Submitted to: Virus Research
Publication Type: Peer reviewed journal
Publication Acceptance Date: 1/29/2004
Publication Date: 5/6/2004
Citation: Wise, M., Sellers, H.S., Alvarez, R., Seal, B.S. 2004. RNA-dependent RNA Polymerase Gene Analysis of Worldwide Newcastle Disease Virus Isolates Representing Different Virulence Types and Their Phylogenetic Relationship with Other Members of the Paramyxoviridae. Virus Research 104 (2004) p71-80. Interpretive Summary: Newcastle disease virus (NDV) is an economically important pathogen for commercial poultry. The polymerase protein is central to viral replication. Consequently, there are not many genetic changes in the sequences encoding the polymerase protein among different virus isolates of the same type. To better understand the relationships among NDV isolates, the polymerase protein genetic sequences were obtained for several highly virulent strains. Although the protein is very similar from one NDV isolate to the next, the genetic sequence is very heterogeneous due to changes occurring that do not affect the protein amino acids. This indicates that creating detection techniques based on polymerase protein genetic sequences may be difficult. During our studies we detected incorrect information that had been submitted to publicly accessible databases which have now been corrected based on the new information for the NDV polymerase gene. Finally, data obtained for the NDV polymerase further supports newly devised classification schemes for this virus type.
Technical Abstract: Nucleotide sequence was determined for the RNA-dependent RNA polymerase (L) gene of sixteen Newcastle disease virus (NDV) isolates from diverse geographic and chronological origins. The observed consensus amino acid sequence conformed to the six domains previously identified among paramyxovirus L proteins, and the putative QGDNQ active site was strictly conserved among all isolates. Analysis of predicted amino acid sequences allowed us to identify a sequencing error in the previously reported L genes for NDV. The correct sequences provided a more accurate alignment with predicted L amino acid sequences of other paramyxoviruses. Comparison of L gene coding sequences among isolates revealed that synonymous substitutions dominated non-synonymous substitutions, as observed previously with other NDV genes. However, the overall substitution rate was lower than other genes examined making the L gene the most conserved of the NDV genome. Phylogenetic analysis of L genes among NDV isolates was consistent with previous results that suggested the existence of two major lineages. One group contained strains isolated in North America prior to 1970 and included virulent and vaccine strains, while the second group included virulent viruses isolated worldwide. A comparison of the NDV L coding sequences to other Paramyxoviridae illustrated the unique clustering of the avian-specific paramyxoviruses, further justifying the newly created Avulavirus genus.