Emergence of a new swine H3N2 and pandemic (H1N1) 2009 influenza A virus reassortant in two Canadian animal populations, mink and swine

Abstract

A swine H3N2 (swH3N2) and pandemic (H1N1) 2009 (pH1N1) influenza A virus reassortant (swH3N2/pH1N1) was detected in Canadian swine at the end of 2010. Simultaneously, a similar virus was also detected in Canadian mink based on partial viral genome sequencing. The origin of the new swH3N2/pH1N1 viral genes was related to the North American swH3N2 triple-reassortant cluster IV (for hemagglutinin [HA] and neuraminidase [NA] genes) and to pH1N1 for all the other genes (M, NP, NS, PB1, PB2, and PA). Data indicate that the swH3N2/pH1N1 virus can be found in several pigs that are housed at different locations.

Fig. 1.

Viral genome sequence homologies of the new swH3N2/pH1N1 reassortant virus with swH3N2 and pH1N1 reference strains. When two squares between an swH3N2/pH1N1 strain and a reference strain possess the same color, it indicates that the viral gene is genetically related. The influenza virus reference strains used for comparison are A/New York/19/2009(H1N1) (GenBank accession no. FJ984388 to FJ984394 and GQ457503) and the swH3N2 cluster IV Quebec reference strain A/swine/Quebec/4001/2005(H3N2) (GenBank accession no. EU826543 to EU826550). Numbers in squares indicate the percentages of nucleotide homology compared to the genetically related strain. n.d., not determined.

Fig. 2.

Phylogenetic tree of the HA gene nucleotide sequences of the swH3N2/pH1N1 strains. The designated clusters I, II, III, and IV classify the North American H3N2 triple-reassortant swine viruses as previously described (4). The phylogenetic tree was generated by the neighbor-joining method using the Geneious v5.4.6 software with a bootstrap resampling method (1,000 replications). Bootstrap confidence levels are indicated at the nodes of the phylogenetic tree. Bootstrap values lower than 50 are not indicated for clarity. GenBank accession numbers for the sequences of all viruses are provided after their names. The horizontal scale indicates the distances between strains; a distance of 0.02 means that the strains possess 98% nucleotide identity. The asterisks and triangle indicate the swine and mink swH3N2/pH1N1 strains, respectively, identified in this study. Those strains have been classified within subclusters IVa and IVb. The arrow indicates the other swH3N2 and pH1N1 reassortant strain that has recently been reported in United States by Ducatez et al. (3); its genes are related to swH3N2 (for HA, NA, NS, PB1, and PB2) and pH1N1 (for M, PA, and NP).

Fig. 3.

Hemagglutination inhibition (HI) titers of convalescent pig sera toward swH3N2/pH1N1 viruses. Twenty sera collected from 6- to 8-week-old pigs housed with the animal experiencing the first confirmed flu case related to the swH3N2/pH1N1 reassortant (A/swine/Quebec/1259260/2010) were tested. The boxes extend from the 25th percentile to the 75th percentile, with a line at the median. The error bars extending below and above each box show the lowest and highest HI values obtained with the 20 pig sera that were tested. When an HI result was negative at the lowest serum dilution (1/10) tested, the value of the HI titer was established to be equal to 0. Labeling of 2 sets of data with different superscript letters indicates that these 2 sets of data are statistically different (P < 0.05). Below the x axis, a table indicates the HI values of the reference sera (ck/150/90 and sw/4001/05) against each of the swine influenza virus strains tested.