The territory of Kazakhstan occupies an important geographical location on the crossroads of the main migration routes of many wild birds in the Eurasian continent and plays a significant role in the ecology of different avian viruses. Isolation of Newcastle Disease Viruses (NDV) circulating in wild bird populations and their study is of particular importance.
In 2014, samples of tracheal and cloacal swabs from wild birds of 36 families were collected from the 9 regions of the Republic of Kazakhstan. Samples were collected from wild birds with no clinical signs of disease and tested using real-time RT-PCR for the presence of NDV. Of the PCR positive samples, 6 NDV were isolated from 9 species of birds from 5 regions of the country by 10-day culture in chicken embryos. Sequencing was performed, and analysis was of the primary sequence of the N-terminal segment of the fusion protein in isolated viruses indicating pathogenic strains of NDV
Sequencing and analysis of the primary sequence of the N-terminal segment of the fusion protein (F protein) in isolated viruses revealed that 13 isolates exhibited the cleavage site sequence 112KRQKR116- F117, which is typical for pathogenic strains of NDV. Analysis of the F-gene nucleotide sequences of the NDV isolated from three bird species (Phalacrocorax carbo, Pelecanus crispus, Acrocephalus dumetorum) in Almaty oblast has shown that they are genetically homogeneous and belong to Genotype VIIb. Strains closest to the Kazakh viruses of the Genotype VIIb were of Chinese origin (2008/China/ZJ-17-08-Ch), as well as the viruses isolated in the territory of the Republic of Kazakhstan from dead poultry (chicken/KZ/Almaty/07/2013, chicken/KZ/Korday/05/2013, and chicken/KZ/SKO/12/2012).
Viruses isolated from eight bird genera (Columbalivia, Mergus, Fulica, Buteo rufinus, Acridotheres, Acridotheres, Phasianus, Phalacrocorax) in Almaty, Zhambyl, Pavlodar, West Kazakhstan and East Kazakhstan oblasts demonstrated genetic homogeneity and were matched to the Genotype VIg. Historic Kazakhstan viruses were identical to the isolated in Russia strains
APMV1/pigeon/Almaty/1064/05(JN806236), 2005/Russia/Pi?Rus/Vladimir/687/05 and 2009/Russia/Pi/Rus/Kemerovo/0267/09.
The current molecular characterization and genome sequencing of NDV strains isolated in Kazakhstan is ongoing and will include sequencing of the complete genome of 5 strains of the NDV from 3 regions of Kazakhstan. The findings provide insights in determining the correlation between the genomic features and the evolution of NVD strains and geographical distribution. Results will elucidate the understanding of the geographical spread and genetic variability of NDV in Central Asia.
Sequencing applications for metagenomics, transcriptomics, diagnostics, and biosurveillanc
