Genetic characterization of an H1N2 influenza virus isolated from a pig in Indiana

Abstract

An H1N2 influenza virus was isolated from a pig during an outbreak of respiratory disease and abortion on an Indiana farm in November 1999. Results of phylogenetic analyses indicate that this virus is a reassortant between a recent classical H1 swine virus and the reassortant H3N2 viruses that have emerged among American pigs since 1998.

FIG. 1

Nucleotide phylogenetic tree for the HA gene of Sw/IN/99. The evolutionary relationship of this gene to HA genes from reference viruses was estimated by the method of maximum parsimony (PAUP software, v.4.0b2; David Swofford, Smithsonian Institution) using the tree-bisection-reconnection branch swapping algorithm and with the MULTREES option in effect. The tree shown represents the best (score = 1,385) of 9,698 rearrangements that were generated. Horizontal line distances are proportional to the minimum number of nucleotide changes needed to join nodes and gene sequences. The vertical lines are simply for spacing the branches and labels. The tree is rooted to an H3 HA sequence. The accession numbers for the reference virus sequences used in this analysis are available upon request.

FIG. 2

Nucleotide phylogenetic trees for the NA (A), M (B), and PA (C) genes of Sw/IN/99. The evolutionary relationships were estimated by the method of maximum parsimony as described in the legend to Fig. 1. The score and number of rearrangements for each tree are as follows: NA, score = 2,011 of 475,664 rearrangements; M, score = 1,020 of 10,892,448 rearrangements; and PA, score = 3,850 of 2,345,030 rearrangements. The reassortant H3N2 viruses isolated from pigs in the Midwestern United States since 1998 (16a, 43) are marked by an asterisk. The NA tree is rooted to an influenza A virus of a different subtype (N1), whereas the M and PA trees are rooted to influenza B viruses.

FIG. 2

Nucleotide phylogenetic trees for the NA (A), M (B), and PA (C) genes of Sw/IN/99. The evolutionary relationships were estimated by the method of maximum parsimony as described in the legend to Fig. 1. The score and number of rearrangements for each tree are as follows: NA, score = 2,011 of 475,664 rearrangements; M, score = 1,020 of 10,892,448 rearrangements; and PA, score = 3,850 of 2,345,030 rearrangements. The reassortant H3N2 viruses isolated from pigs in the Midwestern United States since 1998 (16a, 43) are marked by an asterisk. The NA tree is rooted to an influenza A virus of a different subtype (N1), whereas the M and PA trees are rooted to influenza B viruses.

FIG. 2

Nucleotide phylogenetic trees for the NA (A), M (B), and PA (C) genes of Sw/IN/99. The evolutionary relationships were estimated by the method of maximum parsimony as described in the legend to Fig. 1. The score and number of rearrangements for each tree are as follows: NA, score = 2,011 of 475,664 rearrangements; M, score = 1,020 of 10,892,448 rearrangements; and PA, score = 3,850 of 2,345,030 rearrangements. The reassortant H3N2 viruses isolated from pigs in the Midwestern United States since 1998 (16a, 43) are marked by an asterisk. The NA tree is rooted to an influenza A virus of a different subtype (N1), whereas the M and PA trees are rooted to influenza B viruses.