1 infecting human (A/Iowa/01/2006), and (f) IS of a representative A/H1N1 HA1 (A/Castilla-La Mancha/GP13/2009).

Figure 3

Identification of hot-spots for mutations that may increase A/H1N1/-receptor interaction. (a) Effect of alanine substitution on the amplitude at frequency F(0.295). "In silico" alanine scan of the complete HA1 sequence of the early A/H1N1 isolate A/Mexico/4115/2009 (EPI177288). (b) Homology between HA1 of A/Castilla-La Mancha/GP13/2009 (FJ985753) (identical to US isolate A/South Carolina/09/2009), swine H1N1 viruses infecting human 2005-2007 and A/Mexico/4115/2009 (EPI177288).

Figure 4

Phylogeny of HA gene sequences of representative strains of Novel H1N1 influenza. Strains with specific D274E mutations (black diamond).

Figure 5

A/H1N1 HA trimer and details of the VIN2 region. The informational spectrum and position of the VIN2 domain (yellow) in the 3D structure of A/H1N1 isolate A/California/04/2009.