Whole Genomes of Avian orthoavulavirus 1 (Newcastle Disease Virus Genotypes VIg or new genotype XXI.) in Wild Birds in Kazakhstan

Background: The remarkable diversity and mobility of Newcastle disease viruses (NDV) includes virulent viruses of genotype VI. These viruses are often referred to as pigeon paramyxoviruses 1 because they are normally isolated and cause clinical disease in birds from the Columbidae family. Genotype VI viruses occasionally infect, and may also cause clinical disease in poultry. Thus, the evolution, current spread and detection of NDV are relevant to avian health. Methods: Nucleotide sequencing and phylogenetic studies of three Kazakhstan isolations were performed to characterize the complete fusion (F)-protein gene as well as whole genome sequence. Sequence data were compared with 106 Fusion genes representing different NDV genotypes and sub-genotypes, as well as 225 fusion genes and 37 whole genome of class VI NDV strains from different regions of the world at different time periods. Phylogenetic trees were constructed to determine evolutionary relationships among these strains. We analysed fusion (F) protein gene and whole genome sequences, including the cleavage site. Results: The complete genome of these 3 isolates contained 15142bp, 15085bp and 15102bp in length, similar to those of Newcastle disease virus (NDV) strains in genotypes VIg, with the gene order 3’-NP-P-M-F-HN-L-5’. The cleavage site of the fusion protein was 112KRQKR116-F117, a feature generally associated with virulent NDV strains. Phylogenetic analysis, based on genomic sequences, SNP and fusion gene sequences, revealed that three isolates should be classified as class II genotype VIg NDVs. Phylogenetic analysis revealed that the NDV from various sites in Kazakhstan was highly similar genetically and that it clustered together with NDV of genotype VIg. Based on our data analysis, VIg isolates shared highest sequence identity with Russian and Ukraine isolates of the VIg subgenotype, suggests the possible spread of velogenic NDV in this region through cross-border live bird trade. Conclusion: Our study provides baseline information on the genetic characteristics of NDV circulating in Kazakhstan and we propose that the evolutionary and epidemiological study of virulent NDV could help to provide accurate molecular data about variants circulating in this region, thus aiding in the design of more efficient recombinant vaccines.