Submitted to: Infection, Genetics and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 12, 2012
Publication Date: September 11, 2012
Repository URL: http://handle.nal.usda.gov/10113/57472
Citation: Diel, D.G., Da Silva, L.A., Liu, H., Wang, Z., Miller, P.J., Afonso, C.L. 2012. Genetic diversity of avian paramyxovirus type 1: Proposal for a unified nomenclature and classification system of Newcastle disease virus genotypes. Infection, Genetics and Evolution. 12(8):1770-1779. Interpretive Summary: The avian paramyxovirus type 1 (APMV-1), or Newcastle disease virus (NDV), comprise a diverse group of viruses with a single-stranded, negative-sense RNA genome. Historically, two systems have been simultaneously used to classify NDV isolates into lineages or genotypes, generating confusion in the nomenclature and discrepancies in the assignment of genetic groups. In the present study we assessed the genetic diversity of APMV-1 and propose a unified nomenclature and a classification system based on objective criteria to classify NDV into genotypes. We have analyzed 1,995 partial F (fusion) gene sequences, 704 complete F gene sequences, and 109 complete genome sequences and, as a result, developed a genotype classification based on the full F gene sequences of NDV isolates. Complete F gene sequences of class I (n =102) and class II (n = 602) viruses were used for the final phylogenetic reconstruction and to identify distinct taxonomic groups. The mean evolutionary distance between genetic groups was determined (0.1 or 10%) and set as the cutoff value to assign new genotypes. Results of our study revealed that class I viruses comprise a single genotype (designated here as genotype 1), while class II contains at least fifteen genetic groups including ten previously established (I, II, III, IV, V, VI, VII, VIII, IX, and XI) and five new genotypes (X, XII, XIII, XIV and XV). Sub-genotypes were also identified among class I and class II genotypes. Adoption of a unified nomenclature and of objective criteria to classify new NDV isolates will facilitate studies on NDV epidemiology, evolution, disease control and diagnostics.
Technical Abstract: Genetically diverse Newcastle disease virus (NDV) isolates circulate and cause disease in different geographic locations of the world. The differences found on the genome of distinct NDV isolates have been used to classify different isolates into genetic groups called genotypes or lineages. Both lineage and genotype classification systems have been used to classify NDV isolates as they are discovered, which generates confusion in the nomenclature and sometimes in erroneous classification of these isolates. Here we developed and propose a unified nomenclature to define NDV genetic groups which is based on objective criteria to be used for future classification of new isolates. Results of our analysis demonstrated that class I contains only one genetic group (named genotype 1), while class II viruses is divided in 15 genetic groups. Potential benefits associated with the adoption of the NDV classification system proposed in the present study, include a better understanding of NDV epidemiology and evolution, disease control and diagnostics.