Fig 1.
Phylogenetic analysis of the hemagglutinin (HA) gene of six Ontario H1 subtype viruses isolated from pigs in 2012(▲).
Influenza A virus in swine (IAV-S) H1 α (blue), β (black), γ (turquoise), δ1 (green), δ2 (brown), δ3 (pink) clusters and pandemic (H1N1pdm09) (red) Canadian H1N1 viruses have been included in analysis.
Fig 2.
Phylogenetic analysis of neuraminidase (NA) gene of 5 Ontario H1N1 and 1 H1N2 viruses isolated from pigs in 2012 (purple with ▲).
The H3N2 viruses isolated from Ontario swine between 2011 and 2012 (black), human-like H1N1 bearing seasonal human H1 and N1 genes together with the triple-reassortant internal gene (TRIG) cassette (green), A(H1N1)pdm09 (red), and contemporary influenza A viruses from swine (conIAV-S) which contain HA and NA genes of classical H1N1 in combination with the North American TRIG cassette (blue) have been included in analysis.
Fig 3.
Phylogenetic analysis of the matrix (M) gene of 5 Ontario H1N1 and 1 H1N2 viruses isolated from pigs in 2012 (purple with ▲).
The H3N2 viruses isolated from Ontario swine between 2011 and 2012 containing M gene from trH3N2 (black), contemporary influenza A viruses from swine (conIAV-S) which contain HA and NA genes of classical H1N1 in combination with the North American triple-reassortant internal gene (TRIG) cassette (blue), A(H1N1)pdm09 (red), and H3N2 viruses (green) isolated from Ontario swine between 2011 and 2012 containing M gene from pandemic H1N1 (A(H1N1)pdm09) have been included in analysis.
Table 1.
Top BLAST matches of the 8 gene segments from 5 Ontario H1N1 and 1 Ontario H1N2 virus obtained from NCBI influenza A virus nucleotides and amino acid database.
Fig 4.
Phylogenetic analysis of the polymerase A (PA) gene of 5 Ontario H1N1 and 1 H1N2 viruses isolated from pigs in 2012 (purple with).
Classical swine H1N1 (brown), Ontario H3N2 viruses isolated in 2011 and 2012 (black), and pandemic A(H1N1)pdm09 (red) have been included in analysis.
Fig 5.
Phylogenetic analysis of nonstructural (NS) gene segments of 5 Ontario H1N1 and 1 Ontario H1N2 viruses isolated from pigs in 2012 (purple with ▲).
Analysis includes contemporary influenza A viruses from swine (conIAV-S) which contain HA and NA genes of classical H1N1 in combination with the North American triple-reassortant internal gene (TRIG) cassette (blue), A(H1N1)pdm09 (red), and 2011–2012 Ontario H3N2 viruses (black).
Fig 6.
Potential resistance of 5 Ontario H1N1 and 1 H1N2 isolate to the M2 blocker amantadine.
Alignment analysis of M2 sequences of Ontario H1N1 isolates showing amino acid substitution S31N. The M2 transmembrane is underlined.
Table 2.
Amino acid sequence alignment of the NA protein of 2012 Ontario H1N1 influenza A viruses from pigs.
Fig 7.
Presentation of polymerase B1-F2 (PB1-F2) variants of mammalian and avian influenza A viruses.
Nine PB1 lineages (A to I) have been described and presented. Colored lines at the top represent amino acids of the predicted helical region (black) and the putative mitochondrial targeting sequence (red). Amino acids that are considered to enhance viral pathogenesis are marked in gray (T51, V56, N66S, E87). The first stop codon has been shown by asterisk and following stop codons are indicated by asterisk.
Fig 8.
Phylogenetic analysis of 28 polymerase B1-F2 (PB1-F2) sequences.
Representatives of the nine PB1 lineages (A to I) were selected. The pandemic strains of 1918 (H1N1), 1957 (H2N2), 1968 (H3N2) and H1N1pdm09 are marked with (●). The H1N1 and H1N2 viruses isolated from pigs in 2012 are marked with (▲).
Fig 9.
Predicted HA1 proteins of the 2012 Ontario H1 viruses.
The six 2012 Ontario H1 predicted HA1 proteins were aligned and compared to that of 2009 pandemic H1N1 (A/Mexico/InDRE4487/2009) as reference. Amino acid differences are visible in the antigenic sites Cb (1), Sa (3), Ca2 (2), Ca1 (6), Sb (1). Receptor-binding pocket residures are indicated by a diamond.
Fig 10.
Positions of the amino acid alterations at major antigenic sites of the HA1 molecule in the H3 crystal structure.
The HA monomer in cartoon format with major antigenic sites: Sa (green), Sb (cyan), Ca1 (magenta), Ca2 (yello) and Cb (blue) shown in spheres (I). The positions of changed amino acids are shown in red for each of 6 Ontario 2012 viruses: II (A/SW/ON/13-1/12/H1N1), III (A/SW/ON/16/12/H1N1), IV(A/SW/ON/84/12/H1N1), V (A/SW/ON/68/12/H1N1, VI (A/SW/ON/46/12/H1N1, VII (A/SW/ON/62/12/H1N1). The view of panels I to VII is rotated 180°C along Y-axis and positions of changed amino acids are shown in red (VIII, IX, X, XI, XII, XIII, XIV).
Table 3.
Amino acid sequence alignment of the HA1 and HA2 protein of 2012 Ontario H1N1 and H1N2 influenza A viruses from pigs.