Phylogenetic analysis of H7 avian influenza viruses isolated from the live bird markets of the Northeast United States

Abstract

The presence of low-pathogenic H7 avian influenza virus (AIV), which is associated with live-bird markets (LBM) in the Northeast United States, was first detected in 1994 and, despite efforts to eradicate the virus, surveillance of these markets has resulted in numerous isolations of H7 AIVs from several states from 1994 through 1998. The hemagglutinin, nonstructural, and matrix genes from representative H7 isolates from the LBM and elsewhere were sequenced, and the sequences were compared phylogenetically. The hemagglutinin gene of most LBM isolates examined appeared to have been the result of a single introduction of the hemagglutinin gene. Evidence for evolutionary changes were observed with three definable steps. The first isolate from 1994 had the amino acid threonine at the -2 position of the hemagglutinin cleavage site, which is the most commonly observed amino acid at this site for North American H7 AIVs. In January 1995 a new genotype with a proline at the -2 position was detected, and this genotype eventually became the predominant virus isolate. A third viral genotype, detected in November 1996, had an eight-amino-acid deletion within the putative receptor binding site. This viral genotype appeared to be the predominant isolate, although isolates with proline at the -2 position without the deletion were still observed in viruses from the last sampling date. Evidence for reassortment of multiple viral genes was evident. The combination of possible adaptive evolution of the virus and reassortment with different influenza virus genes makes it difficult to determine the risk of pathogenesis of this group of H7 AIVs.

FIG. 1

Amino acid sequence comparison of the HA1 coding region of three North American H7 isolates selected to display unique structural features of the HA1 coding region. The amino acids which have been shown by molecular modeling to correspond to the receptor binding site identified in the H3 structure are in boldface and are underlined. The serine insertion in the quail isolate between positions 136 and 137 is indicated by the dash at that position in the two 1996 isolates. The amino acid numbering system is based upon the consensus H7 amino acid sequence. The cleavage site separating the HA1 and HA2 is indicated by the gap.

FIG. 2

Phylogenetic trees from the H7 hemagglutinin (H7) subtype, NS subtypes (groups A and B), and the M gene from H7 isolates from the LBMs in the Northeast United States and other representative AIV isolates are presented. All trees were generated with PAUP 3.1 computer program, are the result of 100 bootstrap replicates, and are midpoint rooted. Branch lengths are included on each tree. The H7 LBM isolates are grouped (1 to 4 for the H7 and NS trees and 1 to 3 for the M tree) according to their associations on the tree. Abbreviations: CK, chicken; TK, turkey; GF, guinea fowl; and FPV, Fowl plague virus. Standard two-letter abbreviations are used for states in the United States.

FIG. 3

Comparison of the evolutionary rate of the HA1 segment of the hemagglutinin gene from H7 AIV isolates from the LBMs of the Northeastern United States. The number of nucleotide changes from the earliest H7 isolate, A/CK/NJ/15086-3/94, are given on the y axis, and the number of months after each virus was isolated compared to the index case is given on the x axis. Linear regression analysis was performed to determine the evolutionary rate, and the equation for the line is indicated.