Matrix protein gene nucleotide and predicted amino acid sequence demonstrate that the first US avian pneumovirus isolate is distinct from European strains

Abstract

Avian pneumovirus (APV) is the etiological agent of turkey rhinotracheitis (TRT). Outbreaks of TRT first occurred in the US during May, 1996 and continued through June, 1997. This is the first report of these virus types in the US that was previously considered exotic to the US and Canada. The US isolate, APV/CO, was replicated in chick embryo fibroblasts (CEF) and poly-A RNA from APV/CO infected CEF cells was purified for cDNA synthesis. Degenerate oligonucleotide primers were used to amplify nucleotide sequences coding for the matrix (M) protein gene. Although the type A and B European APV M genes share 75% identity in their coding sequences, they have only 60% identity with the US APV/CO M protein gene. Predicted M proteins of European APV type A and B isolates share 89% identity in their amino acid sequence. However, the predicted M protein of APV/CO has only 78% identity with APV type A and 77% identity with APV type B protein sequences. Phylogenetically the US APV/CO isolate separates as a unique virus relative to European APV type A and B strains that cluster together. Sequence information for the APV/CO M protein gene and predicted amino acids of the M protein confirm the unique nature of this isolate compared to its European counterparts. This correlates with the inability to serologically detect the US APV/CO isolate using diagnostics based on European viruses.