Recombination resulting in virulence shift in avian influenza outbreak, Chile

Abstract

Influenza A viruses occur worldwide in wild birds and are occasionally associated with outbreaks in commercial chickens and turkeys. However, avian influenza viruses have not been isolated from wild birds or poultry in South America. A recent outbreak in chickens of H7N3 low pathogenic avian influenza (LPAI) occurred in Chile. One month later, after a sudden increase in deaths, H7N3 highly pathogenic avian influenza (HPAI) virus was isolated. Sequence analysis of all eight genes of the LPAI virus and the HPAI viruses showed minor differences between the viruses except at the hemagglutinin (HA) cleavage site. The LPAI virus had a cleavage site similar to other low pathogenic H7 viruses, but the HPAI isolates had a 30-nucleotide insert. The insertion likely occurred by recombination between the HA and nucleoprotein genes of the LPAI virus, resulting in a virulence shift. Sequence comparison of all eight gene segments showed the Chilean viruses were also distinct from all other avian influenza viruses and represent a distinct South American clade.

Figure 1

Phylogenetic tree of the hemagglutinin subtype 7 nucleotide sequence, which includes both low pathogenic and highly pathogenic avian influenza viruses from Chile. Representative avian and equine H7 influenza gene sequences are also included. The tree was generated with PAUP 4.0b4 computer program with bootstrap replication (500 bootstraps) and a heuristic search method. The tree is rooted to A/Equine/London/1416/73, and branch lengths are included on the tree. Standard two-letter postal codes are used for states in the United States. TK, turkey; CK, chicken; DK, duck; and FPV, fowl plague virus.

Figure 2

Phylogenetic tree of the nucleoprotein nucleotide sequence, which includes both low pathogenic and highly pathogenic avian influenza viruses from Chile. Representative avian, human, swine, and equine influenza gene sequences are also included. The tree was generated with PAUP 4.0b4 computer program with bootstrap replication (500 bootstraps) and a heuristic search method. The tree is rooted to A/Equine/Prague/1/56, and branch lengths are included on the tree. Standard two-letter postal codes are used for states in the United States. TK, turkey; CK, chicken; DK, duck; and FPV, fowl plague virus. For isolates without a species, it is assumed to be an isolate from a human.

Figure 3

Unrooted phylograms of partial nucleotide sequences of the PB2 and NS genes of selected influenza A viruses including those from poultry in Chile in 2002 (indicated in boxes). Nucleotides 14–188 of PB2and 50–481 of NS were used for the analyses. The lengths of the horizontal lines are proportional to the number of nucleotide differences.