Whole-genome sequencing and molecular characterization of Newcastle disease virus isolates from Kazakhstan

Abstract

Newcastle disease virus (NDV) remains an important threat to poultry health, while complete genome data from Kazakhstan remain limited. In this study, two NDV-positive samples obtained from domestic chicken carcasses in the Almaty region were propagated in embryonated chicken eggs and characterized by diagnostic PCR/RT-PCR, infectivity assessment, whole-genome sequencing, phylogenetic analysis, and comparative molecular analysis. Both isolates replicated efficiently in embryonated eggs, reaching 9.6–9.7 log10 EID50/mL, with HA titers of 1:128–1:256 and no virus-attributable embryo mortality or marked embryo lesions. The complete consensus genomes of NDV_KZ_I and NDV_KZ_II were 15,186 bp and contained six major coding sequences arranged in the canonical 3′-N-P-M-F-HN-L-5′ order. Both isolates were closely related to the lentogenic vaccine-like strain AVIVAK-NDV-LaSota, and the F protein cleavage site motif was 112GRQGRL117, consistent with a lentogenic molecular profile. The F and HN proteins were identical between the isolates, with conserved predicted N-linked glycosylation motifs and predicted linear B-cell epitope profiles. The complete genome sequences were submitted to GenBank under submission number SUB16299204. Because the vaccination history of the source birds was unavailable and ICPI/MDT assays were not performed, the isolates should be interpreted as vaccine-like NDV detected during diagnostic investigation rather than confirmed causative agents of mortality. These data expand available NDV genomic information from Kazakhstan and support future molecular surveillance.