Novel swine influenza virus subtype H3N1, United States

Abstract

Influenza A virus infects various animal species and transmits among different hosts, especially between humans and swine. Swine may serve as a mixing vessel to create new reassortants that could infect humans. Thus, monitoring and characterizing influenza viruses in swine are important in preventing interspecies transmission. We report the emergence and characterization of a novel H3N1 subtype of swine influenza virus (SIV) in the United States. Phylogenetic analysis showed that the H3N1 SIVs may have acquired the hemagglutinin gene from an H3N2 turkey isolate, the neuraminidase gene from a human H1N1 isolate, and the remaining genes from currently circulating SIVs. The H3N1 SIVs were antigenically related to the turkey virus. Lung lesions and nasal shedding occurred in swine infected with the H3N1 SIVs, suggesting the potential to transmit among swine and to humans. Further surveillance will help determine whether this novel subtype will continue to circulate in swine populations.

Figure 1

Genetic relationships of the hemagglutinin (HA) 1 region of HA gene and neuraminidase (NA) gene of the H3N1 swine influenza viruses (SIVs) with other influenza viruses. The tree was created by maximum parsimony method and bootstrapped with 1,000 replicates. The bootstrap numbers are given for each node. A) Phylogenetic trees demonstrating genetic relationship of the closely related H3N2 turkey isolates, recent H3N2 SIVs, and human H3N2s. The tree was created from the HA1 region of HA and rooted to an unrelated sequence, the H4 HA of A/duck/Alberta/28/76. B) Phylogenetic analysis of the N1 subtype of NA genes of human, swine, and avian influenza viruses. N2 of A/Chicken/CA/6643/01 was used as an outgroup sequence.

Figure 2

Alignment of deduced amino acid sequences within the hemagglutinin (HA) 1 region of HA genes of H3N2 swine influenza viruses (SIVs), H3N2 turkey isolates, and H3N1 SIVs. The amino acid sequence represents the consensus sequence, and the amino acid at position 1 is the first amino acid following the signal peptide (37). Dots represent amino acids similar to the consensus. Note that according to H3 structure (37), the residues representing the antigenic sites are underlined and the receptor binding sites are in boldface. The alignment shows that PU243 and PU542 may have emerged from the H3N2 turkey isolates. The residues within the receptor-binding site are relatively conserved.