May Newly Defined Genotypes XVII and XVIII of Newcastle Disease Virus in Poultry from West and Central Africa Be Considered a Single Genotype (XVII)?

LETTER

We read with great interest the article by Snoeck et al. (1), where the authors reported great genetic diversity among Newcastle disease virus (NDV) strains circulating in the poultry population of West and Central Africa along with two newly defined genotypes, genotypes XVII and XVIII, based on fusion (F) gene sequence analysis. More than 90% identity was noticed between the sequences belonging to genotypes XVII and XVIII in NCBI BLAST analysis. We analyzed the report and determined the mean distance within a genotype, mean distance between the genotypes, and net mean distances between genotypes XVII (n = 56) and XVIII (n = 15) using complete F gene sequences of NDVs, which were used in the report by Snoeck et al. (1). The mean evolutionary distance was calculated in MEGA6 software as follows. The number of nucleotide base substitutions per site from an estimation of the net average from comparisons between groups of sequences was analyzed using the maximum composite likelihood model (2). The rate of variation among sites was modeled with a gamma distribution (shape parameter = 1). The analysis involved 71 gene sequences available in NCBI GenBank. The codon positions included were 1st plus 2nd plus 3rd plus noncoding. The nucleotide positions containing gaps and missing data were eliminated. The standard error estimate was obtained by a bootstrap procedure (500 replicates) (2).

The analysis results revealed that the mean distance within genotype XVII is 0.031 (3.1%) with a standard error of 0.002 and within genotype XVII is 0.044 (4.4%) with a standard error of 0.004. The mean distance between genotypes XVII and XVIII was determined to be 0.108 (10.8%) with a standard error of 0.008, whereas the net mean distance between genotypes XVII and XVIII was determined to be 0.071 (7.1%) with a standard error of 0.007. The net mean distances between the genotypes showed agreement with the sequence identity determined in the NCBI BLAST analysis. A minimum of a 10% mean evolutionary distance between NDV genotypes has been recommended to define a new genotype (3). We conclude that newly defined genotypes XVII and XVIII of NDV (1) may be considered a single genotype, genotype XVII.