Newcastle disease virus fusion and haemagglutinin-neuraminidase gene motifs as markers for viral lineage.

Reverse transcriptase polymerase chain reaction was used to generate sequence data for 91 Australian Newcastle disease viruses (NDV) isolated from 1932 to 2000 covering the cleavage site of the fusion (F) protein and the C-terminus of the haemagglutinin-neuraminidase (HN) protein. Comparison of sequences at these two sites indicates distinct evolutionary relationships between these viruses. Typically, HN gene relationships revealed by phylogenetic analyses were also maintained in comparisons between F gene cleavage sites; however, the former analyses appeared to give a clearer indication of the lineage of a virus isolate. This data supports and extends earlier observations in that there is no evidence for gene exchange by recombination but that different strains appear to have evolved through synonymous mutations. Inter-relationships, especially between Australian NDV isolates, appear to be associated with lineages having the same C-terminal HN extensions rather than associated with virulence of the virus. A proposed mechanism for this observation is discussed.