Genetic characterization of swine influenza viruses (H3N2) isolated from Minnesota in 2006–2007

Abstract

Triple-reassortant (TR) H3N2 swine influenza viruses (SIV) are a major cause of respiratory disease in swine worldwide, causing considerable morbidity and mortality. Continuous surveillance of circulating SIV strains is imperative for effective control and prediction of new emerging strains with interspecies transmission potential. The current study characterized SIV isolates from commercial swine population in USA (2006-2007). Nine isolates were completely sequenced, and the molecular evolution of all gene segments was analyzed. Phylogenetic analysis of the nine H3N2 viruses indicated that these strains belonged to cluster-IV of the human/swine/avian TR genotype, grouping with H3N2 viruses of turkey origin, while forming a separate sub-lineage from those of human and avian origin strains. Ten amino acid changes were observed at the major antigenic sites of HA1 region compared to the cluster-III reference strain, with differences in glycosylation sites. All the nine strains were antigenically related to the cluster-IV turkey strain than the cluster-III reference strain. The results of this study suggest that contemporary TR H3N2 strains circulating in North America share the same genetic constellation, thus maintaining the gene pool without any further event of genetic reassortment unlike swine-origin pandemic strain A/California/04/2009/H1N1. These findings strongly support the need for continuous surveillance and monitoring of genetic changes in SIV, to identify evolving strains that might pose a threat to human or animal health.

Pathogenicity and Transmission in Pigs of the Novel A(H3N2)v Influenza Virus Isolated from Humans and Characterization of Swine H3N2 Viruses Isolated in 2010-2011

“…Since the introduction of the H3N2-TRIG in 1998 until 2009, all descendant H3N2 viruses have demonstrated the human-like surface HA and NA genes with a similar TRIG cassette, suggesting that this combination of gene segments favored optimal adaptation to and transmission between swine hosts. A previous publication showed that nine H3N2 viruses obtained from Minnesota in 2006-2007 maintained the same human (HA, NA, and PB1), avian (PB2 and PA), and swine (NP, M, and NS) virus genes that were demonstrated in earlier strains (19), confirming limited reassortment events had taken place at the time. However, the appearance of pH1N1 in swine led to reassortment between pH1N1 and endemic H3N2-TRIG viruses in pigs.…”

“…Differences were detected only in the amino acid sequence of the HA1 region of the Sw/PA virus between the original virus and viruses passaged through the principal and contact pigs. Amino acid sequences at the major antigenic sites (A, B, C, and D) were also compared to a prototypic strain of H3 cluster I (A/Swine/ Texas/4199-1/1998) commonly used as a reference virus and to a cluster IV isolate (A/Swine/Ontario/33853/2005) to assess changes in the antigenic sites (19,35,45). Pairwise amino acid identities of the HA1 protein between the three H3N2 isolates and cluster I and IV prototype viruses is 85.4 to 89.4% and 95.8 to 97.4%, respectively.…”

Genotype patterns of contemporary reassorted H3N2 virus in US swine

“…In 2005, a separate monophyletic H3 cluster (c4) evolved from c3 viruses and was detected in Canada (Olsen et al, 2006) and subsequently in US swine populations (Kumar et al, 2011). The HA gene of all H3 viruses reported here evolved from the H3 c4 that was relatively evolutionarily stable in North American swine since 2005.…”

PhyloFlu, a DNA Microarray for Determining the Phylogenetic Origin of Influenza A Virus Gene Segments and the Genomic Fingerprint of Viral Strains

“…The swine H1N1 viruses from Mexico shared a genomic pattern with H1N1 triple reassortants reported between 1995 and 2009 in the United States (Table 6) (21,22). Similarly, the H3N2 swine viruses had the same fingerprint as the H3N2 triple reassortant strains detected first in 1990 and then reported continuously until 2010 (23,24) (Table 6). To our knowledge, this is the first description of triple reassortant viruses circulating in pigs in Mexico.…”